overlapCalc: Function to calculate overlap and Fishing Effort Index

In GlobalSharkMovement/GSMP_rpackage: Fishing Exposure Index based on telemetry data

Description

This function calculates the monthly overlap and fishing effort index of each individual in gridded data

Usage

overlapCalc(mon = c('01','02','03','04','05','06','07','08','09','10','11','12'),
                        sp, boatPath, shkPath, analyse = 'overlap', ncores = 1)

Arguments

mon	Character vector of months to calculate overlap, with double digits. Eg: January is '01'. Defaults to c('01','02','03','04','05','06','07','08','09','10','11','12')
sp	Character of unique species to analyse
boatPath	Path to boat files of monthly rasters
shkPath	Path to individual dit (density of tracking data) files
analyse	Analysis type: 'effort' or 'overlap'. Defaults to 'overlap'
ncores	Number of cores to use in parallel. Defaults to 1 (no parallel run).

Details

This function can be time-consuming and requires high memory capacity. We advice to use up to 75 percent of available cores and/or break data into chunks whenever possible.

Value

Returns a list of data.frames, where each level is a different month within a species

Author(s)

Marisa Vedor, Ivo da Costa, Nuno Queiroz

See Also

boatFun ditFun

Examples

fld <- '~/r_scripts/2_fei/examples/'

# Shark raster path
shkPath <- list.files(fld,'.tif', recursive = TRUE, full.names = TRUE)

  # Species names
  spp <- basename(dirname(shkPath))

  # Exclude other rasters
  shkPath <- shkPath[!is.na(spp)]
  spp <- spp[!is.na(spp)]


# Boat file path
boatFiles <- list.files(boatFld, '.tif', full.names = TRUE)

# Calculate species overlap or effort for each month
spOverLs <- overlapCalc(mon = c('01', '02'), sp = 'bk',
                   boatPath = boatFiles,
                   shkPath = shkPath[grepl(paste0('^',sp, '_'), basename(shkPath))],
                   analyse)

GlobalSharkMovement/GSMP_rpackage documentation built on Feb. 13, 2021, 8:01 a.m.