The aim of this document is to keep track of the changes made to the different versions of the `R`

package `pencal`

.

The numbering of package versions follows the convention a.b.c, where a and b are non-negative integers, and c is a positive integer. When minor changes are made to the package, a and b are kept fixed and only c is increased. Major changes to the package, instead, are made apparent by changing a or b.

Each section of this document corresponds to a major change in the package - in other words, within a section you will find all those package versions a.b.x where a and b are fixed whereas x = 1, 2, 3, … Each subsection corresponds to a specific package version.

- Released: May 2021
- Function
`survpred_prc`

replaced by two distinct functions:`survpred_prclmm`

for the PRC-LMM model, and`survpred_prcmlpmm`

for the PRC-MLPMM model - Documentation and vignette updated accordingly

- Released: April 2021
`fit_lmms`

is now more memory efficient (`keep.data = F`

when calling lme)`fit_mlpmms`

is now faster (parallelization implemented also before the CBOCP is started)- Added functions
`pencox_baseline`

and`performance_pencox_baseline`

- Minor updates to the vignette

- Released: March 2021
- Fixed CRAN error in PRC MLPMM examples (replaced
`T`

with`TRUE`

) - Corrected typos in vignette

- Released: March 2021
- Added a set of functions that can be used to fit the PRC-MLPMM model(s):
`simulate_prcmlpmm_data`

,`fit_mlpmms`

,`summarize_mlpmms`

and`fit_prcmlpmm`

- Renamed
`performance_prclmm`

to`performance_prc`

, and`survpred_prclmm`

to`survpred_prc`

(the functions work both for the PRC-LMM, and the PRC-MLPMM) - Vignettes and documentation updated to reflect the changes

- Released: January 2021
- Fixed CRAN error caused by parallel::detectCores()
- Added link to arXiv preprint in package description and vignette
- Added CITATION file
- Vignettes updated and revised
- Updated references in help pages

- Released: January 2021
- Added the vignette “An introduction to the R package pencal”

- Released: December 2020
- Added the function
`survpred_prclmm`

, which computes predicted survival probabilities from the fitted PRC-LMM model - Added
`fitted_prclmm`

data object and related documentation (it is used in the examples of`performance_prclmm`

) - Several corrections and clarifications added to the documentation
- Changed displaying style for function arguments in the documentation

- Released: November 2020
- This is the first public release of the
`pencal`

package. It comprises the skeleton around which the rest of the R package will be built - This version comprises functions to perform the following tasks:
- simulate data corresponding to the PRC-LMM model (functions
`simulate_t_weibull`

and`simulate_prclmm_data`

); - estimate the PRC-LMM model and its associated cluster bootstrap optimism correction procedure (functions
`fit_lmms`

,`summarize_lmms`

and`fit_prclmm`

); - compute the optimism-corrected estimates of the C index and time-dependent AUC (function
`performance_prclmm`

)

- simulate data corresponding to the PRC-LMM model (functions
- Note: developing an
`R`

package that is user-friendly, comprehensive and well-documented is an effort that takes months, sometimes even years. This package is*currently under active development*, and many additional features and functionalities (including vignettes!) will be added incrementally with the next releases. If you notice a bug or something unclear in the documentation, feel free to get in touch with the maintainer of the package!