# Main functions: binary data

## Complete code example

Here are presented, in a full and complete example, all main functions (starting with `BIOMOD_[...]`) of `biomod2`.

The data set used is the DataSpecies containing presence/absence data.
Similar examples are presented for count data on the Main functions (abund) webpage.

### Load dataset and variables

    library(biomod2)
    library(terra)

    # Load species occurrences (6 species available)
    data('DataSpecies')
    head(DataSpecies)

    # Select the name of the studied species
    myRespName <- 'GuloGulo'

    # Get corresponding presence/absence data
    myResp <- as.numeric(DataSpecies[, myRespName])

    # Get corresponding XY coordinates
    myRespXY <- DataSpecies[, c('X_WGS84', 'Y_WGS84')]

    # Load environmental variables extracted from BIOCLIM (bio_3, bio_4, bio_7, bio_11 & bio_12)
    data('bioclim_current')
    myExpl <- rast(bioclim_current)

### Prepare data & parameters

#### Format data (observations & explanatory variables)

    # Format data with true absences
    myBiomodData <- BIOMOD_FormatingData(resp.name = myRespName,
                                         resp.var = myResp,
                                         resp.xy = myRespXY,
                                         expl.var = myExpl)
    myBiomodData
    plot(myBiomodData)

#### Pseudo-absences extraction

Single or multiple set of pseudo-absences can be selected with the `BIOMOD_FormatingData` function, which calls the `bm_PseudoAbsences` function to do so. More examples are presented on the Auxiliary functions webpage.

    # # Transform true absences into potential pseudo-absences
    # myResp.PA <- ifelse(myResp == 1, 1, NA)
    #
    # # Format data with pseudo-absences : random method
    # myBiomodData.r <- BIOMOD_FormatingData(resp.var = myResp.PA,
    #                                        expl.var = myExpl,
    #                                        resp.xy = myRespXY,
    #                                        resp.name = myRespName,
    #                                        PA.nb.rep = 4,
    #                                        PA.nb.absences = 1000,
    #                                        PA.strategy = 'random')
    #
    # myBiomodData.r
    # plot(myBiomodData.r)

    # # Select multiple sets of pseudo-absences
    #
    # # Transform true absences into potential pseudo-absences
    # myResp.PA <- ifelse(myResp == 1, 1, NA)
    #
    # # Format Data with pseudo-absences : random method
    # myBiomodData.multi <- BIOMOD_FormatingData(resp.var = myResp.PA,
    #                                            expl.var = myExpl,
    #                                            resp.xy = myRespXY,
    #                                            resp.name = myRespName,
    #                                            PA.nb.rep = 4,
    #                                            PA.nb.absences = c(1000, 500, 500, 200),
    #                                            PA.strategy = 'random')
    # myBiomodData.multi
    # summary(myBiomodData.multi)
    # plot(myBiomodData.multi)

#### Cross-validation datasets

Several cross-validation methods are available and can be selected with the `BIOMOD_Modeling` function, which calls the `bm_CrossValidation` function to do so. More examples are presented on the Auxiliary functions webpage.

    # # k-fold selection
    # cv.k <- bm_CrossValidation(bm.format = myBiomodData,
    #                            strategy = 'kfold',
    #                            nb.rep = 2,
    #                            k = 3)
    #
    # # stratified selection (geographic)
    # cv.s <- bm_CrossValidation(bm.format = myBiomodData,
    #                            strategy = 'strat',
    #                            k = 2,
    #                            balance = 'presences',
    #                            strat = 'x')
    # head(cv.k)
    # head(cv.s)

#### Retrieve modeling options

Modeling options are automatically retrieved from selected models within the `BIOMOD_Modeling` function, which calls the `bm_ModelingOptions` function to do so. Model parameters can also be automatically tuned to a specific dataset, by calling the `bm_Tuning` function, however it can be quite long. More examples are presented on the Auxiliary functions webpage.

    # # bigboss parameters
    # opt.b <- bm_ModelingOptions(data.type = 'binary',
    #                             models = c('SRE', 'XGBOOST'),
    #                             strategy = 'bigboss')
    #
    # # tuned parameters with formated data
    # opt.t <- bm_ModelingOptions(data.type = 'binary',
    #                             models = c('SRE', 'XGBOOST'),
    #                             strategy = 'tuned',
    #                             bm.format = myBiomodData)
    #
    # opt.b
    # opt.t

### Run modeling

#### Single models

    # Model single models
    myBiomodModelOut <- BIOMOD_Modeling(bm.format = myBiomodData,
                                        modeling.id = 'AllModels',
                                        CV.strategy = 'random',
                                        CV.nb.rep = 2,
                                        CV.perc = 0.8,
                                        OPT.strategy = 'bigboss',
                                        metric.eval = c('TSS', 'AUCroc', 'BOYCE'),
                                        var.import = 3)
                                        # seed.val = 123)
                                        # nb.cpu = 8)
    myBiomodModelOut

    # Get evaluation scores & variables importance
    get_evaluations(myBiomodModelOut)
    get_variables_importance(myBiomodModelOut)

    # Represent evaluation scores & variables importance
    bm_PlotEvalMean(bm.out = myBiomodModelOut, dataset = 'calibration')
    bm_PlotEvalMean(bm.out = myBiomodModelOut, dataset = 'validation')
    bm_PlotEvalBoxplot(bm.out = myBiomodModelOut, dataset = 'calibration', group.by = c('algo', 'algo'))
    bm_PlotEvalBoxplot(bm.out = myBiomodModelOut, dataset = 'calibration', group.by = c('algo', 'run'))
    bm_PlotVarImpBoxplot(bm.out = myBiomodModelOut, group.by = c('expl.var', 'algo', 'algo'))
    bm_PlotVarImpBoxplot(bm.out = myBiomodModelOut, group.by = c('expl.var', 'algo', 'run'))
    bm_PlotVarImpBoxplot(bm.out = myBiomodModelOut, group.by = c('algo', 'expl.var', 'run'))

