View source: R/4.f.calibration.R
calib_mdl_b | R Documentation |
This function will read a list of objects of class ENMevaluation (See ?ENMeval::ENMevaluate for details) and return selected maxent model calibrations and predictions. Each element on the list is usually a species. a.proj.l, a.calib.l, occ.l are lists with occurence data, projection and calibration/predictor data. Species in these lists must all be in the same order of species in ENMeval.o.
calib_mdl_b(
ENMeval.o.l,
a.calib.l,
occ.l = NULL,
use.ENMeval.bgpts = TRUE,
format = "raster",
pred.args = c("outputformat=cloglog", "doclamp=true", "pictures=true"),
mSel = c("AvgAIC", "LowAIC", "OR", "AUC"),
wAICsum = 0.99,
dAICc = 2,
AUCmin = 0.7,
randomseed = FALSE,
responsecurves = TRUE,
arg1 = "noaddsamplestobackground",
arg2 = "noautofeature",
numCores = 1,
parallelTunning = TRUE
)
ENMeval.o.l |
List of objects of class ENMevaluation |
a.calib.l |
List of predictors (cropped environmental variables) for model tuning. Used in model calibration. Argument 'x' of dismo::maxent. Raster* object or SpatialGridDataFrame, containing grids with predictor variables. These will be used to extract values from for the point locations. Can also be a data.frame, in which case each column should be a predictor variable and each row a presence or background record.. |
occ.l |
List of occurence data. See argument "occ" in calib_mdl. |
use.ENMeval.bgpts |
Logical. Use background points from ENMeval or sample new ones? |
format |
Character. Output file type. Argument 'format' of raster::writeRaster |
pred.args |
Charater. Argument 'args' of dismo::maxent. Additional argument that can be passed to MaxEnt. See the MaxEnt help for more information. The R maxent function only uses the arguments relevant to model fitting. There is no point in using args='outputformat=raw' when *fitting* the model; but you can use arguments relevant for *prediction* when using the predict function. Some other arguments do not apply at all to the R implementation. An example is 'outputfiletype', because the 'predict' function has its own 'filename' argument for that. |
mSel |
Character vector. Which criteria to use when selecting model(s). Currently implemented: "AvgAIC", "LowAIC", "OR", "AUC" |
wAICsum |
Cumulative sum of top ranked models for which arguments will be created |
dAICc |
Maximum delta AICc of models to be selected. |
AUCmin |
Minimum AUC value to select models using EBPM criteria. |
randomseed |
logical. Args to be passed to dismo::maxent. See ?dismo::maxent and the MaxEnt help for more information. |
responsecurves |
logical. Args to be passed to dismo::maxent. See ?dismo::maxent and the MaxEnt help for more information. |
arg1 |
charater. Args to be passed to dismo::maxent. See ?dismo::maxent and the MaxEnt help for more information. |
arg2 |
charater. Args to be passed to dismo::maxent. See ?dismo::maxent and the MaxEnt help for more information. |
numCores |
Number of cores to use for parallelization. If set to 1, no paralellization is performed |
parallelTunning |
Should parallelize within species (parallelTunning=TRUE) or between species (parallelTunning=FALSE) |
A 'mcm.l' object. A list of 'mcm' (calib.mdls, Maxent Calibrated Models), returned from function "calib_mdl"
mod_sel
, calib_mdl
, ENMevaluate_b
, ENMevaluate
,
maxent
, proj_mdl
, proj_mdl_b
## Not run:
mxnt.mdls.preds.lst <- calib_mdl_b(ENMeval.o.l=ENMeval.res.lst,
a.calib.l=occ.b.env, a.proj.l=areas.projection, occ.l=occ, wAICsum=0.99)
mxnt.mdls.preds.lst[[1]][[1]] # models [ENMevaluate]d and selected using sum of wAIC
mxnt.mdls.preds.lst[[1]][[2]] # MaxEnt models
mxnt.mdls.preds.lst[[1]][[3]] # used prediction arguments
plot(mxnt.mdls.preds.lst[[1]][[4]]) # MaxEnt predictions, based on the model selection criteria
## End(Not run)
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