SEERaBomb: SEER and Atomic Bomb Survivor Data Analysis Tools

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

Author
Tomas Radivoyevitch
Date of publication
2016-11-11 17:26:27
Maintainer
Tomas Radivoyevitch <radivot@ccf.org>
License
GPL (>= 2)
Version
2016.2
URLs

View on CRAN

Man pages

csd
Cancer risk vs years Since Diagnosis of other cancer
fillPYM
Fills age-year person year (PY) matrix
getBinInfo
Gets the lower and upper limit and index of a tsd bin
getDF
Converts a seerSet$L series to a data.frame
getE
Get expected numbers of cases
getFields
Get fields from SEER SAS file
getPY
Get tsd interval PY
mapCancs
Map ICD9 and ICD-O3 codes to cancers
mapRegs
Map registry codes to acronyms
mapTrts
Map treatment codes to factor
mk2D
Make 2D-spline fits of incidences
mkAbomb
Make Abomb SQLite database
mkDF
Converts seerSet$L series to a data.frame
mkExcelCsd
Make RR Excel file from csd output
mkExcelTsd
Make RR Excel file from tsd function output
mkSEER
Make R binaries of SEER data.
mkSEERold
Make SEER binaries as before
msd
Mortality vs years Since Diagnosis
nvsr
National Vital Statistic Report (nvsr) Data
nvsr01
National Vital Statistic Report (nvsr01) Data
pickFields
Pick SEER fields of interest
plot2D
Plot 2D cancer incidence splines
post1PYO
Get person-years at risk and observed cases after first...
post1PYOc
Get person-years at risk and observed cases after first...
post1PYOm
Get person-years at risk and observed deaths after cancer
print.seerSet.summary
Prints seerSet.summary objects
SEERaBomb-package
SEER and A-Bomb Data Analysis Tools
seerSet
Join SEER cancers and PY
seerStats
Summarize SEER data.
Sigurdson
Chromosome translocation versus age data
simSeerSet
Simulate SEER cancers and population person years
stdUS
The standard population of the US in 2000
summary.seerSet
Summary of seerSet object
tsd
Compute RR vs tsd

