In GerkeLab/SEERreadr: Read SEER Fixed Width Data Files

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
library(SEERreadr)

SEERreadr

A small package for reading SEER fixed width files.

Installation

SEERreadr can be installed from GitHub with

# install.packages("remotes")
remotes::install_github("gerkelab/SEERreadr", upgrade = FALSE)

What does this package do?

Read SEER Data Files

The main workhorse of this package is seer_read_fwf(). This function wraps readr::read_fwf() to import the SEER fixed-width ASCII data files, using the column names and field width definitions in the SEER SAS script.

The data files are available from the SEER Data & Software page, where users must request access prior to downloading. The SAS script is included in the file download, or avilable online. The online version is used by seer_read_fwf(), but a local version can be specified in the helper function seer_read_col_positions("local_file.sas").

library(SEERreadr)
x <- seer_read_fwf("incidence/yr1973_2015.seer9/MALEGEN.TXT")

Recode SEER Variables

Two additional functions are provided to help recode the SEER data. seer_recode() uses the seer_data_dictionary data provided in this package to automatically recode all variables with a one-to-one correspondence, for example:

seer_data_dictionary$SEX

The package also includes the function seer_rename_site_specific() that can be used to replace the site-specific variables with their corresponding labels, formatted appropriately to serve as variable names. As an example, CSSSF variables for Breast cancer would be renamed according to the following table.

seer_data_dictionary$CSSSF %>% 
  dplyr::filter(`Schema Name` == "Breast") %>% 
  dplyr::mutate(label = snakecase::to_snake_case(label)) %>% 
  dplyr::select(`Original Variable` = variable, `New Variable Name` = label) %>% 
  knitr::kable()