model_maxent Generate maxent.jar or maxnet model

This functions generates maxent.jar or maxnet models using ENMeval 2.0 and user provided tuning parameters.

Usage

model_maxent(
  occs,
  bg,
  user.grp,
  bgMsk,
  rms,
  rmsStep,
  fcs,
  clampSel,
  algMaxent,
  catEnvs = NULL,
  parallel = FALSE,
  numCores = NULL,
  logger = NULL,
  spN = NULL
)

Arguments

occs: data frame of cleaned or processed occurrences obtained from components occs: Obtain occurrence data or, poccs: Process occurrence data.
bg: coordinates of background points to be used for modeling.
user.grp: a list of two vectors containing group assignments for occurrences (occs.grp) and background points (bg.grp).
bgMsk: a RasterStack or a RasterBrick of environmental layers cropped and masked to match the provided background extent.
rms: vector of range of regularization multipliers to be used in the ENMeval run.
rmsStep: step to be used when defining regularization multipliers to be used from the provided range.
fcs: feature classes to be tested in the ENMeval run.
clampSel: Boolean use of clamping in the model.
algMaxent: character. algorithm to be used in modeling. A selection of "maxnet" or "maxent.jar".
catEnvs: if categorical predictor variables are included must provide the names.
parallel: logical. Whether to use parallel in the generation of models. Default is FALSE
numCores: numeric. If using parallel how many cores to use. Default is NULL.
logger: Stores all notification messages to be displayed in the Log Window of Wallace GUI. Insert the logger reactive list here for running in shiny, otherwise leave the default NULL.
spN: character. Species name to be used for all logger messages.

Value

Function returns an ENMevaluate object with all the evaluated models and a selection of appropriate fields.

Details

The function generates model in ENMeval using a user provided partition of occurrences from previous components in the GUI. User can activate clamping and input tuning arguments to be used for model building.

Author

Jamie M. Kass <jamie.m.kass@gmail.com>

Gonzalo E. Pinilla-Buitrago <gepinillab@gmail.com>

Examples

if (FALSE) { # \dontrun{
envs <- envs_userEnvs(rasPath = list.files(system.file("extdata/wc",
                                           package = "wallace"),
                      pattern = ".tif$", full.names = TRUE),
                      rasName = list.files(system.file("extdata/wc",
                                           package = "wallace"),
                      pattern = ".tif$", full.names = FALSE))
occs <- read.csv(system.file("extdata/Bassaricyon_alleni.csv",
                 package = "wallace"))
bg <- read.csv(system.file("extdata/Bassaricyon_alleni_bgPoints.csv",
               package = "wallace"))
partblock <- part_partitionOccs(occs, bg, method = 'block')
rms <- c(1:2)
rmsStep <- 1
fcs <- c('L', 'LQ')
m <- model_maxent(occs = occs, bg = bg, user.grp = partblock,
                  bgMsk = envs, rms = rms, rmsStep, fcs,
                  clampSel = TRUE, algMaxent = "maxnet",
                  parallel = FALSE)
} # }