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.

Install the latest version of this package by entering the following in R:
install.packages("SEERaBomb")
AuthorTomas Radivoyevitch
Date of publication2017-04-26 05:33:58 UTC
MaintainerTomas Radivoyevitch <radivot@ccf.org>
LicenseGPL (>= 2)
Version2017.1
http://epbi-radivot.cwru.edu/SEERaBomb/SEERaBomb.html

View on CRAN

Man pages

canc2py: Converts canc made by mkSEER into a data.frame with py at...

csd: Cancer risk vs years Since Diagnosis of other cancer

esd: Event vs years Since Diagnosis

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

riskVsAge: Second cancer risk vs attained age after first cancer

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

Functions

canc2py Man page
csd Man page
esd Man page
fillPYM Man page
getBinInfo Man page
getDF Man page
getE Man page
getFields Man page
getPY Man page
mapCancs Man page
mapRegs Man page
mapTrts Man page
mk2D Man page
mkAbomb Man page
mkDF Man page
mkExcelCsd Man page
mkExcelTsd Man page
mkSEER Man page
mkSEERold Man page
msd Man page
nvsr Man page
nvsr01 Man page
pickFields Man page
plot2D Man page
post1PYO Man page
post1PYOc Man page
post1PYOm Man page
print.seerSet.summary Man page
riskVsAge Man page
SEERaBomb_fillPYM Man page
SEERaBomb-package Man page
seerSet Man page
seerStats Man page
Sigurdson Man page
simSeerSet Man page
stdUS Man page
summary.seerSet Man page
tsd Man page

