calc_SpeciesRA: Species' relative abundance calculation and summary

In nevilamos/FAMEFMR: Functions For DELWP FAME Fire Analysis

Species' relative abundance calculation and summary

Description

Species' relative abundance calculation and summary

Usage

calc_SpeciesRA(
  myFHAnalysis,
  myAllCombs = allCombs,
  myHDMSpp_NO = HDMSpp_NO,
  myWriteSpRasters = TRUE,
  myLU_List = LU_List,
  myResultsDir = ResultsDir,
  myTaxonList = TaxonList,
  writeYears = NULL,
  myWriteSp = writeSp,
  myCropRasters = cropRasters
)

Arguments

myFHAnalysis	list containing all the fire history spatial attributes created by function fhProcess
myAllCombs	all combinations of raster values object produced by function calc_U_AllCombs
myHDMSpp_NO	vector of TAXON_IDs for species to be included in output
myWriteSpRasters	logical: whether to also write species abundance rasters to disk
myLU_List	list of species abundance lookup arrays created by function make_Spp_LU_list()
myResultsDir	path of directory where raster results will be written usually generated by FAME script
myTaxonList	data.frame of species attributes (read from default or user provided .csv) including field HDMPaths with the relative or absolute path to the HDM raster used in the analysis.
writeYears	vector for SEASONS for which rasters are to be written otherwise if writeSpRasters == TRUE, if writeYears == NULL then all SEASONS are written out
myWriteSp	vector of TAXON_IDs provided if only subset of species rasters are required as output.
myCropRasters	object containing cell indices and values of input rasters cropped to area of interest created by cropToOutput()

Details

Calculates the relative abundance of species for each raster cell in analysis and summaries these as summed abundance each season. Optionally it also write relative abundance rasters for species to disk

Value

list of two or three data frames:

• SpYearSummWide summary of relative abundance of species by pivoted wide by SEASONS

• SpYearSummLong Long Format summary of relative abundance of species by SEASONS

• grpSpYearSumm summary of abundance of species by pivoted wide by SEASONS grouped by myAllCombs

nevilamos/FAMEFMR documentation built on April 17, 2025, 9:32 p.m.