Skip to contents

Changelog

Source: NEWS.md

tbl.now 1.0.0

example_engine() no longer emits duplicate prediction rows

get_latest_reported_cases() answers by the censoring flag as well as by the event date and the strata, so a cell holding both an exactly-dated and a censored arrival comes back as two rows – and answers by a declared covariate the same way. example_engine() passed those rows straight through, so its predictions repeated the (event date, stratum, quantile level) key that a tbl_nowcast is built on.

Nothing complained at the time. It surfaced much later and much further away: tidy() died with an unreadable recycling error (Size 116: Existing data. Size 118: Column estimate.) and autoplot() with is.finite(x): default method not implemented for type 'list', because pivot_wider() had folded the repeated key into a list-column.

The engine now pools the counts down to the event date and the stratum, which is the only key its result has. This is the same summarise(.by = key) step the Adding your own nowcasting model article already shows; the counts themselves are unchanged, and so is every other engine.

A trailing comma no longer aborts nowcast_ensemble() or nowcast_backtest()

Both take their members through ..., collected with list() – and list() turns a trailing comma into argument is missing, with no default, an error naming neither the argument nor the call. Every verb accepts one, so there was no reason for a reader to expect otherwise. They now collect with rlang::list2(), which tolerates the trailing comma (and accepts !!! splicing). An empty argument in the middle of a call is still refused, and now says which one it was.

engine_surveillance() works on Sunday-start weeks

surveillance::nowcast() refuses a now, a when or a control$dRange that is not the first day of one of its epochs – a Monday for weekly data. An epidemiological week starts on a Sunday, so weekly tbl_now objects built the ordinary way died with The variables 'now' and 'when' needs to be at the first of each epoch.

get_surveillance_when() and get_surveillance_range() now snap their grids to the epoch start, which is what surveillance::linelist2sts() already does to the data, and run_nowcast() shifts the estimates back onto the object’s own weekday on the way out – so the predictions are still indexed by the event dates you supplied. Event dates that sit on no common weekday are refused up front, naming align_weeks(), rather than after a fit.

Breaking: case_autocorrelation() and reporting_completeness() are gone

Both were written by an AI and never reviewed by a human. They were taken out of summary() earlier for that reason and kept exported behind a warning on every call; shipping an unverified statistic in a CRAN release is a different proposition, so they are now removed from the package entirely and parked, tests and all, in devel/unreviewed_summaries.R. There is no deprecation shim.

The autocorrelation and completeness components no longer exist anywhere, and nowcast_summary_components documents the ten remaining blocks. Nothing else in the family changes.

The Get Started vignette is now a five-minute tour

vignette("tbl.now") used to be a 1,500-line reference that opened with the tidyverse and ended with format converters. It is now a five-minute walk of the whole workflow – clean, tbl_now(), diagnose(), summary(), autoplot(), and then the fork between tbl_now_to_*() and run_nowcast()/nowcast_backtest() – drawn as a diagram and run on the same dengue data as the README, with every stop linking to the article that covers it properly.

Everything that was cut moved, unchanged, to a new article: More on the tbl_now object (https://rodrigozepeda.github.io/tbl.now/articles/more-on-tbl-now.html). It keeps the attribute reference (now complete: revision_date, revision_type and revision_units were missing), the three data types, censoring, temporal effects, the revision process, the dplyr methods and the utilities. The plotting and diagnostics sections were dropped in favour of the articles that already cover them.

The website’s articles are now grouped into Tutorials, Diagnosing and visualizing and Miscellaneous rather than listed flat.

?tbl_now_workflows is gone; the vignette says the same thing with an example you can run.

Smaller installation

LazyDataCompression: xz plus the shorter vignette take the installed package from 5.1 Mb to 3.4 Mb, comfortably back under CRAN’s threshold. The datasets themselves are unchanged.

list_nowcast_methods() no longer loads the modelling packages

installed_only = TRUE asked requireNamespace() whether each backend was available, which loads the namespace to find out. Listing the methods therefore pulled , and the rest into the session – several seconds of Stan machinery, and six namespaces attached as a side effect of a question about the library path. It now asks system.file(package = ), which is the cheap form of the same question. The only behavioural difference is that a package which is installed but cannot be loaded is now listed; run_nowcast() still says so, clearly, when you try to use it.

Upstream examples now guard converter and fit equivalence

The shipped examples from epinowcast, NobBS, surveillance, EpiNow2 and epidist now exercise both halves of each integration: the package-native input is compared with the matching tbl_now_to_*() result, and a seeded native fit is compared with the native fit retained by run_nowcast() (or, for epidist, with the same delay-model pipeline, since epidist is not a nowcasting engine).

  • Fixed: tbl_now_to_epinowcast(max_delay = ...) no longer applies the modelling delay cap while completing observations. Later observations are retained long enough for enw_preprocess_data() to calculate max_confirm, matching epinowcast’s documented complete-then-preprocess workflow.
  • Missing-reference reports retained by a tbl_now now make tbl_now_to_epinowcast() select epinowcast’s missing_reference = TRUE behavior automatically. Ordinary inputs continue to use FALSE and do not gain synthetic missing-reference rows.
  • Fixed: the epinowcast and EpiNow2 fixtures built their inputs with data.table’s [ query syntax. A test file is evaluated in the package namespace, which imports no data.table, so data.table:::cedta() sent DT[i] to [.data.frame instead – a filter expression became an unknown object and a row index became a column index, erroring under R CMD check while passing from the global environment. The fixtures now subset with base semantics that mean the same thing under either dispatch.
  • ?sari_bh credits the nowcaster package as the proximate source. The OpenDataSUS portal link it carried has been redirecting to an unreachable host.

autoplot() is now one column per process

The gallery used to flow left to right in two columns, so which process a panel belonged to was something you read off its colour. It is now a matrix: the epidemic process is the first column, the reporting process the second, and the revision process – on an object that declares one – the third, with each row asking the same question of every process. A two-date object is therefore two columns wide and a three-date object three, and a row a process cannot answer (weekly data has no day-of-week panel) leaves that cell empty rather than sliding the next panel into the wrong column.

The number of columns follows the selection, because the columns are the processes: panels = "calendar" or panels = "delay_calendar" now comes back as a single column rather than a two-wide flow.

(breaking)

plot_revision_delay() drew the report-to-resolution delay as boxplots split by outcome, and was the one delay picture that was not a panel of autoplot().

  • Breaking: plot_revision_delay() is gone. Use plot_delay_distribution(x, axis = "revision"), which draws the same delays, split the same way, as the histogram the reporting delay already got. diagnose_revision_delay(), the Wilcoxon test behind the picture, is unchanged.
  • plot_delay_distribution() gains axis, matching plot_reporting_process() and plot_epidemic_process(): "report" (default) is the reporting delay, "revision" the report-to-resolution delay, drawn in the revision process’s ochre.
  • New autoplot() panel "revision_distribution", which is that panel inside the gallery, and fills the revision column’s first row.

Delays and arrivals can be split by revision outcome

plot_delay_distribution() and plot_reporting_process() gain by_revision_type (default TRUE). It splits the panel by how each case eventually resolved – confirmed, pending, retracted and unknown – so “do negative results come back faster than positive ones?” and “was that spike a day of retractions?” are visible rather than inferred.

  • tbl_now_palette() gains a retracted role, the counterpart of revision, so the four outcomes draw as ochre / white / blue / grey and re-theme as a unit.
  • It is ignored on an object with no revision axis, and when by_strata = TRUE, which already spends the fill on the strata. count-cumulative data records running totals rather than cases and cannot carry an outcome, so plot_reporting_process() says so and draws the unsplit bars.
  • autoplot() also takes by_revision_type, but defaults it to FALSE: the gallery is read as a grid of shapes, and diagnostic_plot() keeps its reporting panel in the reporting colour for the same reason.

as_forecast_point() is no longer exported (breaking)

as_forecast_point() is a generic, and this package supplied both a method for it and an exported function of the same name. The exported copy masked the generic: after library(scoringutils); library(tbl.now) a bare as_forecast_point() reached tbl.now’s version, which is not a generic and aborts on anything that is not a tbl_nowcast or a nowcast_backtest(). as_forecast_quantile() and as_forecast_sample() were never exported this way, so the three were also inconsistent with each other.

diagnose() stops reporting the revision axis as a defect

Declaring a revision axis made diagnose() complain about the two things that axis exists to record. A pending case has no revision date yet, and that NA was read as a value.

  • Fixed: rows carrying an NA anywhere in the uniqueness key are no longer compared against each other. Two pending cases in one (event, report) cell are byte-identical apart from a resolution neither has, yet they may still resolve on different days – calling them an “exact duplicate” and advising dplyr::distinct() would have deleted a real case. Rows with a complete key are checked exactly as before, so a genuine repeat still warns.
  • Fixed: the duplicates/key message now names the key it actually checked. It always included the revision columns, the strata, the covariates and the censoring flags, but it read "(event, report)" whatever else was declared.
  • Fixed: missing/<revision date> no longer counts the missing resolution of a case the object says is "pending" – that is the definition of pending, not a defect. A revision date missing from a case recorded as "confirmed" or "retracted" is still reported.
  • Fixed: the pooled strata/pending note said “% of the stratum” when it was reporting every stratum at once; it now says “% of all cases”.
  • Fixed: infer_units() drops NA before reading the spacing of a date column. A column holding one real date plus missings slipped past the “fewer than two dates” guard, and min() warned about its own empty arguments before the abort that followed blamed the spacing.

The delay-distribution converters return one row per observed delay

tbl_now_to_epidist() and tbl_now_to_EpiNow2(target = "estimate_dist") are the two converters that keep the is_censored_report flag, and they were also the two that never pooled. Neither carries an undeclared column or the revision axis onto its result, so rows separated only by those arrived as duplicates that nothing downstream could tell apart: covid_colombia (which carries an undeclared sex) came back from tbl_now_to_epidist() as 3456 rows covering 1898 distinct delays.

  • Fixed: both converters now pool over undeclared columns, exactly as tbl_now_to_baselinenowcast() and tbl_now_to_tsibble() do, and report what they pooled under verbose = TRUE. Case totals are unchanged.
  • Fixed: the revision axis is now removed before that pooling. It was already dropped from the result (with a warning), but its columns stayed in the cell key, so the rows they separated stayed split. Pooling over it gives the "total" case count – every case has exactly one outcome, so no case is counted twice.
  • Fixed: on the aggregate/count shape, rows describing the same delay observation are summed. This closes the last collision: a censored report inside its own event period is widened to the window an uncensored report in that period already has.
  • Declared strata, covariates and materialised temporal-effect columns are untouched – they reach the target package, so they still keep rows apart. Line lists are untouched too: one row is already one case.
  • Fixed: remove_revision_date() no longer loses the object’s now. It rebuilt without passing it, so the constructor re-inferred now from the dates that were left – and the revision axis is the one that usually holds the latest of them. This reached tbl_now_to_epidist() as a wrong obs_date, epidist’s right-truncation clock.

plot_scalogram() is removed

The wavelet scalogram was shipped as very experimental and never earned its keep: it was never confirmed to identify batches reliably, and the two packages it needed to do so – and – were carried in Suggests for that one plot alone.

Most of the package is now stable

The lifecycle badges have been promoted: every exported topic now reads stable, except the surfaces still being worked on — update(), summary(<tbl_now>), diagnose(), diagnose_batches(), diagnose_batches2(), simulate_batch(), transport_discriminant(), autoplot() (both methods), tbl_now_to_EpiNow2() and tbl_now_to_epidist(), which keep experimental.

No behaviour changed; this is a statement about which signatures are now expected to hold still.

autoplot(<tbl_nowcast>) gains date_lim and ylim

A nowcast covers the whole series but only corrects its final periods, so almost every call was followed by a coord_cartesian() to zoom on to them.

  • New: autoplot(fit, date_lim = c(from, to)) and autoplot(fit, ylim = c(lo, hi)). NA in either position leaves that end free; NULL (the default) leaves the axis alone.
  • Both are applied with ggplot2::coord_cartesian(), so they crop the drawn plot instead of filtering the data. That is the point: a scale limit drops the out-of-range rows before the ribbon is built, which cuts the fan off at the boundary rather than letting it run to the edge of the panel.

Two fixes the revisions article turned up

  • Fix (run_nowcast() lost the engine’s label): the fit recorded the backend’s package name as its @method while nowcast_backtest() scored the same engines under their labels. Two configurations of one backend – exactly what label exists for – were therefore indistinguishable once fitted, and nowcast_ensemble(weights = "inverse_score", backtest = ) aborted with “the backtest has no scores for method "diseasenowcasting"”. run_nowcast() now records the label. An unlabelled engine is unaffected: its label defaults to its package name. A backend that returns a tbl_nowcast directly ( does) keeps its own name unless the caller supplied a label. run_nowcast(verbose = TRUE) now names the label as well, so two configurations no longer print the same line.
  • Fix (diagnose()’s pending note printed an R object): the strata/pending note built its “how overdue are they” clause as a deferred .diagnose_text() and then interpolated it into the outer template as {against}. cli deparsed the object, and the note read “… 3.4% of the stratum; list(list(args = list(…), envir = )).” The two fragments are now joined rather than nested, and the note reads as prose in both of its branches.

A revisions walk-through

Site

  • The package version in the pkgdown navbar was the only item there that changed colour with the light switch: pkgdown renders it inside .text-muted, whose Bootstrap 5.3 definition follows the theme. It is now pinned to the same white as the package name in both modes.

complete_zeroes() keeps temporal effects computed

complete_zeroes() adds rows, and materialised [temporal_effects()] columns are a per-row property, so the new cells joined in as NA while computed_temporal_effect_cols went on claiming the columns were computed. The function announced this with a cli_alert_warning() and left the caller to repair it.

  • Fix (stale columns): the effect columns are now recomputed on the completed grid before the result is returned, so every added row carries its own calendar effects. The alert is gone – there is nothing left to warn about. A lazy specification that was never computed stays lazy. The one case that cannot be repaired – computed columns with the specification stripped by hand – still warns, and now says so accurately.
  • Fix (the advice did not work): the alert told callers to run compute_temporal_effects() afterwards, which errored, because the columns were already present; overwrite = TRUE was needed and unmentioned.
  • Fix (overwrite = TRUE was inert for seasonal effects): the guard in add_temporal_effects.data.frame() read cos_exists || (sin_exists && !overwrite) – && binds tighter than || – so an existing _cos column aborted the call whatever overwrite was set to. A computed seasonal effect could therefore never be refreshed, by complete_zeroes() or by anyone else.

Reported downstream in diseasenowcasting#126, where every count-cumulative fit calls complete_zeroes() and so emitted the alert.

rowwise() demotes cleanly

rowwise() stays deliberately unimplemented for tbl_now – but it now says so properly and gets out of the way properly.

  • Fix (leaky demotion): rowwise() returned a rowwise_df that still carried event_date, report_date, now, strata and the rest as attributes, describing a class the object was no longer an instance of. It now goes through the same demotion door as every other downgrade in the package, so the returned object carries none of them.
  • Fix (wrong condition type): the notice was a cli_alert_warning(), which signals a message. suppressWarnings() did not silence it and tryCatch(warning = ) did not see it. It is a real cli_warn() now, and names the columns (.event_num, .report_num, .delay) that have to be dropped before as_tbl_now() will rebuild the object – the previous advice to just call as_tbl_now() errored.
  • Fix (silent grouped path): rowwise() on a grouped_tbl_now dispatched to dplyr’s rowwise.grouped_df, which sits before tbl_now in the class vector. That path demoted just as leakily and emitted nothing at all. A rowwise.grouped_tbl_now method now routes it through the same code.

Implementing rowwise() properly was considered and rejected: it would need a second parallel rowwise_tbl_now class carrying the same dozen dplyr methods grouped_tbl_now already needs, and dplyr::group_vars() reports the rowwise variables while dplyr::is_grouped_df() is FALSE – so every function here that reads group_vars() to pick an aggregation key (to_count(), complete_zeroes(), censor_delays(), align_weeks(), …) would silently read a rowwise variable as a stratifying one.

Sharper epidist integration

Findings from the epidist audit against epidist 0.4.1:

  • Fix (right truncation): tbl_now_to_epidist() now writes an obs_date column set to get_now(x) + w (the end of the now period, widened by the censoring window), instead of letting epidist default it to max(sdate_upr). Without this the right-truncation clock ended at the last observed report, so a silent-tail series or a backtest under-corrected silently. Matches what tbl_now_to_EpiNow2(target = "estimate_dist") has always done.
  • New argument: tbl_now_to_epidist(obs_date = ) lets the caller override the auto-set value (a single Date, or one per row).
  • Fix (round trip): tbl_now_from_epidist() now recovers now from epidist’s obs_date column on the "auto" path (now = max(obs_date) - w), so to_epidist() |> from_epidist() preserves now.
  • New warning: tbl_now_to_epidist() warns once (silenced by quiet = TRUE) when the input carries a revision process (has_revision(x) or is_censored_revision), because epidist models one delay and the revision axis is dropped from the converted object.
  • Docs: the stale “Model choice for count data” section is removed; the Stan compilation failure it warned about was fixed in epidist 0.4.1 (NEWS #583). as_epidist_marginal_model() is now recommended for aggregated counts.
  • Tests: new tests/testthat/test-converter-epidist.R locks the three contracts above (obs_date on every format, round-trip recovery, revision warning) and extends tidy.epidist_fit()’s bookkeeping filter so epidist’s n/weight/.observation/.row cannot leak into the tidy output as bogus parameters.

Sharper epinowcast integration

Findings from the epinowcast audit against epinowcast 0.7.0:

  • Fix: tbl_now_to_epinowcast() no longer reports materialised temporal-effect columns as “dropped covariates”. Those columns are actually threaded onto metareference / metareport – the earlier warning contradicted the docstring and confused users who had run compute_temporal_effects() before conversion.
  • New warning: tbl_now_to_epinowcast() now warns (silenced by quiet = TRUE) when it attaches temporal-effect columns to the preprocessed object, listing the column names and showing an example enw_reference(parametric = ~ 1 + .event_day_of_week, ...) call. Nothing in epinowcast() auto-wires those columns into a module formula.
  • New fit-time check: engine_epinowcast() / nowcast_fit.epinowcast() now warns when the caller’s expectation / reference / report / missing do not reference any of the declared temporal-effect columns – so a caller who forgets to name them in a module formula sees a warning at fit time, rather than a fit that silently ignores them.
  • Docs: engine_epinowcast() clarifies that enw_fit_opts() has no seed argument of its own (checked against formals(epinowcast::enw_fit_opts) on 0.7.0); seed rides through its ... to the sampler (enw_sample()). Also documents the 0.7.0 additions enw_obs(delay_only = TRUE) and enw_report(structural = ...) / enw_dayofweek_structural_reporting().
  • Docs: tbl_now_epinowcast gains a Per-cell observation flags section explaining that epinowcast’s enw_obs(observation_indicator = ) is a cell-level flag rather than the case-level is_censored_report, and cannot be built from is_censored_report alone.
  • Robustness: tidy.epinowcast() no longer hard-codes q5/q95. It picks the widest symmetric pair (qp, q(100-p)) present in the summary(fit, type = "nowcast") frame, so a caller who passes non-default probs to enw_nowcast_summary() no longer causes a $q5 / $q95 lookup crash. The level is derived from the pair; the median stays the estimate.
  • Robustness: nowcast_tidy.epinowcast()’s fallback quantile summary now passes type = "nowcast" to summary(fit) explicitly, rather than relying on the default.
  • Test: new grouped test for tbl_now_to_epinowcast(); the converter ungroups internally, and this now asserts that.

Native strata dispatch on baselinenowcast

baselinenowcast >= 0.2.1 accepts a long tidy data.frame with a strata_cols argument and returns a single baselinenowcast_df with the strata columns still attached. engine_baselinenowcast() uses that path for stratified objects instead of looping one triangle at a time, which enables sharing estimates across strata and drops an internal wrapper class.

