From 073ee5303a215f9d5728d86c41be7b7dfa16f766 Mon Sep 17 00:00:00 2001 From: MayaGueguen Date: Mon, 6 May 2024 13:14:40 +0200 Subject: [PATCH] Update website --- DESCRIPTION | 2 +- README.md | 5 +- _pkgdown.yml | 5 + docs/404.html | 7 + docs/articles/examples_1_mainFunctions.html | 7 + .../examples_2_secundaryFunctions.html | 7 + docs/articles/index.html | 9 + docs/articles/news.html | 7 + docs/articles/vignette_crossValidation.html | 7 + docs/articles/vignette_dataPreparation.html | 7 + docs/articles/vignette_modelingOptions.html | 9 +- docs/articles/vignette_presentation.html | 258 ++++++++++++++++++ docs/articles/vignette_pseudoAbsences.html | 7 + docs/articles/vignette_variability.html | 7 + docs/articles/vignette_videos.html | 7 + docs/authors.html | 7 + docs/index.html | 11 +- .../reference/BIOMOD.ensemble.models.out.html | 7 + docs/reference/BIOMOD.formated.data.PA.html | 7 + docs/reference/BIOMOD.formated.data.html | 7 + docs/reference/BIOMOD.models.options.html | 7 + docs/reference/BIOMOD.models.out.html | 7 + docs/reference/BIOMOD.options.dataset.html | 7 + docs/reference/BIOMOD.options.default.html | 7 + docs/reference/BIOMOD.projection.out.html | 7 + docs/reference/BIOMOD.stored.data.html | 7 + .../BIOMOD_CrossValidation-deprecated.html | 7 + .../reference/BIOMOD_EnsembleForecasting.html | 7 + docs/reference/BIOMOD_EnsembleModeling.html | 7 + docs/reference/BIOMOD_FormatingData.html | 7 + docs/reference/BIOMOD_LoadModels.html | 7 + docs/reference/BIOMOD_Modeling.html | 7 + .../BIOMOD_PresenceOnly-deprecated.html | 7 + docs/reference/BIOMOD_Projection.html | 7 + docs/reference/BIOMOD_RangeSize.html | 7 + docs/reference/BIOMOD_tuning-deprecated.html | 7 + .../BinaryTransformation-deprecated.html | 7 + docs/reference/DataSpecies.html | 7 + .../reference/Find.Optim.Stat-deprecated.html | 7 + docs/reference/ModelsTable.html | 7 + docs/reference/OptionsBigboss.html | 7 + docs/reference/ProbDensFunc-deprecated.html | 7 + docs/reference/bioclim_current.html | 7 + docs/reference/bioclim_future.html | 7 + docs/reference/biomod2-deprecated.html | 7 + docs/reference/biomod2_ensemble_model.html | 7 + docs/reference/biomod2_model.html | 7 + docs/reference/bm_BinaryTransformation.html | 7 + docs/reference/bm_CrossValidation.html | 7 + docs/reference/bm_FindOptimStat.html | 7 + docs/reference/bm_MakeFormula.html | 7 + docs/reference/bm_ModelingOptions.html | 7 + docs/reference/bm_PlotEvalBoxplot.html | 7 + docs/reference/bm_PlotEvalMean.html | 7 + docs/reference/bm_PlotRangeSize.html | 7 + docs/reference/bm_PlotResponseCurves.html | 7 + docs/reference/bm_PlotVarImpBoxplot.html | 7 + docs/reference/bm_PseudoAbsences.html | 7 + docs/reference/bm_RunModelsLoop.html | 7 + docs/reference/bm_SRE.html | 7 + docs/reference/bm_SampleBinaryVector.html | 7 + docs/reference/bm_SampleFactorLevels.html | 7 + docs/reference/bm_Tuning.html | 7 + docs/reference/bm_VariablesImportance.html | 7 + docs/reference/calculate.stat-deprecated.html | 7 + docs/reference/check_duplicated_cells.html | 7 + docs/reference/dot-categorical2numeric.html | 7 + docs/reference/dot-get_categorical_names.html | 7 + docs/reference/dot-get_env_class.html | 7 + docs/reference/dot-load_gam_namespace.html | 7 + ...dot-transform.outputs.list-deprecated.html | 7 + .../reference/dot-transform_model.as.col.html | 7 + .../getStatOptimValue-deprecated.html | 7 + docs/reference/getters.bm.html | 7 + docs/reference/getters.out.html | 7 + docs/reference/index.html | 7 + docs/reference/load_stored_object.html | 7 + docs/reference/makeFormula-deprecated.html | 7 + .../models_scores_graph-deprecated.html | 7 + docs/reference/plot.html | 7 + docs/reference/predict.bm.html | 7 + docs/reference/predict.em.html | 7 + docs/reference/predict2.bm.html | 7 + docs/reference/predict2.em.html | 7 + docs/reference/rast.has.values.html | 7 + docs/reference/response.plot2-deprecated.html | 7 + .../sample.factor.levels-deprecated.html | 7 + docs/reference/sre-deprecated.html | 7 + docs/reference/summary.html | 7 + .../variables_importance-deprecated.html | 7 + docs/reference/zzz_bm.html | 7 + 91 files changed, 883 insertions(+), 4 deletions(-) create mode 100644 docs/articles/vignette_presentation.html 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 +
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  • Modeling Options
    +
    Presentation
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    Pseudo-absences
    Variability in results
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  • 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 + + + + + + + + + + + + +
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    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)

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

      + +
      • +
    +
    +
    +

    + Single models : BIOMOD_Modeling +

    + +
    +
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    + Ensemble models : BIOMOD_EnsembleModeling +

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

    + Exploring outputs +

    + +
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    + Projecting models : BIOMOD_Projection, BIOMOD_EnsembleForecasting +

    +
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    • Project models onto new conditions
      • +
    • Transform predicted probabilities in binary values (through bm_BinaryTransformation)
      • +
    +
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    + Species range change : BIOMOD_RangeSize +

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    +

    +

    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.

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    + + + + + + + + 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

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

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    Main workflow

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