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

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, including the ensemble-based SuperLearner ('h2oEnsemble'). 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.

Author
Oleg Sofrygin [aut, cre], Mark J. van der Laan [aut], Romain Neugebauer [aut]
Date of publication
2016-10-03 08:17:49
Maintainer
Oleg Sofrygin <oleg.sofrygin@gmail.com>
License
GPL (>= 2)
Version
0.2
URLs

View on CRAN

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)...
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
h2o.glm_nn
h2o glm wrapper for non-negative least squares
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...

Files in this package

stremr
stremr/inst
stremr/inst/report
stremr/inst/report/report-script-rmd.R
stremr/tests
stremr/tests/examples
stremr/tests/examples/1_stremr_example.R
stremr/tests/examples/0_defineIntervention.R
stremr/tests/examples/2_building_blocks_example.R
stremr/tests/examples/4_survMSM_example.R
stremr/tests/RUnit
stremr/tests/RUnit/RUnit_tests_04d_sims10K_tmle_speedglm.R
stremr/tests/RUnit/0_simulate_data_1.R
stremr/tests/RUnit/RUnit_tests_09_ContinuousExposure.R
stremr/tests/RUnit/RUnit_tests_05_stremr_example_SL.R
stremr/tests/RUnit/RUnit_tests_04c_sims10K_h2o_ALL_ML.R
stremr/tests/RUnit/RUnit_tests_08_h2oQuasiBinomGLM.R
stremr/tests/RUnit/RUnit_tests_01_stratify.R
stremr/tests/RUnit/RUnit_tests_06_direct_regression_def.R
stremr/tests/RUnit/RUnit_tests_00.R
stremr/tests/RUnit/RUnit_tests_04a_sims10K_speedglm.R
stremr/tests/RUnit/0_simulate_data_2.R
stremr/tests/RUnit/RUnit_tests_03_buildingblocks.R
stremr/tests/RUnit/RUnit_tests_04b_sims10K_h2oGLM.R
stremr/tests/RUnit/RUnit_tests_00_DataStorageClass.R
stremr/tests/RUnit/RUnit_tests_07_iterativeTMLE.R
stremr/tests/RUnit/RUnit_tests_02_categCENS.R
stremr/tests/test-all.R
stremr/src
stremr/src/RcppExports.cpp
stremr/src/glm_binom_family.cpp
stremr/NAMESPACE
stremr/NEWS
stremr/data
stremr/data/OdatDT_10K.rda
stremr/data/OdataCatCENS.rda
stremr/data/OdataNoCENS.rda
stremr/R
stremr/R/IC.R
stremr/R/stremr.R
stremr/R/SL.R
stremr/R/RegressionControlClasses.R
stremr/R/stremr-package.R
stremr/R/summaryS3methods.R
stremr/R/main_estimation.R
stremr/R/DataStorageClass.R
stremr/R/tmle.R
stremr/R/BinomialMLclass.R
stremr/R/RcppExports.R
stremr/R/QlearningClasses.R
stremr/R/GenericModelingClasses.R
stremr/R/reports.R
stremr/R/BinomialGLMsClass.R
stremr/R/BinomialModelClass.R
stremr/R/helper_routines.R
stremr/R/zzz.R
stremr/README.md
stremr/MD5
stremr/DESCRIPTION
stremr/man
stremr/man/summary.H2Omodel.Rd
stremr/man/summary.GLMmodel.Rd
stremr/man/fitSeqGcomp.Rd
stremr/man/GenericModel.Rd
stremr/man/OdataNoCENS.Rd
stremr/man/survDirectIPW.Rd
stremr/man/StratifiedModel.Rd
stremr/man/summary.H2Oensemblemodel.Rd
stremr/man/get_wtsummary.Rd
stremr/man/get_MSM_RDs.Rd
stremr/man/getIPWeights.Rd
stremr/man/survNPMSM.Rd
stremr/man/set_all_stremr_options.Rd
stremr/man/OdatDT_10K.Rd
stremr/man/BinaryOutcomeModel.Rd
stremr/man/fitPropensity.Rd
stremr/man/print.H2Oensemblemodel.Rd
stremr/man/defineIntervedTRT.Rd
stremr/man/fitIterTMLE.Rd
stremr/man/stremr-package.Rd
stremr/man/CategorModel.Rd
stremr/man/make_report_rmd.Rd
stremr/man/survMSM.Rd
stremr/man/get_TMLE_RDs.Rd
stremr/man/QlearnModel.Rd
stremr/man/defineMONITORvars.Rd
stremr/man/openFileInOS.Rd
stremr/man/RegressionClass.Rd
stremr/man/BinomialGLM.Rd
stremr/man/stremrOptions.Rd
stremr/man/OdataCatCENS.Rd
stremr/man/DataStorageClass.Rd
stremr/man/ContinModel.Rd
stremr/man/print_stremr_opts.Rd
stremr/man/fitTMLE.Rd
stremr/man/stremr.Rd
stremr/man/pander.H2OBinomialMetrics.Rd
stremr/man/h2o.glm_nn.Rd
stremr/man/print.GLMmodel.Rd
stremr/man/pander.H2ORegressionMetrics.Rd
stremr/man/importData.Rd
stremr/man/define_single_regression.Rd
stremr/man/print.H2Omodel.Rd