Species library — species

The library combines the read-only example species shipped with the package and the species saved by the user with save_species(), which are kept in tools::R_user_dir("FLOSS", "data") (override with options(FLOSS.user_dir = ...)). A user species with the same id as an example takes precedence.

Usage

species_library()

load_species(id)

save_species(x, overwrite = FALSE)

delete_species(id)

Arguments

id: species id (see species_library()$id).
x: a floss_species.
overwrite: overwrite an existing user species with the same id.

Value

species_library(): a data frame with one row per species (id, species, common_name, msy, source, file).

Examples

species_library()
#>                          id                   species             common_name
#> 1 carcharhinus_melanopterus Carcharhinus melanopterus     Blacktip reef shark
#> 2         lethrinus_mahsena         Lethrinus mahsena         Mahsena emperor
#> 3            lutjanus_bohar            Lutjanus bohar    Two-spot red snapper
#> 4             siganus_sutor             Siganus sutor Whitespotted rabbitfish
#>    msy  source                                                             file
#> 1   75 example /root/R/lib/FLOSS/extdata/species/carcharhinus_melanopterus.yaml
#> 2 1000 example         /root/R/lib/FLOSS/extdata/species/lethrinus_mahsena.yaml
#> 3  600 example            /root/R/lib/FLOSS/extdata/species/lutjanus_bohar.yaml
#> 4  750 example             /root/R/lib/FLOSS/extdata/species/siganus_sutor.yaml
load_species("siganus_sutor")
#> FLOSS species: Siganus sutor (Whitespotted rabbitfish)
#>   MSY = 750  productivity: High 
#>   life history: linf=37.2, k=0.712, t0=-1, a=0.01, b=3.04, lm=25.8, tm=2.22, tmax=9, M=0.975, s=0.599, sigR=0.735, rho=0.321 
#>     fleet                               selectivity relq
#>     traps dnormal(Lpeak=20, sd_left=5, sd_right=15) 1.00
#>   gillnet                    normal(Lpeak=32, sd=8) 0.30
#>  linefish                  logistic(L50=28, L95=32) 0.05