BatchMaxent: BatchMaxent - A function to execute Maxent niche modeling...

In narayanibarve/ENMGadgets: Pre and Post Processing in ENM Workflow

Description

Function BatchMaxent executes Maxent algorithm using dismo and it gives the flexibility of projecting the model to multiple projection areas. This process is done iteratively if the species list contains more than on species. To run this function successfully specific directory structure should be maintained.

Usage

BatchMaxent(projpath = NA, InpFlName = NA, MNameSameAsSpecies = FALSE,
  arglist = NA)

Arguments

projpath	- Project path where all the required files for model calibrations are stored. e.g. "c:/SpDist/Model"
InpFlName	- Name of the input file containing SpeciesName (OccurrenceFileName), M_folderName
MNameSameAsSpecies	- Logical variable, to designate, if the M_folderName is same as OccurrenceFileName or not.
arglist	- List of arguments to be passed to Maxent for model fitting and prediction.

Details

In the projpath parameter, specify the path where the data is residing. MNameSameAsSpecies parameter is also required. This parameter is set to TRUE when M_folderName in the Calibration folder is same as species name. And is set to FALSE when M_folderName is different than species name. This scenario exists, when a single M_folderName can be used for multiple species for calibration. This in this case, specify M_folderName in species list file. arglist parameter is a list of arguments to be passed to Maxent. See documentation of Maxent for more details.

See the description below for projpath directory structure. Within the project path directory, there should be one species list file in .csv format and 3 subfolders as mentioned below. Species list file should be passed as parameter in parameter named InpFlName. The structure of this species list file is SpeciesName, M_folderName. Species name is the name of the file which contains species occurrences and this occurrence file should be stored in Occurrences folder. M_folderName is the name of the directory which contains the background environmental data for model calibration. If M_folderName is same as SpeciesName, then set the parameter MNameSameAsSpecies to TRUE. In that case M_folderName column in species list file can be ignored. The structure of the directory should be as given below. 1) Calibration - This folder should contain subfolders with name as specified in M_folder name in the species list file. These subfolders must contain the background environmental data. 2)Occurrences - This folder should contain occurrence data for each species in separate file with species name as mentioned in species list file. 3) Projections - This folder should contain the background environmental data for projections and data should be stored in subfolders, so if one has to project it only to one area, still data should go in subfolder. Name of the subfolder can be user choice. Output will be stored in ModelOutput folder within project path. This ModelOutput folder will contain subfolders CaliOutput, which contains output of model calibration, for each species there are 3 files, one is model prediction, standard deviation of the bootstrapped model, and variable contribution. Other subfolders are projection folders with 2 files per species, model prediction, and standard deviation of bootstrapped model

Examples

## Not run: 
BatchMaxent()

## End(Not run)

narayanibarve/ENMGadgets documentation built on May 25, 2019, 10:34 p.m.