stremr: Streamlined Estimation of Survival for Static, Dynamic and Stochastic Treatment and Monitoring Regimes
Version 0.4

Analysis of longitudinal time-to-event or time-to-failure data. Estimates the counterfactual discrete survival curve under static, dynamic and stochastic interventions on treatment (exposure) and monitoring events over time. Estimators (IPW, MSM-IPW, GCOMP, longitudinal TMLE) adjust for measured time-varying confounding and informative right-censoring. Model fitting can be performed either with GLM or H2O-3 machine learning libraries. The exposure, monitoring and censoring variables can be coded as either binary, categorical or continuous. Each can be multivariate (e.g., can use more than one column of dummy indicators for different censoring events). The input data needs to be in long format.

AuthorOleg Sofrygin [aut, cre], Mark J. van der Laan [aut], Romain Neugebauer [aut]
Date of publication2017-01-06 10:09:22
MaintainerOleg Sofrygin <oleg.sofrygin@gmail.com>
LicenseGPL (>= 2)
Version0.4
URL https://github.com/osofr/stremr
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("stremr")

Getting started

Package overview
README.md

Popular man pages

BinaryOutcomeModel: R6 class for fitting and making predictions for a single...
fitSeqGcomp: Fit sequential GCOMP and TMLE for survival
getIPWeights: Inverse Probability Weights.
get_TMLE_RDs: Risk Difference Estimates and SEs for a list of TMLE outputs
print_stremr_opts: Print Current Option Settings for 'stremr'
stremr: Estimate Survival with Interventions on Exposure and...
stremr-package: Estimate the Survival of Intervention on Exposures and...
See all...

All man pages Function index File listing

Man pages

BinaryOutcomeModel: R6 class for fitting and making predictions for a single...
BinomialGLM: R6 class for storing the design matrix and the binary outcome...
CategorModel: R6 class for fitting and predicting joint probability for a...
ContinModel: R6 class for fitting and predicting joint probability for a...
DataStorageClass: R6 class for storing, managing, subsetting and manipulating...
defineIntervedTRT: Define counterfactual dynamic treatment
defineMONITORvars: Helper routine to define the monitoring indicator and time...
define_single_regression: Define regression models
fitIterTMLE: Iterative TMLE wrapper for 'fitSeqGcomp'
fitPropensity: Define and fit propensity score models.
fitSeqGcomp: Fit sequential GCOMP and TMLE for survival
fitTMLE: TMLE wrapper for 'fitSeqGcomp'
GenericModel: Generic R6 class for modeling (fitting and predicting)...
get_FUPtimes: Follow-up times by regimen
getIPWeights: Inverse Probability Weights.
get_MSM_RDs: Risk Difference Estimates and SEs for IPW-MSM
get_TMLE_RDs: Risk Difference Estimates and SEs for a list of TMLE outputs
get_wtsummary: IP-Weights Summary Tables
importData: Import data, define various nodes, define dummies for factor...
make_report_rmd: Generate report(s) with modeling stats and survival estimates...
OdataCatCENS: An example of a dataset in long format with categorical...
OdataNoCENS: An example of a dataset in long format with random monitoring...
OdatDT_10K: An example of a dataset in long format with random monitoring...
openFileInOS: Open file
pander.H2OBinomialMetrics: Pander method for H2OBinomialMetrics class
pander.H2ORegressionMetrics: Pander method for H2ORegressionMetrics class
print.GLMmodel: S3 methods for printing model fit summary for glmfit class...
print.H2Oensemblemodel: S3 methods for printing model fit summary for H2Omodel class...
print.H2Omodel: S3 methods for printing model fit summary for H2Omodel class...
print_stremr_opts: Print Current Option Settings for 'stremr'
QlearnModel: R6 Class for Q-Learning
RegressionClass: R6 class that defines regression models evaluating P(sA|sW),...
set_all_stremr_options: Setting 'stremr' Options
StratifiedModel: R6 class for fitting and predicting with several stratified...
stremr: Estimate Survival with Interventions on Exposure and...
stremrOptions: Querying/setting a single 'stremr' option
stremr-package: Estimate the Survival of Intervention on Exposures and...
summary.GLMmodel: S3 methods for getting model fit summary for glmfit class...
summary.H2Oensemblemodel: S3 methods for getting model fit summary for H2Oensemblemodel...
summary.H2Omodel: S3 methods for getting model fit summary for H2Omodel class...
survDirectIPW: Direct (bounded) IPW estimator of discrete survival function.
survMSM: Estimate Survival with a particular MSM for the...
survNPMSM: Non-parametric (saturated) MSM for survival based on...

