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Last data update: 2014.03.03

R: Generate arguments for Maxent

make.args

R Documentation

Generate arguments for Maxent

Description

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

Usage

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.

Examples

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

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

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(ENMeval)
Loading required package: dismo
Loading required package: raster
Loading required package: sp
Loading required package: rJava
Loading required package: parallel
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/ENMeval/make.args.Rd_%03d_medium.png", width=480, height=480)
> ### Name: make.args 
> ### Title: Generate arguments for Maxent
> ### Aliases: make.args
> 
> ### ** Examples
> 
> make.args(RMvalues=c(1:3), fc=c("L","LQ"))
[[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"             

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

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

> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>