biomod2 (version 4.2-5)

BIOMOD_Modeling: Run a range of species distribution models

Description

This function allows to calibrate and evaluate a range of modeling techniques for a given species distribution. The dataset can be split up in calibration/validation parts, and the predictive power of the different models can be estimated using a range of evaluation metrics (see Details).

Usage

BIOMOD_Modeling(
  bm.format,
  modeling.id = as.character(format(Sys.time(), "%s")),
  models = c("ANN", "CTA", "FDA", "GAM", "GBM", "GLM", "MARS", "MAXENT", "MAXNET", "RF",
    "SRE", "XGBOOST"),
  models.pa = NULL,
  CV.strategy = "random",
  CV.nb.rep = 1,
  CV.perc = NULL,
  CV.k = NULL,
  CV.balance = NULL,
  CV.env.var = NULL,
  CV.strat = NULL,
  CV.user.table = NULL,
  CV.do.full.models = TRUE,
  OPT.data.type = "binary",
  OPT.strategy = "default",
  OPT.user.val = NULL,
  OPT.user.base = "bigboss",
  OPT.user = NULL,
  bm.options,
  nb.rep,
  data.split.perc,
  data.split.table,
  do.full.models,
  weights = NULL,
  prevalence = NULL,
  metric.eval = c("KAPPA", "TSS", "ROC"),
  var.import = 0,
  scale.models = FALSE,
  nb.cpu = 1,
  seed.val = NULL,
  do.progress = TRUE
)

Value

A BIOMOD.models.out object containing models outputs, or links to saved outputs.

Models outputs are stored out of R (for memory storage reasons) in 2 different folders created in the current working directory :

1. a models folder, named after the resp.name argument of BIOMOD_FormatingData, and containing all calibrated models for each repetition and pseudo-absence run

2. a hidden folder, named .BIOMOD_DATA, and containing outputs related files (original dataset, calibration lines, pseudo-absences selected, predictions, variables importance, evaluation values...), that can be retrieved with get_[...] or load functions, and used by other biomod2 functions, like BIOMOD_Projection or BIOMOD_EnsembleModeling

Arguments

bm.format

a BIOMOD.formated.data or BIOMOD.formated.data.PA object returned by the BIOMOD_FormatingData function

modeling.id

a character corresponding to the name (ID) of the simulation set (a random number by default)

models

a vector containing model names to be computed, must be among ANN, CTA, FDA, GAM, GBM, GLM, MARS, MAXENT, MAXNET, RF, SRE, XGBOOST

models.pa

(optional, default NULL)
A list containing for each model a vector defining which pseudo-absence datasets are to be used, must be among colnames([e-mail])

CV.strategy

a character corresponding to the cross-validation selection strategy, must be among random, kfold, block, strat, env or user.defined

CV.nb.rep

(optional, default 0)
If strategy = 'random' or strategy = 'kfold', an integer corresponding to the number of sets (repetitions) of cross-validation points that will be drawn

CV.perc

(optional, default 0)
If strategy = 'random', a numeric between 0 and 1 defining the percentage of data that will be kept for calibration

CV.k

(optional, default 0)
If strategy = 'kfold' or strategy = 'strat' or strategy = 'env', an integer corresponding to the number of partitions

CV.balance

(optional, default 'presences')
If strategy = 'strat' or strategy = 'env', a character corresponding to how data will be balanced between partitions, must be either presences or absences

CV.env.var

(optional)
If strategy = 'env', a character corresponding to the environmental variables used to build the partition. k partitions will be built for each environmental variables. By default the function uses all environmental variables available.

CV.strat

(optional, default 'both')
If strategy = 'env', a character corresponding to how data will partitioned along gradient, must be among x, y, both

CV.user.table

(optional, default NULL)
If strategy = 'user.defined', a matrix or data.frame defining for each repetition (in columns) which observation lines should be used for models calibration (TRUE) and validation (FALSE)

CV.do.full.models

(optional, default TRUE)
A logical value defining whether models should be also calibrated and validated over the whole dataset (and pseudo-absence datasets) or not

OPT.data.type

a character corresponding to the data type to be used, must be either binary, binary.PA, abundance, compositional

OPT.strategy

a character corresponding to the method to select models' parameters values, must be either default, bigboss, user.defined, tuned

OPT.user.val

(optional, default NULL)
A list containing parameters values for some (all) models

OPT.user.base

(optional, default bigboss)
A character, default or bigboss used when OPT.strategy = 'user.defined'. It sets the bases of parameters to be modified by user defined values.