  • New: engine_baselinenowcast(strata_sharing = ) – passed straight through to baselinenowcast::baselinenowcast(). "none" (default) fits every stratum independently; "delay" shares the delay PMF across strata; "uncertainty" shares the uncertainty parameters; both can be combined. Meaningful only when the object has strata.
  • New default: tbl_now_to_baselinenowcast(format = "auto") – returns a reporting-triangle matrix when the object has no strata and the long tidy data.frame (what baselinenowcast() consumes with strata_cols =) when it does. Unstratified callers see no change; a stratified tbl_now used to come back as a pooled matrix (with a warning) and now comes back as the shape baselinenowcast can fit natively.
  • Breaking (internal): the baselinenowcast_strata list class that nowcast_fit.baselinenowcast() used to return for stratified fits is gone. run_nowcast() returns the same tbl_nowcast as before. tidy() on a bare list of baselinenowcast_df fits also stops routing through tidy.list() – pass strata to baselinenowcast(strata_cols = ) (or use run_nowcast()) rather than looping over format = "triangle_list".
  • Bump: baselinenowcast (>= 0.2.1) is now the minimum.

tbl.now 0.35.2

Fixed a bug in the is_weekend() function that made it work solely on an English locale.

tbl.now 0.35.1

One help page for the two delay-distribution tidy() methods

tidy.epidist_fit() and tidy.estimate_dist() now share a single help page, ?tidy.delay_distribution. Both methods return the same delay-shaped table, and documenting them apart duplicated the Value, How mean and sd are obtained and name-collision sections. Nothing about either method’s behaviour changed, and both names still work as topic aliases.

Smaller installed package

The installed size drops from 5.4 Mb to 4.5 Mb, below the 5 Mb R CMD check threshold:

  • man/figures/ no longer ships three README plots that no longer appear in README.md, and the four that do are stored with an 8-bit palette.
  • inst/figures/ (only the hex-sticker source, which nothing loads at run time) is excluded from the build.
  • The introductory vignette renders at 72 dpi. Its wide multi-panel figures were being drawn wider than the 700 px the vignette CSS ever displays, so this costs no visible resolution.

Dataset documentation lives in R/data.R

The roxygen blocks for covid_colombia and hai_bucaramanga moved out of R/data-covid_colombia.R and R/data-hai_bucaramanga.R into R/data.R, which is now the single file documenting every shipped dataset. The rendered help pages are unchanged.

tbl.now 0.35.0

diseasenowcasting engine follows the revision/cumulative API

The diseasenowcasting engine documentation and tests now expect automatic model selection to live in diseasenowcasting::nowcast(). tbl.now passes the tbl_now and engine arguments through without injecting model components.

For count-cumulative data, diseasenowcasting consumes signed changes in the cumulative trajectory and selects its cumulative model unless the caller supplies an explicit model(cumulative = cumulative_process(...)).

tbl.now 0.34.0

Documentation clarifies scoring, covariates and article endings

The documentation now states that scoring and backtests use the resolved truth defined by truth_axis and truth_type, rather than an ambiguous “eventual” quantity. It also makes the covariate as-of rule explicit: covariates used in a fit or backtest snapshot should be values available at that snapshot’s now.

The introductory and custom-model vignettes now end with the shared learning-more fragment, and the ensemble article places its References header before that final fragment.

as_forecast_point() exposes scoringutils point forecasts

as_forecast_point() now converts a tbl_nowcast, ensemble or nowcast_backtest() to a scoringutils point forecast using the median prediction. The old as_scoringutils() quantile-frame helper is now internal; use scoringutils::as_forecast_quantile() directly for quantile scoring.

Reporting hexamap labels are more robust

plot_reporting_hexamap() now keeps its custom event, report and delay labels outside the plotted lattice with range-aware spacing, so axis titles are less likely to overlap tick labels or data marks when article or user figure sizes change.

Revision-axis hexamaps now use revision_units for their arrival grid instead of always using report_units.

Ensemble validation is stricter

nowcast_ensemble() now rejects non-finite fixed weights, duplicated or unknown weight names, duplicate prediction/draw keys inside a member, and invalid n_draws values before doing ensemble arithmetic. These inputs previously led to low-level errors, silently ignored weights, or ensemble predictions whose values were NA.

The ensemble documentation now states that members are assumed to target the same reporting or revision quantity, and that the result should be scored with the matching truth_axis and truth_type.

Autoplot can show revision-date calendar effects

The calendar-effect helpers now accept type = "revision", and autoplot() includes revision calendar and cycle panels whenever a tbl_now has a revision process. Revision panels use the new revision palette role, #C79800 by default.

Temporal effects can target revision dates

add_temporal_effects() now accepts date_type = "revision_date" for revision-aware tbl_now objects. compute_temporal_effects() materialises those specs as .revision_* columns using the revision date and .revision_num. Revision-date changers now preserve lazy temporal-effect specs while invalidating computed columns, and remove_revision_date() drops revision-date specs while keeping event/report specs.

Temporal-effect columns are inrevised when date columns change

change_event_date() and change_report_date() now drop already materialised temporal-effect columns and clear their tracking attribute. The lazy temporal_effects() specification is preserved, so later calls to compute_temporal_effects() or converters that carry temporal effects rebuild fresh columns from the current event/report date declarations.

complete_zeroes() preserves missing counts and completes coarser grids

complete_zeroes() now preserves explicit NA counts in the input instead of rewriting them as observed zeroes. Generated incidence cells are still filled with zero, and generated cumulative cells carry forward the previous known cumulative total.

complete_zeroes() now reconstructs generated report dates through the shared delay helper, so monthly and yearly count grids are completed through now instead of silently returning only the originally observed periods.

Backtesting and scoring are stricter about fairness

score_nowcast() and as_scoringutils() now warn when predictions contain targets outside the supplied truth grid. Missing observed rows inside the tbl_now truth grid are scored as zero, because tbl_now objects need not store zero-count cells; targets outside that grid are still omitted because there is no observed value to score.

score_nowcast(), as_scoringutils() and nowcast_backtest() gained explicit truth_axis and truth_type arguments. The default remains reported totals (truth_axis = "report", truth_type = "total"), and revision-aware truth can now be scored with truth_axis = "revision".

nowcast_backtest() now validates explicit now_dates: they must be non-missing Dates within the observed surveillance window and cannot be after the object’s now. A now_date equal to the object’s now is allowed with a warning, because today’s data may still be incomplete.

nowcast_weights() gained now and include_now arguments. When nowcast_ensemble() derives performance weights from a backtest, rows at the members’ own now dates are excluded by default so weights are trained on a holdout window unless include_now = TRUE is set explicitly.

Constructors and dplyr rebuilds are stricter

mutate() and $<- now rebuild generated numeric date columns when event, report, or revision dates are edited, including .revision_num and .revision_delay for revision-aware objects.

Demotion after renaming protected generated columns now drops all tbl_now attributes, and count-data revision now errors when the declared count column is not numeric. Empty tbl_now() inputs remain unsupported, and one-row inputs must declare their units.

EpiNow2 converter and engine checks are stricter

tbl_now_to_EpiNow2() now validates accumulate, complete, and snapshots before building the target object. accumulate and complete must be TRUE, FALSE, or "auto"; snapshots must be NULL or a single positive whole number.

The EpiNow2 converter now warns when lazy temporal-effect specs are dropped by the date/confirm series targets. engine_epinow2() maps the supported report-date day_of_week temporal effect to EpiNow2’s native observation model with EpiNow2::obs_opts(week_effect = TRUE) when the caller has not supplied obs; temporal effects with no EpiNow2 equivalent warn before being dropped.

The ensemble-nowcasting article now tolerates older cached display data that lacks member_predictions, falling back to the cached baseline member predictions so the comparison plot still renders.

Nowcasts and backtests convert directly to scoringutils (#20, #69)

as_scoringutils() now accepts a nowcast_backtest and reuses the truth already stored in it. The result keeps now as a forecast unit, so the same target predicted at different retrospective dates remains distinct.

scoringutils::as_forecast_quantile() now accepts a tbl_nowcast directly, including the result of run_nowcast() and nowcast_ensemble(), as well as a nowcast_backtest. A full tbl_now can be supplied as truth; a backtest uses its stored truth by default.

scoringutils::as_forecast_sample() now does the same for a tbl_nowcast that retains posterior draws and for a draw-based ensemble. Quantile ensembles are refused because samples cannot be recovered from reported quantiles. A nowcast_backtest() can opt into retaining draws with keep_draws = TRUE; its sample coercion checks that every successful engine/date fit supplied them, rather than silently dropping quantile-only members.

Nested ensembles are now covered explicitly: a quantile ensemble can be a member of another quantile ensemble, and a linear-pool ensemble can be a member of another linear pool when it carries draws.

tidy() on a backtest now returns the predictions, not only the truth (#70)

tidy() on a nowcast_backtest reported what was observed and how each method scored against it, but not what the method had actually said – so the one table you would plot a backtest from was missing half the comparison, and recovering it meant reshaping the object’s long $predictions by hand.

It now carries estimate, conf.low, conf.high and level, named as [tidy()] names them everywhere else: estimate is the 0.5 quantile and level the width of the widest symmetric pair of quantile levels actually present. nowcast_backtest() refuses engines whose quantile_levels disagree, so level is one number for the whole table. Where the levels cannot support a bound the column is NA rather than a guess, exactly as on a tbl_nowcast.

The full column order is now method, now, event_date, stratum, observed, estimate, conf.low, conf.high, level, wis, ae_median, coverage_50, coverage_90. Nothing was removed or renamed and no rows were added – (method, now, stratum, event_date) is still the unique key – so code that selects columns by name is unaffected; code that assumed the frame had exactly nine columns is not.

diseasenowcasting is installed from GitHub, and the error now says so (#72)

Asking for engine_diseasenowcasting() without the package installed suggested install.packages("diseasenowcasting", repos = c(options('repos'), epinowcast = ...)), which cannot work: the package is on GitHub and in no CRAN-style repository. The error now gives the instruction that does work:

install.packages("pak")
pak::pkg_install("RodrigoZepeda/diseasenowcasting")

The internal helper behind these messages takes a character vector now, one bullet per line, and interpolates the instruction rather than pasting it into the cli template – an install call carrying a brace (a git ref, say) used to be read as a glue expression and abort while formatting the abort.

tbl.now 0.33.0

aggregate_time_units() now coarsens the temporal-effect specification (#65)

Aggregating dropped the materialised temporal-effect columns but kept the lazy temporal_effects() spec untouched, so the next compute_temporal_effects() rebuilt a day-of-week column on dates that are all the same weekday. The spec now moves onto the new grid with the dates:

  • day_of_week, weekend, day_of_month, holiday_lags and weekend_lags are properties of a day, so they survive only to = "days".
  • week_of_year survives "weeks", month_of_year survives "months".
  • seasons are rescaled rather than dropped – a Fourier period is a length, so a 365-day season becomes a 52.14-week one, and seasons = 52, season_length = 7 becomes seasons = 52 in weeks. A period that comes out at two units or shorter is dropped: it is at or below the new grid’s Nyquist limit.
  • holidays are kept. On a grid coarser than days the holiday column stops being a 0/1 indicator and becomes the share of the period’s days that the calendar marks (1/7 for a week containing Christmas Day). On daily data it is the same integer indicator as before.

A specification left with nothing in it is removed. verbose = TRUE reports what was dropped and what was rescaled.

add_temporal_effects() (the data.frame method) gained a units argument for this; compute_temporal_effects() reads it off the object.

Breaking: the palette is named by ROLE, not by hue

Every colour in the package now comes from the exported tbl_now_palette(), and every element of it is named for the role it plays rather than for the colour it happens to be. The old names encoded the hue (primary_green, accent_red, near_black), which made the palette impossible to re-theme: somebody handing in a blue-and-orange palette had to call their orange primary_green for the plots to find it.

was is
accent_red reporting
light_red reporting_light
primary_green epidemic
light_green epidemic_light
medium_green epidemic_mid
dark_green epidemic_dark
near_black ink
muted_green ink_muted

The red/green grammar is unchanged – red is still the reporting process and green still the epidemic one. What changed is that the names now say that instead of naming the pigment.

There is no deprecation shim. A palette argument carrying the old names is rejected with an error listing the roles it is missing.

The palette also grew the colours that used to be written into the plotting code as literals ("grey60", "white", "#C4D5DE"): ink_inverse, surface, surface_muted, surface_dark, grid_major, grid_minor, guide, guide_strong, annotation, neutral, zero, pending and observed. A re-theme now reaches every mark on the page, and no plotting function contains a hex code.

tbl_now_palette() fills every role from its own defaults, so a partial override is still a complete palette:

plot_reporting_triangle(x, palette = tbl_now_palette(reporting = "#5B4B8A"))

New: plot_weekend_effects(), and the day-type panels are normalized only

plot_weekend_effects() is plot_holiday_effects() for the common case of wanting to see the weekend without first writing the specification down. It attaches temporal_effects(weekend = TRUE) when the object does not already ask for a weekend effect – on a copy, so your object is unchanged – and then draws the same day-type panel. A holiday calendar that is already attached still contributes its Holiday box, and a weekend_days argument sets the weekend definition when this is the call that has to attach it. It needs daily data, and says so rather than drawing a single box:

plot_weekend_effects(daily_now)                  # the weekend, in one call
plot_weekend_effects(daily_now, type = "report") # ... and in the delay
plot_weekend_effects(weekly_now)
#> Error: A weekend effect needs daily data.
#> x `event_units` is "weeks".

Breaking: the four holiday panels – "calendar_holiday", "calendar_holiday_lag" and their delay_* twins – are now always drawn measure = "normalized", and measure is gone from the signatures of plot_holiday_effects() and plot_holiday_lag_effects() (it stays on plot_day_of_week_effects(), plot_week_of_year_effects() and plot_month_of_year_effects()). autoplot() keeps the argument and simply ignores it for those four panels.

A percentage share only means something when the groups are comparable slices of the block it is taken over. A weekend is two days in seven, so “29% of the cases at the weekend” is exactly average and reads as low; the same goes for “1 working day after a holiday”, which is however many days the calendar happens to put there. Normalizing against the mean asks the question the panel is for – is this day type unusual? – and 1 is the answer for “no”.

The day-type panels are also retitled “Weekend and/or holiday effects” (and “Weekend and/or holiday delay effects” for the reporting twin), because that is what their categories are: the panel has never been only about holidays. The holiday-lag panels keep their own titles.

Every plot takes size and linewidth

Point, label and line sizes were hard-coded, so a figure drawn large had marks too small to see. Outside plot_reporting_hexamap() they are multipliers defaulting to 1, which leaves every existing figure unchanged and, unlike an absolute size, preserves a panel’s own hierarchy: plot_transport_discriminant(x, size = 2) doubles both the unflagged points (1.1) and the confirmed batches (2.6) rather than flattening them to one value.

Where a function draws a reference grid of its own – not ’s panel grid, which these plots switch off – that grid has its own absolute argument:

plot_reporting_process(), plot_epidemic_process(), plot_scalogram() and plot_revision_status() draw only bars, tiles or areas, so they take neither, and say so in their documentation rather than offering an argument that would do nothing.

plot_revision_delay() and plot_revision_status() also gained the palette argument they had been missing – they used to call the default palette internally – and now use the shared package theme instead of a bare ggplot2::theme_minimal().

Breaking: the hexamap draws points, not hexagons

plot_reporting_hexamap() marks each (event, delay) cell with a point at the centre of the hexagon it used to fill. A hexagon is drawn in data units: it tiles at any zoom, and that is exactly why it cannot be made bigger – there is no room. A point is drawn in millimetres, so size is a free knob, which is what the plot needed. The projection, the triangular grid and the axes are unchanged; shape = 15 gives squares, which tile the lattice closely.

Because a point is sized in millimetres and the lattice in data units, no default size can suit every combination of cell count and figure size. That is the argument’s reason for existing: raise it until the marks nearly touch at the size you are actually drawing.

Code reading the built plot changes with it – the marks are one row per cell in a geom_point layer rather than six polygon vertices per hexagon.

A batch screen you have subset stops claiming to be one

diagnose_batches() and transport_discriminant() return tibbles with a print() method that summarises the screen. Taking a few columns out of one – the obvious way to look at a result –

flagged <- screened[screened$batch, ]
flagged[order(flagged$p_transport_bh), c("report_date", "reported", "baseline")]

kept the class, so auto-print went looking for the batch column it needed and aborted inside the print method, which is the hardest place to read an error:

Error: Can't subset rows with `!is.na(x$batch) & x$batch`.
x Logical subscript must be size 1 or 4, not 0.

Both classes now demote to a plain tibble when a subset drops a column their summary reads, taking the screen’s own attributes (lookback, alpha, …) with them – the same rule as a tbl_now losing a protected column, silently rather than with a warning, since what is lost here is a print format and not the ability to nowcast. [, dplyr::select() and dplyr::mutate() all follow it; row subsetting, head() and dplyr::filter() keep every column and so keep the screen. As a backstop, both print() methods now fall back to printing the table when a column has gone missing some other way (x$batch <- NULL), rather than erroring.

diagnose_batches() and transport_discriminant() print properly again

Both classes have a print() method, and neither was reached. They were registered with a plain @export, which puts the method in the package’s own methods table; the namespace defines an S7 print generic that shadows base::print once tbl.now is attached, so auto-printing either object fell through to the default and showed a bare tibble instead of the batch screen or the discriminant summary. Both are now registered with @exportS3Method base::print, as every other print() method in the package already was, and there is a regression test asserting auto-print dispatch for each.

Plot backgrounds match the site in dark mode

On the pkgdown site every figure was a black rectangle on a charcoal page. The cause was not in the R code: pkgdown ships one PNG for both themes and relies on a bslib CSS filter, invert(100%) hue-rotate(180deg), which takes a ggplot2 background from white to #000000 while the body is #212529.

pkgdown/extra.css now overrides that filter with brightness(0.871) invert(100%) hue-rotate(180deg) plus mix-blend-mode: lighten. The brightness() before the invert maps white to #212121 while still taking black to white, so no contrast is lost; the blend closes the remaining few units to the page’s slightly blue #212529 and, since nothing in the filtered image is darker than #212121, touches nothing else. The page background is unchanged, and light mode is untouched.

Breaking: diagnose_batch_shape() is now diagnose_batches2()

The shape test is the second half of one question – diagnose_batches() asks how many records arrived on a date, diagnose_batches2() asks which event dates they came from – and the old name read as an unrelated function. It is a straight rename with no deprecation shim: the function is experimental and warns on every call.

Breaking: summary() no longer reports autocorrelation or completeness

case_autocorrelation() and reporting_completeness() were written by an AI and have not been reviewed by a human. They were part of summary(), so every reader of a summary got two numbers nobody had checked, with nothing in the output saying so.

Both are still exported, and both now warn on every call – deliberately not throttled, unlike the experimental diagnostics, because the caveat belongs to the number rather than to the session that produced it. summary() loses its lags, completeness_delays and mature_only arguments, which only ever fed those two blocks; the autocorrelation and completeness components are gone from its output.

summary(x)                        # no longer contains those two components
case_autocorrelation(x, lags = 1) # still there, and says what it is
reporting_completeness(x)

The batch family ignores censored arrival dates

The batch tests – diagnose_batches(), diagnose_batches2() and transport_discriminant() – now drop the rows flagged censored on the axis they are scanning: is_censored_report for axis = "report", is_censored_revision for axis = "revision".

Only those three. The flag is a statement about the arrival axis and about nothing else, so a row censored on the report axis is still a case that happened on its event date: every plot, including plot_epidemic_process() and the diagnostic_plot() panels other than transport, keeps every row.

A censored date is a bound, not the date the record arrived. Censoring is usually applied because something was already known about those dates, and the censored rows all carry the same bound, so leaving them in piles them onto one date and the detector rediscovers, as a finding, the artefact it was told about. Pass drop_censored = FALSE to scan them anyway.

diagnose_batches2() no longer errors on a date with no arrivals

A line list cannot represent a zero, so a report date on which nothing arrived has no rows at all. That is the observation “no arrivals”, not a missing date, and the test now reports n_at = 0 for it instead of aborting. A date off the object’s report grid – where there is nothing to compare against – is still an error, and the message now says the grid’s step.

plot_transport_discriminant() is usable as a plotly widget

  • The axis labels were expression()s. ggplotly() cannot render plotmath and drops them silently, so the interactive plot had unnamed axes. They are now plain text (“Creation z”, “Transport z”).
  • Hovering a point shows the dates behind it: the report (or revision) date the point is, the mean event date of the records that arrived then, the mean delay that implies, and the arrivals against their baseline. The two z-scores are what the point is already positioned by, so they are no longer all the tooltip says.

summary() says what n and total count

One shared schema means the two count columns mean different things in different blocks, and printing them side by side left the reader guessing. Each block now prints a one-line gloss: total is always cases, and n is the block’s own unit – dates on the grid for cases, runs for zero_run, (event, report) cells for delay and composition.

complete_zeroes() works when a date is missing (#66)

A single NA report date made every bound of the grid NA: max_delay came out NA and seq(0, NA) aborted with 'to' must be a finite number, which says nothing about the missing date that caused it. The only workaround was to censor_reports() first, which is a real answer but not the only one a user might want.

