ENMdetails class

An S4 class that details packages, functions, messages associated with a specific species distribution model (SDM) or ecological niche model (ENM). Objects of this class are generated by ENMdetails(). For examples, look in the package's R folder for scripts beginning with "enm" – these are pre-made ENMdetails object specifications that work with ENMeval out of the box.

Usage

# S4 method for class 'ENMdetails'
show(object)

Arguments

object

ENMdetails object

Slots

name

character: name of algorithm

fun

function: function that runs the algorithm

errors

function: returns errors chosen by the user to prevent any malfunction in the analysis. The available arguments are: occs, envs, bg, tune.args, partitions, algorithm, partition.settings, other.settings, categoricals, doClamp, clamp.directions.

msgs

function: prints messages showing the package version number, etc., and those related to the input tuning parameters tune.args. The available arguments are: tune.args, other.settings.

args

function: returns the parameters needed to run the algorithm function. The available arguments are: occs.z, bg.z, tune.tbl.i, other.settings (where x.z is a data.frame of the envs values at coordinates of x, and tune.tbl.i is a single set of tuning parameters).

predict

function: specifies how to calculate a model prediction for a Raster* or a data frame. The available arguments are: mod, envs, other.settings.

ncoefs

function: counts the number of non-zero model coefficients. The available arguments are: mod.

variable.importance

function: generates a data frame of variable importance from the model object (if functionality is available). The available arguments are: mod.

Author

Jamie M. Kass, jamie.m.kass@gmail.com