Files

inst
inst/doc
inst/doc/papers
inst/doc/papers/leukemia2016
inst/doc/papers/leukemia2016/interactions2D.R inst/doc/papers/leukemia2016/amlMDScomputing.R inst/doc/papers/leukemia2016/mkExcelDemo.R inst/doc/papers/leukemia2016/amlAbombAge.R inst/doc/papers/leukemia2016/timeCoursePlots.R inst/doc/papers/leukemia2016/incidAllFirsts.R inst/doc/papers/leukemia2016/consort.R inst/doc/papers/leukemia2016/amlAbombTsx.R inst/doc/papers/leukemia2016/specificFirst.R inst/doc/papers/leukemia2016/specificFirstRRR.R inst/doc/papers/leukemia2016/setup.R inst/doc/papers/leukemia2016/simulate.R inst/doc/papers/leukemia2016/aveAge.R inst/doc/papers/leukemia2016/lymphoidFirsts.R inst/doc/papers/leukemia2016/APL.R inst/doc/papers/leukemia2016/PYnMDSvsDBs.R inst/doc/papers/leukemia2016/tables.R
inst/doc/papers/REB2014
inst/doc/papers/REB2014/supplementAbomb.R
inst/doc/papers/REB2014/baseGraphics
inst/doc/papers/REB2014/baseGraphics/Supplement87.R inst/doc/papers/REB2014/baseGraphics/CMLincid.R inst/doc/papers/REB2014/baseGraphics/CMLdoseAgex3MF.R inst/doc/papers/REB2014/baseGraphics/kageSeerCI.R inst/doc/papers/REB2014/baseGraphics/CMLincidRace.R inst/doc/papers/REB2014/baseGraphics/supplementAbombSave.R inst/doc/papers/REB2014/baseGraphics/tauDiffsSeer.R inst/doc/papers/REB2014/baseGraphics/CMLagexDev.R inst/doc/papers/REB2014/baseGraphics/CMLwait.R inst/doc/papers/REB2014/baseGraphics/racePvalues.R inst/doc/papers/REB2014/baseGraphics/CMLincidDec.r inst/doc/papers/REB2014/baseGraphics/CMMLincid.R inst/doc/papers/REB2014/baseGraphics/CMLwaitCI.R inst/doc/papers/REB2014/baseGraphics/CMLhistO3.r inst/doc/papers/REB2014/SupplementSEER.R
inst/doc/papers/leukemiaRes2016
inst/doc/papers/leukemiaRes2016/prosBreastTimeCrs.R inst/doc/papers/leukemiaRes2016/allTimeRRtab1.R inst/doc/papers/leukemiaRes2016/timeCrs.R inst/doc/papers/leukemiaRes2016/CLLcomputing.R
inst/doc/papers/AAPSJ2016
inst/doc/papers/AAPSJ2016/CMLmortRRtimeCrs.R
inst/doc/papers/blood2012
inst/doc/papers/blood2012/blood2012fig4.R inst/doc/papers/blood2012/vIncidAPLCML.r inst/doc/papers/blood2012/blood2012fig5bc.R inst/doc/papers/blood2012/blood2012fig5a.R inst/doc/papers/blood2012/dingliCMLFINAL3.R inst/doc/papers/blood2012/blood2012fig6.R
inst/doc/papers/JCO2013
inst/doc/papers/JCO2013/MDSAMLsurvMF.R
inst/doc/index.html
inst/doc/examples
inst/doc/examples/aBombDplyr.R inst/doc/examples/lungSurv.R inst/doc/examples/lungIncid.R inst/doc/examples/seerDplyr.R inst/doc/examples/mkDataBinaries.R inst/doc/examples/casesPerYearInUS.R inst/doc/examples/poisRegCI.R inst/doc/examples/registryDiffs.R inst/doc/examples/incidAllgg.R inst/doc/examples/mk2Dsplines.R
inst/doc/gettingData.pdf
inst/doc/fieldNames.html
inst/doc/changes.txt
inst/doc/overview.pdf
inst/doc/extraFuncs
inst/doc/extraFuncs/mkPYM.R
inst/doc/extraFuncs/mkPYM.c
inst/doc/extraFuncs/mkPYMR.R
src
src/SEERaBomb_init.c
src/fillPYM.cpp
src/RcppExports.cpp
NAMESPACE
NEWS
data
data/nvsr.rda
data/Sigurdson.rda
data/nvsr01.rda
data/stdUS.rda
R
R/riskVsAge.R R/mkExcelCsd.R R/mk2D.R R/getDF.R R/mapTrts.R R/simSeerSet.R R/getPY.R R/getFields.R R/tsd.R R/mkSEERold.R R/seerStats.R R/getE.R R/mapRegs.R R/RcppExports.R R/summary.seerSet.R R/getBinInfo.R R/print.seerSet.summary.R R/mkAbomb.R R/pickFields.R R/post1PYOm.R R/esd.R R/post1PYO.R R/plot2D.R R/mkDF.R R/csd.R R/mkExcelTsd.R R/mapCancs.R R/canc2py.R R/msd.R R/seerSet.R R/mkSEER.R R/post1PYOc.R
MD5
DESCRIPTION
man
man/tsd.Rd
man/figures
man/figures/mkSEERfig.png
man/stdUS.Rd man/mkExcelCsd.Rd man/nvsr.Rd man/getFields.Rd man/nvsr01.Rd man/SEERaBomb-package.Rd man/seerSet.Rd man/mkDF.Rd man/mkSEERold.Rd man/mapCancs.Rd man/mkAbomb.Rd man/fillPYM.Rd man/getDF.Rd man/getBinInfo.Rd man/simSeerSet.Rd man/pickFields.Rd man/getPY.Rd man/msd.Rd man/summary.seerSet.Rd man/post1PYOc.Rd man/post1PYO.Rd man/seerStats.Rd man/Sigurdson.Rd man/riskVsAge.Rd man/getE.Rd man/plot2D.Rd man/canc2py.Rd man/mkSEER.Rd man/mapRegs.Rd man/print.seerSet.summary.Rd man/csd.Rd man/mk2D.Rd man/mkExcelTsd.Rd man/esd.Rd man/mapTrts.Rd man/post1PYOm.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.