evaluate | R Documentation |
Evaluation of SDM or ESDM habitat suitability predictions or evalaution of SSDM floristic composition with Pottier et al, 2013 method (see reference below)
evaluate(obj, ...)
## S4 method for signature 'Algorithm.SDM'
evaluate(
obj,
cv,
cv.param,
final.fit.data = "all",
bin.thresh = "SES",
metric = NULL,
thresh = 1001,
Env,
...
)
## S4 method for signature 'MAXENT.SDM'
evaluate(
obj,
cv,
cv.param,
final.fit.data = "all",
bin.thresh = "SES",
metric = NULL,
thresh = 1001,
Env,
...
)
## S4 method for signature 'Stacked.SDM'
evaluate(obj, ...)
obj |
Stacked.SDM. SSDM to evaluate |
... |
arguments for internal use (get_model), such as argument lists to be passed to the source functions (e.g. glm.args=list(test="AIC",singular.ok=FALSE)) |
cv |
character. Method of cross-validation used to evaluate the SDM (see details below). |
cv.param |
numeric. Parameters associated to the method of cross-validation used to evaluate the SDM (see details below). |
final.fit.data |
strategy used for fitting the final model to be returned: 'holdout'= use same train and test data as in (last) evaluation, 'all'= train model with all data (i.e. no test data) or numeric (0-1)= sample a custom training fraction (left out fraction is set aside as test data) |
bin.thresh |
character. Classification threshold ( |
metric |
(deprecated) character. Classification threshold ( |
thresh |
(deprecated) integer. Number of equally spaced thresholds in the interval 0-1 ( |
Env |
raster object. Stacked raster object of environmental variables
(can be processed first by |
SDM/ESDM/SSDM evaluation in a data.frame
Pottier, J., Dubuis, A., Pellissier, L., Maiorano, L., Rossier, L., Randin, C. F., Guisan, A. (2013). The .accuracy of plant assemblage prediction from species distribution models varies along environmental gradients. Global Ecology and Biogeography, 22(1), 52-63. https://doi.org/10.1111/j.1466-8238.2012.00790.x
## Not run:
# Loading data
data(Env)
data(Occurrences)
# SSDM building
SSDM <- stack_modelling(c('CTA', 'SVM'), Occurrences, Env, rep = 1,
Xcol = 'LONGITUDE', Ycol = 'LATITUDE',
Spcol = 'SPECIES')
# Evaluation
evaluate(SSDM)
## End(Not run)
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