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Interface for the DORIS system of WHO

Source: R/doris.R
doris.Rd

Provides an interface for the DORIS https://icd.who.int/doris system by the World Health Organization. Obtains the underlying cause of death using the rules of the Doris system. The fields provided are fields of a standard death certificate.

Usage

doris(
  token,
  sex = NULL,
  age = NULL,
  date_of_birth = NULL,
  date_of_death = NULL,
  cause_of_death_code_a = NULL,
  cause_of_death_code_b = NULL,
  cause_of_death_code_c = NULL,
  cause_of_death_code_d = NULL,
  cause_of_death_code_e = NULL,
  cause_of_death_uri_a = NULL,
  cause_of_death_uri_b = NULL,
  cause_of_death_uri_c = NULL,
  cause_of_death_uri_d = NULL,
  cause_of_death_uri_e = NULL,
  cause_of_death_code_part2 = NULL,
  cause_of_death_uri_part2 = NULL,
  interval_a = NULL,
  interval_b = NULL,
  interval_c = NULL,
  interval_d = NULL,
  interval_e = NULL,
  surgery_was_performed = NULL,
  surgery_date = NULL,
  surgery_reason = NULL,
  autopsy_was_requested = NULL,
  autopsy_findings = NULL,
  manner_of_death = NULL,
  manner_of_death_date_of_external_cause_or_poisoning = NULL,
  manner_of_death_description_external_cause = NULL,
  manner_of_death_place_of_occurrence_external_cause = NULL,
  fetal_or_infant_death_multiple_pregnancy = NULL,
  fetal_or_infant_death_stillborn = NULL,
  fetal_or_infant_death_within_24h = NULL,
  fetal_or_infant_death_birth_weight = NULL,
  fetal_or_infant_death_pregnancy_weeks = NULL,
  fetal_or_infant_death_age_mother = NULL,
  fetal_or_infant_death_perinatal_description = NULL,
  maternal_death_was_pregnant = NULL,
  maternal_death_time_from_pregnancy = NULL,
  maternal_death_pregnancy_contribute = NULL,
  release = "2024-01",
  language = "en",
  stop_on_error = FALSE,
  auto_update = TRUE
)

Arguments

token

(list) Access token to the API obtained from get_token()

sex

Can be either numeric (1 for Male, 2 for Female and 9 for Unknown) or can be a character with those words.

age

Estimated age of the individual in ISO-8601 format. Use iso_8601() to create the age in the appropriate format.

date_of_birth

Date of birth of the individual (date or datetime object)

date_of_death

Date of death of the individual (date or datetime object)

cause_of_death_code_a

String. Cause field A classification codes, comma separated.

cause_of_death_code_b

String. Cause field B classification codes, comma separated.

cause_of_death_code_c

String. Cause field C classification codes, comma separated.

cause_of_death_code_d

String. Cause field D classification codes, comma separated.

cause_of_death_code_e

String. Cause field E classification codes, comma separated.

cause_of_death_uri_a

String. Cause field A classification URIs, comma separated.

cause_of_death_uri_b

String. Cause field B classification URIs, comma separated.

cause_of_death_uri_c

String. Cause field C classification URIs, comma separated.

cause_of_death_uri_d

String. Cause field D classification URIs, comma separated.

cause_of_death_uri_e

String. Cause field E classification URIs, comma separated.

cause_of_death_code_part2

String. Cause field Part2 classification codes, comma separated.

cause_of_death_uri_part2

String. Cause field Part2 classification URIs, comma separated.

interval_a

Time interval from onset to death for Field A, in ISO 8601 format. Use iso_8601() to construct that duration.

interval_b

Time interval from onset to death for Field B, in ISO 8601 format. Use iso_8601() to construct that duration.

interval_c

Time interval from onset to death for Field C, in ISO 8601 format. Use iso_8601() to construct that duration.

interval_d

Time interval from onset to death for Field D, in ISO 8601 format. Use iso_8601() to construct that duration.

interval_e

Time interval from onset to death for Field E, in ISO 8601 format. Use iso_8601() to construct that duration.

surgery_was_performed

Whether surgery was performed on the individual (0 or No, 1 or Yes, and 9 or Unknown)

surgery_date

Date of surgery on the individual if surgery_was_performed

surgery_reason

String. Reason for surgery.

autopsy_was_requested

Whether an autposy was performed on the individual (0 or No, 1 or Yes, and 9 or Unknown)

autopsy_findings

Whether findings from the autopsy were used in the certification (0 or No, 1 or Yes, and 9 or Unknown).

manner_of_death

Either code or word: 0: Disease, 1: Accident, 2: Intentional self-harm, 3: Assault, 4: Legal intervention, 5: War, 6: Could not be determined, 7: Pending investigation, 9: Unknown.

manner_of_death_date_of_external_cause_or_poisoning

Date of external cause or poisoning of the individual according to manner_of_death

manner_of_death_description_external_cause

String. Description of external cause.

