A small package for reading SEER fixed width files.
SEERreadr can be installed from GitHub with
# install.packages("remotes")
remotes::install_github("gerkelab/SEERreadr", upgrade = FALSE)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")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
#> # A tibble: 2 x 2
#> Code Description
#> * <chr> <chr>
#> 1 1 Male
#> 2 2 FemaleThe 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.
| Original Variable | New Variable Name |
|---|---|
| CS1SITE | estrogen_receptor_er_assay_2004 |
| CS2SITE | progesterone_receptor_pr_assay_2004 |
| CS3SITE | number_of_positive_ipsilateral_level_i_ii_axillary_lymph_nodes_2004 |
| CS4SITE | immunohistochemistry_ihc_of_regional_lymph_nodes_2004 |
| CS5SITE | molecular_mol_studies_of_regional_lymph_nodes_2004 |
| CS6SITE | size_of_tumor_invasive_component_2004 |
| CS7SITE | nottingham_or_bloom_richardson_br_score_grade_2010 |
| CS15SITE | her_2_summary_result_of_testing_2010 |
Thank you to Vincent Major for making available the scripts in SEER_read_fwf, which provided a foundation for this package.