OPT.user

(optional, default TRUE)
A BIOMOD.models.options object returned by the bm_ModelingOptions function

bm.options

a BIOMOD.models.options object returned by the bm_ModelingOptions function

nb.rep

deprecated, now called CV.nb.rep

data.split.perc

deprecated, now called CV.perc

data.split.table

deprecated, now called CV.user.table

do.full.models

deprecated, now called CV.do.full.models

weights

(optional, default NULL)
A vector of numeric values corresponding to observation weights (one per observation, see Details)

prevalence

(optional, default NULL)
A numeric between 0 and 1 corresponding to the species prevalence to build 'weighted response weights' (see Details)

metric.eval

a vector containing evaluation metric names to be used, must be among ROC, TSS, KAPPA, ACCURACY, BIAS, POD, FAR, POFD, SR, CSI, ETS, HK, HSS, OR, ORSS, BOYCE, MPA

var.import

(optional, default NULL)
An integer corresponding to the number of permutations to be done for each variable to estimate variable importance

scale.models

(optional, default FALSE)
A logical value defining whether all models predictions should be scaled with a binomial GLM or not

nb.cpu

(optional, default 1)
An integer value corresponding to the number of computing resources to be used to parallelize the single models computation

seed.val

(optional, default NULL)
An integer value corresponding to the new seed value to be set

do.progress

(optional, default TRUE)
A logical value defining whether the progress bar is to be rendered or not

Author

Wilfried Thuiller, Damien Georges, Robin Engler

Details

bm.format

If pseudo absences have been added to the original dataset (see BIOMOD_FormatingData),
PA.nb.rep *(nb.rep + 1) models will be created.

models

The set of models to be calibrated on the data. 12 modeling techniques are currently available :

• ANN : Artificial Neural Network (nnet)

• CTA : Classification Tree Analysis (rpart)

• FDA : Flexible Discriminant Analysis (fda)

• GAM : Generalized Additive Model (gam, gam or bam)
  (see bm_ModelingOptions for details on algorithm selection)

• GBM : Generalized Boosting Model, or usually called Boosted Regression Trees (gbm)

• GLM : Generalized Linear Model (glm)

• MARS : Multiple Adaptive Regression Splines (earth)

• MAXENT : Maximum Entropy (https://biodiversityinformatics.amnh.org/open_source/maxent/)

• MAXNET : Maximum Entropy (maxnet)

• RF : Random Forest (randomForest)

• SRE : Surface Range Envelop or usually called BIOCLIM (bm_SRE)

• XGBOOST : eXtreme Gradient Boosting Training (xgboost)

models.pa

Different models might respond differently to different numbers of pseudo-absences. It is possible to create sets of pseudo-absences with different numbers of points (see BIOMOD_FormatingData) and to assign only some of these datasets to each single model.

CV.[...] parameters

Different methods are available to calibrate/validate the single models (see bm_CrossValidation).

OPT.[...] parameters

Different methods are available to parameterize the single models (see bm_ModelingOptions and BIOMOD.options.dataset). Note that only binary data type is allowed currently.

• default : only default parameter values of default parameters of the single models functions are retrieved. Nothing is changed so it might not give good results.

• bigboss : uses parameters pre-defined by biomod2 team and that are available in the dataset OptionsBigboss.
  to be optimized in near future

• user.defined : updates default or bigboss parameters with some parameters values defined by the user (but matching the format of a BIOMOD.models.options object)

• tuned : calling the bm_Tuning function to try and optimize some default values

weights & prevalence

More or less weight can be given to some specific observations.

• If weights = prevalence = NULL, each observation (presence or absence) will have the same weight, no matter the total number of presences and absences.

• If prevalence = 0.5, presences and absences will be weighted equally (i.e. the weighted sum of presences equals the weighted sum of absences).

• If prevalence is set below (above) 0.5, more weight will be given to absences (presences).

• If weights is defined, prevalence argument will be ignored, and each observation will have its own weight.

