make.args: Generate arguments for Maxent

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/make.args.R

Description

This function generates a list of arguments to pass to Maxent or to use as convenient labels for plotting.

Usage

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make.args(RMvalues = seq(0.5, 4, 0.5), 
	fc = c("L", "LQ", "H", "LQH", "LQHP", "LQHPT"), 
	labels = FALSE)

Arguments

RMvalues

Vector of (non-negative) values to use for the regularization multiplier.

fc

Character vector of feature class combinations to be included in analysis.

labels

logical; If FALSE (default), provides arguments to pass directly to Maxent; if TRUE, provides more intuitive labels to use, for example, in plotting.

Details

When labels = FALSE, the following additional arguments are added:

noaddsamplestobackground, noremoveDuplicates, noautofeature.

For details on these arguments, see Phillips et al. (2006) and the help documentation and tutorial of the Maxent software and the tutorial that can be downloaded from this website.

Value

If labels = FALSE, a list the length of the total number of unique combinations of feature class(es) and regularization multiplier(s).

If labels = TRUE, a list of two items:

$

character vector of feature class combinations in the same order they were provided.

$

numeric vector of regularization multiplier values in the same order they were provided.

Author(s)

Robert Muscarella <bob.muscarella@gmail.com> and Jamie M. Kass <jkass@gc.cuny.edu>

References

Phillips, S. J., Anderson, R. P. and Schapire, R. E. 2006. Maximum entropy modeling of species geographic distributions. Ecological Modelling, 190: 231-259.

See Also

maxent in the dismo package.

Examples

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make.args(RMvalues=c(1:3), fc=c("L","LQ"))

make.args(RMvalues=c(1:3), fc=c("L","LQ"), labels=TRUE)

Example output

Loading required package: dismo
Loading required package: raster
Loading required package: sp
Loading required package: rJava
Loading required package: parallel
[[1]]
[1] "betamultiplier=1"         "noaddsamplestobackground"
[3] "noremoveDuplicates"       "noautofeature"           
[5] "noquadratic"              "nohinge"                 
[7] "noproduct"                "nothreshold"             

[[2]]
[1] "betamultiplier=1"         "noaddsamplestobackground"
[3] "noremoveDuplicates"       "noautofeature"           
[5] "nohinge"                  "noproduct"               
[7] "nothreshold"             

[[3]]
[1] "betamultiplier=2"         "noaddsamplestobackground"
[3] "noremoveDuplicates"       "noautofeature"           
[5] "noquadratic"              "nohinge"                 
[7] "noproduct"                "nothreshold"             

[[4]]
[1] "betamultiplier=2"         "noaddsamplestobackground"
[3] "noremoveDuplicates"       "noautofeature"           
[5] "nohinge"                  "noproduct"               
[7] "nothreshold"             

[[5]]
[1] "betamultiplier=3"         "noaddsamplestobackground"
[3] "noremoveDuplicates"       "noautofeature"           
[5] "noquadratic"              "nohinge"                 
[7] "noproduct"                "nothreshold"             

[[6]]
[1] "betamultiplier=3"         "noaddsamplestobackground"
[3] "noremoveDuplicates"       "noautofeature"           
[5] "nohinge"                  "noproduct"               
[7] "nothreshold"             

[[1]]
[1] "L"  "LQ" "L"  "LQ" "L"  "LQ"

[[2]]
[1] 1 1 2 2 3 3

ENMeval documentation built on Jan. 13, 2021, 8:08 p.m.