readSEER: Read SEER cancer data (ASCII)
In UScancer: Create US cancer datasets from SEER, IARC, and US Census data

Description Usage Arguments Value Author(s) See Also Examples

Reads an ASCII text version of SEER data for one or more given years, states and cancer sites. Data is freely available (after completing a signed SEER Research Data Agreement form) at http://seer.cancer.gov/data/access.html.

1	readSEER(file,year,state,cancer,site,fips)

`file`	A vector of filenames specifying where to find the SEER data. For example, for respiratory cancers between 1973-2010, one could specify the following path from the default directory structure of SEER data `"SEER_1973_2010_TEXTDATA/incidence/yr1973_2010.seer9/RESPIR.TXT"`
`year`	A numeric vector specifying which years of the data to look at. If not specified, defaults to all years.
`state`	A character vector specifying which states to extract. Should be one or more of "Georgia", "California", "New Jersey", "Kentucky", "Louisiana", "Connecticut", "Michigan", "Hawaii", "Iowa", "New Mexico", "Utah", "Washington". If not specified, defaults to all states.
`cancer`	A character vector specifying which cancers. This is passed to `siteLookup` to convert to a regular expression matching the proper site codes. Should be one or more of cancers from `listCancers`. If not specified, `site` is used instead. If neither are specified, then defaults to all cancers.
`site`	A character vector of regular expressions to match cancer site codes on. This takes precidence over `cancer`. If neither are specified, then defaults to all cancers.
`fips`	A `data.frame` object with 5-digit FIPS codes as row numbers and two columns (state,county) with names of the state and county matching the FIPS code. A complete object is included in this package, see the `fipslookup` dataset.

Returns a data.frame of cancer cases with sex, age of diagnosis, year of diagnosis, site, state, county, and 5-digit state+county FIPS code. This format is compatible for use with the getSMR function from the diseasemapping package.

Jonathan Lee jonathan@utstat.utoronto.ca

fipslookup

data(fipslookup)

## Not run: 
#file should point to the proper TXT file containing the cancer data you are interested in
seerData <- readSEER(file="RESPIR.TXT",year=2005,state="Kentucky",cancer="Larynx",fips=fipslookup)
## End(Not run)