death_xxx_count: Summarize NCHS causes of deaths

In PHSKC-APDE/rads: Assisted computation of King County public health data

Summarize NCHS causes of deaths

Description

Generalized function that is called upon by death_113_count() and death_130_count(). Generates death counts for the National Center for Health Statistics (NCHS) Selected Causes of Death (COD). Needs line-level death data with a properly formatted ICD10 column.

In addition to the causes of death you specify with causeids or cause, it will automatically return the total deaths as well as COVID-19 deaths (since they do not have their own NCHS category).

Usage

death_xxx_count(
  ph.data,
  causeids = NULL,
  cause = NULL,
  icdcol = "underlying_cod_code",
  kingco = TRUE,
  group_by = NULL,
  ypll_age = NULL,
  death_age_col = NULL,
  nchsnum = NULL
)

Arguments

ph.data	a data.table or data.frame. Must contain death data structured with one person per row and with at least one column of ICD10 death codes.
causeids	an integer vector, with a minimum value of 1 and a maximum value of dependent upon the NCHS reference table.
cause	an OPTIONAL character vector specifying the complete or partial keyword for the cause of death of interest. It is not case sensitive and you can specify it in two ways: 1) cause = c('viral', 'cough') or 2) cause = c("viral|cough"). If you specify any keyword(s), the function will ignore the causeids argument. The default is NULL, i.e., the function will rely on the causeids argument to identify the causes of death.
icdcol	a character vector of length one that specifies the name of the column in ph.data that contains the ICD10 death codes of interest. The default is underlying_cod_code, which is found in the properly formatted death data obtained using the get_data_death() function.
kingco	a logical vector of length one. It specifies whether you want to limit the analysis to King County. NOTE this only works with data imported with the get_data_death() function because it needs the logical variable chi_geo_kc. The default is kingco = TRUE.
group_by	a character vector of indeterminate length. This is used to specify all the variables by which you want to group (a.k.a. stratify) the results. For example, if you specified group_by = c('chi_sex', 'chi_race_6'), the results would be stratified by each combination of sex and race. The default is group_by = NULL
ypll_age	an optional numeric vector of length 1. When specified, it should be the age (an integer) used for Years of Potential Life Lost (YPLL) calculations. Valid values are between 1 & 99 (inclusive), though 65 and 85 are the most common. For example, ypll_age = 65 would sum the total number of years that could have been lived had everyone in the data lived to at least 65. Note that this function returns the total number of YPLL. Additional processing is necessary to calculate rates per 100,000. The default is ypll_age = NULL, which will skip YPLL calculations.
death_age_col	an optional character vector of length one that specifies the name of the column in ph.data with the decedents' age at death in years. It is only needed if ypll_age is specified AND if ph.data lacks a column named chi_age. The default is death_age_col = NULL.
nchsnum	specifies whether the function should reference NCHS 113 Selected COD (rads::death_113()) or NCHS 130 Selected Causes of Infant Death (rads::death_130()).

Details

See rads::death_113() & rads::death_130() for a complete list of available causesid and cause values.

Value

Generates a table with three columns, causeid, cause.of.death, and deaths. If ypll_age is specified, a ypll_## column will also be added to the table. Columns in the group_by argument will also be returned.

By default, it will return all relevant causes of death. You can specify which causes of death you want to assess using the causeids or cause arguments.

References

https://www.cdc.gov/nchs/data/dvs/Part9InstructionManual2020-508.pdf & https://secureaccess.wa.gov/doh/chat/Content/FilesForDownload/CodeSetDefinitions/NCHS113CausesOfDeath.pdf https://secureaccess.wa.gov/doh/chat/Content/FilesForDownload/TechnicalNotes.pdf

Examples

# example 1: death count only
set.seed(98104)
deathdata <- data.table::data.table(
  cod.icd10 = c(rep("A85.2", round(runif(1, 30, 100000), 0)),
                rep("B51", round(runif(1, 30, 100000), 0)),
                rep("U071", round(runif(1, 30, 100000), 0)),
                rep("E44", round(runif(1, 30, 100000), 0)),
                rep("E62", round(runif(1, 30, 100000), 0)),
                rep("G00", round(runif(1, 30, 100000), 0)),
                rep("J10", round(runif(1, 30, 100000), 0)),
                rep("J15", round(runif(1, 30, 100000), 0)),
                rep("V874", round(runif(1, 30, 100000), 0)))
)
eg1 <- death_xxx_count(ph.data = deathdata,
                       causeids = seq(1, 113, 1),
                       cause = NULL,
                       icdcol = "cod.icd10",
                       kingco = FALSE,
                       ypll_age = NULL,
                       death_age_col = NULL,
                       nchsnum = 113)
head(eg1)

PHSKC-APDE/rads documentation built on April 14, 2025, 10:47 a.m.