BioIndex {BioIndex} | R Documentation |
R code to perform analysis of trawl survey data using MEDITS file format
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 )
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 |
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)