Every bound is now computed ignoring the missing dates. A row whose event or report date is NA has no cell on the rectangle, so it takes no part in the grid – but it is still a case, and it is carried through unchanged rather than deleted by the closing report_date <= bound filter (NA <= bound is NA, which dplyr::filter() drops). Only an object in which every row is missing one of the two dates is refused, with a message saying so.

Two things fixed alongside it:

  • .event_num was read off the completing join, so any row with no counterpart on the grid – a negative delay, a missing report date – had its event number blanked even though its event date was perfectly well known. It is now numbered from the event date itself.
  • max_delay = NULL on data whose delays are all negative built a decreasing seq(0, max_delay). The floor is now 0.

Breaking (behaviour): a stratified baselinenowcast fit completes its grid (#67)

run_nowcast(x, engine_baselinenowcast()) returned a different nowcast for a line list than for the same object passed through to_count() |> complete_zeroes() – with the same seed. The stratified path built its triangles from tbl_now_to_baselinenowcast(format = "long"), which is a tidy data frame with no grid and so is deliberately never completed. A line list has no row at all for an event period in which nothing was reported, so the reference axis silently stopped short: 54 reference times where the completed counts gave 81.

nowcast_fit.baselinenowcast() now asks for format = "triangle_list", which is the format that exists for exactly this – one triangle per stratum. It completes the grid, restores the not-yet-observed cells to NA, and absorbs negative increments, none of which the hand-rolled split did. Stratified fits on line-list input will change, and they now agree with the count path.

Because the triangle really does drop declared covariates, a stratified fit on an object carrying them now warns that it did; the long format used to carry them into a frame the fit then ignored.

tbl_now_to_EpiNow2() completes a line list’s grid (#67, audit)

Found by auditing every converter for the defect behind #67. A line list has no row for an event period in which nothing was reported, and .epinow2_series_data() built its date/confirm series from the rows it was handed: on daily data the series stopped at the last period carrying a report rather than at the object’s [get_now()], which is the period the nowcast is about. estimate_truncation() was worse – .epinow2_snapshots() completes each snapshot with complete_zeroes(), which refuses a line list, and the surrounding tryCatch() swallowed the refusal and kept the short snapshot, though ?estimate_truncation asks for “a complete vector of dates”.

tbl_now_to_EpiNow2() gains a complete argument with the same contract as tbl_now_to_baselinenowcast()’s: "auto" (the default) completes line-list input only, because count data can say “observed zero” itself and filling those cells would claim reporting was complete when it was not. TRUE / FALSE force either behaviour. All three series targets (estimate_infections, regional_epinow, estimate_truncation) now reach the now.

The rest of the audit came back clean, and is now pinned by tests: epinowcast completes through enw_complete_dates(), NobBS and surveillance are handed the now by their fit methods (NobBS(now =), get_surveillance_range()), and epidist fits a delay distribution with no event grid at all. tests/testthat/test-engines-linelist-equivalence.R asserts that every engine returns the same nowcast, under the same seed, from a line list and from the equivalent to_count() |> complete_zeroes() object.

tbl.now 0.32.0

Breaking: diagnose() no longer signposts the statistical tests

diagnose_signposts() is removed, along with the "signposts" check, and the not_run status is gone from the findings schema – status is now error > warning > note > ok > skipped.

diagnose() still runs no statistical test, and for the same reason: drift and batching are statements about a distribution, and answering them means choosing a method, a window and a multiplicity correction. What changed is that it no longer spends four rows of every report saying so. Call the tests yourself when you want them:

diagnose_drift(x, axis = "report")
diagnose_batches(x, axis = "report")

They are listed under @seealso on diagnose(), which is where a pointer belongs.

diagnose() findings

  • Right-truncation no longer reports an estimated 0%. An event date can sit past the 95th percentile of the delay with its eventual total already in – the percentile is a bound on the delay, not a promise that something is outstanding. That case is now an ok finding (“none of their eventual total is still to arrive”) instead of a note asking the reader to act on a 0%.
  • A truncation estimate with no mature history is skipped, not a note. Without mature event dates there is no arrival curve to read the recent ones against, and the old code reported the resulting 0% as if it were an estimate.
  • The sparsity finding now carries its denominator and a baseline. It read “87% of the event dates on the grid carry no cases at all”, which is both self-contradictory (a date on the grid is not an event date until it has a case) and unreadable without knowing how sparse the object is as a whole. It now reads “2489 of the 2861 dates on the event grid carry no cases at all (87%, against 73.2% pooled over every stratum)”, and the hint says that when every stratum is mostly zeros the grid is finer than the data and aggregate_time_units() is the fix.

Documentation

  • The covid_colombia example no longer wraps itself in requireNamespace("tbl.now") – a package’s own example can assume the package.

tbl.now 0.31.0

Breaking: the *_confirmed() counters are gone, replaced by a revised-cases family (#64)

get_latest_confirmed(), get_net_confirmed(), get_initial_confirmed() and get_nth_confirmed() are removed. They answered a version of the question get_latest_reported_cases() already answered, in a different return shape (a plain tibble), with a delay measured from a different anchor – so the two families could not be read against each other.

In their place, the reporting getters have an exact twin on the revision axis:

get_initial_revised_cases(x)                     # as of the FIRST result back
get_latest_revised_cases(x)                      # everything settled so far
get_nth_revised_cases(x, delay = 7)              # settled within 7 periods
get_latest_revised_cases(x, type = "confirmed")  # was get_latest_confirmed()
get_latest_revised_cases(x, type = "net")        # was get_net_confirmed()
get_latest_revised_cases(x, type = "by_type")    # every outcome, side by side
  • They return the same count-cumulative tbl_now the reporting getters return, carrying all three dates and the generated numeric columns, rather than a bare tibble.
  • type = is new on both families, so the reporting axis can be filtered the same way: "total" (default), "confirmed", "retracted", "pending", "unknown", "net", or "by_type" for one row per outcome. On an object with no revision process anything but "total" warns and pools.
  • get_nth_revised_cases() counts the delay from the event, so it and get_nth_reported_cases() describe the same period. get_nth_confirmed() measured from the report, which is .revision_delay – a different quantity. Reading the old and new numbers as the same thing is the one migration hazard.
  • A pending case has no revision date, so it never appears on the revision axis; type = "pending" is refused there and belongs on the reporting axis.
  • An empty selection – nothing revised yet, no case with that outcome, no arrival within the delay – is an error naming the reason, rather than a failure inside tbl_now() about an empty data frame.

The reported-cases getters respect a grouping; to_count() says it does not (#61)

get_latest_reported_cases(), get_initial_reported_cases() and get_nth_reported_cases() (and the three new revised ones) now keep the caller’s grouping and answer by it: the grouping columns join the event date and the strata as keys, and come back on the result.

tn |> dplyr::group_by(hospital) |> get_latest_reported_cases()

This is the only way to ask for a count by a covariate – a column that matters without being something you nowcast by. These verbs can do it because they select a point in the process rather than reshaping the object.

to_count() cannot, and now warns rather than dropping the grouping in silence: after aggregating, one row is an (event, report) cell rather than one of the rows that were grouped, so the grouping describes nothing that is left. Declare the column with add_strata() or add_covariates() to keep it out of the sum.

is_tbl_now() is a class check again, not a revision run (#62)

is_tbl_now() used to call validate_tbl_now() inside a tryCatch() that caught errors but not warnings, so the object’s findings escaped from wherever the predicate was called – which is every .assert_tbl_now() in the package. A verb that fixed a problem warned about it twice, after the fix.

It is now a structural check: the class, the attributes a tbl_now cannot do without, and the columns those attributes name. Cheap, and silent.

  • tbl_now_can_reconstruct() suppresses warnings while asking its hypothetical.
  • An object can be a tbl_now and still have data validate_tbl_now() warns about. That is the point: the class is a container, and a container is not a claim that what is in it is clean.

Fractional delays are refused where they are created, and reported where they are found (#63)

A calendar has no half-days, so a fractional delay had to become something. It became round() – round-half-to-even, so 2.5 went down and 3.5 went up, silently – while the numeric axis refused the same value outright.

  • censor_reporting_delays(to_delay =), censor_revision_delays(to_delay =) and tbl_now(delay =) now abort on a delay that is not a whole number of the axis’s units, on every axis. Round it yourself if that is what you mean.
  • validate_tbl_now() warns when an object’s .delay is fractional; it was a diagnose()-only note. The remaining way in is two date columns on different weekday grids, which is exactly what align_weeks() fixes – so this stays a warning rather than an error, and the object you need to hand to align_weeks() can still be built.

tbl.now 0.30.0

New: coarsen the time grid in one call (#56)

aggregate_time_units() moves a tbl_now onto a bigger time unit – daily to weekly, weekly to monthly, monthly to yearly – and updates the object so that .delay, the converters and the models all count in the new unit:

hai <- hai_bucaramanga |>
  tbl_now(event_date = specimen_date, report_date = report_date,
          strata = sex, data_type = "linelist", units = "days")

hai |> aggregate_time_units(to = "weeks")
  • Counts are added up, not merely relabelled. count-cumulative totals are de-accumulated first, aggregated as increments and accumulated again on the new grid, because a cumulative total is not additive.
  • axes = picks which axes move ("all", "event", "report", "revision"), and label = picks whether a period is named by its first or its last day. Use label = "end" when you coarsen only a later axis, or a report lands before its own event.
  • Weeks go through the same epi/ISO machinery as align_weeks(), so type and align_on_day mean what they mean there.
  • It only ever coarsens: asking a weekly object for "days" is an error, not a guess. So is aggregating a numeric axis, which has no calendar.
  • Weeks do not nest inside months. Aggregating to weeks and then to months is not the same as going straight to months; aggregate once, to the unit you want.

New: censor by condition, and replace the date (#57)

censor_reports() and censor_reporting_delays() take a filter()-style condition and record the matching rows as bounds rather than measurements – optionally replacing the date at the same time. This is the fix for the two dates that are not really dates: the missing one, and the sentinel far in the future.

hai |> censor_reports(is.na(report_date), to_report = Sys.Date())
hai |> censor_reports(report_date == as.Date("2222-02-22"), to_report = Sys.Date())
tn  |> censor_reporting_delays(.delay > 60, to_delay = 60)

The censoring family is now six verbs, two axes by three ways to select

by date by delay threshold
reporting (is_censored_report) censor_reports() censor_reporting_delays() censor_reporting_delays_above()
revision (is_censored_revision) censor_revisions() censor_revision_delays() censor_revision_delays_above()

"pending" cases are skipped when a revision date would be written, with a warning saying how many. A pending case is reported and still waiting, so it has no resolution date; writing one would assert a resolution that never happened and make the case look resolved to everything counting arrivals on that axis. Set revision_type to "confirmed" or "retracted" first if the case really was resolved. Flagging without a replacement is unaffected – no date is written, so nothing is contradicted.

  • NA is not a match: a condition that cannot be evaluated on a row is not a condition that row met.
  • Existing censoring flags are merged, never cleared, and the flag column is created as .is_censored_report when the object has none.
  • Replacing a date moves now forward when the replacement lands after it, never backwards, and drops any .report_* temporal-effect column that the move has made stale.

New: one units argument instead of three (#58)

tbl_now() gains units, the shared default for event_units, report_units and revision_units:

tbl_now(hai_bucaramanga, event_date = specimen_date, report_date = report_date,
        strata = sex, data_type = "linelist", units = "days")

Anything given explicitly still wins, so units = "days", report_units = "weeks" reads a daily event date against a weekly report date, and an explicit event_units = "auto" still means infer.

Fixes

  • group_by() (with no grouping variables), summarise() and reframe() copied the event units onto the report axis when rebuilding, so a mixed-unit object silently became a uniform one. They now carry report_units across.
  • infer_units() on a column with a single distinct date warned about min() returning Inf before aborting with an unrelated message. It now says which column it is, and points at units.
  • Censoring a grouped tbl_now aborted inside add_is_censored_report() / add_is_censored_revision(), which refuse a grouped_tbl_now. All four censoring verbs – censor_reports(), censor_reporting_delays(), censor_reporting_delays_above() and censor_revision_delays_above() – now ungroup, work, and put the grouping back.
  • The two censoring axes share one implementation of “merge this flag in without un-censoring anything”, rather than a copy each.
  • Demotion is now one operation. Dropping a protected column returns a plain tibble, and that used to be as_tibble() – which leaves unknown attributes alone on a tibble but rebuilds a grouped_df and drops them. So a demoted object kept the class’s attributes, or lost them, according to whether the caller had grouped it. It now strips them explicitly, either way.
  • align_weeks() failed on a grouped tbl_now with Column "now" not found in data: it read get_now() and nine other attributes off its own input after demoting it, and worked only by the asymmetry above. It now reads them first, and returns the grouping.
  • complete_zeroes() aborted on a grouped tbl_now ('length = 2' in coercion to 'logical(1)'): every bound it computes is a filter()/distinct()/pull() that a grouping turns into one value per group, so the date grid was built from a vector. The grid is a property of the object, not of how the caller grouped it.
  • tbl_now_to_epidist() aborted on a grouped tbl_now; it was the only converter that did.
  • DEVELOPMENT_SKILL.md gains Every new function gets a grouped test (§8) and a line in the definition of done, because the six grouping fixes above are all the same bug; devel/audit_grouped_verbs.R sweeps every exported function for it. Three verbs drop the grouping deliberately and are left for #61 to decide: to_count(), get_latest_reported_cases() and get_initial_reported_cases().

tbl.now 0.29.0

Breaking: is_censored is now is_censored_report (#54)

There are two censoring axes now, so the unqualified name had to go. The old spelling is removed outright, not deprecated:

was is
tbl_now(is_censored = ) tbl_now(is_censored_report = )
get_is_censored() get_is_censored_report()
add_is_censored(), change_is_censored(), remove_is_censored() add_is_censored_report(), change_is_censored_report(), remove_is_censored_report()
is_censored attribute is_censored_report attribute
.is_censored (the column censor_reporting_delays_above() creates) .is_censored_report

New: is_censored_revision, the revision-axis censoring flag (#53)

The twin of is_censored_report, for models that use censored revision delays. It marks rows whose time from report to resolution is a bound rather than a measurement.

Breaking: censor_revision_delays_above() flags instead of erasing

It used to set the offending rows’ revision_type to "pending" and delete their revision date. That was wrong: a case confirmed after 200 days is still a confirmed case, and the object should say so. It now sets is_censored_revision and leaves the date and the outcome alone, exactly as censor_reporting_delays_above() does on the report axis. get_latest_confirmed() therefore still counts those cases.

New: revision_levels, for data not recorded in English (#54)

revision_type may hold only "confirmed", "retracted", "pending" or NA – that was already enforced, and the error now names the way out. tbl_now(revision_levels = ) is that way out: a named dictionary whose names are the labels in your data and whose values are the canonical four.

tbl_now(casos,
  revision_type   = desenlace,
  revision_levels = c(
    confirmado = "confirmed", retractado = "retracted", pendiente = "pending"
  ),
  ...
)

The column is rewritten to the canonical values; the dictionary is kept on the object and read back with get_revision_levels(). A dictionary that would recode a canonical value into a different one is refused, because it would flip the column on every rebuild.

Fixed: change_now() re-censors instead of erroring (#51)

Moving now backwards is what change_now() is for – it is how a backtest walks through time. On an object carrying a revision process it aborted for every now earlier than the last revision, which is nearly every historical as-of date.

It now masks revisions dated after the new now: the revision date becomes NA and the outcome returns to "pending", because a resolution that has not happened yet is not a resolution. change_now() and update_now() gain verbose to silence the report of how many rows were masked.

covid_us carries a revision process (#52)

No shipped dataset had one, so every example fabricated an outcome by row position. covid_us is rebuilt from the same CDC source with the two date columns that were being left on the floor, and it now runs onset -> positive specimen -> registration at CDC:

was is
cdc_case_earliest_dt, cdc_report_dt, n (2020-2021) onset_dt, pos_spec_dt, cdc_report_dt, current_status, sex, n (2020)

cdc_case_earliest_dt is CDC-derived and equals onset_dt for 99.997% of the rows kept, so it is gone as redundant; sex is a stratum, and current_status is the revision outcome – in CDC’s own words, so that mapping it is a worked example of revision_levels. The relationship between outcome and revision delay is real rather than fabricated: probable cases are registered a median of 2 days after the specimen, laboratory-confirmed ones 4 days. CDC does not withdraw cases, so "retracted" does not occur.

tbl.now 0.28.0

Breaking: the confirmation process is now the revision process

The optional third date a tbl_now can carry is called a revision rather than a confirmation, throughout. The old spelling is gone, not deprecated – it had not shipped.

was is
add_confirmation(), change_confirmation(), remove_confirmation() add_revision_date(), change_revision_date(), remove_revision_date()
get_confirmation_date(), get_confirmation_type(), get_confirmation_units(), has_confirmation() get_revision_date(), get_revision_type(), get_revision_units(), has_revision()
confirmation_counts, confirmation_delay revision_counts, revision_delay
censor_confirmation_delays_above(), diagnose_confirmation_delay() censor_revision_delays_above(), diagnose_revision_delay()
plot_confirmation_delay(), plot_confirmation_status(), prop_confirmation_type() plot_revision_delay(), plot_revision_status(), prop_revision_type()
confirmation_date, confirmation_type, confirmation_units arguments revision_date, revision_type, revision_units
.confirmation_num, .confirmation_delay columns .revision_num, .revision_delay
axis = "confirmation" axis = "revision"
"event_to_confirmation", "report_to_confirmation" "event_to_revision", "report_to_revision"

The outcome values are unchanged: a case is still "confirmed", "retracted" or "pending". Revision is what the process does; confirmed is one of the things it can conclude.

diseasenowcasting now uses revision_process() for row-level report resolution and cumulative_process() for count-cumulative signed changes.

Documentation: fewer, fuller reference pages

  • The revision getters now live on ?nowcast_data_getters, next to get_event_date(), and the revision setters on ?add, next to change_event_date(). Someone asking “what did this object record, and how do I change it” now finds every answer on one page instead of four.
  • Describing and diagnosing a tbl_now and Diagnosing reporting batches are now one article, Diagnosing a tbl_now, running structure-first: what is in the data (summary()), what is structurally wrong with it (diagnose()), and then the statistical tests diagnose() signposts but refuses to run.
  • The attribute diagrams in the README now appear on the pkgdown site. They lived in inst/figures/, which pkgdown does not copy; man/figures/ is the directory it publishes, and GitHub renders it just as happily.
  • summary()’s "completeness" and "growth" rows are distributions over event dates, so they populate mean/sd/the quantiles (and, for completeness, prop) and leave the scalar value column empty. The documented examples selected value and got a column of NA; they now select the columns that carry the answer.

Fixed: baselinenowcast on a snapshot (“as of”) series

A snapshot stream restates the whole history in every snapshot, so its delay axis is as long as the series itself and the reporting triangle comes out square. baselinenowcast needs more reference dates than delay columns – it spends max_delay of them estimating the delay distribution and keeps two back for the uncertainty model – so it refused, with a message about reference-time arithmetic that mentioned neither the delay axis nor anything to do about it. Three of the six shipped datasets are that shape.

  • engine_baselinenowcast() gains max_delay, the number of delay periods to keep, forwarded to tbl_now_to_baselinenowcast(). ?run_nowcast already documented it (“max_delay caps the triangle’s width”); what actually happened is that it fell into ... and reached the modelling call, which has no such argument and ignored it.

  • A triangle too wide to fit is now refused by tbl.now, naming the delay axis and a concrete cap – the delay covering 99% of the reported cases:

Note that a snapshot series must be declared data_type = "count-cumulative". infer_data_type() reads a single downward revision as incidence, by design, and a revised running total has them; left to the inference, every delay carries a whole period’s count instead of an increment and nothing downstream can tell.

New: diagnose() and summary() print as reports

Both still return the tibbles they always returned, and every dplyr verb still works on them. What changed is what you see when you print one.

  • diagnose() – and each of its blocks – prints the errors, warnings and notes in full, each with its hint, and counts the checks that passed, that were deliberately not run, and that could not be assessed. print(x, all = TRUE) spells those out too.
  • summary() – and each of its blocks – prints one block per component, dropping the columns that component does not populate. The schema is wide because it holds every block at once; no block fills more than a handful of it.
  • tibble::as_tibble() gives the plain table back in both cases.

New: a nowcast prints its value at the now edge

print() on a tbl_nowcast now leads with the number it was fitted to produce – the estimate and interval at the last event date it covers, one line per stratum – before the quantile table, which starts at the oldest event date.

tbl.now 0.27.0

Breaking: a nowcast is specified with an engine()

run_nowcast() and nowcast_backtest() used to take a method name plus a ... (and, for the backtest, a method_args list of lists keyed by label). Both failed the same silent way: an argument that missed its backend simply vanished, and you got a fitted model at its default with nothing on the object to say so.