Functions

BinaryOutcomeModel Man page
BinomialGLM Man page
CVmetrics_H2Obasemodel Source code
CVsummary_H2Obasemodel Source code
CategorModel Man page
CheckExistFactors Source code
CheckVarNameExists Source code
ContinModel Man page
DataStorageClass Man page
GenericModel Man page
GetWarningsToSuppress Source code
OdatDT_10K Man page
OdataCatCENS Man page
OdataNoCENS Man page
QlearnModel Man page
RegressionClass Man page
SLfit.h2oLearner Source code
SLfit.h2ogrid Source code
StratifiedModel Man page
SuppressGivenWarnings Source code
checkpkgs Source code
create_subset_expr Source code
define.intervals Source code
defineIntervedTRT Man page Source code
defineMONITORvars Man page Source code
defineNodeGstarGComp Source code
defineNodeGstarIPW Source code
define_single_regression Man page Source code
detect.col.types Source code
fit Source code
fit.glm Source code
fit.h2odeeplearning Source code
fit.h2ogbm Source code
fit.h2oglm Source code
fit.h2orandomForest Source code
fit.speedglm Source code
fitIterTMLE Man page Source code
fitPropensity Man page Source code
fitSeqGcomp Man page Source code
fitSeqGcomp_onet Source code
fitTMLE Man page Source code
format_wts_data Source code
get.misval Source code
getIPWeights Man page Source code
getSE.RD.d1.minus.d2 Source code
getSE.S Source code
getSE_table_d_by_d Source code
getSEcoef Source code
get_FUPtimes Man page Source code
get_MSM_RDs Man page Source code
get_TMLE_RDs Man page Source code
get_n_regs Source code
get_n_regs.ListOfRegressionForms Source code
get_n_regs.RegressionClass Source code
get_n_regs.SingleRegressionFormClass Source code
get_outvars Source code
get_outvars.ListOfRegressionForms Source code
get_subset_exprs Source code
get_subset_exprs.ListOfRegressionForms Source code
get_vars_fromlist Source code
get_wtsummary Man page Source code
getopt Source code
importData Man page Source code
internal_define_reg Source code
is.DataStorageClass Source code
is.H2OFrame Source code
is.integerish Source code
iterTMLE_onet Source code
keep_only_fun_args Source code
logit_linkinv Source code
make.bins_mtx_1 Source code
make.bins_mtx_cens Source code
make.ordinal Source code
make.table.m0 Source code
makeFreqTable Source code
make_report_rmd Man page Source code
newsummarymodel Source code
newsummarymodel.Qlearn Source code
newsummarymodel.binary Source code
newsummarymodel.categor Source code
newsummarymodel.contin Source code
newsummarymodel.deterministic Source code
newsummarymodel.generic Source code
newsummarymodel.stratify Source code
normalize Source code
onAttach Source code
onLoad Source code
openFileInOS Man page Source code
pander.H2OBinomialMetrics Man page Source code
pander.H2ORegressionMetrics Man page Source code
predictP1 Source code
predictP1.GLMmodel Source code
predictP1.H2Oensemblemodel Source code
predictP1.H2Omodel Source code
prettyprint_GenericModel Source code
print.GLMmodel Man page Source code
print.H2Oensemblemodel Man page Source code
print.H2Omodel Man page Source code
print.SingleRegressionFormClass Source code
print_stremr_opts Man page Source code
process_opt_wts Source code
process_regform Source code
process_regforms Source code
replace_add_user_args Source code
runglmMSM Source code
select_reg Source code
select_reg.ListOfRegressionForms Source code
select_reg.RegressionClass Source code
set.misval Source code
set_all_stremr_options Man page Source code
set_subset_exprs Source code
set_subset_exprs.ListOfRegressionForms Source code
stratify_by_uncensored Source code
stremr Man page Source code
stremr-package Man page
stremrOptions Man page Source code
summary.GLMmodel Man page Source code
summary.H2Oensemblemodel Man page Source code
summary.H2Omodel Man page Source code
survDirectIPW Man page Source code
survMSM Man page Source code
survNPMSM Man page Source code
testmisfun Source code
tmle.update Source code
tryCatch.W.E Source code