Files in this package

SEERaBomb
SEERaBomb/inst
SEERaBomb/inst/doc
SEERaBomb/inst/doc/papers
SEERaBomb/inst/doc/papers/leukemia2016
SEERaBomb/inst/doc/papers/leukemia2016/interactions2D.R
SEERaBomb/inst/doc/papers/leukemia2016/amlMDScomputing.R
SEERaBomb/inst/doc/papers/leukemia2016/mkExcelDemo.R
SEERaBomb/inst/doc/papers/leukemia2016/amlAbombAge.R
SEERaBomb/inst/doc/papers/leukemia2016/timeCoursePlots.R
SEERaBomb/inst/doc/papers/leukemia2016/incidAllFirsts.R
SEERaBomb/inst/doc/papers/leukemia2016/consort.R
SEERaBomb/inst/doc/papers/leukemia2016/amlAbombTsx.R
SEERaBomb/inst/doc/papers/leukemia2016/specificFirst.R
SEERaBomb/inst/doc/papers/leukemia2016/specificFirstRRR.R
SEERaBomb/inst/doc/papers/leukemia2016/setup.R
SEERaBomb/inst/doc/papers/leukemia2016/simulate.R
SEERaBomb/inst/doc/papers/leukemia2016/aveAge.R
SEERaBomb/inst/doc/papers/leukemia2016/lymphoidFirsts.R
SEERaBomb/inst/doc/papers/leukemia2016/APL.R
SEERaBomb/inst/doc/papers/leukemia2016/PYnMDSvsDBs.R
SEERaBomb/inst/doc/papers/leukemia2016/tables.R
SEERaBomb/inst/doc/papers/REB2014
SEERaBomb/inst/doc/papers/REB2014/supplementAbomb.R
SEERaBomb/inst/doc/papers/REB2014/baseGraphics
SEERaBomb/inst/doc/papers/REB2014/baseGraphics/Supplement87.R
SEERaBomb/inst/doc/papers/REB2014/baseGraphics/CMLincid.R
SEERaBomb/inst/doc/papers/REB2014/baseGraphics/CMLdoseAgex3MF.R
SEERaBomb/inst/doc/papers/REB2014/baseGraphics/kageSeerCI.R
SEERaBomb/inst/doc/papers/REB2014/baseGraphics/CMLincidRace.R
SEERaBomb/inst/doc/papers/REB2014/baseGraphics/supplementAbombSave.R
SEERaBomb/inst/doc/papers/REB2014/baseGraphics/tauDiffsSeer.R
SEERaBomb/inst/doc/papers/REB2014/baseGraphics/CMLagexDev.R
SEERaBomb/inst/doc/papers/REB2014/baseGraphics/CMLwait.R
SEERaBomb/inst/doc/papers/REB2014/baseGraphics/racePvalues.R
SEERaBomb/inst/doc/papers/REB2014/baseGraphics/CMLincidDec.r
SEERaBomb/inst/doc/papers/REB2014/baseGraphics/CMMLincid.R
SEERaBomb/inst/doc/papers/REB2014/baseGraphics/CMLwaitCI.R
SEERaBomb/inst/doc/papers/REB2014/baseGraphics/CMLhistO3.r
SEERaBomb/inst/doc/papers/REB2014/SupplementSEER.R
SEERaBomb/inst/doc/papers/leukemiaRes2016
SEERaBomb/inst/doc/papers/leukemiaRes2016/prosBreastTimeCrs.R
SEERaBomb/inst/doc/papers/leukemiaRes2016/allTimeRRtab1.R
SEERaBomb/inst/doc/papers/leukemiaRes2016/timeCrs.R
SEERaBomb/inst/doc/papers/leukemiaRes2016/CLLcomputing.R
SEERaBomb/inst/doc/papers/AAPSJ2016
SEERaBomb/inst/doc/papers/AAPSJ2016/CMLmortRRtimeCrs.R
SEERaBomb/inst/doc/papers/blood2012
SEERaBomb/inst/doc/papers/blood2012/blood2012fig4.R
SEERaBomb/inst/doc/papers/blood2012/vIncidAPLCML.r
SEERaBomb/inst/doc/papers/blood2012/blood2012fig5bc.R
SEERaBomb/inst/doc/papers/blood2012/blood2012fig5a.R
SEERaBomb/inst/doc/papers/blood2012/dingliCMLFINAL3.R