An engine is one modelling package plus every argument it needs:

run_nowcast(x, engine_nobbs(max_D = 10, moving_window = 64))

nowcast_backtest(x,
  engine_baselinenowcast(draws = 1000),
  engine_nobbs(max_D = 10),
  now_dates = dates, seed = 20260824
)
  • One constructor per supported package – engine_diseasenowcasting(), engine_baselinenowcast(), engine_epinowcast(), engine_nobbs(), engine_surveillance(), engine_epinow2() – each naming that package’s own arguments, so they are visible in the signature and a typo is an error at the call rather than a default nobody notices. ... still carries anything a named argument does not cover.
  • engine(method, ...) is the general constructor and works for any registered method, including a backend you wrote yourself.
  • The data and verbose are the only arguments outside the engine. quantile_levels moved onto it, because for NobBS it is a fit-time model argument (it lands in specs$quantiles, and NobBS keeps no draws, so a level it was never asked for cannot be recovered) rather than a way of summarising afterwards.
  • nowcast_backtest(x, ...) now takes the engines variadically, or as one list. methods and method_args are gone. An engine’s label is its name in the result; labels must be unique, and every engine must report the same quantile levels – the WIS averages over the levels reported, so mismatched engines are not scoring the same quantity.
  • nowcast_method() is removed. The engine is the object nowcast_fit() and nowcast_tidy() dispatch on, so an existing backend needs no change; write engine("mymodel") where you wrote nowcast_method("mymodel").
  • A bare method string is an error that names the constructor to use.

New: min_date, per engine

Every engine takes min_date, saying how much history to fit on:

min_date means
NULL (default) the whole series
a Date keep event dates on or after it
a number keep the last n periods before now, in the object’s own units

It is per engine on purpose. baselinenowcast and diseasenowcasting take a long series in their stride, while epinowcast and EpiNow2 scale with the number of reference dates and are best given a window – so one global filter() over all of them was the wrong tool.

Prefer the number inside a nowcast_backtest(): now moves between fits, so a fixed calendar cut makes the fitted window grow as the backtest walks forward and the last fit is trained on more data than the first.

min_date trims the event axis, not now, and the trimmed object is what the result carries – so score_nowcast() and autoplot()’s reported counts describe the series the model was actually shown.

Breaking: score_nowcast() / as_scoringutils() take a tbl_now as truth

observed_col is removed, and a plain data frame is no longer accepted. The tbl_now already knows which column holds the observed counts – it is get_case_count(), or the count to_count() produces from a line list – so naming it was a burden on the caller and the old default (“the last column that is neither the event date nor a stratum”) was a guess that could mis-score silently.

score_nowcast(nc, truth = dengue)     # the FULL tbl_now, line list or counts
as_scoringutils(nc, truth = dengue)

Breaking: argument names made consistent

A documentation audit read every exported function and found the same argument wearing different names in different places. 116 of the 148 exports already took x first; these were the exceptions.

  • nowcast_fit() and nowcast_tidy() take engine, not method. This is the one that affects code outside the package: if you wrote a backend, rename the first argument of your methods.

    # before
nowcast_fit.mymodel  <- function(method, x, ..., quantile_levels, verbose) { }
nowcast_tidy.mymodel <- function(method, fit, x, ..., quantile_levels) { }

# after
nowcast_fit.mymodel  <- function(engine, x, ..., quantile_levels, verbose) { }
nowcast_tidy.mymodel <- function(engine, fit, x, ..., quantile_levels) { }

    What arrives has always been the engine – engine()’s own documentation defines an engine as “the object nowcast_fit() and nowcast_tidy() dispatch on” – and the old name was left over from the removed nowcast_method(). The argument is only a dispatch handle, so no method body needed changing; R CMD check’s S3 consistency check will flag yours until you rename it.

    engine(method = ) and list_nowcast_methods() keep “method”, where it correctly means the name of a backend rather than a configured engine.

  • data becomes x in diagnose_batches(), diagnose_batch_shape(), simulate_batch(), transport_discriminant(), censor_reporting_delays_above() and censor_confirmation_delays_above(). Positional calls are unaffected. Two internal helpers also named data in their error messages, so diagnose_batches(x = <not a tbl_now>) used to complain about an argument that did not exist.

  • quiet becomes verbose in censor_reporting_delays_above() and censor_confirmation_delays_above(), with the sense inverted and defaulting to TRUE, matching the twenty other functions that control messaging this way. Write verbose = FALSE where you wrote quiet = TRUE.

    The converters that carry both verbose and quiet keep both: they are different channels – verbose is the conversion summary, quiet is the lossy-conversion warning – and the documentation now says so.

Breaking: align_weeks() numbers weekdays the ISO way

align_weeks(align_on_day = ) counted weekdays from Sunday while is_weekday(weekend_days = ) counted them from Monday. align_weeks() now uses ISO numbering too – 1 = Monday … 7 = Sunday – so the two agree. is_weekday() is unchanged.

The default is unchanged. It becomes 7, which is still Sunday, so align_weeks(x) – and tbl_now(..., align_weeks = TRUE), which is where nearly everyone meets it – behaves exactly as before. Only an explicit align_on_day changes meaning, and the migration is to subtract one, wrapping 1 to 7:

you wrote you meant now write
1 Sunday 7
2 Monday 1
3 Tuesday 2
… … …
7 Saturday 6

New: example_engine(), a toy engine for examples

Every real engine needs its modelling package, so every example that fitted a nowcast sat inside \donttest{} behind a requireNamespace() guard – and none of them ran on a default check. example_engine() needs nothing, is deterministic, and returns in milliseconds, so the examples for run_nowcast(), nowcast_backtest(), nowcast_weights(), score_nowcast() and tidy() on a backtest now show real output.

It is not a nowcasting method. It ignores the reporting delay entirely – reporting the counts that have arrived and putting a spread-wide band around them – so it under-predicts recent dates by construction. That is useful to see and useless to rely on; the examples say so. Its source is also the shortest complete nowcast_fit() / nowcast_tidy() pair in the package, if you are writing a backend.

New: tbl_now() warns on misspelled argument names

tbl_now() keeps unmatched ... names as user metadata, which meant a typo in a real argument name was accepted in silence. case_col = "n" set a useless attribute and left count data typed as a line list – as it had been doing in one of this package’s own examples.

Names close enough to a real argument to be a typo now warn and name the intended one. Deliberate metadata (data_source, citation, population) stays silent: a match needs a shared first letter and an edit distance under a third of the longer name, which is what keeps source from being read as a misspelling of force.

autoplot() on a nowcast draws the reported counts as columns

The cases reported so far were points floating in the middle of the fan, which reads as a second estimate. They are now grey columns under it, so they read as a count measured from zero and the correction the nowcast applies is the visible gap between the top of a bar and the band. The bars are one period wide, taken from get_event_units().

EpiNow2 keeps its draws

nowcast_tidy.EpiNow2() now reads the posterior samples with EpiNow2::get_predictions(format = "sample") instead of the fit’s lower_<pct>/upper_<pct> summary. Before, EpiNow2 could report only a median and the two tails of whatever CrIs it happened to be fitted with – three levels – so quantile_levels could not be honoured, tidy(probs =) was an error, and it could not join a type = "linear_pool" ensemble. It now does all three. The summary path remains as a fallback for a fit get_predictions() cannot read.

This has a visible knock-on: an ensemble containing EpiNow2 now shares all nine of nowcast_quantile_levels() rather than collapsing to three.

Performance: tbl_now() and every dplyr verb on one

No behaviour changed, but the class got substantially cheaper. tbl_now() is about 3x faster and validate_tbl_now() – which runs on every dplyr verb via tbl_now_reconstruct() – about 4x.

Almost all of the cost was building findings that were then discarded. validate_tbl_now() reports at floor = "note", so on a clean object it formatted eleven cli messages and showed one; formatting is the expensive part (a hint interpolating a vector of row numbers costs ~15 ms), and each finding also built its own one-row tibble (~2 ms).

  • .diagnose_text() now returns a template rather than a formatted string, and .diagnose_finalise() filters by the reporting floor before formatting, so only a finding somebody will read is paid for.
  • Findings are plain lists until .diagnose_finalise() assembles the one tibble the caller sees.

diagnose() returns exactly the same tibble, and validate_tbl_now() the same conditions.

Documentation

Every reference page was read once, function by function, for an audience of public-health practitioners first and statisticians second.

  • Eleven defects, most of them found by running examples that had never been run. tbl_now() documented two attributes that do not exist (repot_num – a typo – and event_num) and omitted four that do. The align_weeks example passed case_col =, which ... swallowed, building count data as a line list. The change example referenced an undefined object that only survived because R never forced the promise. update()’s example built from the whole dataset and then “updated” it with rows it already held.

  • Fifteen pages shipped with an empty Description. A block opening with a bare `r lifecycle::badge()` paragraph gets that badge as its entire @description, pushing the prose into Details; ?diagnose_drift and fourteen others showed a badge and nothing else, in the help viewer and in the reference index.

  • Article links. vignettes/articles is .Rbuildignored, so vignette("nowcasting-models") and vignette("custom-nowcast-models") resolved to nothing in an installed package. All article references now use URLs.

  • Ten pages merged into five, with aliases preserved so ?change and existing links still resolve: change and remove onto add; plot_reporting_process onto plot_epidemic_process; names_tbl_now and money_tbl_now onto assign_tbl; as_scoringutils onto score_nowcast; censor_confirmation_delays_above onto censor_reporting_delays_above; is_tbl_now onto validate_tbl_now; week_2_date onto align_weeks; compute_temporal_effects onto add_temporal_effects.

  • Every exported topic now has @seealso, @return and a runnable example; every internal function carries @noRd. Both @examplesIf FALSE blocks are gone, and nothing in man/ contains if (FALSE) or \dontrun{}.

  • ?tbl.now was the DESCRIPTION text and nothing else. It now lays out the workflow – declare, describe, diagnose, reshape, fit, check – with a link into each step.

  • Three slow examples trimmed: align_weeks ran the whole 452,567-row FluSight table (15.4s to 1.5s), tbl_now_summary computed summary() four times over, and both Stan examples fitted on twenty years of dengue data.

  • vignette("ensemble-nowcasting") gains a figure of the ensemble against each of its members, and a section on min_date explaining why the engines are not all shown the same data.

  • data-raw/ensemble_comparison.R fits both Stan back-ends with approximate inference (epinowcast through enw_pathfinder(), EpiNow2 through stan_opts(method = "pathfinder")), so the article rebuilds in minutes rather than overnight. The article says so, so no member’s band is mistaken for that package’s tuned answer.

  • It also no longer fits three epidemics. It scored every member on mpox and covid as well as dengue and cached the result as forecasts; no chunk in the article ever read that table, and it was roughly two thirds of the run time.

  • DEVELOPMENT_SKILL.md records why the CRAN test path cannot be measured with testthat::test_local(), and devel/TEST_SPEEDUP_BRIEF.md is a standalone brief on the suite’s runtime with measured per-file timings.

tbl.now 0.26.0

One surveillance line list per stratum

tbl_now_to_surveillance() gains format = "linelist_list", which returns one line list per stratum as a tbl_now_surveillance_list instead of one frame with a pasted strata column. surveillance::nowcast() has no strata argument, so a stratified analysis is one fit per stratum, and the split no longer has to be done by hand:

pieces <- tbl_now_to_surveillance(x, format = "linelist_list")
lapply(pieces, function(piece) surveillance::nowcast(data = piece, ...))

It mirrors tbl_now_to_baselinenowcast(format = "triangle_list") throughout: the result is a plain list, so lapply(), [[ and friends work unchanged; it is length one and named "all" when the object declares no strata, so the return type never depends on whether strata happen to be attached; it prints what it is; and as_tbl_now() binds it back into a tbl_now, restoring the original date-column names, the strata and the covariates. Count input comes back as a "linelist" – one row per case, totals unchanged – because that is what a surveillance line list holds.

format = "linelist" remains the default and is unchanged.

Documentation

  • The surveillance and NobBS sections of vignette("nowcasting-models") now say that the credible interval is in their figures and is simply too narrow to see: the median band over the plotted window is under 1% of the estimate for both, against 37% for epinowcast. The numbers quoted are computed from the cached tidy() tables rather than typed.
  • EpiNow2 gained the nowcast-vs-truth figure every other engine’s section already had.
  • The surveillance section fits its strata through the new format = "linelist_list".

tbl.now 0.25.0

A vignette on writing your own back-end

vignette("custom-nowcast-models") is the full account of the nowcast_fit() / nowcast_tidy() contract: what a method may assume about the tbl_now it is handed (get the column names from the getters, work on .event_num/.delay rather than the calendar, run the grid to get_now(), remember that a line list cannot hold a zero), how to reuse the tbl_now_to_*() converters and as_tbl_now() instead of reshaping by hand, and what shipping a back-end in a package involves.

The worked example is a delay-ratio nowcast: for each delay it takes the median of the factor by which past mature event dates grew from that delay to their eventual total, and applies the empirical quantiles of that factor to the counts reported so far. It needs no modelling package, so the article runs every line of its own code – including the scoring, the backtest and the ensemble – and it is written twice, once returning predictions and once returning draws, to show both branches of the contract.

vignette("ensemble-nowcasting")’s section 4 now points here instead of carrying its own smaller version of the same material.

Bug fixes

  • autoplot() on a tbl_nowcast drew only the 50% band. The tails of each central interval were matched to the requested width by exact equality, and (1 - (1 - 2 * 0.05)) / 2 is not 0.05, so every other band came out as an NA ribbon and was silently dropped by ggplot2. The default nine quantile levels now draw all four bands, and levels = is matched with a tolerance too.

Documentation

  • ?nowcast_tidy said its ... was “available to your own” methods. It is not: run_nowcast() forwards the user’s ... to nowcast_fit() only, so anything the tidying step needs has to travel inside the fit object. Both help pages now say so.

tbl.now 0.24.0

diagnose(): a structural health check

summary() describes a tbl_now; diagnose() looks for what is wrong with it. One row is one finding, sorted worst first, and the offending row indices come with it:

findings <- diagnose(dengue_now)
findings |> dplyr::filter(status <= "note")

bad <- findings |> dplyr::filter(check == "ordering")
dengue_now[bad$rows[[1]], ]

Ten checks: declarations (attribute types, the columns they name, role collisions, columns the object was never told about, temporal effects added but never materialised), ordering (event <= report <= confirmation, including the transitive leg that a missing report_date would otherwise hide), missing, duplicates, units, negatives, now, truncation, strata and signposts. Each is also an exported function of its own – see ?nowcast_diagnose_components – and diagnose(x) is exactly the dplyr::bind_rows() of them.

status is an ordered factor, worst first, which is why the tibble sorts itself and why status <= "note" reads as “anything worth acting on”: error > warning > note > ok > not_run > skipped.

Four decisions worth knowing about:

  • It runs no statistical test, ever. Whether the reporting delay drifts, and whether reports arrive in batches, are statements about a distribution. Answering them means choosing a method, a maturity window and a multiplicity correction, and diagnose() has no business choosing those on your behalf. It emits not_run rows carrying the call instead – diagnose_drift(x, axis =) and diagnose_batches(x, axis =).
  • Reporting outages are deliberately not detected. A tbl_now does not carry the zeroes, so an absent row means “nothing was reported” and a quiet Sunday is structurally identical to a three-week outage. Telling them apart requires asking whether a run of zero-arrival dates is improbably long, which is a test. The descriptive answer is zero_run_summary(); the inferential one is diagnose_batches().
  • An NA count is reported neutrally. In a reporting triangle it means not yet observed – correct data, and the thing that tells a nowcast the cell is still open – so diagnose_missing() counts it without calling it a defect. An NA date is a different matter and stays a warning.
  • diagnose_strata() uses no thresholds. “Too small to fit separately” depends on the engine and on the epidemic, so it names the extremes – the smallest stratum, its case count and its share; the sparsest stratum and how much of the event grid it leaves empty – and lets you judge.

validate_tbl_now() is the same engine, presented as conditions

validate_tbl_now() no longer has a check list of its own. It calls the findings engine and re-emits the result as the cli conditions it has always emitted: it aborts on the errors and warns about the warnings. One implementation, two presentations.

What that changes for you:

  • validate_tbl_now() now warns when a confirmation precedes its report. That check existed, but only ran at construction, so an object that acquired the problem later never mentioned it again. tbl_now() no longer runs it separately, so it warns once rather than twice.
  • Everything else aborts and warns exactly as before, including warn_non_uniqueness, which stays FALSE there. diagnose() defaults it TRUE.
  • A note is never emitted as a warning. validate_tbl_now() runs inside every dplyr verb, and turning a diagnose() observation into a warning there would make construction noisy for data the class has always accepted.
  • One warning was reworded. The missing-date warning said “N rows have NULL or NA values in column event_date = "event_date"” – it printed the literal string rather than the column, and a column cannot hold NULL. It now reads “N rows have NA values in the event_date column "onset_week"”.

Breaking: the statistical tests take the diagnose_ prefix

The five tests are named for what they are for rather than for the fact that they are tests. The old names are gone, not deprecated:

was is now
test_delay_drift() diagnose_drift()
test_delay_changepoint() diagnose_changepoint()
test_confirmation_delay() diagnose_confirmation_delay()
batch_test() diagnose_batches()
batch_shape_test() diagnose_batch_shape()

The S3 class batch_test, and with it print.batch_test(), is renamed to diagnose_batches to match.

Documentation and website

summary() and diagnose() are now documented where people actually meet the package:

  • A new article, Describing and diagnosing a tbl_now, treats the two as one workflow: what the schema means, what the six statuses mean, why skipped is not ok, and why diagnose() refuses to run a statistical test.
  • The worked example article is restructured. It now builds the tbl_now before cleaning and lets diagnose() report the defects, rather than checking for them by hand and hoping the list was complete. The hand-written cleaning is still there — it is now the fix for what was reported, and it keeps the one check diagnose() deliberately will not do for a line list (deduplicating on a record id).
  • The README and the introductory vignette gain a compact section on each.
  • The reference index is now explicit. _pkgdown.yml gained a reference: section grouping every exported topic, so summary(), diagnose() and their components are findable rather than buried in one alphabetical list. Note for contributors: pkgdown now fails the build on an exported topic that is not listed. pkgdown::check_pkgdown() catches it without building the site.

Fixed: the light/dark switch never rendered

template: light-switch: true was set and lightswitch.js was being loaded, but the site had no toggle. The control is a navbar component, and _pkgdown.yml named an explicit navbar: structure: right: that replaced pkgdown’s default [search, github, lightswitch] without listing it. The script loaded, the button did not exist, and nothing errored. lightswitch is now listed explicitly.

tbl.now 0.23.0

summary() describes the object the way a nowcaster reads it

summary() on a tbl_now now returns a tibble rather than the column-by-column listing summary.data.frame() produces, which said nothing about the structure the class exists to carry. One row is one statistic of one quantity of one stratum:

summary(dengue_now) |> dplyr::filter(component == "delay")

It covers the case counts on each of the object’s time axes (event, report and, where there is one, confirmation), the delay distributions between them, the lengths of the runs of zero dates, the compositional shares (censored, per confirmation outcome, per stratum, per categorical covariate level), the lag-1 autocorrelation of each series, the reporting-completeness curve, the totals, the date ranges and now, and how full the reporting triangle is.

Three decisions worth knowing about:

  • The date grids run to now, not to the last row present. “Cases per event date” is a statement about a calendar; a date with no rows is a zero, not an absence. This is what makes prop_zero and the zero-run lengths mean anything, and it is why a line list – which cannot represent a zero – summarises to exactly the same numbers as its counts. The grid is global, so a stratum whose cases start late shows its leading zeros and the strata stay comparable. So does the triangle-occupancy denominator.
  • Quantiles are the inverse-ECDF (type 1) estimator, not stats::quantile()’s default: q50 is the smallest value whose cumulative weight reaches 0.5. This is the estimator autoplot() and test_delay_drift() already use, so the table and the figures agree, and it always returns a delay that was actually observed. The mean and standard deviation are the ordinary case-weighted ones, equal to expanding the counts to one row per case.
  • Not-yet-observed cells are dropped. An NA count means the cell has not been observed yet, unlike a 0, which was observed and was zero. Those rows carry no cases and are excluded, rather than turning every total they touch into NA – which is what flusight did to an earlier draft. The "unobserved_cells" coverage row says how many were dropped.
  • count-cumulative data gets no delay rows. A cumulative total is not additive across delays, so a case-weighted delay distribution would be meaningless; delay_summary() refuses it outright and points at to_count(). The new "growth" rows take its place, giving the ratio of each event date’s running total from one delay to the next.

