tsd
(Package: SEERaBomb) :
Compute RR vs tsd
Computes relative risks (RR) over specified times since diagnoses (tsd) of a 1st cancer. 2D spline fits are used to produce expected cases E controlling for background risk dedepence on age and calendar year. RR is then O/E where O is the number of observed cases. WARNING: Use of this function is deprecated, please use csd() instead.
● Data Source:
CranContrib
● Keywords: internal
● Alias: tsd
●
0 images
|
getFields
(Package: SEERaBomb) :
Get fields from SEER SAS file
Converts the SAS file in the SEER ‘incidence’ directory into a data frame in R.
● Data Source:
CranContrib
● Keywords: IO
● Alias: getFields
●
0 images
|
Creates SEER (Surveillance, Epidemiology and End Results) and Japanese A-bomb survivor data binaries from ASCII sources and provides tools for estimating SEER second cancer risks. Depicted below, mkSEER merges cancers and populations of all three of the SEER databases into single cancer and population data frames.
● Data Source:
CranContrib
● Keywords: package
● Alias: SEERaBomb-package
●
0 images
|
seerSet
(Package: SEERaBomb) :
Join SEER cancers and PY
Creates a sex-specific list of cancer and population person year (PY) data frames, possibly specific to a race and interval of ages at diagnosis.
● Data Source:
CranContrib
● Keywords: IO
● Alias: seerSet
●
0 images
|
mkDF
(Package: SEERaBomb) :
Converts seerSet$L series to a data.frame
Creates a data.frame of observed and expected cases for each first and second cancer and treatment. Use of this function is deprecated. Use getDF() instead, if needed: csd now calls getDF internally for the most recent time series, so even it may not need to be called directly.
● Data Source:
CranContrib
● Keywords: internal
● Alias: mkDF
●
0 images
|
mkSEERold
(Package: SEERaBomb) :
Make SEER binaries as before
Converts SEER ASCII text files into smaller R binaries. This is being maintained to avoid fixing old scripts. Please use mkSEER for new scripts.
● Data Source:
CranContrib
● Keywords: IO
● Alias: mkSEERold
●
0 images
|
mapCancs
(Package: SEERaBomb) :
Map ICD9 and ICD-O3 codes to cancers
Adds a factor cancer with easily recognizable levels to a SEER cancer data.frame.
● Data Source:
CranContrib
● Keywords: IO
● Alias: mapCancs
●
0 images
|
mkAbomb
(Package: SEERaBomb) :
Make Abomb SQLite database
Converts Abomb files ‘lsshempy.csv’ and ‘lssinc07.csv’ into tables heme and solid, respectively, in SQLite database ‘abomb.db’.
● Data Source:
CranContrib
● Keywords: IO
● Alias: mkAbomb
●
0 images
|
fillPYM
(Package: SEERaBomb) :
Fills age-year person year (PY) matrix
This internal function converts a matrix with lots of individual PY contributions and starting ages and years as rows, into a population-level PY histrogram matrix of (1-year age)x(1-year year) resolution bins. The output matrix is more square-like (currently at 40 calendar years by 126 age years) than the tall dataframe-like input matrix.
● Data Source:
CranContrib
● Keywords: internal
● Alias: fillPYM
●
0 images
|
getDF
(Package: SEERaBomb) :
Converts a seerSet$L series to a data.frame
Creates a data.frame of observed and expected cases for each first and second cancer and treatment. csd() calls this internally for the most recent time series, so it may not need to be called directly.
● Data Source:
CranContrib
● Keywords: IO
● Alias: getDF
●
0 images
|
providing 
.