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SEERaBomb (version 2019.2)

SEER and Atomic Bomb Survivor Data Analysis Tools

Description

Creates SEER (Surveillance, Epidemiology and End Results) and A-bomb data binaries from ASCII sources and provides tools for estimating SEER second cancer risks. Methods are described in .

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Version

Install

install.packages('SEERaBomb')

Monthly Downloads

243

Version

2019.2

License

GPL (>= 2)

Maintainer

Tomas Radivoyevitch

Last Published

December 12th, 2019

Functions in SEERaBomb (2019.2)

Sigurdson

Chromosome translocation versus age data
csd

Cancer risk vs years Since Diagnosis of other cancer
getDF

Converts a seerSet$L series to a data.frame
esd

Event vs years Since Diagnosis
SEERaBomb-package

SEER and A-Bomb Data Analysis Tools
getE

Get expected numbers of cases
fillPYM

Fills age-year person year (PY) matrix
getBinInfo

Gets the lower and upper limit and index of a tsd bin
canc2py

Converts canc made by mkSEER into a data.frame with py at risk after firsts
getFields

Get fields from SEER SAS file
incidSEER

Computes SEER incidences
incidAbomb

Computes A-bomb incidences
getPY

Get tsd interval PY
mapRegs

Map registry codes to acronyms
mapCancs

Map ICD9 and ICD-O3 codes to cancers
mkDF

Converts seerSet$L series to a data.frame
mkSEERold

Make SEER binaries as before
mkSEER

Make R binaries of SEER data.
mkExcelCsd

Make RR Excel file from csd output
mkAbomb

Make Abomb Binaries
mkDemographics

Make Demographics Tables
pickFields

Pick SEER fields of interest
mapCODs

Map CODs to strings
mapTrts

Map treatment codes to factor
riskVsAge

Second cancer risk vs attained age after first cancer
seerSet

Join SEER cancers and PY
summary.seerSet

Summary of seerSet object
tsd

Compute RR vs tsd
nvsr

National Vital Statistic Report (nvsr) Data
msd

Mortality vs years Since Diagnosis
print.seerSet.summary

Prints seerSet.summary objects
post1PYOm

Get person-years at risk and observed deaths after cancer
mk2D

Make 2D-spline fits of incidences
mkExcelTsd

Make RR Excel file from tsd function output
stdUS

The standard population of the US in 2000
simSurv

Simulate Survival Times
plot2D

Plot 2D cancer incidence splines
post1PYOc

Get person-years at risk and observed cases after first cancers
post1PYO

Get person-years at risk and observed cases after first cancers
mkLT

Make Life Tables
mkMrt

Make mortality binaries
p2s

Primary to Secondary
mkMrtLocal

Make mortality binaries from local HMD data files
seerStats

Summarize SEER data.
nvsr01

National Vital Statistic Report (nvsr01) Data
simSeerSet

Simulate SEER cancers and population person years