SEERaBomb: SEER and Atomic Bomb Survivor Data Analysis Tools

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

AuthorTomas Radivoyevitch
Date of publication2016-11-11 17:26:27
MaintainerTomas Radivoyevitch <radivot@ccf.org>
LicenseGPL (>= 2)
Version2016.2
http://epbi-radivot.cwru.edu/SEERaBomb/SEERaBomb.html

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

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