diff --git a/DESCRIPTION b/DESCRIPTION index 79bd39e..f63e482 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: pcadapt Type: Package Title: Fast Principal Component Analysis for Outlier Detection Version: 4.4.0 -Date: 2024-04-15 +Date: 2024-09-24 Authors@R: c( person("Keurcien", "Luu", role = "aut"), person("Michael", "Blum", role = "aut"), diff --git a/README.md b/README.md index a1aa5a6..6e51ef3 100644 --- a/README.md +++ b/README.md @@ -1,17 +1,17 @@ -# pcadapt - [![DOI](https://zenodo.org/badge/doi/10.1093/molbev/msaa053.svg)](https://doi.org/10.1093/molbev/msaa053) -[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/pcadapt)](https://cran.r-project.org/package=pcadapt) +[![CRAN status](https://www.r-pkg.org/badges/version/pcadapt)](https://CRAN.R-project.org/package=pcadapt) [![R-CMD-check](https://github.com/bcm-uga/pcadapt/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/bcm-uga/pcadapt/actions/workflows/R-CMD-check.yaml) -R package {pcadapt} has been developed to detect genetic markers involved in biological adaptation. +# pcadapt + +R package {pcadapt} was developed to detect genetic markers involved in biological adaptation. This package uses statistical tools for outlier detection based on Principal Component Analysis (PCA). A tutorial for {pcadapt} is available on [pcadapt's website](https://bcm-uga.github.io/pcadapt/articles/pcadapt.html). -**News:** A new paper is finally out describing version 4 of pcadapt (which has been available for quite some time now). Please cite the new paper. +**News:** Our paper describing version 4 of pcadapt (which has been available for quite some time now) is out. Please cite the newest paper (see Refs below). ## Installation diff --git a/docs/articles/pcadapt.html b/docs/articles/pcadapt.html index 1001ab2..9c189de 100644 --- a/docs/articles/pcadapt.html +++ b/docs/articles/pcadapt.html @@ -167,10 +167,10 @@

B.1. Scree plot## Warning: The `<scale>` argument of `guides()` cannot be `FALSE`. Use "none" instead as ## of ggplot2 3.3.4. ## ℹ The deprecated feature was likely used in the pcadapt package. -## Please report the issue at < -## This warning is displayed once every 8 hours. -## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was -## generated. +## Please report the issue at <https://github.com/bcm-uga/pcadapt/issues>. +## This warning is displayed once every 8 hours. +## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was +## generated.

By default, the number of principal components shown in the scree plot is K, but it can be reduced via the argument @@ -353,10 +353,10 @@

D.3. Histogra 
## Warning: The dot-dot notation (`..density..`) was deprecated in ggplot2 3.4.0.
 ## ℹ Please use `after_stat(density)` instead.
 ## ℹ The deprecated feature was likely used in the pcadapt package.
-##   Please report the issue at <
-## This warning is displayed once every 8 hours.
-## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
-## generated.
+## Please report the issue at <https://github.com/bcm-uga/pcadapt/issues>. +## This warning is displayed once every 8 hours. +## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was +## generated.

diff --git a/docs/articles/pcadapt_files/figure-html/unnamed-chunk-10-1.png b/docs/articles/pcadapt_files/figure-html/unnamed-chunk-10-1.png index d35187d..e6b7d24 100644 Binary files a/docs/articles/pcadapt_files/figure-html/unnamed-chunk-10-1.png and b/docs/articles/pcadapt_files/figure-html/unnamed-chunk-10-1.png differ diff --git a/docs/articles/pcadapt_files/figure-html/unnamed-chunk-8-1.png b/docs/articles/pcadapt_files/figure-html/unnamed-chunk-8-1.png index 2cba946..79f9341 100644 Binary files a/docs/articles/pcadapt_files/figure-html/unnamed-chunk-8-1.png and b/docs/articles/pcadapt_files/figure-html/unnamed-chunk-8-1.png differ diff --git a/docs/articles/pcadapt_files/figure-html/unnamed-chunk-9-1.png b/docs/articles/pcadapt_files/figure-html/unnamed-chunk-9-1.png index 5229709..aad2261 100644 Binary files a/docs/articles/pcadapt_files/figure-html/unnamed-chunk-9-1.png and b/docs/articles/pcadapt_files/figure-html/unnamed-chunk-9-1.png differ diff --git a/docs/index.html b/docs/index.html index 54a22a1..3e3de2a 100644 --- a/docs/index.html +++ b/docs/index.html @@ -72,14 +72,14 @@
+ +

pcadapt

- - -

R package {pcadapt} has been developed to detect genetic markers involved in biological adaptation. This package uses statistical tools for outlier detection based on Principal Component Analysis (PCA).

+

R package {pcadapt} was developed to detect genetic markers involved in biological adaptation. This package uses statistical tools for outlier detection based on Principal Component Analysis (PCA).

A tutorial for {pcadapt} is available on pcadapt’s website.

-

News: A new paper is finally out describing version 4 of pcadapt (which has been available for quite some time now). Please cite the new paper.

+

News: Our paper describing version 4 of pcadapt (which has been available for quite some time now) is out. Please cite the newest paper (see Refs below).

Installation

@@ -100,6 +100,7 @@

References @@ -141,7 +142,7 @@

Developers

Dev status

  • DOI
    • -
  • CRAN_Status_Badge
    • +
  • CRAN status
  • R-CMD-check

diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index cb4a0f6..80b8b28 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -3,5 +3,5 @@ pkgdown: 2.0.6 pkgdown_sha: ~ articles: pcadapt: pcadapt.html -last_built: 2024-04-15T13:03Z +last_built: 2024-09-24T12:48Z diff --git a/src/Makevars b/src/Makevars index 516e51b..9bf3c5f 100644 --- a/src/Makevars +++ b/src/Makevars @@ -1,3 +1,2 @@ PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) PKG_CPPFLAGS = -I../inst/include -DARMA_DONT_PRINT_OPENMP_WARNING -DSTRICT_R_HEADERS -CXX_STD = CXX11