Every block of the summary is its own function

summary() is exactly the bind_rows() of these, and each returns the same schema, so they stack:

cases_per_date(), delay_summary(), zero_run_summary(), prop_censored(), prop_confirmation_type(), prop_strata(), prop_covariate_levels(), case_autocorrelation(), date_ranges(), triangle_occupancy(), reporting_completeness() and cumulative_growth().

delay_summary() names the three delays explicitly – "event_to_report", "event_to_confirmation" and "report_to_confirmation" – because the first two are measured from the event and the last is the laboratory’s own turnaround, measured from the report, and confusing them is a documented hazard.

Internal

One date-grid helper replaces three inlined copies of the same seq(from, to, by = <units>) logic, including the one in complete_zeroes() that only knew about days and weeks.

tbl.now 0.22.0

The back-ends that stratify by ONE column

NobBS::NobBS.strat() takes a single strata column name, EpiNow2::regional_epinow() a single region, and surveillance::nowcast() takes no strata argument at all. A tbl_now may declare several stratifying columns, and their interaction – “nowcast each observed combination separately” – is exactly one stratum to those back-ends. The converters now build that column, so there is an argument to write:

  • tbl_now_to_nobbs() and tbl_now_to_surveillance() gain strata_col (default "strata") and strata_sep (default " | "). The declared strata are pasted into that one column, which NobBS.strat(strata = "strata") takes directly and which split() splits a surveillance line list on. The original columns ride along unchanged, and strata_col = NULL opts out.
  • Pasting is refused rather than fudged when a stratum value already contains the separator: the label could not be split back apart, and a nowcast silently attached to the wrong stratum is worse than a failed conversion. The error names strata_sep. tbl_now_to_EpiNow2(target = "regional_epinow") gained the same check, which it did not have.
  • Writing into an existing column is refused too, so a declared covariate called strata is not overwritten.

Previously tbl_now_to_nobbs() handed back the strata as ordinary columns and nothing else, so there was no way to call NobBS.strat() on a multiply stratified object at all. run_nowcast(x, "NobBS") had its own copy of the pasting logic; it now uses the converter’s column, so the two cannot disagree.

tidy() also learned the last per-stratum shape it did not know: a list of stsNC fits, which is what split()-ing a surveillance line list and looping produces.

tidy() returns the quantiles a NobBS fit was asked for

NobBS keeps no draws, so tidy(fit, probs = ...) refused every probs outright. But NobBS(specs = list(quantiles = c(0.1, 0.5, 0.9))) computes those levels at fit time and puts them in estimates – reading them back is a lookup, not an approximation, and refusing it made the documented workflow (“ask at fit time, then request them with probs”) impossible to complete.

tidy() now returns them. A level the fit was not asked for still aborts, because that one really is unrecoverable, and the message now names the missing levels and the specs = list(quantiles = ...) call that would have produced them.

The two date grids surveillance::nowcast() needs

  • get_surveillance_when(x, length = 30) – the dates to estimate, the most recent length steps ending exactly at get_now().
  • get_surveillance_range(x) – the whole time axis, passed as control$dRange.

Both read the step off the object’s own event units and abort on a "numeric" grid rather than anchoring integer indices at the 1970 epoch. dRange matters more than it looks: left to itself nowcast() infers the axis from the line list it was handed, and a line list cannot express a zero – the quiet days at the now edge have no rows, so the inferred axis stops short of exactly the days being nowcast.

The article now runs the code it shows

vignettes/articles/nowcasting-models.Rmd displayed cached results next to code that a separate script, data-raw/nowcast_comparison.R, kept its own copy of. The two drifted, invisibly, because the article never ran what it printed.

data-raw/nowcast_models_precompute.R replaces it: it knitr::purl()s the article, runs the article’s own chunks with the fits live, and reads the displayed objects back out by name. The code that produced every number is now literally the code printed above it. Renaming an object in the article stops the script with a list of what is missing instead of quietly saving a shorter file.

Fixed along the way, all of it drift the old arrangement hid:

  • the Summary figure showed an unnamed grey NA line, because EpiNow2 had no entry in the figure’s colour scale and the factor dropped it to NA;
  • two chunk labels were duplicated and two chunks called tidy() on objects the article never created, so the article could not be knitted at all;
  • the EpiNow2 delay section tidied a dist_fit that was never fitted, and the epinowcast seasonal fit was never assigned to a name;
  • regional_epinow() was called without truncation, which is the one argument that makes it a nowcast – the same trap the pooled section spends a warning box on;
  • epidist’s marginal model is used, now that it compiles. It reads the aggregated weights the converter produces instead of expanding 6.1M cases back to one row each, which is why the latent model was there;
  • the epinowcast sections filtered to two years of daily reference dates while every other engine used 60 days, and the article claimed that “keeps the Stan fit tractable”. It does not: one chain spent six hours in a bad region of the posterior while the other chain of the same fit finished in sixteen minutes. The cached numbers had come from a 180-day fit that took six minutes, so the article had never run its own window. It is 180 days now, with the discrepancy explained in the text;
  • the epinowcast fits were unseeded – epinowcast() does not take R’s set.seed(), so Stan drew its own each run and the same fit took 41 minutes once and six hours the next. Both now pass seed through enw_fit_opts().

tbl.now 0.21.0

The confirmation process

A tbl_now can now carry a third date. Influenza is the picture to keep in mind: symptoms begin (the event), the patient visits a doctor (the report), and days later a swab comes back positive (the confirmation) or negative (a retraction – reported, but not a case after all). The assumed timeline is event <= report <= confirmation <= now.

  • tbl_now() gains confirmation_date, confirmation_type and confirmation_units. confirmation_type takes "confirmed", "retracted", "pending" or NA; pending means reported and still waiting, so it has no confirmation date, which is a different thing from a result you never recorded (NA). Two columns are derived: .confirmation_num (on the same numeric grid as the other dates) and .confirmation_delay, the laboratory’s turnaround, measured from the report.
  • add_confirmation(), change_confirmation(), remove_confirmation(), get_confirmation_date(), get_confirmation_type(), get_confirmation_units() and has_confirmation().
  • A date with no type warns rather than guessing: a date alone cannot say whether the case was confirmed or retracted. A confirmation before its own report warns too.
  • now is confirmation-aware. A result issued on a date means the system was still being observed then, so now is never earlier than the last confirmation, and setting one earlier is an error.
  • The confirmation columns survive dplyr verbs, update(), align_weeks() (which now aligns all three dates) and to_count() (which groups by the confirmation, so a case is never summed together with its own retraction).
  • The print footer gains a confirmation line: the column, its units, and how many cases are resolved.

Counting when cases can be undone

get_latest_confirmed(), get_net_confirmed() (confirmed minus retracted), get_nth_confirmed(x, delay) and get_initial_confirmed() – the confirmation mirrors of the report-axis getters. censor_confirmation_delays_above() returns implausibly long confirmations to "pending", which is what they really were.

Diagnostics on the confirmation axis

A laboratory clearing a backlog looks exactly like a surveillance system clearing its inbox, so rather than duplicate every diagnostic, they take an axis = c("report", "confirmation") argument: batch_test(), batch_screen(), batch_shape_test(), transport_discriminant(), plot_reporting_process(), plot_epidemic_process(), plot_reporting_triangle(), plot_delay_profiles(), plot_reporting_hexamap(), plot_scalogram(), plot_delay_drift(), test_delay_drift(), test_delay_changepoint() and diagnostic_plot().

On the confirmation axis, delays are still measured from the event, so the two axes are directly comparable and the gap between them is the time the laboratory adds. Cases still "pending" are excluded – counting them would invent an arrival on a date they do not have.

New in their own right: plot_confirmation_status() (the confirmed / retracted / pending shares over time), and test_confirmation_delay() / plot_confirmation_delay(), which ask whether retractions come back faster than confirmations – a laboratory that rules cases out sooner than it confirms them biases any nowcast that treats the two alike.

Other changes

  • Calendar temporal effects are now factors. day_of_week, day_of_month, month_of_year and week_of_year are factors with their full level sets (all seven weekdays, 1-31, 1-12, 1-52) rather than character or numeric columns, so a model gets dummy coding rather than treating “Tuesday” as twice “Monday”, and a level absent from a stratum still exists. weekend stays 0/1 and the Fourier seasons stay numeric, as both are already correctly numeric.
  • Fixed: the non-uniqueness warning fired on every confirmed/retracted pair. A case and its own retraction share an (event, report) combination and are still two different rows; the confirmation columns are now part of the key.
  • run_nowcast(x, "diseasenowcasting") passes straight through to diseasenowcasting::nowcast(). The confirmation process belongs to that package’s model(), not to tbl.now, so pass it there.

tbl.now 0.20.0

Bugs found by the new engine test suite

Every one of these was found by writing the tests, not before:

  • count-cumulative data failed on diseasenowcasting before automatic cumulative selection lived in that package. diseasenowcasting::nowcast() now auto-detects cumulative data and selects its cumulative signed-change model unless the caller supplies an explicit cumulative process.

    De-accumulating to incidence first would also “work”, and is wrong: it discards the downward revisions the cumulative likelihood exists to model.

  • A censored report’s window started before its own event date. For is_censored rows, .delay_censoring_windows() bounded the secondary window below by the earliest event in the data rather than by that row’s event, so every censored row implied a possibly-negative delay, and the zero-width guard pushed one strictly negative. refuses it outright (“Assertion on data$stime_lwr failed: not >= 0”) and EpiNow2::estimate_dist() would have fitted a delay distribution with mass below zero. The window is now [event_date, report_date], and the zero-width guard widens upward.

  • as_tbl_now(x, verbose = ) failed on two classes. as_tbl_now.tbl_now_triangle_list() and as_tbl_now.tbl_now_epinow2_snapshots() passed verbose both explicitly and through ...: “formal argument ‘verbose’ matched by multiple actual arguments”. Both now default it into the dots, so the caller still wins.

  • verbose = FALSE was suppressing warnings, not just chatter. .quietly_if() wrapped every backend in suppressWarnings(), which hid exactly the messages that say what the model actually saw – strata pooled, a censoring flag collapsed, covariates dropped. It now suppresses messages only. This is the same failure mode DEVELOPMENT_SKILL section 9 records for run_engine().

  • diseasenowcasting and NobBS were pooling multi-column strata needlessly. diseasenowcasting models any number of strata and labels each combination "F|N"; tbl.now only ever read the one-column case and pooled otherwise. NobBS.strat() takes one column, so several are now joined into their interaction and split back apart. Both take any number of strata, and ?run_nowcast’s table says so.

Covariates and censoring are no longer dropped in silence

  • tbl_now_to_baselinenowcast() (matrix and triangle formats), tbl_now_to_epinowcast() and tbl_now_to_EpiNow2() now warn when declared covariates cannot be carried, naming them and saying what to do instead. Materialised temporal-effect columns count as covariates: they are the case where somebody asked for an effect and would otherwise never learn it was ignored.
  • The censoring collapse already warned; it is now reachable through run_nowcast(verbose = FALSE) because of the .quietly_if() fix above.

nowcast_truth() removed

Dropped entirely rather than kept internal. It was get_latest_reported_cases() reshaped. score_nowcast() and as_scoringutils() take the tbl_now itself as truth.

covidat removed

covid_us is kept: it is the only shipped dataset that actually exhibits backlog dumps, which vignette("batch-reporting") is about. Measured against a 15-day rolling baseline, covid_us has 21 report days above 2x and 5 above 3x; covid_colombia has one above 2x and none above 3x.

New tests

All skip_on_cran(), all on synthetic fixtures built by tests/testthat/helper-engines.R rather than on shipped data, so one axis can be varied at a time:

  • test-engines-matrix.R – 24 real fits per fast engine ({0,2 covariates} x {0,2 strata} x {days, weeks} x the three data types), plus numeric-grid refusals, weekly-grid preservation, strata labelling for 0/1/2 columns, counts-are-cases, and run_nowcast() against the hand-written call.
  • test-engines-covariates.R – used, or complained about, per converter.
  • test-engines-censoring.R – used, or announced, per converter.
  • test-converter-roundtrip-all.R – a registry of every tbl_now_to_*() shape and whether as_tbl_now() brings it back; fails when a converter is missing from it.
  • test-coercion-methods.R – every converter must expose the target package’s own coercion generic (as_reporting_triangle(), as_tsibble(), …) as a thin wrapper, or record why that package has none. It re-checks the “has none” claims against the installed package, so we find out if one gains a verb.

Articles

  • vignette("nowcasting-models"): EpiNow2 is now a two-step fit. Given only a reporting delay it does not nowcast at all – its median stayed flat and sat below the already-reported count. delays says how infections become reports; it does not say the newest days are incomplete. Only truncation does, and that is what the report dimension of a tbl_now measures. Step 1 fits it with estimate_truncation(), step 2 passes it as trunc_opts(). Over the last seven days – about 50% complete – the fit now sits below the reported count on 4 of 21 stratum-days instead of most of them.
  • vignette("ensemble-nowcasting"): the three-epidemic comparison is removed; the article is now about how to use ensembles.

DEVELOPMENT_SKILL

  • A pre-flight grep before writing any new function, with the two questions that decide whether it should exist, and the two times this package got it wrong.
  • The target package’s own coercion verb is now part of “writing a converter”.

tbl.now 0.19.0

Converters no longer make you aggregate first

covid_colombia carries sex. An object built without strata = sex therefore has two rows per (notification_date, diagnosis_date) cell, and a reporting triangle, a tsibble key and an epinowcast observation table each have exactly one slot per cell. Until now that meant tbl_now_to_baselinenowcast() aborted (“duplicate reference_date and report_date combinations”) and tbl_now_to_tsibble() aborted (“a valid tsibble must have distinct rows”), and you had to group_by() |> summarise() before converting.

Both now pool undeclared columns for you, as tbl_now_to_nobbs(), tbl_now_to_surveillance(), tbl_now_to_EpiNow2(), tbl_now_to_epinowcast() and tbl_now_to_data_table() already did. The pooling is to_count(), so case totals are preserved exactly, and it is reported under verbose = TRUE:

i `tbl_now_to_baselinenowcast()`: pooled over 1 undeclared column ("sex");
  18195 rows -> 10129.
i Declare it with `add_strata()` to nowcast it separately.

Line lists are left alone: one row is already one case there, and collapsing would destroy the individual records the target package is being handed.

The non-uniqueness warning now names the culprit

It used to say “Consider using to_count() to aggregate the data or distinct() to remove repeated observations”. The distinct() half is wrong whenever the cause is an undeclared column – those rows are distinct, they differ in sex – so it sends you in a circle, and on data with genuine repeats it silently deletes cases. The warning now inspects the object and says which:

  • undeclared columns: names them, and points at strata = or to_count(), adding that the converters pool them for you so this is information rather than a fault;
  • genuine duplicate rows: says so, and then recommends distinct().

tbl_now_to_baselinenowcast(max_delay = )

A cap on the delay axis, counted exactly as tbl_now_to_epinowcast() counts it – max_delay = 30 keeps delays 0 to 29, giving a 30-column triangle – so the same number means the same triangle in both. NULL (default) keeps every delay, which is the previous behaviour. This replaces the filter(.delay <= 30) |> idiom the docs used to recommend.

nowcast_truth() is now internal

It was get_latest_reported_cases() with the class stripped, undeclared columns summed away and the count renamed .observed – the values were identical. A second public name for that is a second thing to learn for no gain.

score_nowcast() and as_scoringutils() now accept the tbl_now itself as truth and do the reshaping internally, which is shorter than what it replaces:

score_nowcast(nowcast, truth = dengue)          # was: truth = nowcast_truth(dengue)

A data frame of observed counts still works, as does NULL.

?run_nowcast says what the models actually are

Three new sections, because “it calls the package with its defaults” is not enough to read the output:

  • Strata – a table of how many each backend can model and how. baselinenowcast, surveillance, EpiNow2 and epinowcast take any number; diseasenowcasting and NobBS take exactly one and pool with a warning beyond that, because the single array dimension they return cannot be split back into two columns.
  • Temporal effects – the converters materialise them into columns, but only diseasenowcasting uses them automatically. epinowcast needs them named in a module formula; every other backend carries them and ignores them.
  • Censored delays – collapsed with a warning by every backend that goes through a converter; diseasenowcasting receives the flag intact.

And a section on how each engine’s default model is specified, with the two that most need saying out loud:

  • epinowcast defaults to a per-day random effect on the growth rate (a random walk in all but name), a single time-constant lognormal reporting delay, and no day-of-week report effect.
  • EpiNow2 defaults to delays = delay_opts(), which is Fixed(0) – no reporting delay at all – and generation_time = gt_opts(), which is Fixed(1). Those defaults describe a process with nothing to nowcast, so supply the epidemiology yourself. It also models with a Gaussian process rather than a random walk.

Article fixes

  • vignette("nowcasting-models") now cuts at 2021-04-01, on the rising limb of Colombia’s third wave, instead of 2023-03-03 where the epidemic had subsided and a nowcast had nothing to correct. The line-list engines trim to 60 days (278,000 rows; NobBS 24s, surveillance 6s measured) rather than 180.
  • The per-package figures were drawing the wrong quantity. geom_col() was given width = 5.5 on a daily series, so each bar overlapped its neighbours and ggplot2 stacked the overlaps: the grey “reported by now” bars showed sums of about six days. The summary figure at the end of the article used width = 0.8 and was correct, which is why the two disagreed. All the panels now use width = 0.8.
  • The stratified NobBS example handed it count rows, which is the exact mistake the article’s own warning box forbids two screens earlier – it counts rows, so it was nowcasting counts as cases. It now goes through tbl_now_to_nobbs() like the unstratified example.
  • The stratified surveillance example converted the whole series (2.3M cases) at build time and used N.tInf.max = 1000 against per-stratum daily counts of ~4,000, which silently truncates the posterior. It now trims first and uses the same settings as the unstratified fit.
  • vignette("ensemble-nowcasting") gains an experimental badge and note at the top, and a figure showing each member’s median against the ensemble and the eventual truth.

tbl.now 0.18.0

New: one call per model, and ensembles

Until now tbl.now prepared data for six nowcasting packages and normalised what they returned, but running several of them still meant six different calls and six different result shapes to reconcile by hand. This release adds the layer that removes that bookkeeping.

  • run_nowcast(x, method) fits any supported package and always returns a tbl_nowcast: an S7 object holding the predictions as one row per (event date, stratum, quantile level), plus the draws where the backend has them, plus the backend’s own untouched fit. Backends ship for "diseasenowcasting", "baselinenowcast", "epinowcast", "NobBS", "surveillance" and "EpiNow2", each feeding its package through the matching tbl_now_to_*() converter rather than building the input by hand.

    It is called run_nowcast() and not nowcast() because exports nowcast(); keeping the names distinct means both can be attached at once.

  • nowcast_ensemble() combines several of them, either by averaging their quantiles level by level (type = "quantile", vincentization – narrower) or by pooling their draws into a mixture (type = "linear_pool" – wider, and refused outright when a member has no draws, rather than silently dropping it).

  • nowcast_backtest(), score_nowcast() and nowcast_weights() score models retrospectively and turn those scores into ensemble weights ("inverse_score", "optim" or "equal"). as_scoringutils() hands the same object to for its full score suite.

  • nowcast_fit() / nowcast_tidy() are the extension point: two S3 methods, in any package, and run_nowcast() knows about your model. See vignette("ensemble-nowcasting").

  • autoplot() for a tbl_nowcast draws a fan chart, in the palette’s green – a nowcast estimates the epidemic process, not the reporting one.

New: tidy() for a nowcast and for a backtest

tidy() already worked on every raw engine fit. It now also works on what run_nowcast() and nowcast_ensemble() return, which is the way round it should always have been.

  • tidy() on a tbl_nowcast returns the package’s standard frame – event_date, stratum, estimate, conf.low, conf.high, level, engine, plus q* columns for probs. engine is the method (or the ensemble’s name); level is the width of the widest symmetric pair of quantile levels the object actually carries, and is NA, with NA bounds, when no symmetric pair exists. A guessed 0.95 there would defeat the one column that exists to stop a 90% band being compared with a 95% one.

    probs is honoured only when the nowcast carries draws, and errors otherwise: a quantile-only nowcast cannot produce a level it was not summarised at.

    Registered in .onLoad(), because tbl_nowcast is S7 and tidy.tbl.now::tbl_nowcast is not a writable S3 method name.

  • tidy() on a nowcast_backtest gives one row per (method, now date, target), with the internal dot-prefixed columns traded for ordinary ones.

