BioIndex {BioIndex}R Documentation

BioIndex

Description

R code to perform analysis of trawl survey data using MEDITS file format

Usage

BioIndex(
  ta,
  tb,
  tc,
  sspp,
  rec_threshold,
  spaw_threshold,
  haul_threshold = 30,
  sexes = "all",
  depth,
  GSA,
  country = "all",
  map_lim,
  depth_lines = c(10, 200, 800),
  strata = BioIndex::strata_scheme,
  stratification_tab = BioIndex::stratification,
  resolution = 1,
  buffer = 0.1,
  wd,
  zip = TRUE,
  save = TRUE,
  verbose = TRUE
)

Arguments

ta

data frame of the TA table in the MEDITS format

tb

data frame of the TB table in the MEDITS format

tc

data frame of the TC table in the MEDITS format

sspp

reference species for the analysis

rec_threshold

cutoff threshold for recruits

spaw_threshold

cutoff threshold for spawners

haul_threshold

minimum number of individuals to be used in estimation of the spatial indicaticators

sexes

reference sex for the analysis

depth

reference depth range

GSA

reference GSA for the analysis

country

reference country

map_lim

coordinates limits for the maps

depth_lines

depth contours to be plotted in the maps (3 values allowed)

strata

data frame of the reference strata for the study area

stratification_tab

data frame of the stratification scheme

resolution

resolution of the depth line

buffer

buffer around the map

wd

path of the working directory

zip

boolean. If TRUE the results are stored in a zip file into the working directory

save

boolean. If TRUE the results are stored in the working directory

verbose

boolean. If TRUE messages are promted in the console

Examples

BioIndex(ta=TA, tb=TB, tc=TC, sspp="MERLMER",rec_threshold=200, spaw_threshold=210,sexes="all", depth=c(10,800), GSA=10, country="all", map_lim=c(13.3,15.2,39.9,41.3),depth_lines=c(50,200,800), strata=BioIndex::strata_scheme, stratification_tab = BioIndex::stratification, resolution=1, buffer=0.1, wd=tempdir(), zip=TRUE, save=TRUE, verbose=TRUE)


[Package BioIndex version 0.5.02 Index]