# Auxiliary functions

## Small code examples

Here are presented, in small and unlinked examples, auxiliary functions (starting with `bm_[...]`) of `biomod2`. Most of these functions are internally called by some main functions (starting with `BIOMOD_[...]`) of `biomod2`, but can be easily used as such.

### Prepare data

#### Vector data

    ## Generate a binary vector -------------------------------------------------------------
    vec.a <- sample(c(0, 1), 100, replace = TRUE)

    ## Generate a 0-1000 vector (random drawing) --------------------------------------------
    vec.b <- runif(100, min = 0, max = 1000)

    ## Generate a 0-1000 vector (biased drawing) --------------------------------------------
    BiasedDrawing <- function(x, m1 = 300, sd1 = 200, m2 = 700, sd2 = 200) {
      return(ifelse(x < 0.5, rnorm(1, m1, sd1), rnorm(1, m2, sd2)))
    }
    vec.c <- sapply(vec.a, BiasedDrawing)
    vec.c[which(vec.c < 0)] <- 0
    vec.c[which(vec.c > 1000)] <- 1000

    ## Generate a 0-1000 vector (normal distribution) ---------------------------------------
    vec.d <- rnorm(100, 500, 100)

#### Explanatory variables & Observations

    library(biomod2)
    library(terra)

    ## Create simple simulated data ---------------------------------------------------------
    myResp.sim <- sample(c(0, 1), 20, replace = TRUE)
    myExpl.sim <- data.frame(var1 = sample(c(0, 1), 100, replace = TRUE),
                             var2 = rnorm(100),
                             var3 = 1:100)

    ## Create raster data -------------------------------------------------------------------
    ras.1 <- ras.2 <- mask.out <- rast(nrows = 10, ncols = 10)

    ## define 2 variables : 1 categorical, 1 numerical
    ras.1[] <- as.factor(rep(c(1, 2, 3, 4, 5), each = 20))
    ras.1 <- as.factor(ras.1)
    ras.2[] <- rnorm(100)
    stk <- c(ras.1, ras.2)
    names(stk) <- c('varFact', 'varNorm')

    ## define a mask for already sampled points
    mask.out[1:40] <- 1

    ## define a list of masks where we want to sample in priority
    mask.in <- list(ras.1, ras.1)
    mask.in[[1]][1:80] <- NA ## only level 5 should be sampled in this mask
    mask.in[[1]][21:80] <- NA ## only levels 1 and 5 should be sampled in this mask

    ## Load real data : CLIMATE -------------------------------------------------------------
    data(bioclim_current)
    myExpl.real <- rast(bioclim_current)
    tmp <- classify(subset(myExpl.real, 1), matrix(c(-Inf, Inf, 0), ncol = 3))

    ## Load real data : BINARY --------------------------------------------------------------
    data(DataSpecies)
    myResp.real <- as.numeric(DataSpecies[, 'GuloGulo'])
    myCoord.real <- DataSpecies[, c('X_WGS84', 'Y_WGS84')]
    myCoord.real.1 <- DataSpecies[which(myResp.real == 1), c('X_WGS84', 'Y_WGS84')]
    myResp.real.raster <- tmp
    myResp.real.raster[cellFromXY(myResp.real.raster, myCoord.real.1)] <- 1

    ## Load real data : ABUNDANCE -----------------------------------------------------------
    data(DataSTOC)
    myResp.AB <- as.numeric(DataSTOC[, 'Periparus.ater'])
    myCoord.AB <- DataSTOC[, c('X_WGS84', 'Y_WGS84')]

### Auxiliary functions : vector data

#### Generate calibration / evaluation datasets

    bm_SampleBinaryVector(obs = vec.a, ratio = 0.7)

#### Find optimal threshold for a specific evaluation metric

    # Vary the number of thresholds to test
    bm_FindOptimStat(metric.eval = 'TSS', obs = vec.a, fit = vec.b, nb.thresh = 5)
    bm_FindOptimStat(metric.eval = 'TSS', obs = vec.a, fit = vec.b, nb.thresh = 100)

    # Compute different metrics
    bm_FindOptimStat(metric.eval = 'TSS', obs = vec.a, fit = vec.c)
    bm_FindOptimStat(metric.eval = 'AUCroc', obs = vec.a, fit = vec.c)
    bm_FindOptimStat(metric.eval = 'BOYCE', obs = vec.a, fit = vec.c)