manner_of_death_place_of_occurrence_external_cause

Integer. 0: At home, 1: Residential institution, 2: School, other institution, public administration area, 3: Sports and athletics area, 4: Street and highway, 5: Trade and service area, 6: Industrial and construction area, 7: Farm, 8: Other place, 9: Unknown.

fetal_or_infant_death_multiple_pregnancy

(0 or No, 1 or Yes, and 9 or Unknown)

fetal_or_infant_death_stillborn

(0 or No, 1 or Yes, and 9 or Unknown)

fetal_or_infant_death_within_24h

Hours survived if death occurred within 24 hours.

fetal_or_infant_death_birth_weight

Birth weight in grams.

fetal_or_infant_death_pregnancy_weeks

Integer. Number of completed weeks of pregnancy.

fetal_or_infant_death_age_mother

Integer. Age of mother in years.

fetal_or_infant_death_perinatal_description

String. Condition of mother affecting the fetus and newborn.

maternal_death_was_pregnant

For women, was the deceased pregnant? (0 or No, 1 or Yes, and 9 or Unknown)

maternal_death_time_from_pregnancy

Integer. 0: At time of death, 1: Within 42 days before death, 2: Between 43 days and 1 year before death, 3: One year or more before death, 9: Unknown.

maternal_death_pregnancy_contribute

Did pregnancy contribute to death? (0 or No, 1 or Yes, and 9 or Unknown)

release

Release version as listed in https://icd.who.int/docs/icd-api/SupportedClassifications/#supported-classifications-and-versions the default is 2024-01.

language

(character) Language for the request. Available languages are listed in https://icd.who.int/docs/icd-api/SupportedClassifications/ the default is English (language = "en").

stop_on_error

Whether to stop if API throws an error or just throw it as a warning.

auto_update

Attempts to update token automatically

Value

List with the cause of death report

Details

All of the parameters are optional. In case of a missing parameter don't use it.

Note

IMPORTANT!. This endpoint is pre-release. The results may have issues and the API may change in the next releases. Underlying cause of death detection using the rules of the Doris system (https://icd.who.int/doris) The fields provided are fields of a standard death certificate. You don't need to provide causeOfDeathUri fields if you provide causeOfDeathCode fields or vice versa

Examples

# Assuming that the CLIENT ID and CLIENT SECRET are set up. Substitute accordingly
if (exists("CLIENT_ID") & exists("CLIENT_SECRET")) {
  # Get the Token
  token <- get_token(CLIENT_ID, CLIENT_SECRET)

  # Check a 25 year old male with immediate cause 1C8Z
  # due to 1C62.3Z
  doris(token,
    sex = "Male", age = iso_8601(years = 25), cause_of_death_code_a = "1C8Z",
    cause_of_death_code_b = "1C62.3Z"
  )

  # Check a 52 year old with immediate cause "GB61.Z" due to GB60.Z
  # due to 5A11 due to BA00.Z with other significant issues contributing to death
  # being 3A9Z and BC45
  doris(token,
    sex = "Male", age = iso_8601(years = 25), cause_of_death_code_a = "GB61.Z",
    cause_of_death_code_b = "GB60.Z", cause_of_death_code_c = "5A11",
    cause_of_death_code_d = "BA00.Z", cause_of_death_code_part2 = c("3A9Z", "BC45")
  )
}
#> $`Underlying cause of death (UCOD)`
#> [1] "5A11"
#> 
#> $`UCOD URI`
#> [1] "http://id.who.int/icd/entity/119724091"
#> 
#> $`UCOD with postcoordinated information (if available)`
#> [1] "5A11/BA00.Z"
#> 
#> $`UCOD postcoordinated URI`
#> [1] "http://id.who.int/icd/release/11/mms/119724091 / http://id.who.int/icd/release/11/mms/761947693/unspecified"
#> 
#> $`Detailed explanation (report)`
#> [1] "SP4: 5A11 is the starting point of the first-mentioned sequence (GB61.Z due to GB60.Z due to 5A11), which is selected as the tentative starting point (TSP).\nGB61.Z, GB60.Z, BA00.Z, BC45 is a manifestation of the selected underlying cause of death 5A11/BA00.Z and it is added as a postcoordination.\n\n\nFull report:\nSP1: is not applicable.\nSP2: is not applicable.\nSP3: is not applicable.\nSP4: 5A11 is the starting point of the first-mentioned sequence (GB61.Z due to GB60.Z due to 5A11), which is selected as the tentative starting point (TSP).\nSP6: is not applicable.\nSP7: is not applicable.\nSP8: is not applicable.\nM1: There is no special instruction applicable with TUC 5A11.\nM2: is not applicable.\nM3: The tentative underlying cause is the same as the starting point selected in Steps SP1 to SP8.\nGB61.Z, GB60.Z, BA00.Z, BC45 is a manifestation of the selected underlying cause of death 5A11/BA00.Z and it is added as a postcoordination.\n"
#> 
#> $reject
#> [1] FALSE
#> 
#> $error
#> NULL
#> 
#> $warning
#> NULL
#>