SEERaBomb/inst/doc/papers/blood2012/blood2012fig6.R
SEERaBomb/inst/doc/papers/JCO2013
SEERaBomb/inst/doc/papers/JCO2013/MDSAMLsurvMF.R
SEERaBomb/inst/doc/index.html
SEERaBomb/inst/doc/examples
SEERaBomb/inst/doc/examples/aBombDplyr.R
SEERaBomb/inst/doc/examples/lungSurv.R
SEERaBomb/inst/doc/examples/lungIncid.R
SEERaBomb/inst/doc/examples/seerDplyr.R
SEERaBomb/inst/doc/examples/mkDataBinaries.R
SEERaBomb/inst/doc/examples/casesPerYearInUS.R
SEERaBomb/inst/doc/examples/poisRegCI.R
SEERaBomb/inst/doc/examples/registryDiffs.R
SEERaBomb/inst/doc/examples/incidAllgg.R
SEERaBomb/inst/doc/examples/mk2Dsplines.R
SEERaBomb/inst/doc/gettingData.pdf
SEERaBomb/inst/doc/fieldNames.html
SEERaBomb/inst/doc/changes.txt
SEERaBomb/inst/doc/overview.pdf
SEERaBomb/inst/doc/extraFuncs
SEERaBomb/inst/doc/extraFuncs/mkPYM.R
SEERaBomb/inst/doc/extraFuncs/mkPYM.c
SEERaBomb/inst/doc/extraFuncs/mkPYMR.R
SEERaBomb/src
SEERaBomb/src/fillPYM.cpp
SEERaBomb/src/RcppExports.cpp
SEERaBomb/NAMESPACE
SEERaBomb/NEWS
SEERaBomb/data
SEERaBomb/data/nvsr.rda
SEERaBomb/data/Sigurdson.rda
SEERaBomb/data/nvsr01.rda
SEERaBomb/data/stdUS.rda
SEERaBomb/R
SEERaBomb/R/mkExcelCsd.R
SEERaBomb/R/mk2D.R
SEERaBomb/R/getDF.R
SEERaBomb/R/mapTrts.R
SEERaBomb/R/simSeerSet.R
SEERaBomb/R/getPY.R
SEERaBomb/R/getFields.R
SEERaBomb/R/tsd.R
SEERaBomb/R/mkSEERold.R
SEERaBomb/R/seerStats.R
SEERaBomb/R/getE.R
SEERaBomb/R/mapRegs.R
SEERaBomb/R/RcppExports.R
SEERaBomb/R/summary.seerSet.R
SEERaBomb/R/getBinInfo.R
SEERaBomb/R/print.seerSet.summary.R
SEERaBomb/R/mkAbomb.R
SEERaBomb/R/pickFields.R
SEERaBomb/R/post1PYOm.R
SEERaBomb/R/post1PYO.R
SEERaBomb/R/plot2D.R
SEERaBomb/R/mkDF.R
SEERaBomb/R/csd.R
SEERaBomb/R/mkExcelTsd.R
SEERaBomb/R/mapCancs.R
SEERaBomb/R/msd.R
SEERaBomb/R/seerSet.R
SEERaBomb/R/mkSEER.R
SEERaBomb/R/post1PYOc.R
SEERaBomb/MD5
SEERaBomb/DESCRIPTION
SEERaBomb/man
SEERaBomb/man/tsd.Rd
SEERaBomb/man/figures
SEERaBomb/man/figures/mkSEERfig.png
SEERaBomb/man/stdUS.Rd
SEERaBomb/man/mkExcelCsd.Rd
SEERaBomb/man/nvsr.Rd
SEERaBomb/man/getFields.Rd
SEERaBomb/man/nvsr01.Rd
SEERaBomb/man/SEERaBomb-package.Rd
SEERaBomb/man/seerSet.Rd
SEERaBomb/man/mkDF.Rd
SEERaBomb/man/mkSEERold.Rd
SEERaBomb/man/mapCancs.Rd
SEERaBomb/man/mkAbomb.Rd
SEERaBomb/man/fillPYM.Rd
SEERaBomb/man/getDF.Rd
SEERaBomb/man/getBinInfo.Rd
SEERaBomb/man/simSeerSet.Rd
SEERaBomb/man/pickFields.Rd
SEERaBomb/man/getPY.Rd
SEERaBomb/man/msd.Rd
SEERaBomb/man/summary.seerSet.Rd
SEERaBomb/man/post1PYOc.Rd
SEERaBomb/man/post1PYO.Rd
SEERaBomb/man/seerStats.Rd
SEERaBomb/man/Sigurdson.Rd
SEERaBomb/man/getE.Rd
SEERaBomb/man/plot2D.Rd
SEERaBomb/man/mkSEER.Rd
SEERaBomb/man/mapRegs.Rd
SEERaBomb/man/print.seerSet.summary.Rd
SEERaBomb/man/csd.Rd
SEERaBomb/man/mk2D.Rd
SEERaBomb/man/mkExcelTsd.Rd
SEERaBomb/man/mapTrts.Rd
SEERaBomb/man/post1PYOm.Rd