icenReg: Regression Models for Interval Censored Data
Version 2.0.1

Regression models for interval censored data. Currently supports Cox-PH, proportional odds, and accelerated failure time models. Allows for semi and fully parametric models (parametric only for accelerated failure time models) and Bayesian parametric models. Includes functions for easy visual diagnostics of model fits and imputation of censored data.

AuthorClifford Anderson-Bergman
Date of publication2017-04-19 15:53:30 UTC
MaintainerClifford Anderson-Bergman <pistacliffcho@gmail.com>
LicenseLGPL (>= 2.0, < 3)
Version2.0.1
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("icenReg")

Popular man pages

bayesControls: Control parameters for ic_bayes
cs2ic: Convert current status data into interval censored format
diag_covar: Evaluate covariate effect for regression model
ic_bayes: Bayesian Regression Models for Interval Censored Data
ic_np: Non-Parametric Estimator for Interval Censored Data
ic_sample: Draw samples from an icenReg model
ic_sp: Semi-Parametric models for Interval Censored Data
See all...

All man pages Function index File listing

Man pages

bayesControls: Control parameters for ic_bayes
cs2ic: Convert current status data into interval censored format
diag_baseline: Compare parametric baseline distributions with...
diag_covar: Evaluate covariate effect for regression model
getFitEsts: Get Survival Curve Estimates from icenReg Model
getSCurves: Get Estimated Survival Curves from Semi-parametric Model for...
ic_bayes: Bayesian Regression Models for Interval Censored Data
ic_np: Non-Parametric Estimator for Interval Censored Data
ic_par: Parametric Regression Models for Interval Censored Data
ic_sample: Draw samples from an icenReg model
ic_sp: Semi-Parametric models for Interval Censored Data
imputeCens: Impute Interval Censored Data from icenReg Regression Model
IR_diabetes: Interval censored time from diabetes onset to diabetic...
makeCtrls_icsp: Control Parameters for ic_sp
miceData: Lung Tumor Interval Censored Data from Hoel and Walburg 1972
predict.icenReg_fit: Predictions from icenReg Regression Model
sampleSurv: Samples fitted survival function
simCS_weib: Simulate Current Status Data
simDC_weib: Simulate Doubly Censored Data
simIC_weib: Simulates interval censored data from regression model with a...
survCIs: Confidence/Credible intervals for survival curves

Functions

ICNPMLE Source code
IR_diabetes Man page
PCAFit2OrgParFit Source code
R_ic_bayes Source code
abs_inv Source code
addIfMissing Source code
addListIfMissing Source code
adjustIntervals Source code
bayesControls Man page Source code
bs_sampleData Source code
checkMatrix Source code
checkWeights Source code
computeConditional_p Source code
computeConditional_q Source code
cs2ic Man page Source code
dGeneralGamma Source code
default_baseline Source code
default_reg_pars Source code
diag_baseline Man page Source code
diag_covar Man page Source code
evalCV Source code
expandX Source code
expandY Source code
fastMatrixInsert Source code
fastNumericInsert Source code
findMaximalIntersections Source code
findUpperBound Source code
fit_ICPH Source code
fit_bayes Source code
fit_par Source code
formula_has_plus Source code
fullParamFit Source code
fullParamFit_exp Source code
getBSParSample Source code
getBS_coef Source code
getData Source code
getFactorFromData Source code
getFitEsts Man page Source code
getFormula Source code
getMaxLength Source code
getNumCovars Source code
getResponse Source code
getSCurves Man page Source code
getSamplablePars Source code
getSamplableVar Source code
getSurvProbs Source code
getSurvTimes Source code
getVarNames_fromFormula Source code
getVar_fromRHS Source code
get_dataframe_row Source code
get_etas Source code
get_link_fun Source code
get_s_fun Source code
get_tbull_mid_p Source code
get_tbull_mid_q Source code
ic_bayes Man page Source code
ic_np Man page Source code
ic_npSINGLE Source code
ic_par Man page Source code
ic_parList Source code
ic_sample Man page Source code
ic_sp Man page Source code
icenReg_cv Source code
icqqplot Source code
icr_colMeans Source code
icr_ncol Source code
icr_nrow Source code
imputeCens Man page Source code
imputeCensoredData_exp Source code
initICNPMLE Source code
lines.ic_npList Source code
lines.icenReg_fit Source code
lines.sp_curves Source code
lines.surv_cis Source code
makeCtrls_icsp Man page Source code
makeFactorSplitInfo Source code
makeIntervals Source code
makeNumericSplitInfo Source code
makeQQFit Source code
make_par_fitList Source code
miceData Man page
names.icenReg_fit Source code
no_link Source code
optCliq Source code
pGeneralGamma Source code
ph_link Source code
plot.ic_npList Source code
plot.icenReg_fit Source code
plot.sp_curves Source code
po_link Source code
predict.icenReg_fit Man page Source code
qGeneralGamma Source code
removeSurvFromFormula Source code
removeVarFromCall Source code
s_exp Source code
s_gamma Source code
s_lnorm Source code
s_loglgst Source code
s_weib Source code
sampBayesPar Source code
sampPars Source code
sampleSurv Man page Source code
sampleSurv_slow Source code
sample_etas_and_base Source code
sample_in_interval Source code
sample_pars Source code
setSamplablePars Source code
simBVCen Source code
simCS_weib Man page Source code
simDC_weib Man page Source code
simEventTime Source code
simICPO_beta Source code
simIC_weib Man page Source code Source code
simPars_fromFit Source code
simRawExpTimes Source code
simRawTimes Source code
splitAndFit Source code
splitData Source code
subSampleData Source code
subsetData_ifNeeded Source code
summary.ic_npList Source code
summary.icenReg_fit Source code
survCIs Man page Source code
updateDistPars Source code
vcov.icenReg_fit Source code