#### From continuous to binary / filtered vector

    vec.d_bin <- bm_BinaryTransformation(data = vec.d, threshold = 500)
    vec.d_filt <- bm_BinaryTransformation(data = vec.d, threshold = 500, do.filtering = TRUE)
    cbind(vec.d, vec.d_bin, vec.d_filt)

### Auxiliary functions : explanatory variables

#### Generate automatic formula

    bm_MakeFormula(resp.name = 'myResp.sim',
                   expl.var = head(myExpl.sim),
                   type = 'quadratic',
                   interaction.level = 0)

#### Sample all factor levels

    samp1 <- bm_SampleFactorLevels(expl.var = stk, mask.out = mask.out)
    samp2 <- bm_SampleFactorLevels(expl.var = stk, mask.in = mask.in)
    samp3 <- bm_SampleFactorLevels(expl.var = stk, mask.out = mask.out, mask.in = mask.in)

#### Compute Species Range Envelop model

    # Compute SRE for several quantile values
    sre.100 <- bm_SRE(resp.var = myResp.real.raster,
                      expl.var = myExpl.real,
                      new.env = myExpl.real,
                      quant = 0)
    sre.095 <- bm_SRE(resp.var = myResp.real.raster,
                      expl.var = myExpl.real,
                      new.env = myExpl.real,
                      quant = 0.025)
    sre.090 <- bm_SRE(resp.var = myResp.real.raster,
                      expl.var = myExpl.real,
                      new.env = myExpl.real,
                      quant = 0.05)

    # Visualize results
    res <- c(myResp.real.raster, sre.100, sre.095, sre.090)
    names(res) <- c("Original distribution", "Full data calibration", "Over 95 percent", "Over 90 percent")
    plot(res, zlim = c(0, 1))

#### Compute variables importance

    mod <- glm(var1 ~ var2 + var3, data = myExpl.sim)
    bm_VariablesImportance(bm.model = mod,
                           expl.var = myExpl.sim[, c('var2', 'var3')],
                           method = 'full_rand',
                           nb.rep = 3)

### Auxiliary functions : `biomod2` data

    # Format count ABUNDANCE data
    myBiomodDataAB <- BIOMOD_FormatingData(resp.name = 'Virus',
                                           resp.var = myResp.AB,
                                           resp.xy = myCoord.AB,
                                           expl.var = myExpl.real,
                                           data.type = 'count')

    # Format BINARY data with true absences
    myBiomodData <- BIOMOD_FormatingData(resp.name = 'Alien',
                                         resp.var = myResp.real,
                                         resp.xy = myCoord.real,
                                         expl.var = myExpl.real)

    # Transform true absences into potential pseudo-absences
    myResp.real.PA <- ifelse(myResp.real == 1, 1, NA)
    myResp.real.PA.vect <- vect(cbind(myCoord.real, myResp.real.PA), geom = c('X_WGS84','Y_WGS84'))

#### Generate pseudo-absence datasets

    # random method
    PA.r <- bm_PseudoAbsences(resp.var = myResp.real.PA.vect,
                              expl.var = myExpl.real,
                              nb.rep = 4,
                              nb.absences = 1000,
                              strategy = 'random')

    # disk method
    PA.d <- bm_PseudoAbsences(resp.var = myResp.real.PA.vect,
                              expl.var = myExpl.real,
                              nb.rep = 4,
                              nb.absences = 500,
                              strategy = 'disk',
                              dist.min = 5,
                              dist.max = 35)

    # SRE method
    PA.s <- bm_PseudoAbsences(resp.var = myResp.real.PA.vect,
                              expl.var = myExpl.real,
                              nb.rep = 4,
                              nb.absences = 1000,
                              strategy = 'sre',
                              sre.quant = 0.025)

    # user.defined method
    myPAtable <- data.frame(PA1 = ifelse(myResp.real == 1, TRUE, FALSE),
                            PA2 = ifelse(myResp.real == 1, TRUE, FALSE))
    for (i in 1:ncol(myPAtable)) myPAtable[sample(which(myPAtable[, i] == FALSE), 500), i] = TRUE
    PA.u <- bm_PseudoAbsences(resp.var = myResp.real.PA.vect,
                              expl.var = myExpl.real,
                              strategy = 'user.defined',
                              user.table = myPAtable)

    str(PA.r)
    head(PA.r$pa.tab)
    apply(PA.r$pa.tab, 2, table)

    head(PA.d$pa.tab)
    apply(PA.d$pa.tab, 2, table)

    head(PA.s$pa.tab)
    apply(PA.s$pa.tab, 2, table)

    tail(PA.u$pa.tab)
    apply(PA.u$pa.tab, 2, table)

