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Changelog

Source: NEWS.md

trtswitch 0.2.8

  • added summary methods for rpsftm, ipe, tsesimp, tsegest, ipcw, and msm with analysis populations, ordered TSD 24 reporting checklists, model parameter estimates, treatment effect estimates, weight summaries where applicable, and bootstrap summaries
  • added matched function calls to rpsftm, ipe, tsesimp, tsegest, ipcw, and msm output; MSM summaries distinguish exclusion of post-switching data from switching models and inclusion of post-switching data in the weighted outcome model
  • expanded rpsftm, ipe, tsesimp, tsegest, ipcw, and msm summaries with guidance to inspect relevant model diagnostics and plots, alongside reporting items requiring external justification or separately fitted sensitivity analyses
  • added pre-filter missingness summaries for AFT-model covariates in tsesimp and switching-model covariates in tsegest, ipcw, and msm, grouped by treatment arm and relevant model candidates
  • added p_kmstar to plot.ipe and added p_km_switch to plot.tsesimp and plot.tsegest
  • added data_switch and km_switch to tsesimp output
  • added a small positive value to avoid zero time in survival_analysis.cpp

trtswitch 0.2.7

CRAN release: 2026-06-25

  • clarified documentation for multiple-root handling of psi estimation in rpsftm, ipe, and tsegest: grid search selects the root closest to zero for point estimates and uses minimum/maximum roots for conservative confidence bounds, while root-finding (Brent or bisection) returns one bracketed root without guaranteeing selection of the root closest to zero
  • fixed a typo in tsegest.R
  • fixed a typo in the settings output of phregr
  • fixed a bug in plot.rpsftm, plot.ipe, plot.tsesimp, plot.tsegest, plot.ipcw, and plot.msm for KM plot number at risk tables
  • added a check for an empty input vector in the nscpp call in ipcw, msm, and tsegest
  • fixed a bug in bootstrap for tsegest by adding bootstrapped values for psi
  • added the missing append of oidc_local in bootstrap for tsesimp
  • fixed a typo in bootstrap mean_sd for psi for the experimental group in tsesimp
  • included only subjects with positive observable follow-up in tssim
  • returned an empty matrix if ncol == 0 in splines.cpp
  • checked signed K before converting to unsigned K in splines.cpp
  • handled an edge case when all ‘x’ values lie outsided boundary knots in splines.cpp
  • set the anyWarning flag to true if either lrEq0 or lrEq1 holds in splines.cpp
  • handled an edge case when a stratum does not contain both treatment groups in kmdiff

trtswitch 0.2.5

CRAN release: 2026-03-13

  • replace std::mt19937 with boost::random::mt19937 for random number generation in the bootstrap procedures

trtswitch 0.2.4

CRAN release: 2026-02-12

  • updated the concat_flatmatrix function for empty flat matrices
  • utilized column-major storage of flat matrices for cholesky decomposition
  • simplified the bygroup function

trtswitch 0.2.3

CRAN release: 2026-01-10

  • added assess_phregr to assess the proportional hazards assumption for the Cox model using the supremum test of Lin et al. (1993)
  • added an internal data pbc for testing assess_phregr
  • updated the censoring of post switch survival times in ipcw and msm to be consistent with the swtrt_control_only parameter value
  • added zph_phregr to compute the Schoenfeld residuals and test statistics for the proportional hazards assumption for the Cox model
  • refactored the code in pure c++ and RcppParallel for core computations to improve computational speed

