From 3e34052db06e788eb5a307143a09ebc733b7255e Mon Sep 17 00:00:00 2001 From: ThimotheeV Date: Wed, 7 Oct 2026 15:37:50 +0200 Subject: [PATCH 1/3] New version --- DESCRIPTION | 2 +- R/zzz.R | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 2a7e18d..2c21f41 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: treepplr Title: R Interface to TreePPL -Version: 0.15.0 +Version: 0.5.0 Authors@R: c( person("Mariana", "P Braga", , "mpiresbr@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-1253-2536")), diff --git a/R/zzz.R b/R/zzz.R index 6e256fd..e96e7ed 100644 --- a/R/zzz.R +++ b/R/zzz.R @@ -11,7 +11,7 @@ #' @description #' TreePPL program version in use for this package version #'@export -TPPLC_VERSION <- "0.4" +TPPLC_VERSION <- "0.5" .onLoad <- function(libname, pkgname){ tp_installing_treeppl(download = FALSE) From f900c3de105750b58bd619750eaba5b097be3354 Mon Sep 17 00:00:00 2001 From: ThimotheeV Date: Tue, 3 Nov 2026 15:45:53 +0100 Subject: [PATCH 2/3] add changelog --- CHANGELOG.md | 47 +++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 CHANGELOG.md diff --git a/CHANGELOG.md b/CHANGELOG.md new file mode 100644 index 0000000..a59aefa --- /dev/null +++ b/CHANGELOG.md @@ -0,0 +1,47 @@ +# treepplr + +## [Unreleased] + +### Added + +### Changed + +### Deprecated + +### Removed + +### Fixed + +### Security + +## v0.5.0 + +### Added +- ([treepplr#12](https://github.com/treeppl/treepplr/pull/12)) Add `tp_runtime_options` +- ([treepplr#13](https://github.com/treeppl/treepplr/pull/13)) `tp_run(n_runs)` to run multiple sweeps/runs +- ([treepplr#13](https://github.com/treeppl/treepplr/pull/13)) `tp_run(n_processes)` to run MCMC or SMC in parallel using n cores +- ([treepplr#13](https://github.com/treeppl/treepplr/pull/13)) `tp_compile_methods()` to find available methods +- ([treepplr#14](https://github.com/treeppl/treepplr/pull/14)) Tim and Stenio as package authors in DESCRIPTION. +- ([treepplr#31](https://github.com/treeppl/treepplr/pull/31)) At the end of a run, `tp_run()` now prints a summary with runtime information and output directories/files. +- ([treepplr#31](https://github.com/treeppl/treepplr/pull/31)) New argument `wide` in `tp_parse_smc()` and `tp_parse_mcmc()` to choose between wide (standard in other software) and long (good for plotting) format. Default = `TRUE`. + +### Changed +- ([treepplr#12](https://github.com/treeppl/treepplr/pull/12)) Change "compiled_model" to "sampler" (temporary) +- ([treepplr#13](https://github.com/treeppl/treepplr/pull/13)) Updated the documentation +- ([treepplr#14](https://github.com/treeppl/treepplr/pull/14)) treepplr package installation should be done with `pak::pak` because `devtools::install_github` will soon be deprecated. +- ([treepplr#30](https://github.com/treeppl/treepplr/pull/30)) Updated roxygen documentation for `tp_parse_smc()` and `tp_parse_mcmc()`. Changed their output objects to tidy data frames. +- ([treepplr#31](https://github.com/treeppl/treepplr/pull/31)) `tp_run()` now returns a tidy data frame (in wide format by default) instead of a list. It automatically calls `tp_parse_smc()` or `tp_parse_mcmc()`, depending on the inference method and model passed to `tp_compile()`. For models without a parser yet (e.g., models that return trees), it returns the path to the output JSON file along with a message. +- ([treepplr#31](https://github.com/treeppl/treepplr/pull/31)) `tp_parse_smc()` and `tp_parse_mcmc()` now take a character vector with the path(s) to the JSON output file(s) instead of the list returned by `tp_run()`. +- ([treepplr#31](https://github.com/treeppl/treepplr/pull/31)) `tp_mcmc_convergence()` and `tp_smc_convergence()` now accept data frames in either long or wide format. + +### Deprecated +- ([treepplr#12](https://github.com/treeppl/treepplr/pull/12)) all references to `n_runs` have been remove + +### Removed + +### Fixed +- ([treepplr#12](https://github.com/treeppl/treepplr/pull/12)) Always check if tpplc is installed before calling it +- ([treepplr#12](https://github.com/treeppl/treepplr/pull/12)) `tp_compile_options` update for new `--help` format +- ([treepplr#30](https://github.com/treeppl/treepplr/pull/30)) `tp_parse_smc()` and `tp_parse_mcmc()` now parse per-particle/iteration with explicit indices and (for SMC) join weights by index using `left_join(..., by = "particle")` instead of relying on positional recycling, which is the default behavior of `data.frame()` when handling vectors of different lengths. + +### Security \ No newline at end of file From feca0a030c4f0f74c1d1cdbce2a2f7b5efcce391 Mon Sep 17 00:00:00 2001 From: Tim Virgoulay Date: Tue, 3 Nov 2026 16:56:47 +0100 Subject: [PATCH 3/3] Update project title in CHANGELOG.md --- CHANGELOG.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index a59aefa..9d62355 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,4 +1,4 @@ -# treepplr +# treepplr : an R package for TreePPL ## [Unreleased] @@ -44,4 +44,4 @@ - ([treepplr#12](https://github.com/treeppl/treepplr/pull/12)) `tp_compile_options` update for new `--help` format - ([treepplr#30](https://github.com/treeppl/treepplr/pull/30)) `tp_parse_smc()` and `tp_parse_mcmc()` now parse per-particle/iteration with explicit indices and (for SMC) join weights by index using `left_join(..., by = "particle")` instead of relying on positional recycling, which is the default behavior of `data.frame()` when handling vectors of different lengths. -### Security \ No newline at end of file +### Security