New: reproducible backtests

nowcast_backtest() gains a seed argument. When given, the RNG is seeded immediately before each fit, from the seed and the method and date that fit is for. One set.seed() before the whole backtest only pins anything if every method draws the same random numbers in the same order – which stops being true the moment a method is dropped or one date is refitted. This is the same lesson data-raw/nowcast_comparison.R already records.

nowcast_weights(type = "optim") now falls back to equal weights, with a warning, when the optimiser does not converge on a usable point. It used to return NA weights, which do not fail until much later inside nowcast_ensemble(), as an all-NA nowcast that reads like a modelling problem rather than an optimisation one.

Removed: the nowcaster backend

nowcaster was dropped in 0.16.0 along with its converters, for the reasons recorded there. The run_nowcast() backend for it is not shipped: it called tbl_now_to_nowcaster() and get_nowcaster_strata(), which no longer exist. Neither nowcaster nor INLA is reintroduced to DESCRIPTION.

Other

  • scoringutils added to Suggests (CRAN, so no Additional_repositories entry is needed). is deliberately not added: it is GitHub-only and sits in no repository R CMD check --as-cran can resolve, so declaring it would trade an undeclared-import warning for a CRAN-incoming NOTE about a dependency that cannot be found. nowcast_fit.diseasenowcasting() therefore looks its entry point up with getExportedValue() after .need_pkg() has confirmed the package is installed, rather than writing a literal diseasenowcasting::.
  • LICENSE / LICENSE.md copyright year updated to 2026. The hand-rolled .wis() is now cross-checked against it in the test suite: two implementations agreeing is worth more than either alone.
  • New article, vignette("ensemble-nowcasting"), with the fits precomputed by data-raw/ensemble_comparison.R so the build never fits anything. It reports WIS per model and per ensemble across three epidemics, and answers “does the ensemble beat its best member?” and “does performance weighting beat equal weighting?” from the cached numbers rather than by assertion.
  • vignette("nowcasting-models") gains a run_nowcast() column in its package table, and a pointer to the new article.

tbl.now 0.17.0

New: support

tbl_now_to_EpiNow2() and tbl_now_from_EpiNow2(), against EpiNow2 1.9.0 (now the minimum in Suggests). EpiNow2 takes four different input shapes, one per entry point, so target names the function the result is passed to and it can be handed over unchanged:

  • "estimate_infections" (default) – data.frame(date, confirm), the series as known at get_now(). Also what epinow() takes.
  • "regional_epinow" – the same plus a region column built from the object’s strata (" | "-joined for several, matching the triangle_list convention). The other targets pool strata with a warning.
  • "estimate_truncation" – a tbl_now_epinow2_snapshots list, one date/confirm snapshot per report date. This is the one EpiNow2 model that uses the report dimension a tbl_now exists to carry.
  • "estimate_dist" – the interval-censored frame EpiNow2::estimate_dist() fits a delay distribution to. New in EpiNow2 1.9.0, and it documents the schema exactly, so it shares .delay_censoring_windows() with tbl_now_to_epidist() rather than growing a second copy.

Three things worth knowing:

  • EpiNow2 models a daily process and has no timestep. As of 1.9.0 there is no timestep, interval or period argument on any entry point (all four formals checked), so a weekly series passed as one row per week is read as one row per day – no error, just an epidemic seven times too fast. The converter lays it on the daily grid with EpiNow2’s own accumulate column instead – built by [EpiNow2::fill_missing()] rather than by hand, because a hand-rolled version put each period’s count on the period’s last day where fill_missing() leaves it on the date given, shifting every weekly fit six days with no error. Units coarser than a week, and the "numeric" grid, are refused by name rather than approximated.

    initial_accumulate is passed explicitly rather than inferred: with by, EpiNow2 1.9.0’s inference drops each group’s first observation (a two-region weekly series of 336/167 cases came back as 295/147). Single-series inference is unaffected.

  • The snapshot form has a real inverse. Snapshot k is the series as known at report date k, so differencing consecutive snapshots recovers count-incidence exactly. tbl_now_epinow2_snapshots carries the report dates so as_tbl_now() can do it; a bare list needs report_dates. Verified against EpiNow2::example_truncated, which round-trips to the case for the case. (The commented-out draft of this converter asserted no inverse was possible. For a single series that is true; for snapshots it is not.)

  • estimate_secondary() and estimate_delay() get no target. The first models two data streams against each other and one tbl_now is one stream; the second is superseded by estimate_dist() by EpiNow2’s own help and throws away the censoring a tbl_now carries.

obs_date and the censoring windows are different quantities, and the converter now treats them as such. [sdate_lwr, sdate_upr) brackets when the report happened – at weekly resolution [W, W + 7), a half-open interval whose upper bound is the end of that week, not a claim that anything happened on day W + 7. obs_date is when observation stopped, which estimate_dist() asserts is >= sdate_upr on every row. A tbl_now’s now labels a period, so the instant observation stopped is the end of it: obs_date = now + w. That makes the assertion hold by construction, and nothing is observed after it. Clamping the windows at now instead was tried and rejected – it moves reports in the final period into an earlier one, which the epidist round-trip test caught.

The nowcasting-models article now covers across all three strata, with its results precomputed into nowcast-comparison.rds like every other engine. Two caveats are stated in the article itself: the delay distributions are ’s shipped examples rather than distributions fitted to the Colombian data, and sampling is lighter than the default (500 draws, 250 warmup, 2 chains) because it is much the slowest engine in the comparison.

data-raw/nowcast_comparison.R now takes engine names (Rscript data-raw/nowcast_comparison.R EpiNow2) and merges them into the existing file, leaving every other engine’s rows and recorded timings alone; with no arguments it rebuilds everything as before. This replaces a second script that re-created the setup by parsing the first one.

Two correctness fixes came out of that. Every engine is now seeded per (engine, stratum) immediately before its fit, rather than relying on a single set.seed() at the top of the script – which only pins results if every engine consumes the same random numbers in the same order, and so does not survive refitting a subset. Refitting baselinenowcast alone had been silently changing its estimates, and one EpiNow2 fit produced a stratum whose upper credible bound sat at 1e8 for all 181 days and would not reproduce. Both now refit to max abs diff == 0. The script also refuses to cache any fit whose scale exceeds 100x the observed maximum for its stratum, since an unconverged Stan or INLA fit returns numbers rather than an error.

tidy() gained methods for estimate_infections, epinow, estimate_truncation and estimate_dist, plus a regional_epinow branch in tidy.list() giving one block per region.

tidy.estimate_dist() reports the fitted distribution’s mean and sd alongside its parameters, so its output is directly comparable with tidy.epidist_fit(). They are derived from the distribution, not from the family’s algebra: each draw’s parameters go back into the fit’s own dist_spec and through [EpiNow2::discretise()], which knows the families, and the moments follow by summation over the PMF. Nothing in this package names a distribution, so a family adds later works as soon as discretise() supports it. Against the closed forms the mean is exact and the sd runs about 1% high – the variance a discrete grid adds – so expect a difference of that order against , which reports continuous-distribution moments.

It also honours probs and takes a level argument, matching tidy.epidist_fit(). (An earlier draft rejected probs with a message claiming the engine keeps no draws. It does: summary.estimate_dist() reads them.)

tbl_now_to_EpiNow2(target = "estimate_dist") warns when it pools strata – estimate_dist() has no grouping argument, so it fits one distribution to everything – and warns when a large share of delays are exactly zero, since a lognormal has zero density there and will inflate its variance rather than fail. The message points at the families that do have positive density at zero ("exp", or "gamma"/"weibull" with shape below 1) rather than at a constant shift, which would silently bias every parameter.

Two more points of care:

  • level is read off the lower_<pct>/upper_<pct> column names, because EpiNow2’s CrIs is a user argument – a fit made with CrIs = c(0.5, 0.95) has no lower_90 at all, and hard-coding 0.90 would report a width the fit never produced.
  • tidy.estimate_dist() returns the delay schema (term, estimate, …), not the nowcast one – the second instance of the documented exception alongside tidy.epidist_fit(). Note that summary()’s mean/sd columns are the posterior mean and sd of each parameter, while the mean/sd rows this method reports are the delay distribution’s moments. Same words, different quantities.

.epidist_drop_unusable_counts() is now .drop_unusable_counts() and shared: EpiNow2::estimate_dist() asserts n >= 1 with the identical message epidist uses, so the same filter applies to both.

Audit of the converters and tidy() against the target packages’ own docs

Every claim the converters and tidy() methods make about diseasenowcasting, baselinenowcast, epinowcast, epidist, NobBS, surveillance, tsibble and data.table was re-checked against those packages’ installed help pages and source. Five defects came out of it, all of them cases where the code was silently plausible rather than wrong-looking.

  • tidy() no longer pools strata under "all". tidy.nowcast() documents stratum as "all" when the fit is unstratified, so (stratum, event_date) is meant to be a unique key. Two methods broke that:

    • tidy.epinowcast() read summary(fit, type = "nowcast") and ignored both .group and the by columns sitting beside it. A real two-group fit (by = "age_group" on germany_covid19_hosp, age groups 00+ and 80+) came back as 20 rows all labelled "all", with every one of its 10 reference dates duplicated. It now emits one block per by group, and several grouping columns are pasted " | "-separated, matching tbl_now_to_baselinenowcast(format = "triangle_list").
    • tidy.list() recognised a NobBS::NobBS.strat() fit – it has the estimates/onset_date shape the detector looks for – but ignored the stratum column that NobBS.strat() puts there. A two-stratum fit on denguedat returned 44 rows labelled "all", 22 of them duplicate keys. It now reads stratum when present.

    The probs path for epinowcast was mispaired in the same way: it split the posterior samples on reference_date alone, so on a stratified fit each date’s quantiles went to whichever stratum split() sorted first. The split is now keyed on (stratum, reference_date) and indexed by the summary’s own rows.

  • tidy() no longer invents an interval for a baselinenowcast point fit. baselinenowcast(output_type = "point") returns one value per reference date and stamps output_type = "point" on the result. tidy() ignored that column and took the 2.5%/97.5% quantiles of a single number, reporting conf.low == conf.high == estimate with level = 0.95 – a zero-width 95% band. It now returns NA bounds and NA level, and refuses probs rather than returning the point estimate under a quantile’s name.

  • tbl_now_to_nobbs() prints the units string NobBS accepts. Its verbose summary printed the object’s own "weeks", but NobBS::NobBS() documents units as "1 day" or "1 week"; pasting "weeks" into the call produces -Inf/Inf warnings from seq() and then an opaque replacement has 1 row, data has 0. It now prints "1 week", and aborts up front for any grid NobBS cannot model.

  • The line-list back-ends no longer fabricate 1970 dates from a numeric grid. tbl_now_to_nobbs() and tbl_now_to_surveillance() both coerced the event and report columns with as.Date(). On a numeric-unit tbl_now those columns are integer indices, so index 1 became 1970-01-02 and the conversion succeeded, silently, with a line list of invented dates. Both now abort naming the units, as tbl_now_to_baselinenowcast() and tbl_now_to_epinowcast() already did. tbl_now_to_surveillance() also gained "years" -> "1 year"; it previously fell through to "1 week".

The remaining findings were addressed too:

  • A negative delay now warns instead of silently losing cases. A reporting triangle is indexed by delay from 0, so a report that arrived before its event has no cell: 10 cases in gave a triangle summing to 9, with the affected cell reading 0 – an observed zero – rather than NA. Both triangle formats and tbl_now_to_epinowcast() now warn, naming how many rows and cases go and how to filter them yourself. format = "long" has no delay axis, keeps them, and stays quiet.

  • tbl_now_to_epidist() accepts count-cumulative data. epidist asserts n >= 1, and de-accumulating a cumulative series produces a 0 wherever a report added nothing and a negative on any downward revision – so the conversion died on epidist’s own Assertion on 'data$n' failed for essentially any real cumulative input, and for plain incidence data that had been through complete_zeroes(). Rows carrying no case are now dropped before the epidist object is built: a zero contributes nothing to a delay distribution, so that is lossless and only reported under verbose = TRUE; a negative discards a revision, so it warns; and if nothing usable is left the converter aborts saying why. flusight – the one error cell in the article’s converter matrix – now converts.

  • tidy() handles a per-stratum list of baselinenowcast fits. ?tbl_now_triangle_list recommends lapply(triangles, baselinenowcast::baselinenowcast), and tidy() on the result used to error and suggest engine = "NobBS". A list whose elements are all baselinenowcast_df is now recognised: each is tidied and labelled with its list name (or its position, when the list is unnamed), giving the same one-block-per-stratum table the natively stratified engines return. probs passes through.

  • DEVELOPMENT_SKILL.md section 2 corrected. It claimed tbl_now_to_surveillance() sets control$dRange. It does not, and its own help page says so: now and the delay unit are deliberately left to the caller, because the converter cannot know which window you mean to fit.

Behaviour changes

  • tidy() reports level = NA for a fit instead of 0.95. NobBS()’s lower/upper come from specs$conf, and its return value is list(estimates, estimates.inflated, nowcast.post.samps, params.post) – no specs, so the width is genuinely unrecoverable from the fit. A guessed default is worse than NA in the one column that exists to stop widths being compared blindly. Pass tidy(fit, level = 0.95) to fill it in. The assertion in test-tidy.R that recorded the old behaviour was updated.

  • tidy.epidist_fit() warns on a delay model with covariates. epidist::predict_delay_parameters() returns one row per draw and observation, and the reported quantiles pool over both. For mu ~ 1 every observation shares the draw’s value, so that is exactly the posterior interval; with covariates in the delay model the interval is a mixture across covariate levels, which the docs described simply as “Posterior median”. The method now detects a parameter that varies within a single draw and says so, pointing at newdata for a specific covariate combination. The numbers are unchanged – only the silence is.

Tests

  • New test-tidy-strata.R: stratified tidy() for epinowcast and NobBS.strat(), quantile-to-stratum alignment, the point-fit interval, the per-stratum list of baselinenowcast_df fits, and the level argument. The fits are mocked from the shape of real ones, so the file needs neither cmdstan nor JAGS.

  • New test-converter-grids.R: the numeric grid across every converter, zero / negative / very long delays, gaps in the event grid, a trailing event period with no reports under each complete setting, the negative-delay warning, and epidist’s n >= 1 filtering (including flusight).

  • New test-converter-strata-shapes.R: several stratifying columns, a factor level with no rows, and label-to-value pairing when the data order is not alphabetical.

  • test-converter-censoring.R now covers tbl_now_to_nobbs(), which the converter loop skipped because its package name is not its suffix.

  • Removed support: tbl_now_to_nowcaster(), get_nowcaster_strata(), the tidy() branch for its fits, and its sections in the articles are all gone. The converter worked, but the package around it demanded enough special-casing that keeping it cost more than it returned:

    • Dmax and wdw are counted in weeks, whatever grid you hand it. On a daily series, values chosen as days are silently read as weeks: Dmax = 30, wdw = 120 asked for a 30-week horizon over a 2.3-year window, which ran for 45 minutes and had INLA reporting the fit diverging. The same fit with week-scaled values took 24 seconds.
    • It returns weekly estimates from daily data, so its numbers are weekly totals while every other engine reports daily counts – roughly 6x larger on the same axis, and not comparable without re-gridding. Its label is the week start.
    • age_col must be numeric even though the help calls it a stratum column: a character column errors inside cut(), and a character bins_age trips an if (bins_age == "SI-PNI") comparison against a vector. The converter existed largely to encode strata into codes and hand back the matching breaks.
    • Results come back as those codes, not labels, so a tidied stratified fit reported stratum values of "1" and "2" rather than the levels.
    • It takes its maximum observable time from the last event date, not the last report, so cutting the series anywhere except where max(onset) == max(report) made it NA-mask genuinely observed cells and nowcast below what had already been reported.
    • It needs R-INLA, and was itself installable only from GitHub.

    That last point has a side benefit: was the only entry in Remotes:, so removing it drops that field entirely – and with it the reason the package could not be submitted to CRAN as-is.

  • New tbl_now_to_nobbs(), filling a real gap. counts rows, so handing it count-incidence data was silently wrong: a table of 1,174 rows carrying 50,160 cases was nowcast as 1,174 cases, with no error. The converter expands counts to one row per case first. The articles previously recommended as.data.frame(), which is correct only for a line list.

  • Fixed the pkgdown build on CI. The shared “Learning more” fragment was pulled in with a relative child path (../../man/fragments/...). renders into an intermediates directory under tempdir() and copies relative resources alongside it, so a path containing ../.. escapes that directory – harmless where tempdir() is deep, fatal on CI where it sits two levels from the filesystem root (cannot create file '/tmp/RtmpXXXX/../../man/...'). The fragment moved to inst/fragments/ and every caller now locates it with system.file(), which is path-independent and also works under pkgload::load_all().

  • Dependency fixes for CI. almanac is used by the package but was declared nowhere – the Remotes: entry for it was inert, since Remotes only says where to fetch an already-declared dependency. It is now in Suggests, with its r-universe added to Additional_repositories (it was archived from CRAN). nowcaster was declared but unobtainable from any configured repository; it briefly gained a Remotes: entry, and was then dropped altogether (above).

  • tidy() on a fit now works directly. From 2.1.0 that package re-exports the shared generics generic and ships its own method, so tidy(fit) returns the standard nowcast table. tbl.now now registers its own method for diseasenowcasting::nowcast_prediction only when the package does not supply one, so older versions keep working and newer ones are not overridden. The article calls plain tidy(dnc_fit) again.

  • Article fixes so the code on the page reproduces the output shown. Three places displayed results the printed code could not produce: the section tidied the fit rather than predict(fit), and the section hid the trailing-row trim that keeps the final week from exploding. All three now match the precompute.

  • Documented two tidy() masking hazards. library(diseasenowcasting) attaches its own tidy() generic, and library(broom) overwrites tbl.now’s tidy.list() method (which fits dispatch on). Neither errors; both silently return a different table. tbl.now::tidy() disambiguates.

  • New tidy() method for fits. is the one supported package that does not nowcast – it estimates the reporting-delay distribution – so tidy.epidist_fit() returns a delay-shaped table (term, estimate, conf.low, conf.high, level, engine) with one row per distribution parameter, rather than forcing a delay fit into the per-event-date nowcast schema. probs works, because the fit keeps its draws. Note that epidist() returns c("brmsfit", "epidist_fit") in that order, so a loaded wins dispatch; call tidy.epidist_fit() explicitly if that matters.

  • tidy() now returns ’s credible interval, which it previously discarded. surveillance::nowcast() stores a prediction interval in the returned object’s pi slot at the width control$alpha names (95% by default), but the method hard-coded conf.low, conf.high and level to NA, so surveillance was the one engine that appeared to report no uncertainty. Reaching for the JAGS-backed bayes.trunc/bayes.trunc.ddcp methods was never needed to get an interval.

  • Censored delays no longer break the converters. A censoring indicator that is a property of the case rather than of the delay – an administrative “this date is only an upper bound” mark, say – splits one (event_date, report_date) cell into a censored and an uncensored row. A reporting triangle has one slot per cell, so tbl_now_to_baselinenowcast() and tbl_now_to_epinowcast() aborted on duplicate cells, and the converters that expand back to a line list picked the flag up as an unrequested stratifier. The censoring dimension is now collapsed before the conversion, and each route warns:

    • count data: counts are summed over the flag, so case totals are unchanged;
    • line lists: the column is dropped, leaving one row per case.

    tbl_now_to_epidist() is deliberately exempt: estimating a delay distribution is the one job that can use the flag.

  • tbl_now_to_baselinenowcast() now handles a line list on its own. It already aggregated to incidence; it now also completes the zero periods out to the now (new complete = TRUE argument). A reporting triangle is a rectangular grid, and an event period with no reports has no rows, so the triangle used to stop short unless you remembered to_count() |> complete_zeroes() first. Linelist and count-incidence input now produce an identical triangle.

  • tbl_now_to_baselinenowcast() also accepts count-cumulative data, which it used to refuse. De-accumulating produces negative increments wherever a total was revised downward, and ships preprocess_negative_values() for exactly that; the converter applies it and warns. negatives = "error" restores the old refusal.

  • Bug fix: tidy() ignored the strata of a diseasenowcasting fit. A stratified fit reports strata_draws (draws x event times x stratum), but the method read only the pooled draws, so every row came back with stratum = "all" even when the fit itself said “2 strata”. It now returns one block per stratum, matching what the other engines do.

  • Two new test files worth naming, because they exist to stop silent regressions:

    • test-converter-equivalence.R – every converter accepts line-list input, and the triangle/preprocessing targets give the same result from a line list as from the equivalent count-incidence object.
    • test-converter-datasets.R – every converter against every dataset the package ships. This is the testthat counterpart of the article’s matrix: the article documents, this one fails.

