pseval: Methods for Evaluating Principal Surrogates of Treatment Response

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Contains the core methods for the evaluation of principal surrogates in a single clinical trial. Provides a flexible interface for defining models for the risk given treatment and the surrogate, the models for integration over the missing counterfactual surrogate responses, and the estimation methods. Estimated maximum likelihood and pseudo-score can be used for estimation, and the bootstrap for inference. A variety of post-estimation summary methods are provided, including print, summary, plot, and testing.

Author
Michael C Sachs [aut, cre], Erin E Gabriel [aut]
Date of publication
2016-09-23 22:53:05
Maintainer
Michael C Sachs <sachsmc@gmail.com>
License
MIT + file LICENSE
Version
1.3.0

View on CRAN

Man pages

add_bootstrap
Bootstrap resampling parameters
add_estimate
Estimate parameters
add_integration
Integration models
add_riskmodel
Add risk model to a psdesign object
calc_risk
Calculate the risk and functions of the risk
calc_STG
Calculate the Standardized total gain
empirical_TE
Compute the empirical Treatment Efficacy
empirical_VE
Compute the empirical Treatment Efficacy
expand_augdata
Expand augmented data using the integration function
generate_example_data
Generate sample data used for testing
integrate_bivnorm
Bivariate normal integration models for the missing S(1)
integrate_nonparametric
Nonparametric integration model for the missing S(1)
integrate_parametric
Parametric integration model for the missing S(1)
integrate_semiparametric
Semiparametric integration model using the location-scale...
plot.psdesign
Plot summary statistics for a psdesign object
plus-.ps
Modify a psdesign object by adding on new components.
print.psdesign
Concisely print information about a psdesign object
ps_bootstrap
Estimate parameters from a specified model using bootstrap...
psdesign
Specify a design for a principal surrogate evaluation
ps_estimate
Estimate parameters from a specified model using estimated...
pseudo_score
Estimate parameters from a specified model using pseudo-score
risk_binary
Risk model for binary outcome
riskcalc
Calculate risks with handlers for survival data
risk_continuous
Risk model for continuous outcome
risk_exponential
Exponential risk model for time to event outcome
risk.logit
Logit link function
risk_poisson
Poisson risk model for count outcomes
risk.probit
Probit link function
risk_weibull
Weibull risk model for time to event outcome
sp_locscale
Fit the semi-parametric location-scale model
stg
Compute the standardized total gain
summarize_bs
Summarize bootstrap samples
summary.psdesign
Summary method for psdesign objects
TE
Treatment efficacy contrast functions
verify_trt
Check that a variable is suitable for using as binary...
wem_test
Test for wide effect modificiation

Files in this package

pseval
pseval/inst
pseval/inst/CITATION
pseval/inst/doc
pseval/inst/doc/cheatsheet.pdf
pseval/inst/doc/introduction.R
pseval/inst/doc/introduction.html
pseval/inst/doc/introduction.Rmd
pseval/tests
pseval/tests/simulation-study.R
pseval/tests/testthat.R
pseval/tests/testthat
pseval/tests/testthat/test-bootstrap.R
pseval/tests/testthat/test-estimation.R
pseval/NAMESPACE
pseval/NEWS
pseval/R
pseval/R/gen-test-data.R
pseval/R/integrate.R
pseval/R/pseudo-score.R
pseval/R/summarize.R
pseval/R/risk.R
pseval/R/design.R
pseval/R/post-estimation.R
pseval/R/print.R
pseval/R/estimate.R
pseval/R/pseval-constructors.R
pseval/vignettes
pseval/vignettes/psreferences.bib
pseval/vignettes/introduction.Rmd
pseval/README.md
pseval/MD5
pseval/build
pseval/build/vignette.rds
pseval/DESCRIPTION
pseval/man
pseval/man/stg.Rd
pseval/man/summarize_bs.Rd
pseval/man/add_riskmodel.Rd
pseval/man/riskcalc.Rd
pseval/man/empirical_VE.Rd
pseval/man/verify_trt.Rd
pseval/man/integrate_semiparametric.Rd
pseval/man/risk_weibull.Rd
pseval/man/TE.Rd
pseval/man/psdesign.Rd
pseval/man/add_integration.Rd
pseval/man/plus-.ps.Rd
pseval/man/risk_binary.Rd
pseval/man/ps_estimate.Rd
pseval/man/risk_poisson.Rd
pseval/man/integrate_bivnorm.Rd
pseval/man/risk_exponential.Rd
pseval/man/integrate_parametric.Rd
pseval/man/integrate_nonparametric.Rd
pseval/man/print.psdesign.Rd
pseval/man/plot.psdesign.Rd
pseval/man/expand_augdata.Rd
pseval/man/generate_example_data.Rd
pseval/man/risk.logit.Rd
pseval/man/risk_continuous.Rd
pseval/man/calc_risk.Rd
pseval/man/add_estimate.Rd
pseval/man/ps_bootstrap.Rd
pseval/man/empirical_TE.Rd
pseval/man/sp_locscale.Rd
pseval/man/summary.psdesign.Rd
pseval/man/add_bootstrap.Rd
pseval/man/calc_STG.Rd
pseval/man/wem_test.Rd
pseval/man/pseudo_score.Rd
pseval/man/risk.probit.Rd
pseval/LICENSE