load_files: Load SEER tumor group files

In outcomesinsights/seer.tools: Download SEER Data and Create Analysis Files

Description

This function gets tumor group files by name and binds them into a data.frame. Subset the output for the tumor(s) of interest. Use one of the following group files: "BREAST", "COLRECT", "DIGOTHR", "FEMGEN", "LYMYLEUK", "MALEGEN", "RESPIR", "URINARY", and "OTHER" (names do NOT have to be in caps). Select variables to be included in the output file by putting them in a character vector. For example, you could select the following variables: varnames <- c("pubcsnum", "year_dx", "primsite", "histo3v", "beho3v", "grade", "lateral", "dx_conf", "rept_src", "seq_num")

Usage

load_files(group = "", setup_file, vars = NULL)

Arguments

group	Name of the SEER group file to retrieve. Uses grepl on a list of the SEER group filenames so the string can be written flexibly. Use "." to get all files.
setup_file	Setup file generated by setup_incidence() function.
vars	Character vector of variable names to be extracted (default NULL gives all variables).

Value

This function returns a dataframe of the files across SEER years.

Examples

## Not run: 
# get AML data and use data.table to subset and select.  Need to run setup_incidence() first.
s <- setup_incidence()
seer <- load_files("LYMYLEUK", s)
aml <-
    setDT(seer) %>%
    setkey(., siterwho) %>%
    .[J(35021)] %>%
    .[, type := "aml"]
setkey(aml, casenum)
aml <- unique(aml) # removes duplicate aml records (only taking first of each)

## End(Not run)

outcomesinsights/seer.tools documentation built on May 24, 2019, 5:54 p.m.