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. 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
https://github.com/osofr/stremr

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)...

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
CategorModel Man page
ContinModel Man page
DataStorageClass Man page
defineIntervedTRT Man page
defineMONITORvars Man page
define_single_regression Man page
fitIterTMLE Man page
fitPropensity Man page
fitSeqGcomp Man page
fitTMLE Man page
GenericModel Man page
get_FUPtimes Man page
getIPWeights Man page
get_MSM_RDs Man page
get_TMLE_RDs Man page
get_wtsummary Man page
importData Man page
make_report_rmd Man page
OdataCatCENS Man page
OdataNoCENS Man page
OdatDT_10K Man page
openFileInOS Man page
pander.H2OBinomialMetrics Man page
pander.H2ORegressionMetrics Man page
print.GLMmodel Man page
print.H2Oensemblemodel Man page
print.H2Omodel Man page
print_stremr_opts Man page
QlearnModel Man page
RegressionClass Man page
set_all_stremr_options Man page
StratifiedModel Man page
stremr Man page
stremrOptions Man page
stremr-package Man page
summary.GLMmodel Man page
summary.H2Oensemblemodel Man page
summary.H2Omodel Man page
survDirectIPW Man page
survMSM Man page
survNPMSM Man page

Files

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/get_FUPtimes.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/print.GLMmodel.Rd stremr/man/pander.H2ORegressionMetrics.Rd stremr/man/importData.Rd stremr/man/define_single_regression.Rd stremr/man/print.H2Omodel.Rd

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