Merge pull request #111 from sanssouci-org/guillermo-dev

Version 0.13.0

.Rbuildignore

@@ -24,6 +24,7 @@ appveyor.yml
 ^vignettes/.*_cache
 ^inst/shiny-examples/volcano-plot/.*\.rds$
 
+TODO-package.md
 TODO*.txt
 ^doc$
 ^Meta$

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="[email protected]",

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]
 

README.Rmd

@@ -2,8 +2,6 @@
 output: github_document
 ---
 
-<!-- README.md is generated from README.Rmd. Please edit that file -->
-
 ```{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 released version of sanssouci from [CRAN](https://CRAN.R-project.org) with: -->
 
-<!-- ``` r -->
-<!-- install.packages("sanssouci") -->
-<!-- ``` -->
-
 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")
 ```
 

README.md

@@ -1,6 +1,4 @@
 
-<!-- README.md is generated from README.Rmd. Please edit that file -->
-
 # sanssouci
 
 <!-- badges: start -->
@@ -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)
 <!-- badges: end -->
 
 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.
 ```
 
 <img src="man/figures/README-conf-curve-1.png" width="100%" />
@@ -111,14 +113,11 @@ to perform such selections interactively and without programming.
 ## Installation
 
 <!-- You can install the released version of sanssouci from [CRAN](https://CRAN.R-project.org) with: -->
-<!-- ``` r -->
-<!-- install.packages("sanssouci") -->
-<!-- ``` -->
 
 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")
 ```

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}
 ---