diff --git a/.Rbuildignore b/.Rbuildignore index 425ab46..54b98e5 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -24,6 +24,7 @@ appveyor.yml ^vignettes/.*_cache ^inst/shiny-examples/volcano-plot/.*\.rds$ +TODO-package.md TODO*.txt ^doc$ ^Meta$ diff --git a/DESCRIPTION b/DESCRIPTION index 046e8c2..74d7596 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: sanssouci -Version: 0.12.9 -Date: 2023-07-18 +Version: 0.13.0 +Date: 2024-06-17 Title: Post Hoc Multiple Testing Inference Authors@R: c(person("Pierre", "Neuvial", role=c("aut", "cre"), email="pierre.neuvial@math.univ-toulouse.fr", diff --git a/NEWS b/NEWS index 262f93b..2458115 100644 --- a/NEWS +++ b/NEWS @@ -2,10 +2,26 @@ Package: sanssouci ================== +Version 0.13.0 [2024-06-17] + +* New algorithm to compute a curve of post hoc bounds on a path of selection sets +when using a reference family with a forest structure, see DBNR paper (PR #109) +* The DBNR vignette is back in line with the settings used in the simulations +of the paper (PR #110) +* Multiple code optimization and tricks added for the functions linked to DBNR +* According to the points above, new functions: pruning, delete.gaps, +curve.V.star.forest.naive, curve.V.star.forest.fast, forest.completion +* Some functions removed, in particular zetas.tree.refined, now an option of +zetas.tree does the same +* gen.p.values now allow to generate p-values for the three types of alternative +* Multiple issues closed (#86 #88 #89 #101 #102 #106 #107) +* Scripts illustrating the various computationnal time improvements added +* Documentation greatly improved for all the functions linked to DBNR + Version 0.12.9 [2023-07-18] -* export curveMaxFP and formatBounds (#108) -* cleanup in different versions of curveMaxFP +* Export curveMaxFP and formatBounds (#108) +* Cleanup in different versions of curveMaxFP Version 0.12.8 [2022-11-11] diff --git a/README.Rmd b/README.Rmd index 56b36da..6cad459 100644 --- a/README.Rmd +++ b/README.Rmd @@ -2,8 +2,6 @@ output: github_document --- - - ```{r, include = FALSE} knitr::opts_chunk$set( collapse = TRUE, @@ -89,14 +87,10 @@ Importantly, multiple such selections can be made without compromising the valid - - - - You can install the development version from [GitHub](https://github.com/) with: ``` r -# install.packages("remotes") -remotes::install_github("sanssouci-org/sanssouci") +# install.packages("pak") +pak::pkg_install("sanssouci-org/sanssouci") ``` diff --git a/README.md b/README.md index 9515ca8..d58543a 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,4 @@ - - # sanssouci @@ -9,6 +7,7 @@ status](https://github.com/sanssouci-org/sanssouci/workflows/R-CMD-check/badge.svg)](https://github.com/sanssouci-org/sanssouci/actions) [![Coverage Status](https://codecov.io/gh/sanssouci-org/sanssouci/branch/develop/graph/badge.svg)](https://codecov.io/github/sanssouci-org/sanssouci/branch/develop) +[![R-CMD-check](https://github.com/sanssouci-org/sanssouci/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/sanssouci-org/sanssouci/actions/workflows/R-CMD-check.yaml) The goal of sanssouci \[sãsusi\] is to perform **post hoc inference**: @@ -86,6 +85,9 @@ plot(res, xmax = 500) + geom_line(size = 1.5) #> Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. #> ℹ Please use `linewidth` instead. +#> This warning is displayed once every 8 hours. +#> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was +#> generated. ``` @@ -111,14 +113,11 @@ to perform such selections interactively and without programming. ## Installation - - - You can install the development version from [GitHub](https://github.com/) with: ``` r -# install.packages("remotes") -remotes::install_github("sanssouci-org/sanssouci") +# install.packages("pak") +pak::pkg_install("sanssouci-org/sanssouci") ``` diff --git a/vignettes/CopyOfconfidenceCurves_localized.Rmd b/vignettes/CopyOfconfidenceCurves_localized.Rmd index 3c4cd1f..22fa4bf 100644 --- a/vignettes/CopyOfconfidenceCurves_localized.Rmd +++ b/vignettes/CopyOfconfidenceCurves_localized.Rmd @@ -9,7 +9,7 @@ output: keep_tex: true bibliography: sanssouci.bib vignette: > - %\VignetteIndexEntry{Confidence curves for structured hypotheses} + %\VignetteIndexEntry{copy of vignette: Confidence curves for structured hypotheses} %\VignetteEngine{knitr::knitr} ---