getCases: Creates an initial incidence cohort.

In buddha2490/MargotFun: Just a bunch of useful functions to do my job.

Description

This function does most of the tedious work for creating an incidence cohort. It will pull all the required datasets, define the incidence cases based on verified cancers + deaths (but NOT self-reported only cancers). Cases are censored at diagnosis date, date of other cancer diagnosis, date of death, date of last survey, or reported cancer of interest (if not verified). The final returned dataset will include both men and women, and can be merged with other data.

Usage

getCases(outcome, cpsCode, icd9Code, icd10Code, rep_code, inccanv = NULL, sitec = NULL, initialPath = file.path("s:/cps"))

Arguments

outcome	1L character vector describing your outcome. All of the incident cancer variables will be named with this variable, example: "BREAST_FINAL", "BREAST_DIED", etc.
cpsCode	1982 CPS death codes for the cancer of interest - typically unnecessary for a nutrition cohort analysis, but including it anyways.
icd9Code	Character vector: ICD9 death codes for the cancer of interest
icd10Code	Character vector: ICD10 death codes for the cancer of interest
rep_code	Character vector: Codes to pull reported cases from the reported file, corresponds to the (INCCAN97, INCCAN99, etc) variables
inccanv	Character vector: Codes to pull from the verified INCCANV variable.
sitec	Character vector: Codes to pull from the SITEC verified variable.
initialPath	Initial path - points to S:/CPS as default, but I can change it if I want to run locally.

Value

Only a selection of variables will be returned from the original data. I've chosen to drop most of the variables from the survey files, and just include things that can be merged with the rest of an analytic cohort.

ALL the variables included in the verified file will be returned because all cases will need further processing for histology/subtypes/etc.

Also returned:

ID	14-digit CPS2 ID
DXDATE	Diagnosis date from verified file (pre-censoring)
SEX	Sex ("MEN" or "WOMEN")
CODE1	Code1 from Mortality file
CODE2	Code2 from Mortality file
CODE3	Code3 from Mortality file
DEAD	Vital status
DTHDATE	Date of death
LOSTFU	Lost to followup
ANYCANCER	Death from any cancer
DATEFT	Final end of followup variable (post censoring)
PREV82	Prevalent cancer in 1982
PREV92	Prevalent cancer in 1992
PREVCANCER	Prevalent cancer including 1982 and 1992
DTINT92	Date of interview 1992
outcome_FINAL	Final incident cancer variable (post censoring)
outcome_DEATH	Death from cancer of interest (post censoring)
outcome_DIED	Death-only case (post censoring)
outcome_SELF	Self reported cancer of interest (post censoring)
outcome_VERIFIED	Verified cancer of interest (post censoring)

Author(s)

Brian Carter

Examples

breast.cases <- getCases(outcome="BREAST",
                         cpsCode="74",
                         icd9Code=c("174",paste0("174",0:9),"175",paste0("175",0:9)),
                         icd10Code=c("C50",paste0("C50",0:9)),
                         rep_code="C50",
                         inccanv="C50",
                         sitec=NULL)

buddha2490/MargotFun documentation built on Nov. 4, 2019, 8:16 a.m.