Files

inst
inst/CITATION
inst/doc
inst/doc/icenReg.Rnw
inst/doc/icenReg.R
inst/doc/icenReg.pdf
src
src/registeringRoutines.c
src/icenReg.cpp
src/icenReg_files
src/icenReg_files/ic_bayes.h
src/icenReg_files/regressionTransforms_2.h
src/icenReg_files/bivariateNPMLE.h
src/icenReg_files/myPAVAalgorithm.cpp
src/icenReg_files/EMICM.cpp
src/icenReg_files/regressionTransforms.cpp
src/icenReg_files/bivariateNPMLE.cpp
src/icenReg_files/ic_par_aft.cpp
src/icenReg_files/ic_par.cpp
src/icenReg_files/ic_bayes.cpp
src/icenReg_files/ic_par.h
src/icenReg_files/ic_sp_ch.cpp
src/icenReg_files/ic_sp_ch.h
src/icenReg_files/ic_sp_gradDescent.cpp
src/icenReg_files/regressionTransforms_2.cpp
src/icenReg_files/ic_par_aft.h
src/icenReg_files/experimentalCode.cpp
src/icenReg_files/basicUtilities.cpp
src/icenReg_files/EMICM.h
src/icenReg_files/regressionTransforms.h
src/RcppExports.cpp
NAMESPACE
NEWS
data
data/IR_diabetes.RData
data/miceData.RData
R
R/internal_utilities.R
R/plottingFunctions.R
R/simulationFunctions.R
R/ic_np.R
R/user_utilities.R
R/ic_sp.R
R/referenceClasses.R
R/optCliq.R
R/ic_par.R
R/RcppExports.R
R/ic_bayes.R
R/dataRoxygen.R
R/icenReg_CV.R
vignettes
vignettes/icenReg.Rnw
vignettes/inProgress
vignettes/inProgress/StatisticalBackground-009.pdf
vignettes/inProgress/StatisticalBackground-005.pdf
vignettes/inProgress/StatisticalBackground-004.pdf
vignettes/inProgress/StatisticalBackground.tex
vignettes/inProgress/StatisticalBackground.toc
vignettes/inProgress/StatisticalBackground.pdf
vignettes/inProgress/StatisticalBackground-008.pdf
vignettes/inProgress/StatisticalBackground.log
vignettes/inProgress/StatisticalBackground.Rnw
vignettes/inProgress/StatisticalBackground-010.pdf
vignettes/inProgress/StatisticalBackground-concordance.tex
vignettes/inProgress/StatisticalBackground-006.pdf
vignettes/inProgress/StatisticalBackground-003.pdf
vignettes/inProgress/StatisticalBackground.synctex.gz
vignettes/inProgress/StatisticalBackground-007.pdf
MD5
build
build/vignette.rds
DESCRIPTION
man
man/IR_diabetes.Rd
man/diag_covar.Rd
man/ic_sp.Rd
man/ic_par.Rd
man/predict.icenReg_fit.Rd
man/cs2ic.Rd
man/ic_np.Rd
man/miceData.Rd
man/getSCurves.Rd
man/simDC_weib.Rd
man/simCS_weib.Rd
man/makeCtrls_icsp.Rd
man/simIC_weib.Rd
man/bayesControls.Rd
man/imputeCens.Rd
man/ic_bayes.Rd
man/ic_sample.Rd
man/survCIs.Rd
man/sampleSurv.Rd
man/diag_baseline.Rd
man/getFitEsts.Rd
icenReg documentation built on May 19, 2017, 11:24 a.m.

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