Package: SEERaBomb 2019.2

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. Methods are described in <doi:10.1038/leu.2015.258>.

Authors:Tomas Radivoyevitch [aut, cre], R. Molenaar [ctb]

SEERaBomb_2019.2.tar.gz
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SEERaBomb.pdf |SEERaBomb.html✨
SEERaBomb/json (API)
NEWS

# Install 'SEERaBomb' in R:

install.packages('SEERaBomb', repos = c('https://radivot.r-universe.dev', 'https://cloud.r-project.org'))

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

Sigurdson - Chromosome translocation versus age data
nvsr - National Vital Statistic Report (nvsr) Data
nvsr01 - National Vital Statistic Report (nvsr01) Data
stdUS - The standard population of the US in 2000

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

41 exports 1.24 score 183 dependencies 4 mentions 176 scripts 246 downloads

Last updated 5 years agofrom:0342bd4a26. Checks:OK: 9. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Sep 03 2024
R-4.5-win-x86_64	OK	Sep 03 2024
R-4.5-linux-x86_64	OK	Sep 03 2024
R-4.4-win-x86_64	OK	Sep 03 2024
R-4.4-mac-x86_64	OK	Sep 03 2024
R-4.4-mac-aarch64	OK	Sep 03 2024
R-4.3-win-x86_64	OK	Sep 03 2024
R-4.3-mac-x86_64	OK	Sep 03 2024
R-4.3-mac-aarch64	OK	Sep 03 2024

Exports:canc2py csd esd fillPYM getBinInfo getDF getE getFields getPY incidAbomb incidSEER mapCancs mapCODs mapRegs mapTrts mk2D mkAbomb mkDemographics mkDF mkExcelCsd mkExcelTsd mkLT mkMrt mkMrtLocal mkSEER mkSEERold msd p2s pickFields plot2D post1PYO post1PYOc post1PYOm print.seerSet.summary riskVsAge seerSet seerStats simSeerSet simSurv summary.seerSet tsd

Dependencies:abind ash askpass backports base64enc bit bit64 bitops blob boot bslib cachem checkmate class cli clipr cluster cobs colorspace cpp11 crayon curl cvar data.table DBI demography deSolve digest dplyr e1071 ecp evaluate evgam fansi farver fastICA fastmap fBasics fda fdapace fds fGarch FNN fontawesome forcats forecast foreign Formula fracdiff fs ftsa gbutils generics geometry ggplot2 glue GPArotation gridExtra gss gtable haven hdrcde highr HMDHFDplus Hmisc hms htmlTable htmltools htmlwidgets httr isoband janitor jquerylib jsonlite kernlab KernSmooth knitr ks labeling labelled LaF LaplacesDemon lattice lifecycle linprog Lmoments lmtest locfit lpSolve lubridate magic magrittr MASS Matrix MatrixModels mclust memoise mgcv mime mnormt multicool munsell mvtnorm nlme nnet numDeriv openssl openxlsx pcaPP pdfCluster pillar pkgconfig plogr plyr pracma prettyunits progress proxy psych purrr quadprog quantmod quantreg R6 rainbow rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen RcppProgress RCurl Rdpack readr reshape2 rgl rlang rmarkdown ROOPSD rpart RSQLite rstudioapi rvest sandwich sass scales sde selectr snakecase SparseM spatial stabledist stringi stringr strucchange survival sys tibble tidyr tidyselect timechange timeDate timeSeries tinytex tseries TTR tzdb urca utf8 vars vctrs viridis viridisLite vroom withr WriteXLS xfun xml2 xts yaml zip zoo

Citation

Readme and manuals

Help Manual

Help page	Topics
SEER and A-Bomb Data Analysis Tools	SEERaBomb-package
Cancer risk vs years Since Diagnosis of other cancer	csd
Event vs years Since Diagnosis	esd
Converts a seerSet$L series to a data.frame	getDF
Get fields from SEER SAS file	getFields
Computes A-bomb incidences	incidAbomb
Computes SEER incidences	incidSEER
Map ICD9 and ICD-O3 codes to cancers	mapCancs
Map CODs to strings	mapCODs
Map registry codes to acronyms	mapRegs
Map treatment codes to factor	mapTrts
Make 2D-spline fits of incidences	mk2D
Make Abomb Binaries	mkAbomb
Make Demographics Tables	mkDemographics
Make RR Excel file from csd output	mkExcelCsd
Make Life Tables	mkLT
Make mortality binaries	mkMrt
Make mortality binaries from local HMD data files	mkMrtLocal
Make R binaries of SEER data.	mkSEER
Mortality vs years Since Diagnosis	msd
National Vital Statistic Report (nvsr) Data	nvsr
National Vital Statistic Report (nvsr01) Data	nvsr01
Primary to Secondary	p2s
Pick SEER fields of interest	pickFields
Plot 2D cancer incidence splines	plot2D
Second cancer risk vs attained age after first cancer	riskVsAge
Join SEER cancers and PY	seerSet
Summarize SEER data.	seerStats
Chromosome translocation versus age data	Sigurdson
Simulate SEER cancers and population person years	simSeerSet
Simulate Survival Times	simSurv
The standard population of the US in 2000	stdUS
Summary of seerSet object	summary.seerSet

Package: SEERaBomb 2019.2

SEERaBomb: SEER and Atomic Bomb Survivor Data Analysis Tools

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)