readSEER: Reads SEER data from ASCII data file(s).

In mribeirodantas/vidente: Collection of functions to work with SEER Database

Description

Reads SEER data from ASCII data file(s).

Usage

readSEER(path, instructions, read_dir = FALSE, year_dx, primary_site)

Arguments

path	A path or a vector with paths to either folder with SEER ASCII data files or directly to the file(s).
instructions	The output variable from the buildSEERParser function
read_dir	If true, it reads all .TXT files in the directory or directories provided in the path parameter. If this parameter is missing or FALSE, vidente will only read the TXT you explicitly informed. This function does not work with data exported from the SEER*Stat software.
year_dx	Filter the result to this year of diagnosis (or range of years of diagnosis)
primary_site	Filter the result to a primary site (or a vector of primary sites for SEER*Stat files, or a site category from listPrimarySite() for data downloaded from SEER).

Value

A data frame with all SEER data from the ASCII data file(s) you provided, given the criteria you chose in the parameters.

Examples

# First build parsing instructions
## Not run: 
instr <- buildSEERParser(file_path = 'read.seer.research.nov17.sas',
                         file_source = 'download')

# Now you can read it
paths <- c('/home/yourusername/SEER/yr1973_2015.seer9/BREAST.TXT',
          '/home/yourusername/SEER/yr2000_2015.ca_ky_lo_nj_ga/BREAST.TXT')

# I'm interested here in patients with breast cancer diagnosed between 2012
# and 2015
seer_data <- readSEER(path = paths,
                      instructions = instr,
                      year_dx = c(2012:2015),
                      primary_site = 'Breast')
## End(Not run)

mribeirodantas/vidente documentation built on May 15, 2019, 4:47 p.m.