Changelog

CHANGELOG.md

@@ -0,0 +1,47 @@
+# treepplr : an R package for TreePPL
+
+## [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

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")),

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)