Methods for Evaluating Principal Surrogates of Treatment Response

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.


pseval is an R package aimed at implementing existing methods for surrogate evaluation using a flexible and common interface. Development will take place on the Github page, and the current version of the package can be installed as shown below. First you must install the devtools package, if you haven't already install.packages("devtools").

devtools::install_github("sachsmc/pseval")

Check out the vignette for methodological details and information on how to use the package.

Check out the cheat sheet for a quick reference.

News

  • bugfix: inverted poisson parameters
  • enhancement: VE changed to more general TE for treatment efficacy
  • enhancement: Printed results output more closely match that of lm/glm
  • new feature: risk model for continuous outcomes
  • enhancement: improved documentation for joint versus marginal estimands
  • enhancement: Added cheatsheet
  • bugfix: missing sqrt in univariate wald test for WEM.
  • bugfix: inversion of exponential scale parameter.
  • Bugfix: permutation test for STG does not have correct type 1 error in some scenarios. This functionality was removed until we can resolve it.
  • Added newdata argument to calc_risk
  • Bugfix for restricted mean survival
  • Bugfix for lty and col in plot.psdesign
  • Add poisson risk model for count data
  • Total gain estimation
  • Initial release

Reference manual

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install.packages("pseval")

1.3.0 by Michael C Sachs, a year ago


Browse source code at https://github.com/cran/pseval


Authors: Michael C Sachs [aut, cre], Erin E Gabriel [aut]


Documentation:   PDF Manual  


MIT + file LICENSE license


Imports survival

Suggests ggplot2, testthat, knitr, printr, rmarkdown


See at CRAN