    # Represent response curves
    bm_PlotResponseCurves(bm.out = myBiomodModelOut,
                          models.chosen = get_built_models(myBiomodModelOut)[c(1, 4, 8, 10, 13)],
                          fixed.var = 'median')
    bm_PlotResponseCurves(bm.out = myBiomodModelOut,
                          models.chosen = get_built_models(myBiomodModelOut)[c(1, 4, 8, 10, 13)],
                          fixed.var = 'min')
    bm_PlotResponseCurves(bm.out = myBiomodModelOut,
                          models.chosen = get_built_models(myBiomodModelOut)[4],
                          fixed.var = 'median',
                          do.bivariate = TRUE)

    # Explore models' outliers & residuals
    bm_ModelAnalysis(bm.mod = myBiomodModelOut,
                     models.chosen = get_built_models(myBiomodModelOut)[c(1, 4, 8, 10, 13)])

#### Ensemble models

    # Model ensemble models
    myBiomodEM <- BIOMOD_EnsembleModeling(bm.mod = myBiomodModelOut,
                                          models.chosen = 'all',
                                          em.by = 'all',
                                          em.algo = c('EMmedian', 'EMmean', 'EMwmean',
                                                      'EMca', 'EMci', 'EMcv'),
                                          metric.select = c('TSS'),
                                          metric.select.thresh = c(0.7),
                                          metric.eval = c('TSS', 'AUCroc', 'BOYCE'),
                                          var.import = 3,
                                          EMci.alpha = 0.05,
                                          EMwmean.decay = 'proportional')
    myBiomodEM

    # Get evaluation scores & variables importance
    get_evaluations(myBiomodEM)
    get_variables_importance(myBiomodEM)

    # Represent evaluation scores & variables importance
    bm_PlotEvalMean(bm.out = myBiomodEM, dataset = 'calibration', group.by = 'full.name')
    bm_PlotEvalBoxplot(bm.out = myBiomodEM, dataset = 'calibration', group.by = c('full.name', 'full.name'))
    bm_PlotVarImpBoxplot(bm.out = myBiomodEM, group.by = c('expl.var', 'full.name', 'full.name'))
    bm_PlotVarImpBoxplot(bm.out = myBiomodEM, group.by = c('expl.var', 'algo', 'merged.by.run'))
    bm_PlotVarImpBoxplot(bm.out = myBiomodEM, group.by = c('algo', 'expl.var', 'merged.by.run'))

    # Represent response curves
    bm_PlotResponseCurves(bm.out = myBiomodEM,
                          models.chosen = get_built_models(myBiomodEM)[c(1, 6, 7)],
                          fixed.var = 'median')
    bm_PlotResponseCurves(bm.out = myBiomodEM,
                          models.chosen = get_built_models(myBiomodEM)[c(1, 6, 7)],
                          fixed.var = 'min')
    bm_PlotResponseCurves(bm.out = myBiomodEM,
                          models.chosen = get_built_models(myBiomodEM)[7],
                          fixed.var = 'median',
                          do.bivariate = TRUE)

### Project models

#### Single models

    # Project single models
    myBiomodProj <- BIOMOD_Projection(bm.mod = myBiomodModelOut,
                                      proj.name = 'Current',
                                      new.env = myExpl,
                                      models.chosen = 'all',
                                      metric.binary = 'all',
                                      metric.filter = 'all',
                                      build.clamping.mask = TRUE)
    myBiomodProj
    plot(myBiomodProj)

#### Ensemble models

    # Project ensemble models (from single projections)
    myBiomodEMProj <- BIOMOD_EnsembleForecasting(bm.em = myBiomodEM,
                                                 bm.proj = myBiomodProj,
                                                 models.chosen = 'all',
                                                 metric.binary = 'all',
                                                 metric.filter = 'all')

    # Project ensemble models (building single projections)
    myBiomodEMProj <- BIOMOD_EnsembleForecasting(bm.em = myBiomodEM,
                                                 proj.name = 'CurrentEM',
                                                 new.env = myExpl,
                                                 models.chosen = 'all',
                                                 metric.binary = 'all',
                                                 metric.filter = 'all')
    myBiomodEMProj
    plot(myBiomodEMProj)

### Compare range sizes

    # Load environmental variables extracted from BIOCLIM (bio_3, bio_4, bio_7, bio_11 & bio_12)
    data('bioclim_future')
    myExplFuture = rast(bioclim_future)

    # Project onto future conditions
    myBiomodProjFuture <- BIOMOD_Projection(bm.mod = myBiomodModelOut,
                                                  proj.name = 'Future',
                                                  new.env = myExplFuture,
                                                  models.chosen = 'all',
                                                  metric.binary = 'TSS',
                                                  build.clamping.mask = TRUE)

    # Compute differences
    myBiomodRangeSize <- BIOMOD_RangeSize(proj.current = myBiomodProj,
                                          proj.future = myBiomodProjFuture,
                                          metric.binary = 'TSS')

    myBiomodRangeSize@Compt.By.Models
    plot(myBiomodRangeSize@Diff.By.Pixel)

    # Represent main results
    bm_PlotRangeSize(bm.range = myBiomodRangeSize,
                     do.count = TRUE,
                     do.perc = TRUE,
                     do.maps = TRUE,
                     do.mean = TRUE)