  • Website: fixed a regression that drew an empty scrollbar track (“a rectangle”) under every code chunk. The no-wrap rules have to apply to code as well as its container, but overflow-x must apply ONLY to the container – setting it on the inner <code> too made each one a second scroll context that reserved a gutter. Figure captions are now centred, smaller and grey.

  • The nowcasting-models article now shows the real output of every fit and every tidy() call. The fits are far too slow to run on each build, so data-raw/nowcast_comparison.R captures what each one prints and what tidy() returns for it, and the article replays that. Each section pairs a copy-pasteable tidy(fit) (shown, not run) with a hidden head(5) whose output appears beneath it, so nothing in the visible code has to be trimmed for display. The ad-hoc result extraction each section used to do – pulling $estimates out of NobBS, building a data.frame() from epoch() and upperbound() for surveillance – is gone; every section now uses tidy().

  • New article section running every converter, plus a nowcast, against every dataset the package ships (data-raw/converter_matrix.R), recording which combinations work and explaining the ones that do not: count-cumulative cannot become a reporting triangle without inventing negative increments, epidist has no individual delays to censor in a cumulative series, and a tsibble needs a unique index/key. Each attempt is time-limited so the matrix is reproducible.

  • The article states plainly that each modelling package is a separate install that tbl.now does not pull in, with the commands for the ones that are not on CRAN and the note that Stan, JAGS and R-INLA are software outside R.

  • SKILL.md documents tidy(), the surveillance converter, format = "triangle_list", the new complete_zeroes() behaviour, and the zero-period pitfalls.

  • Every package section in that article now shows how to recover its predictions with tidy().

  • The comparison precompute falls back gracefully when rejects a triangle whose most recent reference times are all zero. A thin stratum can hit that after the zero weeks are completed out to now – here the female series has no case in the final week even though the pooled series does – and the fallback completes only as far as the last week holding a case, costing that stratum one week rather than the whole nowcast.

  • New tidy() methods, one shape of answer whatever engine produced the fit. The converters normalise what goes into a nowcasting package; tidy() normalises what comes back out. It returns event_date, stratum, estimate, conf.low, conf.high, level and engine for fits from , , , and .

    • probs adds one column per requested quantile, named after the probability (q5, q50, q2.5, …). Only the engines that keep draws (, , ) can honour it; the others error rather than return an approximation dressed up as a quantile.
    • level records the width each engine’s interval actually has – reports a 90% band by default while the others report 95%, and without it the two get compared as if they were the same.
    • returns an unclassed list, so it is told apart by structure, with an engine argument to override.
    • tidy() deliberately does not re-grid: packages that bin onto their own week starts keep them, because snapping would hide a real difference.
    • The generic comes from (a new, dependency-free Imports), so it composes with rather than masking it.

  • The nowcasting-models article now cuts at the second week of July 2002 rather than the turn of the year: a December cut lands on the holiday reporting slump, which says more about December than about the models. Section headings are now just the package name, each package’s figure carries a caption instead of a heading, each gains a Simple nowcast heading, and packages needing an external backend (Stan, JAGS, R-INLA) carry a coloured requirement callout. The overview table gained an Additional requirements column.

  • Website: .alert-warning callouts now use the attenuated red the plots use for intervals, and code blocks are pinned to scroll sideways rather than wrap – pkgdown’s white-space: pre-wrap on code inside pre was overriding the bare pre rule and folding long lines onto a second line.

  • Print methods now write to stdout instead of emitting messages. print.batch_test(), print.transport_discriminant(), print.tbl_now_triangle_list() and the temporal_effects print method used the cli_*() family, whose output is a message – so it vanished under message = FALSE, sink() or capture.output(), which is exactly where a print method is expected to work. They now use cli’s cat_*() family. The matching tests were switched from cli::cli_fmt() to capture.output().

  • The epinowcast section filtered on a hard-coded 2008-12-20, left over from the old window; against the new data that matched zero rows and aborted the build. It now trims relative to the series, using tbl_now_to_epinowcast(preprocess = FALSE) followed by enw_filter_reference_dates() and enw_preprocess_data().

  • tbl_now_to_baselinenowcast() gained format = "triangle_list": one reporting triangle per stratum, instead of pooling them into a single matrix. Unlike splitting the long format by hand it takes the delay unit and the strata off the object, so neither has to be restated. With no strata attached the result is still a list — of length one, named "all" — so the return type never depends on whether strata happen to be present.

  • The result is a thin tbl_now_triangle_list class: still an ordinary list, so lapply() and [[ work as before, but with a print() method. The class earns its place as a guard: ’s estimate_and_apply_delays() also takes a list of triangles, but retrospective snapshots of one series rather than one per stratum, and would silently accept a per-stratum list and treat the strata as points in time.

  • as_tbl_now() gained a method for tbl_now_triangle_list, rebuilding a count-incidence tbl_now with the strata recoded onto their column. The strata values are stored on the object rather than parsed back out of the element names, so a stratum containing the name separator still round-trips.

  • Bug fix: as_tbl_now() aborted on any weekly reporting triangle. tbl_now_from_baselinenowcast() ignored the triangle’s own delays_unit attribute and read the delay columns as days, so a weekly triangle produced daily report dates against weekly event dates and unit inference contradicted itself (“report_units must be coarser than or equal to event_units”). Both directions now default delays_unit = NULL and resolve it from the attribute; an explicit value still wins.

  • Bug fix in complete_zeroes(): it was silently deleting real cases. The closing “don’t look into the future” filter compared with < rather than <=, so every row reported on the final report date was dropped — in the function’s own documented example, 5 of 55 cases vanished. A function whose job is to add zeroes was removing data at the boundary.

  • complete_zeroes() now completes out to the object’s now, not merely to the last event date present in the data, and gained an until argument to complete to a specific date instead. An event date with no reports at all does not appear in the data, so the old behaviour left a gap exactly at the now edge — where nowcasting matters. A supplied until never truncates below the data. The line-list error message now explains why a line list cannot hold a zero week and points at to_count().

  • plot_reporting_hexamap()’s max_cells is now a real bound. It previously took the delay at position max_cells and kept every cell sharing that delay, so a wide band at the cut overshot the documented cap.

  • The nowcasting-models comparison now runs to the now for every engine. baselinenowcast gets there via complete_zeroes(); surveillance cannot (a zero-count row expands to zero line-list rows, so padding evaporates) and is instead given its grid directly through control$dRange. The article explains both, including that forcing surveillance to estimate a period with no observations is unstable on stratified data.

  • The nowcasting-models article now builds its tbl_now from the whole denguedat series (52,987 cases over 1,091 weeks) instead of a pre-filtered two-year window. Every converter runs on the full object in a few seconds; where a package needs a shorter series to fit, the article now uses that package’s own argument rather than subsetting the data first — moving_window in NobBS (which is what takes the full-series fit from impractical to about six seconds) and when in surveillance. diseasenowcasting (~12 s) and baselinenowcast (~10 s) take all 1,091 weeks as they are. epinowcast is the one engine with no such argument, since the reporting triangle is already built by the time you hold a preprocessed object; the article shows tbl_now_to_epinowcast(preprocess = FALSE) followed by enw_filter_reference_dates() and enw_preprocess_data(), and prints the full and trimmed objects side by side. Each section states which it is doing.

  • Website: .alert-info callouts (pandoc ::: {.alert .alert-info} fenced divs) are restyled from the Bootstrap default blue into the package’s sage green, with a darker green left rule and heading colour.

  • The nowcasting-models article’s baselinenowcast fit referred to a dengue_triangle2 object that no longer existed; it now uses dengue_triangle.

  • The example article was rewritten from scratch around the new hai_bucaramanga dataset and is now a full end-to-end tutorial: cleaning a messy surveillance extract with dplyr + tbl.now (duplicate records, missing dates, and reports dated before the event they describe), reading the data with autoplot() and the standalone plot_*() diagnostics, testing the reporting delay for drift and change points, attaching only the temporal effects the data justifies, and finally nowcasting with diseasenowcasting and five other engines. Each modelling choice at the end is traced back to a diagnostic at the beginning. It moved from vignettes/ to vignettes/articles/ (the pkgdown URL is unchanged) because diseasenowcasting is not on CRAN and so cannot be fitted while building a shipped vignette.

  • New converters for further back-ends:

    • tbl_now_to_surveillance() builds the individual-level line list [surveillance::nowcast()] works from, renaming the event and report dates to ’s own dHospital / dReport defaults. format = "sts" instead returns the observed curve as a surveillance sts object.

    It accepts count data as well as line lists, expanding counts back to one row per case (de-accumulating first when the data is cumulative). is a new Suggests.

  • The nowcasting-models article gained a section for it and a closing comparison of every engine on one set of axes — one plot for the unstratified object and one faceted by stratum, with a colour per package, the incomplete data each engine actually saw, and the counts those weeks eventually reached. The comparison deliberately uses an earlier 2002-2003 window rather than the article’s main dengue_now, because the latter runs to the end of denguedat and so has no ground truth to check against. The fits are precomputed by data-raw/nowcast_comparison.R and read from a saved file, so editing the prose no longer re-runs Stan, JAGS and INLA.

  • flusight no longer ships duplicate rows (#25). The upstream FluSight time-series.csv contains 39,139 exact duplicates, which forced every example to open with a distinct() call; the dataset now goes from 491,706 to 452,567 rows. The removal is lossless — every repeated (as_of, target_end_date, location_name) key carried an identical observation, with no conflicting values — so that triple is now a unique key. The help page documents the change, and the FluSight example vignette drops the de-duplication step.

  • New dataset hai_bucaramanga: 1,423 healthcare-associated infections (IAAS) notified in Bucaramanga, Colombia, 2016-2023, from the Colombian open data portal. Column names and categorical values are translated from Spanish. It is a deliberately unpolished extract and its help page documents the defects in detail — a 1900-01-01 missing-date sentinel, 88 negative reporting delays, 100 exact duplicate records, and a strongly bimodal delay (3-day median, 92-day 90th percentile) — which makes it a realistic exercise for the delay diagnostics rather than a clean modelling example.

  • test_delay_drift() and test_delay_changepoint() now document every column of their output, plus new Interpreting the result sections. The test_delay_drift() help gained a Choosing a method section explaining why "hamed-rao" is the default (deterministic, no AR(1) assumption, effectively instant) and when to cross-check with "block-bootstrap", which is robust to weekly periodicity but stochastic and thousands of times slower.

  • The Get Started vignette now opens the nowcasting problem with a figure showing observed-to-date cases, the reports still in transit, and the nowcast of the eventual total.

  • The “Learning more” links live in a single man/fragments/learning-more.Rmd and are included in the README and at the end of every vignette and article, so they only have to be edited in one place.

  • Website: the “Articles” navbar dropdown was rendering near-black with grey text because the styling targeted .submenu, which Bootstrap 5 does not use; it now targets .dropdown-menu and matches the pale red of the package plots. pkgdown/extra.css is also no longer listed under includes: in_header:, which was pasting raw CSS into <head> where it was ignored.

  • README code blocks no longer wrap mid-tibble: printed output was being split into stacked column blocks by R itself, which no stylesheet could undo.

tbl.now 0.15.0

  • autoplot() panels are now consistently colour-coded by process: red for everything reporting-related (the delay distribution, the delay calendar/holiday effects, the delay periodogram) and green for the epidemic (event-date) process (the observed cases and their calendar/holiday effects). This matches the colours the standalone diagnostic plots (plot_reporting_process() / plot_epidemic_process(), plot_scalogram(), …) already used, so a panel and its standalone twin read the same.
  • Every autoplot() panel now says which process it describes in its subtitle — either “Reporting delay process” or “Epidemic (event-date) process” — replacing the per-panel explanatory subtitles. A single panel therefore reads on its own.
  • The two periodogram panels are renamed “Cycles (periodogram)” (previously “Seasonality” / “Delay periodicity”).
  • Every autoplot() panel now has a standalone plot_*() twin that draws just that panel (identical data, colours and subtitle): plot_day_of_week_effects(), plot_week_of_year_effects(), plot_month_of_year_effects(), plot_holiday_effects(), plot_holiday_lag_effects() (each taking type = "epidemic" or type = "report"), plus plot_cycles(), plot_delay_distribution() and plot_observed_cases(). Use autoplot() for the grid and a plot_*() for one effect on its own.
  • The day-of-week, week-of-year, month-of-year, holiday and weekend/holiday-lag panels gained a measure argument (in autoplot() and every plot_*() twin). measure = "normalized" (the default) is the existing view — each value divided by its overall mean, 1 = average. measure = "percent" instead shows the share of cases falling in each group with its IQR (e.g. “10% of cases at the weekend versus 90% on weekdays”); the reporting version shares out the reports by report date. Percentages need Date event/report columns.
  • Vignettes: the Get Started guide documents the plot_*() twins and the measure argument, and marks the “Holiday effects”, “Do delay distributions drift over time?” and “Detecting batch reporting” sections as AI-written, pointing readers to the human-written batch-reporting article. The FluSight example analysis is flagged as a work in progress.

tbl.now 0.14.1

  • Strata are now carried into the model converters that can use them. tbl_now_to_epidist() keeps the strata as data columns (usable as covariates in an epidist formula), and tbl_now_to_baselinenowcast(format = "long") keeps them so you can build one reporting triangle per stratum. A single reporting-triangle matrix has no strata dimension, so format = "matrix" now pools the strata with a warning instead of erroring on duplicate cells. tbl_now_to_epinowcast() already passed strata as its grouping (by).

  • The nowcasting-models article was restructured: each package is now shown bare (from dengue_now) and then enriched — one dengue_seasonal object carrying a stratum and temporal effects flows through every converter — so the separate “Carrying delay effects into each model” section is gone. It adds a worked per-stratum baselinenowcast loop (one triangle per stratum). The workflow also had a bug: it used the plural estimate_and_apply_delays() (which expects a list of retrospective triangles) on a single triangle; it now uses the one-call baselinenowcast() wrapper for samples and notes the singular estimate_and_apply_delay() for a point nowcast.

  • New plot_reporting_hexamap(): draws the reporting triangle as an age-period-cohort hexamap (Jalal and Burke, 2020). Event date, report date and delay are the cohort, period and age (report = event + delay); each cell is a hexagon coloured by its report count, and a batch — a single report date — reads as a clean vertical stripe. The number of hexagons is bounded by a max_cells safety cap (the delay axis is auto-capped, with a message, rather than drawing an unbounded map). Replaces the reporting-V panel in the batch article.

  • Bug fix for issue #33: autoplot(x, strata = "race", by_strata = TRUE) no longer errors with a strata passed as column name.

  • autoplot() gained four holiday panels, which describe the attached temporal_effects() spec rather than the event unit:

    • "calendar_holiday" / "delay_holiday" — normalized cases / mean reporting delay by day type. The categories follow the spec: a holidays calendar plus weekend = TRUE gives Weekday/Weekend/Holiday, a calendar alone gives Non-holiday/Holiday, and a weekend effect alone gives Weekday/Weekend. A holiday falling on a weekend counts as a holiday.
    • "calendar_holiday_lag" / "delay_holiday_lag" — the same, by position relative to the nearest holiday ("2 before", "1 before", "Holiday", "1 after", …, plus "Other" as the reference), as asked for by holiday_lags. These show exactly the days the ..._holiday_lag_k / ..._holiday_lead_k columns flag, so you can check a lag is worth modelling before you model it. A date that is both after one holiday and before the next is attributed to the nearer one, ties going to the “after” side.

  • Bug fix: tbl_now_to_epinowcast() now passes a timestep to , inferred from the object’s report units ("days" -> "day", "weeks" -> "week") and overridable with the new timestep argument. It previously left on its "day" default whatever the data, so weekly data was laid out on a daily grid.

  • Bug fix: tbl_now_to_epinowcast() now derives the temporal-effect covariates on ’s completed date grid instead of carrying them through enw_complete_dates(). That function fills the (reference, report) grid and extends the reference axis into the nowcast horizon, but sets every non-schema column to NA on the rows it adds — so the covariates previously survived only on the original rows. Becasue the effects are functions of a date alone, they are n ow re-derived from the completed grid and cover every row, including the recent horizon dates a nowcast has to predict.

tbl.now 0.14.0

  • holiday_lags and weekend_lags in temporal_effects() now accept negative depths, placing the effect before the break instead of after it. A negative depth creates ..._holiday_lead_k / ..._weekend_lead_k indicator columns that flag dates exactly k working days before a holiday / weekend, counting backwards from it — so _lead_1 is the working day closest to the break. weekend_lags = -1 flags the Friday, weekend_lags = -3 flags the Wednesday, Thursday and Friday, and holiday_lags = -1 flags Christmas Eve. Working days skip weekends and holidays exactly as they do for positive depths, and holiday_lags still requires a holidays calendar for either sign. Use it to capture the reporting slowdown that precedes a break; attach one specification per direction to model both sides of it. Positive depths are unchanged.
  • ?temporal_effects gained a “Using a different holiday calendar” section. holidays has always accepted any almanac::rcalendar(), but the docs only showed cal_us_federal(); reporting holidays are local, so the section covers the building blocks (built-in hol_*() rules, custom rholiday() rules, weekend observance with hol_observe(), and editing a calendar with cal_add() / cal_remove()), and works through the New York City calendar as an example.

tbl.now 0.13.1

  • Fixed style in the batch reporting vignette
  • Improved the axis title position in the v triangle to better visualize the dates

tbl.now 0.13.0

  • Bug fix: batch_shape_test() no longer errors (“missing value where TRUE/FALSE needed”) on large count data. The standardised rank-sum expands counts to one value per item, so the group sizes could exceed the 32-bit integer range and their product overflowed to NA; the group sizes are now computed as doubles.

  • batch_test() now returns a lean, Benjamini-Hochberg-only result: report_date, stratum, reported, baseline, deficit, delta, p_transport, p_transport_bh and the batch flag, each documented under ?batch_test. The raw per-point classification column (and the p_creation/p_deletion/scale columns behind it) has been dropped: it was not multiplicity-corrected and over-identified, whereas batch controls the false discovery rate. (transport_discriminant() keeps its classification.)

  • batch_test() (and transport_discriminant()) now infer the calendar period from the object’s temporal effects: a day-of-week effect sets period = 7, a week-of-year effect period = 52 (see [add_temporal_effects()]). A period you pass still wins, with a note if it disagrees; and if the data is daily with no temporal effect, the function suggests period = 7.

  • The baseline_method argument of batch_test() and transport_discriminant() has been removed — the baseline is always the repeated-median local line. The running-median (local-constant) alternative had no advantage: it reduces to the same fit on a flat series and is biased the moment the series trends.

  • New covid_us dataset: a compact aggregation of the U.S. CDC COVID-19 Case Surveillance Public Use Data, with both event and report dates in 2020-2021 (a self-consistent “as of the end of 2021” snapshot), built to demonstrate batch reporting. Its reporting delay is huge and heavily right-skewed — cases were released to CDC in large backlog dumps — so batch_test() and the batch plots recover a clear, real signal (and correctly call the biggest December-2021 spikes surges, since they land on the Omicron wave). Prepared with duckdb from the 14 GB source (see data-raw/covid_us.R).

  • New article, Finding batch reporting in CDC COVID-19 case surveillance data, written for public-health practitioners with no maths. It builds a made-up outbreak with a planted batch to show what each plot looks like (including a novel V reporting triangle – the reporting triangle rotated 45° so a batch is a horizontal slice), rehearses on a real dengue epidemic curve with simulated log-normal reporting and self-planted batches, finds the batches in the real covid_us data, adds a wavelet view (window-inner report-vs-event scalograms, via ), and ends with a one-page summary table. A new transport-vs-creation tutorial plants a hold, a batch and a surge in a made-up outbreak and colours each day the same way on the reporting timeline and in the creation/transport plane, so a reader can trace a bar to its dot and see why a batch goes up, a surge goes right, and a hold drifts up-and-left.

  • Every plot function now takes plotly = TRUE to return an interactive widget (hover, zoom) instead of a static plot: plot_reporting_process(), plot_epidemic_process(), plot_reporting_triangle(), plot_delay_profiles(), plot_delay_drift(), plot_transport_discriminant(), plot_reporting_v(), plot_scalogram(), diagnostic_plot() and autoplot(). Needs the (suggested) package.

  • New plot_reporting_v(): the reporting “V” – the same data as plot_reporting_triangle() (the same event-date x delay cells) rotated 45° so report date runs up the page and the data opens into a V (left arm = event date, right arm = delay). A batch, a diagonal in the square triangle, becomes a horizontal slice. The whole observable triangle is filled (pale-blue reported zeros + coloured reports).