trtswitch 0.2.2

CRAN release: 2025-11-16

  • added a check for the class of object for residuals_lieferegr.R, residuals_phregr.R, and survfit_phregr.R
  • added psi_roots for the vector of values at which the Z-statistic is zero, identified using grid search and linear interpolation for rpsftm.
  • added psi_roots and psi_trt_roots for the vector of psi values at which the Z-statistic is zero, identified using grid search and linear interpolation for tsegest
  • separated NumericVector loghrs = log(hrhats[ok]) into two statements: NumericVector subset_hrhats = hrhats[ok]; NumericVector loghrs = log(subset_hrhats); to avoid ASAN errors for ipcw.cpp, ipe.cpp, msm.cpp, rpsftm.cpp, tsegest.cpp, and tsesimp.cpp
  • updated the lrtest call to add the value for the new weight_readj parameter for ipcw.cpp, ipe.cpp, msm.cpp, rpsftm.cpp, tsegest.cpp, and tsesimp.cpp
  • added the weight_readj parameter to lrtest to indicate whether the weight variable at each event time will be readjusted to be proportional to the number at risk by treatment group in survival_analysis.
  • updated the getpsiest function to output multiple roots depending on the new direction parameter value in utilities.cpp and utilities.h
  • updated rpsftm and tsegest to use gridsearch by default
  • added print method for rpsftm, ipe, tsesimp, tsegest, ipcw, and msm
  • added class attribute for rpsftm, ipe, tsesimp, tsegest, ipcw, and msm objects
  • added km_outcome and lr_outcome for rpsftm, ipe, tsesimp, tsegest, ipcw, and msm objects
  • clarified the point estimate of psi when there are multiple roots and grid search is used
  • initialized weights to 1.0 for the Cox switching model in ipcw
  • added event summary and weight summary to output for ipcw and msm
  • added event summary to output for rpsftm, ipe, tsesimp and tsegest
  • added the plot method for rpsftm, ipe, tsesimp, tsegest, ipcw, and msm
  • use settings to store input parameter values for logisregr, liferegr, phregr, rpsftm, ipe, tsesimp, tsegest, ipcw, and msm
  • converted treatment back to a factor variable for output data sets in rpsftm, ipe, tsesimp, tsegest, ipcw, and msm
  • add res_aft to ipe and tsesimp

trtswitch 0.2.1

CRAN release: 2025-11-06

  • fixed the bootstrap procedures for IPCW, MSM, and TSEgest by reconstructing idx, idx1, treatn1, and stratumn1
  • clarified the distinction between IPCW using pooled logistic regression and IPCW using a Cox model with time-dependent covariates
  • excluded existing variables in out\(data\_switch\[\[h]]\)data from add_vars for IPCW and MSM
  • excluded existing variables in out\(analysis\_switch\)data_logis[[h]]$data from add_vars for TSEgest
  • excluded existing variables in out\(data\_aft\[\[h]]\)data from add_vars for TSEsimp
  • replaced chained sorting using logical OR with multiple if–return statements to ensure stable sorting in survival_analysis
  • replaced chained sorting using logical OR with std::tie in IPCW, IPE, MSM, RPSFTM, TSEsimp, and TSEgest
  • added id = “id” in test-ipe.R and test-rpsftm.R
  • combined functions f and g into a single function in test-rpsftm.R
  • added bootstrap testing for test-tsesimp.R
  • removed the target argument from the definition of function f in test-tsegest.R
  • added an option to use a Cox model with robust variance for constructing confidence intervals for the hazard ratio in IPCW and MSM
  • removed robust variance from the switching model in IPCW and MSM to improve computational speed
  • replaced geom_density with geom_histogram in the IPCW and MSM vignettes
  • removed natural spline basis functions for time from the pooled logistic regression model equation in TSEgest and incorporated these effects into time-dependent confounders in the TSEgest vignette
  • replaced event = “died” with event = “event” in bootstrap testing in the TSEgest vignette
  • removed the analysis_switch level from the output of TSEgest and moved its components to the top level of the output list
  • updated getpsiest to return only the first root
  • updated IPCW to apply weight truncation within each treatment group after computing weights for data_outcome
  • updated TSEsimp and TSEgest to use the switch time as the progression time when switching occurs before or in the absence of recorded progression
  • updated kmest to add the weight parameter for adjusted Kaplan-Meier estimate by Xie & Liu (2005)
  • updated lrtest to add the weight parameter for adjusted log-rank test by Xie & Liu (2005, 2011)
  • updated ipcw and msm to add Kaplan-Meier estimates of the survival functions and the log-rank test for the treatment effect based on the weighted outcome data truncated at time of treatment switching