Files

inst
inst/report
inst/report/report-script-rmd.R
tests
tests/examples
tests/examples/1_stremr_example.R
tests/examples/0_defineIntervention.R
tests/examples/2_building_blocks_example.R
tests/examples/4_survMSM_example.R
tests/RUnit
tests/RUnit/RUnit_tests_04d_sims10K_tmle_speedglm.R
tests/RUnit/0_simulate_data_1.R
tests/RUnit/RUnit_tests_09_ContinuousExposure.R
tests/RUnit/RUnit_tests_05_stremr_example_SL.R
tests/RUnit/RUnit_tests_04c_sims10K_h2o_ALL_ML.R
tests/RUnit/RUnit_tests_08_h2oQuasiBinomGLM.R
tests/RUnit/RUnit_tests_01_stratify.R
tests/RUnit/RUnit_tests_06_direct_regression_def.R
tests/RUnit/RUnit_tests_00.R
tests/RUnit/RUnit_tests_04a_sims10K_speedglm.R
tests/RUnit/0_simulate_data_2.R
tests/RUnit/RUnit_tests_03_buildingblocks.R
tests/RUnit/RUnit_tests_04b_sims10K_h2oGLM.R
tests/RUnit/RUnit_tests_00_DataStorageClass.R
tests/RUnit/RUnit_tests_07_iterativeTMLE.R
tests/RUnit/RUnit_tests_02_categCENS.R
tests/test-all.R
src
src/RcppExports.cpp
src/glm_binom_family.cpp
NAMESPACE
NEWS
data
data/OdatDT_10K.rda
data/OdataCatCENS.rda
data/OdataNoCENS.rda
R
R/IC.R
R/stremr.R
R/SL.R
R/RegressionControlClasses.R
R/stremr-package.R
R/summaryS3methods.R
R/main_estimation.R
R/DataStorageClass.R
R/tmle.R
R/BinomialMLclass.R
R/RcppExports.R
R/QlearningClasses.R
R/GenericModelingClasses.R
R/reports.R
R/BinomialGLMsClass.R
R/BinomialModelClass.R
R/helper_routines.R
R/zzz.R
README.md
MD5
DESCRIPTION
man
man/summary.H2Omodel.Rd
man/summary.GLMmodel.Rd
man/fitSeqGcomp.Rd
man/GenericModel.Rd
man/OdataNoCENS.Rd
man/survDirectIPW.Rd
man/StratifiedModel.Rd
man/summary.H2Oensemblemodel.Rd
man/get_wtsummary.Rd
man/get_MSM_RDs.Rd
man/getIPWeights.Rd
man/survNPMSM.Rd
man/set_all_stremr_options.Rd
man/OdatDT_10K.Rd
man/BinaryOutcomeModel.Rd
man/fitPropensity.Rd
man/print.H2Oensemblemodel.Rd
man/get_FUPtimes.Rd
man/defineIntervedTRT.Rd
man/fitIterTMLE.Rd
man/stremr-package.Rd
man/CategorModel.Rd
man/make_report_rmd.Rd
man/survMSM.Rd
man/get_TMLE_RDs.Rd
man/QlearnModel.Rd
man/defineMONITORvars.Rd
man/openFileInOS.Rd
man/RegressionClass.Rd
man/BinomialGLM.Rd
man/stremrOptions.Rd
man/OdataCatCENS.Rd
man/DataStorageClass.Rd
man/ContinModel.Rd
man/print_stremr_opts.Rd
man/fitTMLE.Rd
man/stremr.Rd
man/pander.H2OBinomialMetrics.Rd
man/print.GLMmodel.Rd
man/pander.H2ORegressionMetrics.Rd
man/importData.Rd
man/define_single_regression.Rd
man/print.H2Omodel.Rd
stremr documentation built on May 20, 2017, 4:21 a.m.

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