  • New wavelet scalograms, plot_scalogram(type = "reporting") and plot_scalogram(type = "epidemic"), plus the paired plot_reporting_process() and plot_epidemic_process() bar charts. The scalogram splits the count series into fast wiggles (short periods) and slow swings (long periods) and shows the energy at each: a batch lights up as a bright short-period ridge in the reporting scalogram that the epidemic (event) scalogram lacks. These use a window-inner scalogram (, border_effects = "INNER"): computed from observed data only, with no border padding, so nothing is fabricated at the recent (“now”) edge that matters for nowcasting. Reporting views are drawn in red, epidemic views in green. plot_scalogram() defaults to the PAUL wavelet (wname), which localises a batch more sharply; takes a format argument for the x-axis date labels (default "%d/%b/%y"); and paints the region outside the cone of influence dark grey. The series is analysed on its own integer time grid, so weekly (or monthly) data is handled correctly, and the heat map tiles a uniform index relabelled with dates so it stays gapless even for long series.

  • The conservation monitors — plot_creation_transport() (the two window scores as stacked panels) together with the cumulative-backlog, reporting-lag, dashboard and transport-minus-creation “batch score” plots — live in devel/conservation_extras.R, kept out of the package: clean on large batches but noisy in general. The transport diagnostics keep their exported transport_discriminant() / plot_transport_discriminant().

  • simulate_batch() gains a held_fraction argument: the fraction of each closed date’s reports actually held back and released later (default 1, a full closure). With held_fraction = 0.5, roughly half of each day’s reports are held and half report on time – a realistic partial slow-down rather than a total blackout. Supported for "linelist" and "count-incidence" data (a cumulative total cannot be split).

  • The default lookback for batch_test() and transport_discriminant() is now 7 (a week of daily reporting) rather than 3.

  • The @details of the batch functions (batch_test(), transport_discriminant(), batch_shape_test(), simulate_batch()) and the batch plots were trimmed: the formal theorem / null-distribution derivations were replaced with concise, plain-language explanations.

  • New diagnostic_plot(): a gallery of complementary views of the reporting process for spotting reporting artefacts (above all batch reporting), laid out in two columns. The five panels are the reporting process (reports by report date), the reporting triangle (event date x delay), the per-date delay profiles, the reporting-delay drift (plot_delay_drift()), and the transport discriminant plane. Each is also its own exported function. Choose views with panels (a single one is returned as a plain plot), and every view is facetted by stratum. by = c("report", "event") switches the profiles panel; ... (e.g. period = 7) is routed to whichever panels accept it.

    • Every panel carries a plain-language, grey caption explaining what it shows and what the colours mean, and legends are labelled in words.
    • The reporting process y-axis is capped at the 99th percentile only when a pathological dump (over 30x the median day, e.g. covid’s 1.8M-report day) would otherwise flatten the whole series; an ordinary batch spike – the very thing the plot exists to show – is left to tower.
    • The transport discriminant y-axis is limited to the batch region (with default clipping, so points stop at the panel edge) so the deep-negative “hold” dates do not squash the confirmed batches; the shaded region is now labelled “Potential batch region” and each confirmed batch gets a bold, unclipped date label.
    • The reporting triangle draws a third axis for report date: evenly spaced dashed diagonals (report = event + delay) running up-right at 45°, labelled by report date, so event date (x), delay (y) and report date are all readable off one plot (plot_reporting_triangle(report_ticks =), default 6; mark_batches = optionally highlights the biggest batch stripes). It also distinguishes an observable reported zero (muted blue) from a not yet reportable cell (blank), on the full calendar event axis.
    • The delay profiles draw in a single colour at fixed transparency.
    • The transport discriminant colours red only the batch_test()-confirmed batches (BH-corrected), not the raw per-point classification – which at level alpha painted 10-20% of points batch/surge/hold by construction, ignoring multiplicity and the heavy autocorrelation of the window statistics. The shaded batch region and the ±z* lines are drawn only as a reference for where a batch would sit.

  • New transport_discriminant(): exposes the plane behind batch_test()’s conservation law – for every report date the deficit (the transport axis: reports the preceding window is missing) and the window discriminant (the creation axis: the window total relative to its baseline), with robust standardised transport_z / creation_z and the same quadrant classification. A batch sits top-left (a deficit paid the spike, no net creation); a surge sits bottom-right. Returned as a transport_discriminant tibble and plotted by diagnostic_plot(panels = "transport").

  • The multi-panel autoplot() title changed from “Diagnostic plots” to “Automatic plot of effects” (that phrase now titles diagnostic_plot()).

  • batch_test(null_model = "auto") is now overdispersion-aware. The exact Poisson/Binomial null assumes Poisson counts and a baseline that captures the mean; real surveillance counts are overdispersed, and the conditional transport test is then badly anti-conservative (on clean but overdispersed Poisson data it can fake dozens of batches). auto now reserves the exact null for non-negative counts with no detected overdispersion (dispersion <= 1.5) and otherwise falls back to the dispersion-corrected robust null; signed (count-cumulative) increments still always use the robust null. This makes the default far more realistic on overdispersed data (e.g. filtered covid_colombia drops from ~125 flags to ~18; add period = 7 for its weekly reporting cadence to reach ~4). Force the old behaviour with null_model = "poisson" if you need it.

  • autoplot()’s empirical delay distribution panel now adapts to count-cumulative data: instead of a histogram of increments it shows the cumulative growth by delay — boxplots (on a log scale, with a dashed reference at 1) of the ratio of each event date’s cumulative count at a delay to its count at the previous delay. Ratios above 1 are upward revisions, below 1 downward ones, and they converge to 1 as reporting completes, so you can see the cumulative curve stabilise. The log scale makes a doubling and a halving symmetric about 1. linelist / count-incidence data keep the histogram, and the panel respects by_strata.

  • tbl_now_to_baselinenowcast(delays_unit = ) now defaults to NULL and is inferred from the object’s time units for the "matrix" format: when the event and report units are equal and either "days" or "weeks", that unit is used; otherwise the function errors asking you to supply delays_unit explicitly. (The "long" format never uses it.)

  • Added the covid_colombia dataset from diseasenowcasting to here.

  • Fixed several documentation issues that produced “could not resolve link” warnings when building the docs (links to internal helpers / to the un-declared trend package, a [0, 1] mis-parsed as a link, and a mis-ordered internal roxygen block).

  • to_count() now supports count-cumulative -> count-incidence by de-accumulating the series (increment = cumulative total minus the previous one within each event date and grouping). Because cumulative totals can be revised downward, an increment can be negative. This fixes autoplot() (and the other delay diagnostics) on count-cumulative data such as FluSight, which previously errored with “Transformation from data_type count-cumulative to count-incidence not implemented” (#26).

  • Updated SKILL.md (the AI-agent usage guide) to cover everything added since 0.10.0: reporting-delay autoplot() panels and the panels / by_strata selectors, plot_delay_drift() / test_delay_drift() / test_delay_changepoint(), the model-free batch detectors (batch_test(), batch_shape_test(), simulate_batch()), get_nth_reported_cases(), the after-holiday/weekend temporal-effect lags, as_tibble() / as.data.frame() coercion, and the new count-cumulative -> count-incidence support.

tbl.now 0.12.0

Batch detection, rebuilt around a conservation law

The report-batch detectors were rebuilt on a single, exact principle: a batch moves reports along the report axis without creating them, so a window of report dates spanning both the lull and the release has an unchanged total, whereas a genuine epidemic surge inflates it. The previous heuristic detect_report_batches() / plot_report_batches() (multi-signal robust-z, and the model-based conditional scan) are removed and replaced by three model-free, r lifecycle::badge("experimental") functions. Each derives its mathematics in a “The mathematics” section of its help page.

  • New batch_test() returns, per (report date, stratum), the deficit (reports missing beforehand — sensitive to a batch) and delta (the window total minus its expected value — sensitive to a real surge), and classifies each date as "batch", "surge", "batch_and_surge", "hold_or_deletion" or "none". The transport (batch) test conditions on the window total, so its size does not depend on the unknown incidence nor on the quality of the baseline; the baseline itself is refit from report dates outside each candidate window, which makes delta invariant to a within-window batch pathwise. It handles all data types, including "count-cumulative" (signed increments), and takes a period argument that absorbs a fixed reporting schedule (weekends, holidays).
  • New batch_shape_test() tests whether a flagged report date drew on unusually old event dates, by a permutation rank-sum on the reporting delays. It is exactly distribution-free whenever incidence is locally log-linear.
  • New simulate_batch() plants a known batch (a deterministic close-and-release) in a tbl_now, for revision and teaching.
  • New Batch detection article, with worked examples on dengue (a planted batch), FluSight (count-cumulative), and a weekend reporting schedule.

tbl.now 0.10.1

  • autoplot()’s reporting-delay calendar panels (delay_weekday, delay_week, delay_month) are now normalized: each event date’s mean delay is divided by the overall mean delay, so 1 marks an average delay and a dashed reference line is drawn there. Previously the ungrouped panels plotted the raw mean delay while the by_strata = TRUE panels were already normalized. They now share one scale, matching the case-count calendar panels and making the calendar pattern comparable across strata (y-axis: "Normalized delay").
  • plot_delay_drift()’s window now defaults to 7 periods regardless of the time unit — 7 days for daily data, 7 weeks for weekly data. Previously the default was data-dependent (max(5, n_periods / 20)), which produced a very wide window on long series. Pass window = to smooth a specific series.
  • Internal: replaced the remaining base-R data-frame subsetting and column assignment (df[cond, ], df$col <- ...) outside the converters with the equivalent dplyr verbs (filter(), select(), slice(), mutate()). No user-facing behaviour change. The examples and vignettes now likewise use dplyr::filter() rather than [ (e.g. dplyr::filter(batches, batch)).

tbl.now 0.10.0

  • New get_nth_reported_cases(): the cumulative cases reported for each event date within a given delay. delay = 0 gives the initial snapshot, delay = 1 adds the delay-1 reports, and so on; delay = Inf (or the maximum delay) matches get_latest_reported_cases(). Documented alongside get_initial_reported_cases() and get_latest_reported_cases().

  • Performance: get_latest_reported_cases(), get_initial_reported_cases() and get_nth_reported_cases() are substantially faster (~3-4x on the bundled data) — the aggregation now runs on a declassed data frame and the tbl_now is reconstructed once, with identical output.

  • The experimental diagnostic functions (plot_delay_drift(), test_delay_drift(), test_delay_changepoint(), detect_report_batches(), plot_report_batches()) now carry a lifecycle experimental badge. test_delay_drift() and test_delay_changepoint() additionally emit a cli warning that they are experimental, their results are not guaranteed and their interface may change. Flagged batches, change points and trend changes are surfaced as potential (e.g. “potential batches”, “potential change point”).

  • New detect_report_batches() and plot_report_batches() to detect batch reporting — report dates on which a laboratory releases a backlog of many old cases at once. Working on the report-date axis, it flags a report date using up to four selectable robust-anomaly signals (volume, delay, span, gap), AND-ed together. Requiring the delay (long/dispersed delays) signal alongside volume is what distinguishes a batch from an epidemic peak: a peak also spikes the report volume, but its cases keep the normal short delay distribution, so its delay score stays low. detect_report_batches() returns a per-report-date table with the features, robust scores and a batch flag; plot_report_batches() shows the report-volume and mean-delay timelines with the flagged dates marked.

  • New test_delay_changepoint() complements test_delay_drift(): where the latter tests for a gradual monotonic trend, this tests for a single abrupt change point in the per-period delay summaries using Pettitt’s nonparametric test (implemented directly, no extra dependency). It reports the estimated change date, the before/after level of the statistic, the shift and a changepoint_detected verdict, per stat (median / mean / IQR / 10-90 spread) and per stratum, on mature data only.

  • plot_delay_drift() gained a changepoint argument: set it to TRUE to mark the estimated change point of the median delay on the fan chart with a vertical line.

  • New plot_delay_drift() and test_delay_drift() to answer “do reporting delay distributions drift over time?”.

    • plot_delay_drift() draws a rolling fan chart of the count-weighted delay distribution indexed by event date: a solid rolling median, a dashed rolling mean, and 25-75% / 10-90% quantile bands. The recent, not-yet-fully reported region (after the level incompleteness cutoff) is shaded grey so the truncation-induced dip is not mistaken for drift. Supports by_strata.
    • test_delay_drift() runs an autocorrelation-robust monotonic-trend test (Hamed-Rao modified Mann-Kendall by default, with Yue-Pilon and block-bootstrap options via the new modifiedmk Suggests) on the per-period delay summaries, testing both a location statistic (median/mean) and a dispersion statistic (IQR / 10-90 spread), on mature data only. Returns a tidy tibble with the Kendall tau, Sen’s slope, p-value and a drift verdict, per stat and stratum.

  • autoplot() gained a by_strata argument (default FALSE). When TRUE, every panel is split by stratum: the calendar and delay boxplots become dodged boxes (one per stratum, side by side), the epidemic process and both periodograms become one coloured line per stratum (no area fill), and the delay distribution becomes dodged bars. Boxplots are normalized per stratum (1 = that stratum’s own average) so the calendar pattern is comparable across strata, and strata are coloured with a viridis scale. A companion strata argument chooses which columns to group on (defaults to the object’s strata; pass a subset such as strata = "gender" to override).

  • autoplot() now draws reporting-delay diagnostic panels alongside the case-count ones, so you can see delay effects: the mean reporting delay by day of week / week of year / month (delay_weekday, delay_week, delay_month), and a periodogram of the mean-delay series (delay_seasonality) that reveals periodicity in the delay itself. The delay panels are computed on the complete part of the series (before the incompleteness line) so recent truncation does not bias them.

  • autoplot() gained a panels argument to choose which panels to draw. It accepts the concrete panel keys, or the aliases "all" (default), "calendar" and "delay_calendar". Selecting a single panel returns it as a plain ggplot2 object instead of a patchwork. Unknown panels error; panels that do not apply to the data’s time unit are skipped with a warning.

  • New pkgdown article “One dataset, many nowcasts” now also demonstrates that temporal (delay) effect columns are carried into epinowcast (metareference/metareport), baselinenowcast (long) and epidist, with a table clarifying which target formats can hold covariates and how each model can use them.

  • temporal_effects() gained an after-holiday and after-weekend effect via the new holiday_lags and weekend_lags arguments. Each takes a non-negative integer depth N; materialising the spec then adds indicator columns ..._holiday_lag_1 … ..._holiday_lag_N (and likewise ..._weekend_lag_k) that flag dates falling exactly k working days after a holiday / weekend. Working days skip weekends and holidays, so the effect lands on the first day(s) back at work — designed to capture the rise in cases just after a holiday or weekend. holiday_lags requires a holidays calendar. The columns are picked up automatically by every tbl_now_to_*() converter (as covariate columns) and by diseasenowcasting::nowcast().

  • Documented and tested attaching temporal effects to the report date (in addition to the default event date) via add_temporal_effects(x, spec, date_type = "report_date"). Event- and report-date effects can coexist on the same tbl_now; both sets of columns (.event_* and .report_*) are carried through all converters.

tbl.now 0.9.0

  • Added as_tibble() and as.data.frame() methods for tbl_now with an opt-in compute_temporal_effects argument (default FALSE). Passing compute_temporal_effects = TRUE materialises the lazy temporal_effects() spec (holidays, Fourier terms, calendar effects) into columns before returning a plain tibble / data.frame; the input tbl_now is left unchanged. The default stays lazy on purpose, because dplyr relies on these coercions being cheap, non-materialising declassers internally (e.g. group_by()).
  • The tbl_now_to_*() converters now carry the (lazy) temporal-effect columns (holidays, Fourier seasonal terms, day-of-week / calendar effects) into the target format as covariate columns. The spec is materialised on demand via compute_temporal_effects() at conversion time (the input tbl_now is left unchanged), and the columns are passed to data.table, tsibble, baselinenowcast long format, epidist, and epinowcast (where they appear in the observations and metareference tables for use in the reference module). The baselinenowcast reporting-triangle matrix still cannot hold them.
  • Removed the |> export and changed all the pipes to |>
  • Refactored converters.R for readability (dplyr column operations instead of base indexing, full variable names, lintr-clean).
  • The tbl_now_to_*() converters now keep the covariates and is_censored columns wherever the target format can hold them (data.table, tsibble, baselinenowcast long format, epidist linelist); the fixed modelling objects (enw_preprocess_data, the reporting-triangle matrix, the EpiNow2 series) still cannot carry them.
  • Added S3 methods on the other packages’ coercion generics so they accept a tbl_now directly: as_epidist_linelist_data(), as_reporting_triangle(), as_tsibble() and as.data.table(), each wrapping the matching tbl_now_to_*().
  • Fixed tbl_now_to_data_table() checking for baselinenowcast instead of data.table, and tbl_now_to_baselinenowcast(format = "long") no longer requiring baselinenowcast to be installed.

tbl.now 0.8.0

  • Modified the update as the t_effect argument was not doing anything.
  • Fixed bug that errored complete_zeroes when is_censored was given.
  • Removed explicit zeroes from the converters (tbl_now_from_*) as they are not necessary in tbl_now.
  • Added censor_reporting_delays_above() to flag reports with an implausibly long delay as censored (their delay becomes an upper bound).
  • Improved documentation and README
  • Documented all internal functions with roxygen (@keywords internal + @noRd) and ensured every exported function has a @return.
  • Homogenized lifecycle badges.
  • Brought the censor_reporting_delays_above function from diseasenowcasting to tbl_now.
  • tbl_now_from_epinowcast() now accepts not only the raw long input but also a preprocessed enw_preprocess_data object or a fitted epinowcast object (grouping auto-detected), matching the format epinowcast uses for summaries and plots.
  • tbl_now_to_EpiNow2() gained a model argument: "estimate_infections" (default, the single date/confirm series) and "estimate_truncation" (a list of report-date snapshots, the one EpiNow2 model that uses the report dimension). Documentation clarified accordingly.
  • Fixed two converter requireNamespace() guards: tbl_now_to_data_table() checked for baselinenowcast instead of data.table, and tbl_now_to_baselinenowcast(format = "long") no longer requires baselinenowcast to be installed.

tbl.now 0.7.5

  • Bumped roxygen to version 8.0.0. This also resulted in updated documentation.
  • Changed autoplot()’s default level to 0.95
  • Added tests for converters and pillars.
  • Throws warning when converting to baselinenowcast if data is "count-cumulative".

tbl.now 0.7.3

  • Added the update_now() function to make it more intuitive to update the now.

tbl.now 0.7.0

  • Added an autoplot() method for tbl_now objects that produces a multi-panel diagnostic overview: the empirical delay distribution, the observed epidemic process with an incompleteness line (controlled by level), normalized calendar-effect boxplots (cases relative to the overall mean), and a periodogram to help choose Fourier seasons. Daily data shows both a day-of-week and a week-of-year boxplot panel; weekly data shows week-of-year. Built on ggplot2 and patchwork. The x-axis limits of each panel can be set individually (delay_distribution_xlim, event_date_xlim, calendar_effect_xlim, seasonality_xlim), and holidays from the temporal-effects spec are marked with red dots on the epidemic process.
  • Added converters to and from other packages, all of the form tbl_now_from_*() / tbl_now_to_*(): epinowcast, baselinenowcast, EpiNow2 (to only), epidist, data.table and tsibble. The tbl_now_from_*() functions wrap as_tbl_now() and forward ... to tbl_now(); the tbl_now_to_*() functions call into the target package. All accept a verbose argument that reports the choices made (the inferred now, data type, units, and column mapping).
  • as_tbl_now() gained methods for the classes produced by tbl_now_to_*() (enw_preprocess_data, reporting_triangle, epidist_linelist_data, tbl_ts and data.table), so a converted object can be turned straight back into a tbl_now.
  • Documented autoplot() and the converters in the introduction vignette.

tbl.now 0.6.4

  • Fixed dependency on R >= 4.2.0
  • Update function now defaults the censoring to FALSE if the update is censored but the original is not.

tbl.now 0.6.3

  • Added season length to seasons so we can get weekly seasonality.

tbl.now 0.6.2

  • Removed warning when using columns for temporal effects that cascaded into to_count.
  • Changed DESCRIPTION to fix ortographic error and trigger less messages of unknown words.

tbl.now 0.6.1

  • Changed links in description of tidy-select

tbl.now 0.6.0

  • Changed temporal effects to be lazy (as required by #17) so that now its easier to use dplyr functions without compromising them.
  • Bumped the deprecated dplyr’s *_at functions to use all_of()
  • Fixed to no warnings during test.
  • Users can now pass the .delay column directly (#6) and it will recalculate the missing column (i.e. event or report)
  • Added complete_zeroes to vignette (#13).