trtswitch 0.2.0

CRAN release: 2025-10-06

  • added MSM to package description
  • added the plannedTime argument to the tssim function so that followupTime only refers to the follow-up time in a fixed follow-up design
  • added an extra record for a subject to the tssim output dataset if the observed survival time exceeds the number of regular treatment cycles times days per cycle
  • removed the getAccrualDurationFromN utility function
  • changed the default value of the boot parameter to FALSE for ipcw and msm
  • added the ns_df parameter to the tsegest function
  • added the preptdc function to prepare survival data with time-dependent covariates
  • expanded the findInterval3 function definition to mimic R’s findInterval() behavior with rightmost_closed, all_inside, and left_open options
  • updated the survfit_phregr function to only include time points between the first tstart and the last tstop for each subject with counting process style of input
  • added the exclusion of observations with missing values for survfit_phregr and residuals_phregr
  • added the exclusion of observations with missing values for rpsftm, ipe, tsesimp, tsegest, ipcw, and msm
  • changed to sort the input data by treatment, ID, and time variables for IPCW, MSM, and TSEgest, and by treatment, stratum, ID, and time variables for bootstrap samples
  • changed the default value of treat_alt_interaction from FALSE to TRUE for MSM
  • renamed Y to event for tssim output
  • added the bisect utility function for root finding
  • added the root_finding parameter to rpsftm, ipe, tsegest to allow the user to choose between brent and bisect for root finding

trtswitch 0.1.9

CRAN release: 2025-09-03

  • added fail_boots_data to include the failed bootstrap sample data
  • used strata variable names and values for dummy variables in logistic regression and life regression models
  • updated the tssim function to allow both fixed and variable follow-up designs
  • used stratified bootstrapping for the rpsftm, ipe, tsesimp, tsegest, ipcw, and msm functions
  • allowed event, pd, and swtrt to take real values 1 or 0 in rpsftm, ipe, tsesimp, tsegest, ipcw, and msm functions
  • added martingale residuals for lifereg for event or right-censored survival data
  • added time-dependent covariate visit7on and used cattdc instead of catlag for tsegest sample call
  • added interval splitting if treatment switching occurs between visits for ipcw, msm, and tsegest
  • added a small number to os_time if needed to ensure pd_time is less than os_time for tsesimp and tsegest
  • added getpsiest and getpsiend utility functions for psi estimation of rpsftm, ipe, and tsegest
  • updated the condition to include post progression data up to switching in tsegest
  • updated the condition for time-dependent crossover indicator in tsegest
  • updated the algorithm for generating timePFSobs in tsegestsim
  • removed catlag and xotime_upper from the output data set of tsegestsim
  • applied weights to the next interval for ipcw and msm using logistic regression switching model
  • updated tssim to use Z and A to denote the alternative therapy status at the start instead of end of interval
  • updated logisregr, liferegr and phregr to allow zero events to run with trivial output

trtswitch 0.1.8

CRAN release: 2025-07-12

  • 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

trtswitch 0.1.7

CRAN release: 2025-06-05

  • 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

trtswitch 0.1.6

CRAN release: 2025-04-25

  • fixed an ASAN issue in survQuantile

trtswitch 0.1.5

CRAN release: 2025-04-24

  • 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

trtswitch 0.1.4

CRAN release: 2025-03-20

  • 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

trtswitch 0.1.3

CRAN release: 2025-02-06

  • Updated logistic regression and associated programs

trtswitch 0.1.2

CRAN release: 2024-12-05

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

trtswitch 0.1.1

CRAN release: 2024-11-01

  • 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

trtswitch 0.1.0

CRAN release: 2024-10-17

  • Initial release.