parse_lambdas: Parse Maxent lambdas information
In johnbaums/things: Mostly spatial things

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

Parse Maxent .lambdas files to extract the types, weights, minima and maxima of features, as well as the fitted model's entropy and other values required for predicting to new data.

1	parse_lambdas(lambdas)

lambdas

Either a MaxEnt fitted model object (fitted with the maxent function in the dismo package), or a file path to a Maxent .lambdas file.

A list with five elements:

lambdas: a data.frame describing the features used in a Maxent model, including their weights (lambdas), maxima, minima, and type;
linearPredictorNormalizer: a constant that ensures the linear predictor (the sum of clamped features multiplied by their respective feature weights) is always negative (for numerical stability);
densityNormalizer: a scaling constant that ensures Maxent's raw output sums to 1 over background points;
numBackgroundPoints: the number of background points used in model training; and
entropy: the entropy of the fitted model.

This function is still in development, and no guarantee is made for the accuracy of its projections.

John B. Baumgartner, johnbaums@gmail.com

Wilson, P. W. (2009) Guidelines for computing MaxEnt model output values from a lambdas file.
Maxent software for species habitat modeling, version 3.3.3k help file (software freely available here).

read_mxe project_maxent

# Below we use the dismo::maxent example to fit a Maxent model:
if (require(dismo) && require(rJava) && 
    file.exists(file.path(system.file(package='dismo'), 'java/maxent.jar'))) {
  fnames <- list.files(path=paste(system.file(package="dismo"), '/ex', sep=''),
  pattern='grd', full.names=TRUE )
  predictors <- stack(fnames)
  occurence <- paste(system.file(package="dismo"), '/ex/bradypus.csv', sep='')
  occ <- read.table(occurence, header=TRUE, sep=',')[,-1]
  me <- maxent(predictors, occ, path=file.path(tempdir(), 'example'), 
               factors='biome')

  # ... and then parse the lambdas information:
  parse_lambdas(me)
  parse_lambdas(file.path(tempdir(), 'example/species.lambdas'))
  
}