Collection of similar functions which get specific columns from the Atlantis functionalGroups.csv

This collection of functions uses the dataframe of functional groups created with load_fgs and creates various character strings of group names or acronym names.

Usage

get_groups(fgs)

get_age_groups(fgs)

get_acronyms(fgs)

get_age_acronyms(fgs)

get_nonage_acronyms(fgs)

get_fish_acronyms(fgs)

get_cohorts_acronyms(fgs, numCohorts = 10)

get_fished_acronyms(fgs)

get_turnedon_acronyms(fgs)

Arguments

fgs

Character string giving the connection to the functional groups file. The filename usually contains Groups and does end in .csv.

numCohorts

integer. Number of cohorts by which to filter (Default = 10)

Value

Character string.

Details

Currently, the following character strings can be created

get_groups: Extract column "Name"

get_age_groups: Extract column "Name". Selects groups with 10 ageclasses.

get_acronyms: Extract column "Code"

get_age_acronyms: Extract column "Code". Selects groups with 10 ageclasses.

get_nonage_acronyms: Extracts columns "Code". Only groups with ageclasses different from 10 are selected.

get_fish_acronyms: Extract column "Code". Only groups with InvertType equal to "FISH" or "SHARK" are selected.

get_cohorts_acronyms: Extracts column "Code" based on Cohort size

get_fished_acronyms: Extracts column "Code" based on whether a species is fished in the model (IsFished == 1)

get_turnedon_acronyms: Extracts column "Code" based on whether species are turned on in the model (IsTurnedOn == 1)

See also

Other get functions: get_boundary(), get_colpal(), get_conv_mgnbiot()

Examples

d <- system.file("extdata", "setas-model-new-trunk", package = "atlantistools")
fgs <- file.path(d, "SETasGroupsDem_NoCep.csv")

get_age_groups(fgs)
#> [1] "Planktiv_S_Fish" "Pisciv_S_Fish"  
get_nonage_acronyms(fgs)
#> [1] "CEP" "BML" "PL"  "DL"  "DR"  "DC"