diff --git a/DESCRIPTION b/DESCRIPTION index 7e6cdf4a..67cec58b 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: biomod2 Type: Package Title: Ensemble Platform for Species Distribution Modeling Version: 4.2-5 -Date: 2024-04-30 +Date: 2024-05-30 Authors@R: c(person("Wilfried", "Thuiller", role = c("aut") , email = "wilfried.thuiller@univ-grenoble-alpes.fr"), person("Damien", "Georges", role = c("aut")), diff --git a/README.md b/README.md index 2ff1e442..c7852434 100644 --- a/README.md +++ b/README.md @@ -22,7 +22,10 @@ z-index: 10; } +
+

Logo biomod2

+ ------------------------------------------------------------
Species distribution modeling,
calibration and evaluation,
@@ -81,7 +84,7 @@ devtools::install_github("biomodhub/biomod2", dependencies = TRUE)

Main workflow

-

+


diff --git a/_pkgdown.yml b/_pkgdown.yml index e27ed518..968de97b 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -9,6 +9,7 @@ navbar: left: - home - videos + - presentation - examples - reference right: @@ -22,6 +23,10 @@ navbar: text: Videos icon: fas fa-video href: articles/vignette_videos.html + presentation: + text: Presentation + icon: fas fa-graduation-cap + href: articles/vignette_presentation.html examples: text: Examples icon: fas fa-stethoscope diff --git a/docs/404.html b/docs/404.html index 1de76174..10f488de 100644 --- a/docs/404.html +++ b/docs/404.html @@ -51,6 +51,13 @@ Videos +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
  • Modeling Options
    +
    Presentation
    +
    Pseudo-absences
    Variability in results
    diff --git a/docs/articles/news.html b/docs/articles/news.html index e3ff383e..a6209288 100644 --- a/docs/articles/news.html +++ b/docs/articles/news.html @@ -52,6 +52,13 @@ Videos
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +

  • 1 ANN binary nnet nnet avNNet 2 CTA binary rpart rpart rpart 3 FDA binary mda fda fda -4 GAM binary gam gam gamSpline +4 GAM binary gam gam gamLoess 5 GAM binary mgcv bam bam 6 GAM binary mgcv gam gam 7 GBM binary gbm gbm gbm diff --git a/docs/articles/vignette_presentation.html b/docs/articles/vignette_presentation.html new file mode 100644 index 00000000..d93051e1 --- /dev/null +++ b/docs/articles/vignette_presentation.html @@ -0,0 +1,258 @@ + + + + + + + +Presentation • biomod2 + + + + + + + + + + + + +
    +
    + + + + +
    +
    +
    +

    Presentation

    + + + Source: vignettes/vignette_presentation.Rmd + + +
    + + + +

    +

    To follow biomod2 evolution of organization and +features, the presentation below details the different steps and modules +of the package.

    +



    +
    + +
    +



    + +
    +

    + Data formating : BIOMOD_FormatingData +

    +
      +

    • Formating data : combine observations, +coordinates and explanatory variables,
      and sample pseudo-absences +for presence-only data (through bm_PseudoAbsences)

      • +

    • Cross-validation : create calibration / +validation datasets (through bm_CrossValidation)

      • +
    • +

      Modeling options (with the help of ModelsTable and OptionsBigboss +datasets)

      + +
      • +
    +
    +
    +

    + Single models : BIOMOD_Modeling +

    + +
    +
    +

    + Ensemble models : BIOMOD_EnsembleModeling +

    +
      +
    • Filter single models based on one evaluation metric
      • +
    • Combine them according to different combinations
      • +
    • And build ensemble models
      • +
    +
    +
    +

    + Exploring outputs +

    + +
    +
    +

    + Projecting models : BIOMOD_Projection, BIOMOD_EnsembleForecasting +

    +
      +
    • Project models onto new conditions
      • +
    • Transform predicted probabilities in binary values (through bm_BinaryTransformation)
      • +
    +
    +
    +

    + Species range change : BIOMOD_RangeSize +

    +
    +
    + + + +
    + + + +
    +

    +

    Developed by Wilfried Thuiller, Damien Georges, Maya Gueguen, Robin Engler, Frank Breiner, Bruno Lafourcade, Remi Patin, Helene Blancheteau.

    +
    + +
    +

    +

    Site built with pkgdown 2.0.9.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/articles/vignette_pseudoAbsences.html b/docs/articles/vignette_pseudoAbsences.html index 8fd840cf..00f45ad9 100644 --- a/docs/articles/vignette_pseudoAbsences.html +++ b/docs/articles/vignette_pseudoAbsences.html @@ -52,6 +52,13 @@ Videos

    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +

  • https://biomodhub.github.io/biomod2/

    @@ -203,7 +212,7 @@

    Main workflow

    -



    +




    diff --git a/docs/reference/BIOMOD.ensemble.models.out.html b/docs/reference/BIOMOD.ensemble.models.out.html index 6a27065c..1b12f3b5 100644 --- a/docs/reference/BIOMOD.ensemble.models.out.html +++ b/docs/reference/BIOMOD.ensemble.models.out.html @@ -37,6 +37,13 @@ Videos

    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +
    • +
  • + + + + Presentation + +