THIS IS AN EXPERIMENTAL DRAFT PROJECT NOT TO BE USED AT THIS STAGE!
fishglobr (perhaps to be renamed to fishglob) is an R package for efficiently downloading, caching, and querying the FishGlob database. FISHGLOB is an international consortium of scientists, experts and data providers who collect, curate, standardize, share and analyse data from scientific bottom trawl surveys.
Installation
You can install the development version of fishglobr like so:
# temporary location; to be moved to fishglob group
pak::pak("seananderson/fishglobr")Example
First we load the package and download and install the database locally. We only have to do this once. The data is stored in a local DuckDB database.
library(fishglobr)
install_fishglob_data()
#> Downloading catch ■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■ | 65 MB/ 65 MB ETA: 0s
#> Downloading haul ■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■ | 4.7 MB/4.7 MB ETA: 0s
#> Downloading taxon ■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■ | 49 kB/ 49 kB ETA: 0s
#> Downloading survey ■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■ | 0.7 kB/0.7 kB ETA: 0s
#> Building the local FishGlob DuckDB database
#> FishGlob data are ready in
#> ~/Library/Caches/org.R-project.R/R/fishglobr/fishglob.duckdb
# Find available agency data sources
get_sources()
#> [1] "DATRAS ICES" "DFO" "IMR" "NOAA"
# The full list of available species:
spp <- get_scientific_names()
spp[1:5]
#> [1] "Ablennes hians" "Abudefduf saxatilis"
#> [3] "Acanthemblemaria" "Acantholabrus palloni"
#> [5] "Acantholiparis opercularis"
# All Canary Rockfish data held by DFO
dat <- get_data(
scientific_name = "sebastes pinniger",
source = "DFO"
)
nrow(dat)
#> [1] 1106
# All Sebastes data globally from 2000 to 2021
# using a regular expression
dat <- get_data(
scientific_name = "^sebastes*",
regex = TRUE,
year = 2000:2021
)
head(dat[c("scientific_name", "year", "latitude", "longitude", "wgt_cpue")], n = 3)
#> scientific_name year latitude longitude wgt_cpue
#> 1 Sebastes fasciatus 2021 42.04747 -67.71460 0.06549118
#> 2 Sebastes fasciatus 2021 41.84667 -68.20291 0.25524769
#> 3 Sebastes fasciatus 2021 42.20143 -66.86743 1.13853904