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NEWS

• eliminated redundant code for the logistic regression switching model for ipcw
• added the marginal structural model (msm) method
• added na.action = na.pass for model frame construction involving covariates for all methods
• added the init parameter and the fail flag to the output to logisregr, liferegr, and phregr
• replaced the survreg initial value method with the OLS initial value method for liferegr
• added the fail flag to output of rpsftm, ipe, tsesimp, tsegest, ipcw, and msm

• updated survival_analysis to ignore intervals not at risk within each stratum without creating non overlapping times across strata
• updated documentation for the survsplit utility function
• updated tsegestsim to use the standard definition of weibull scale
• removed bc from logisregr
• removed swtrt_time_upper from tsegest
• removed subject-level adsl data from tsegestsim output
• removed swtrt_time_lower, swtrt_time_upper, and relative_time from ipcw
• removed the robust option for logistic regression treatment switching model in ipcw
• added match3 utility function to match on id and value
• added residuals_liferegr for residuals from parameteric regression models for failure time data
• added the psi_test, aft_dist, and strata_main_effect_only parameters to rpsftm to allow parametric regression and cox regression models to estimate psi
• added baseline covariates to the output Sstar data set of the rpsftm and ipe functions
• added a check for switching time before progression time in tsesimp and tsegest
• added a check for switching time or progression time less than offset in tsesimp and tsegest
• added timeOS and died variables for subject-level data and used event for death status at the end of each time interval for tsegestsim
• added tssim for treatment switching data simulation

• fixed an ASAN issue in survQuantile

• updated the default search interval for psi to [-2,2] at 101 points in rpsftm
• added parameters and output low_psi = -2 and hi_psi = 2 to ipe
• renamed gest to est_psi_tsegest and updated the default search interval for psi to [-2,2] at 101 points in tsegest
• replaced dummy variables with original variables in data_outcome for rpsftm
• replaced dummy variables with original variables in data_outcome and data_aft for ipe
• removed dummy strata variables in data_aft for ipe
• replaced dummy variables with original variables in data_outcome and data_aft for tsesimp
• removed dummy strata variables in data_aft for tsesimp
• renamed time to pps in data_aft for tsesimp
• added pd_time, swtrt_time, and time to data_aft for tsesimp
• added tstart, tstop to data_logis for tsegest
• replaced dummy variables with original variables in data_outcome and data_logis for tsegest
• removed dummy strata variables in data_logis for tsegest
• added tstart, tstop to data_switch for ipcw
• replaced dummy variables with original variables in data_outcome and data_switch for ipcw
• removed dummy strata variables in data_switch for ipcw
• updated liferegr to use better starting values for model parameters
• updated documentations for rpsftm, ipe, tsesimp, tsegest, and ipcw to clarify the variables in output data frames
• added gridsearch parameter to tsegest
• updated unit tests and vignettes to use functions from the survival package
• added maxiter and eps to logisregr, liferegr, and phregr
• added the special case for psilower and psiupper when no root exists when using uniroot finding in rpsftm and tsegest
• updated to shortening survival if patients switched from active treatment to control in tsegestsim
• added subject-level data to tsegestsim

• Added the keep_censor parameter to the kmest function and added the ncensor variable to the output data frame.
• Added time 0 and the ncensor variable to the output data frame of the kmest function
• Added time 0 and the ncensor variable to the output baseline hazard data frame of the phregr function
• Added id to output data

• Updated logistic regression and associated programs

• Added probit and complementary log-log links to logistic regression
• Removed verbatim environment for ggplot in vignettes

• Fixed clang-UBSAN issues.

• Updated description in trtswitch-package.

• Updates to survival.cpp:

  • Changed requirement of positive time to nonnegative time for kmest, kmtest, rmest, and rmdiff.

• Updates to tsegestsimp.cpp:

  • Changed the description of shape1, scale1, shape2, and scale2 parameters.

• Updates to utilities.cpp:

  • Moved untreated and unswitched functions here. These functions are shared by rpsftm and ipe.

• Updates to rpsftm:

  • Added treat variable to Sstar.
  • Changed the default value of admin_recensor_only from FALSE to TRUE.
  • Added data_outcome and fit_outcome to output.
  • Added raw stratum and treat information to data_outcome.

• Updates to ipe:

  • Added treat variable to Sstar.
  • Changed the default value of admin_recensor_only from FALSE to TRUE.
  • Modified Sstar and kmstar to be consistent with rpsftm.
  • Added data_aft and fit_aft to output.
  • Added data_outcome and fit_outcome to output.
  • Added raw stratum and treat information to data_outcome.

• Updates to tsesimp:

  • Changed the default value of admin_recensor_only from FALSE to TRUE.
  • Added data_aft, fit_aft, data_outcome, and fit_outcome to output.
  • Added psi1hats in bootstrap.
  • Added raw stratum information to data_outcome.
  • Added agerand, sex.f, tt_Lnum, rmh_alea.c, and pathway.f as baseline covariates in the example.

• Updates to tsegest:

  • Changed the default value of admin_recensor_only from FALSE to TRUE.
  • Added the parameter n_eval_z to evaluate the Wald statistics at a sequence of psi values.
  • Added data_switch, km_switch, eval_z, data_nullcox, fit_nullcox, data_logis, fit_logis, data_outcome, and fit_outcome to output.
  • Included data_switch, km_switch, eval_z, data_nullcox, fit_nullcox, data_logis, and fit_logis in the analysis_switch list.
  • Added raw stratum information to data_outcome.

• Updates to ipcw:

  • Added relative_time parameter.
  • Added data_switch to output.
  • Added ns_df to output.
  • Renamed df_outcome to data_outcome.
  • Added raw stratum information to data_outcome.

• Added vignettes:

  • rpsftm.Rmd
  • ipe.Rmd
  • tsesimp.Rmd
  • tsegest.Rmd
  • ipcw.Rmd

• Initial release.

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