Read and process SEER cancer incidence and population research data


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("").

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:

#> # A tibble: 2 x 2
#>   Code  Description
#> * <chr> <chr>      
#> 1 1     Male       
#> 2 2     Female

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.

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.