Cross-validation

✘ Definition

Whether independent data is available or not, data-splitting methods allow to divide input data into pieces to calibrate and validate the models on different parts.

Most common procedures either split randomly the original dataset in two parts (random) with higher proportion to calibrate the models ; or in k datasets of equal sizes (k-fold), each of them being used in turn to validate the model, while the remaining is used for calibration. For both methods, the splitting can be repeated several times.
Other procedures are available to test for model overfitting and to assess transferability either in geographic or environmental space : block method described in Muscarella et al. 2014 partitions data in four bins of equal size (bottom-left, bottom-right, top-left and top-right), while x-y-stratification described in Wenger and Olden 2012 uses k partitions along the x-(or y-) gradient and returns 2k partitions ; environmental partitioning returns k partitions for each environmental variable provided.
These methods can be balanced over presences or absences to ensure equal distribution over space, especially if some data is clumped on an edge of the study area.
The user can also define its own data partitioning (user.defined).

✠ How you can select methods

biomod2 allows you to use different strategies to separate your data into a calibration dataset and a validation dataset for the cross-validation. With the argument CV.strategy in BIOMOD_Modeling, you can select :

Random

The most simple method to calibrate and validate a model is to split the original dataset in two datasets : one to calibrate the model and the other one to validate it. The splitting can be repeated nb.rep times. You can adjust the size of the splitting between calibration and validation with perc.

K-fold

The k-fold method splits the original dataset in k datasets of equal sizes : each part is used successively as the validation dataset while the other k-1 parts are used for the calibration, leading to k calibration/validation ensembles. This multiple splitting can be repeated nb.rep times.

Block

It may be used to test for model overfitting and to assess transferability in geographic space. block stratification was described in Muscarella et al. 2014 (see References). Four bins of equal size are partitioned (bottom-left, bottom-right, top-left and top-right).

Stratified

It may be used to test for model overfitting and to assess transferability in geographic space. x and y stratification was described in Wenger and Olden 2012 (see References). y stratification uses k partitions along the y-gradient, x stratification does the same for the x-gradient. both returns 2k partitions: k partitions stratified along the x-gradient and k partitions stratified along the y-gradient. You can choose x, y and both stratification with the argument strat.

Environmental

It may be used to test for model overfitting and to assess transferability in environmental space. It returns k partitions for each variable given in env.var.You can choose if the presences or the absences are balanced over the partitions with balance.

User-defined

Allow the user to give its own cross-validation table. For a presence-absence dataset, column names must be formatted as: _allData_RUNx with x an integer. For a presence-only dataset for which several pseudo-absence dataset were generated, column names must be formatted as: _PAx_RUNy with x an integer and PAx an existing pseudo-absence dataset and y an integer

If you are ensure about the strategy and want to make verification, get_calib_lines() can help you to visualize the split. (TRUE for calibration and FALSE for validation)

✣ Evaluation

biomod2 allows to use a cross-validation method to build (calibration) and validate (validation) the model, but it can also be tested on another independent dataset if available (evaluation). This second independent dataset can be integrated with the eval.resp, eval.xy and eval.env.data parameters in the BIOMOD_FormatingData function.

For example :

• dataset 1 will be used to build the individual models, being split for instance 10 times into 70/30 percentages to cross-validate them.
• dataset 2 will be used to evaluate all models (individual or ensemble).

Note that, if you can have as many evaluation values (with dataset 2) as your number of cross-validation splitting for single models, you can have only one evaluation value for ensemble models.

This can be circumvented by using em.by = 'PA+run' within the BIOMOD_EnsembleModeling function to build for each cross-validation fold an ensemble model across algorithms. You will obtain as many ensemble models as cross-validation split, and thus as many evaluation values. But you will also have several ensemble models, which may defeat your purpose of having a final single model.

✜ Concretly

All the examples are made with the data of the package.
For the beginning of the code, see the main functions vignette.

⛒ Cross-validation

To do a random cross-validation method with 2 runs and with a distribution 80/20 for calibration and validation.

myBiomodModelOut <- BIOMOD_Modeling(bm.format = myBiomodData,  
                                    modeling.id = 'Example',  
                                    models = c('RF', 'GLM'),  
                                    CV.strategy = 'random',  
                                    CV.nb.rep = 2,  
                                    CV.perc = 0.8,  
                                    metric.eval = c('TSS','ROC'))

To get the cross-validation table and visualize it on your BIOMOD.formated.data or BIOMOD.formated.data.PA object.

myCalibLines <- get_calib_lines(myBiomodModelOut)
plot(myBiomodData, calib.lines = myCalibLines)

To create a cross-validation table with bm_CrossValidation.

bm_CrossValidation(bm.format = myBiomodData,
                   strategy = "strat",
                   k = 2,
                   balance = "presences",
                   strat = "x")

Example of a table for the user.defined method : myCVtable.

_PA1_RUN1	_PA1_RUN2	_PA2_RUN1	_PA2_RUN2
FALSE	FALSE	FALSE	TRUE
TRUE	TRUE	FALSE	FALSE
TRUE	TRUE	TRUE	TRUE
…	…	…	…

myBiomodModelOut <- BIOMOD_Modeling(bm.format = myBiomodData,  
                                    modeling.id = 'Example',  
                                    models = c('RF', 'GLM'),  
                                    CV.strategy = 'user.defined',  
                                    CV.user.table = myCVtable,
                                    metric.eval = c('TSS','ROC'))

You can find more examples in the Secondary functions vignette.

☒ Evaluation

To add an independent dataset for evaluation, you will need to provide the correspondent environment variable (myEvalExpl) as a raster, a matrix or a data.frame.

Case 1 : If your evaluation response (myEvalResp) is a raster :

myBiomodData <- BIOMOD_FormatingData(resp.var = myResp,
                                     expl.var = myExpl,
                                     resp.xy = myRespXY,
                                     resp.name = myRespName, 
                                     eval.resp.var = myEvalResp,
                                     eval.expl.var = myEvalExpl)

Case 2 : If your evaluation response (myEvalResp) is a vector :

• you also need the coordinates of your response points : myEvalCoord
• if myEvalExpl is a data.frame or a matrix, be sure the points are in the same order.

myBiomodData <- BIOMOD_FormatingData(resp.var = myResp,
                                     expl.var = myExpl,
                                     resp.xy = myRespXY,
                                     resp.name = myRespName, 
                                     eval.resp.var = myEvalResp,
                                     eval.expl.var = myEvalExpl,
                                     eval.resp.xy = myEvalCoord)                                    

✖ References

• Wenger, S.J. and Olden, J.D. (2012), Assessing transferability of ecological models: an underappreciated aspect of statistical validation. Methods in Ecology and Evolution, 3: 260-267. https://doi.org/10.1111/j.2041-210X.2011.00170.x

• Muscarella, R., Galante, P.J., Soley-Guardia, M., Boria, R.A., Kass, J.M., Uriarte, M. and Anderson, R.P. (2014), ENMeval: An R package for conducting spatially independent evaluations and estimating optimal model complexity for Maxent ecological niche models. Methods in Ecology and Evolution, 5: 1198-1205. https://doi.org/10.1111/2041-210X.12261