Last run: April 22, 2025
Purpose
The ‘get prediction grid’ script should be run before running other scripts. Use the ‘pull data’ file or go to the ‘data’ folder to get the data we are working with then run the ‘main’ file. Other scripts provide supporting functions that are run in the ‘main’ file. Due to the high number of species, effort scenarios, and replicates, the script is very computationally intensive. Reduce the number of species/effort scenarios/replicates when testing.
This repository is under active development and all code, results, and other materials should be considered preliminary. Find code used for various versions in the [releases](https://github.com/nmfs-ost/surveyresamplr/releases section for finalized products and project milestones.
This code is primarally maintained by:
Emily Markowitz (Emily.Markowitz AT noaa.gov; @EmilyMarkowitz-NOAA)
Alaska Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA 98195
Derek Bolser (Derek.Bolser AT noaa.gov; @dgbolser-NOAA)
Office of Science and Technology, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Silver Spring, MD 98195
Elizabeth Perl (Elizabeth.Perl AT noaa.gov; @e-perl-NOAA)
Affiliate with ECS Federal in support of the Office of Science and Technology, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Silver Spring, MD 98195
Ian Taylor (Ian.Taylor AT noaa.gov; @iantaylor-NOAA)
Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA 98195
Installation notes
devtools::install_github("nmfs-ost/surveyresamplr", build_vignettes = TRUE)Windows will not update a package already loaded, so then you have to remove the package and install it from scratch. There are two suggested packages, ‘graph’ and ‘Rgraphviz’, that are on Bioconductor, and you can install those with:
install.packages("INLA",repos=c(getOption("repos"), INLA="https://inla.r-inla-download.org/R/stable"), dep=TRUE)
inla.upgrade() # for the stable version
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(c("graph", "Rgraphviz"), dep=TRUE)
options(repos=c( inlabruorg = "https://inlabru-org.r-universe.dev", INLA = "https://inla.r-inla-download.org/R/testing", CRAN = "https://cran.rstudio.com") )
install.packages("fmesher")Cite data used in analysis
NOAA Fisheries Alaska Fisheries Science Center (2024)
Suggestions and Comments
If you see that the data, product, or metadata can be improved, you are invited to create a pull request, submit an issue to the GitHub organization, or submit an issue to the code’s repository.
R Version Metadata
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FALSE time zone: America/Los_Angeles
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FALSE attached base packages:
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FALSE loaded via a namespace (and not attached):
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NOAA README
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