    # random method : different number of PA
    PA.r_mult <- bm_PseudoAbsences(resp.var = myResp.real.PA.vect,
                                   expl.var = myExpl.real,
                                   nb.rep = 4,
                                   nb.absences = c(1000, 500, 500, 200),
                                   strategy = 'random')

    str(PA.r_mult)
    head(PA.r_mult$pa.tab)
    apply(PA.r_mult$pa.tab, 2, table)

#### Generate calibration / evaluation datasets

    # random selection
    cv.r <- bm_CrossValidation(bm.format = myBiomodData,
                               strategy = 'random',
                               nb.rep = 3,
                               k = 0.8)

    # k-fold selection
    cv.k <- bm_CrossValidation(bm.format = myBiomodData,
                               strategy = 'kfold',
                               nb.rep = 2,
                               k = 3)

    # block selection
    cv.b <- bm_CrossValidation(bm.format = myBiomodData,
                               strategy = 'block')

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

    # stratified selection (environmental)
    cv.e <- bm_CrossValidation(bm.format = myBiomodData,
                               strategy = 'env',
                               k = 2,
                               balance = 'presences')

    head(cv.r)
    apply(cv.r, 2, table)
    head(cv.k)
    apply(cv.k, 2, table)
    head(cv.b)
    apply(cv.b, 2, table)
    head(cv.s)
    apply(cv.s, 2, table)
    head(cv.e)
    apply(cv.e, 2, table)

#### Retrieve modeling options

All models currently available in `biomod2` (and their related package and function) are listed within a small dataset. Some of them can be tuned through the `train` function of the `caret` package and corresponding training function to be used is also indicated.

    data(ModelsTable)
    ModelsTable

    allModels <- c('ANN', 'CTA', 'FDA', 'GAM', 'GBM', 'GLM'
                   , 'MARS', 'MAXENT', 'MAXNET', 'RF', 'SRE', 'XGBOOST')

    # default parameters
    opt.d <- bm_ModelingOptions(data.type = 'binary',
                                models = allModels,
                                strategy = 'default')

    # providing formated data
    opt.df <- bm_ModelingOptions(data.type = 'binary',
                                 models = allModels,
                                 strategy = 'default',
                                 bm.format = myBiomodData,
                                 calib.lines = cv.k)

    opt.d
    opt.d@models
    opt.d@options$ANN.binary.nnet.nnet
    names(opt.d@options$ANN.binary.nnet.nnet@args.values)

    opt.df@options$ANN.binary.nnet.nnet
    names(opt.df@options$ANN.binary.nnet.nnet@args.values)

    # bigboss parameters
    opt.b <- bm_ModelingOptions(data.type = 'binary',
                                models = allModels,
                                strategy = 'bigboss')

    # user.defined parameters
    user.SRE <- list('_allData_allRun' = list(quant = 0.01))
    user.XGBOOST <- list('_allData_allRun' = list(nrounds = 10))
    user.val <- list(SRE.binary.biomod2.bm_SRE = user.SRE
                     , XGBOOST.binary.xgboost.xgboost = user.XGBOOST)

    opt.u <- bm_ModelingOptions(data.type = 'binary',
                                models = c('SRE', 'XGBOOST'),
                                strategy = 'user.defined',
                                user.val = user.val)

    opt.b
    opt.u

    # Tune parameters for Random Forest model
    tuned.rf <- bm_Tuning(model = 'RF',
                          tuning.fun = 'rf', ## see in ModelsTable
                          do.formula = TRUE,
                          bm.options = opt.d@options$RF.binary.randomForest.randomForest,
                          bm.format = myBiomodData)
    tuned.rf ## list object

    # Tune parameters for GAM (from mgcv package) model
    tuned.gam <- bm_Tuning(model = 'GAM',
                           tuning.fun = 'gam', ## see in ModelsTable
                           do.formula = TRUE,
                           do.stepAIC = TRUE,
                           bm.options = opt.d@options$GAM.binary.mgcv.gam,
                           bm.format = myBiomodData)
    tuned.gam ##list object

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

    opt.t ## BIOMOD.modeling.options object