• If pseudo-absences have been generated (PA.nb.rep > 0 in BIOMOD_FormatingData), weights are by default calculated such that prevalence = 0.5. Automatically created weights will be integer values to prevent some modeling issues.

metric.eval

simple

• POD : Probability of detection (hit rate)

• FAR : False alarm ratio

• POFD : Probability of false detection (fall-out)

• SR : Success ratio

• ACCURACY : Accuracy (fraction correct)

• BIAS : Bias score (frequency bias)

complex

• ROC : Relative operating characteristic

• TSS : True skill statistic (Hanssen and Kuipers discriminant, Peirce's skill score)

• KAPPA : Cohen's Kappa (Heidke skill score)

• OR : Odds Ratio

• ORSS : Odds ratio skill score (Yule's Q)

• CSI : Critical success index (threat score)

• ETS : Equitable threat score (Gilbert skill score)

presence-only

• BOYCE : Boyce index

• MPA : Minimal predicted area (cutoff optimising MPA to predict 90% of presences)

Optimal value of each method can be obtained with the get_optim_value function. Several evaluation metrics can be selected. Please refer to the CAWRC website (section "Methods for dichotomous forecasts") to get detailed description of each metric. Results after modeling can be obtained through the get_evaluations function.
Evaluation metric are calculated on the calibrating data (column calibration), on the cross-validation data (column validation) or on the evaluation data (column evaluation).
For cross-validation data, see CV.[...] parameters in BIOMOD_Modeling function ; for evaluation data, see eval.[...] parameters in BIOMOD_FormatingData.

var.import

A value caracterizing how much each variable has an impact on each model predictions can be calculated by randomizing the variable of interest and computing the correlation between original and shuffled variables (see bm_VariablesImportance).

scale.models

This parameter is quite experimental and it is recommended not to use it. It may lead to reduction in projection scale amplitude. Some categorical models always have to be scaled (FDA, ANN), but it may be interesting to scale all computed models to ensure comparable predictions (0-1000 range). It might be particularly useful when doing ensemble forecasting to remove the scale prediction effect (the more extended projections are, the more they influence ensemble forecasting results).

See Also

glm, gam, gam, bam, gbm, rpart, nnet, fda, earth, randomForest, maxnet, xgboost, BIOMOD_FormatingData, bm_ModelingOptions, bm_Tuning, bm_CrossValidation, bm_VariablesImportance, BIOMOD_Projection, BIOMOD_EnsembleModeling, bm_PlotEvalMean, bm_PlotEvalBoxplot, bm_PlotVarImpBoxplot, bm_PlotResponseCurves

Other Main functions: BIOMOD_EnsembleForecasting(), BIOMOD_EnsembleModeling(), BIOMOD_FormatingData(), BIOMOD_LoadModels(), BIOMOD_Projection(), BIOMOD_RangeSize()

Examples

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 <- terra::rast(bioclim_current)

# \dontshow{
myExtent <- terra::ext(0,30,45,70)
myExpl <- terra::crop(myExpl, myExtent)
# }

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


# ---------------------------------------------------------------------------- #
# Model single models
myBiomodModelOut <- BIOMOD_Modeling(bm.format = myBiomodData,
                                    modeling.id = 'AllModels',
                                    models = c('RF', 'GLM'),
                                    CV.strategy = 'random',
                                    CV.nb.rep = 2,
                                    CV.perc = 0.8,
                                    OPT.strategy = 'bigboss',
                                    metric.eval = c('TSS','ROC'),
                                    var.import = 2,
                                    seed.val = 42)
myBiomodModelOut

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

# Represent evaluation scores 
bm_PlotEvalMean(bm.out = myBiomodModelOut, dataset = 'calibration')
bm_PlotEvalMean(bm.out = myBiomodModelOut, dataset = 'validation')
bm_PlotEvalBoxplot(bm.out = myBiomodModelOut, group.by = c('algo', 'run'))

# # Represent variables importance 
# 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 
# mods <- get_built_models(myBiomodModelOut, run = 'RUN1')
# bm_PlotResponseCurves(bm.out = myBiomodModelOut, 
#                       models.chosen = mods,
#                       fixed.var = 'median')
# bm_PlotResponseCurves(bm.out = myBiomodModelOut, 
#                       models.chosen = mods,
#                       fixed.var = 'min')
# mods <- get_built_models(myBiomodModelOut, full.name = 'GuloGulo_allData_RUN2_RF')
# bm_PlotResponseCurves(bm.out = myBiomodModelOut, 
#                       models.chosen = mods,
#                       fixed.var = 'median',
#                       do.bivariate = TRUE)