diff --git a/README.md b/README.md index 4133cae..f6e87ca 100644 --- a/README.md +++ b/README.md @@ -1,25 +1,27 @@ # EFHSDM (in progress) -A package is designed to produce SDMs and SDM visualizations as part of the 2022 EFH 5-year review. It is designed to be moderately flexible and can be expanded in the future, but for now assumes that abundance prediction is the end goal. +A package is designed to produce SDMs and SDM visualizations as part of the 2023 EFH 5-year review. It is designed to be moderately flexible and can be expanded in the future, but for now assumes that abundance prediction is the end goal. -The most recent version of this package was built in R 4.1.2. +The most recent version of this package was built in R 4.4.1. Authors: @jeremyharris7 @James-Thorson-NOAA -@Ned-Laman-NOAA +@MasonSmith-NOAA @MargaretSiple-NOAA @jodipirtle - +@Ned-Laman-NOAA # Installation `EFHSDM` can be installed using the following code: ```r devtools::install_github("afsc-gap-products/akgfmaps", build_vignettes=TRUE) - devtools::install_github("alaska-groundfish-efh/EFHSDM@main", dependencies = TRUE, build_vignettes = FALSE) + +# Development version - not currently recommended unless you are an active developer +# devtools::install_github("alaska-groundfish-efh/EFHSDM@dev", dependencies = TRUE, build_vignettes = FALSE) ``` @@ -34,7 +36,7 @@ xtable, XML, raster, rgdal, gstat, sp, sf, stars, akgfmaps, ggplot, viridis, gri # Roadmap Sections of the analysis are included as separate scripts. The general strategy is to use the functions provided in `Functions_Maxent.R` and `Functions_GamModel.R` to produce models, abundance rasters, effects estimates, and other outputs in a standard-ish format. Then, the scripts `Functions_LoadMap.R` and `Functions_Ensemble.R` provide more general methods for mapping or plotting model outputs and combining inferences from multiple models. -The `Meatgrinder.R` script provides an example of a workflow that combines these functions to make an ensemble SDM and the accompanying maps. It contains control logic designed to accommodate the needs of the 2022 EFH 5-year Review process, which involved running and keeping track of over 200 individual species/lifestages. +The `Meatgrinder.R` script provides an example of a workflow that combines these functions to make an ensemble SDM and the accompanying maps. It contains control logic designed to accommodate the needs of the 2023 EFH 5-year Review process, which involved running and keeping track of over 200 individual species/lifestages. 1) `Functions_Maxent.R` - this script provides the functions for quickly using maxnet models. @@ -97,9 +99,9 @@ The functions are typically called top to bottom. Begin by fitting a model using ## Simple example -All of the rasters used for the EFH 2022 Five-Year Review are stored on a shared drive at NOAA. For the purposes of the following example, the datasets are embedded in the package. For additional rasters and datasets, contact the package developers or submit a data [product request](https://github.com/alaska-groundfish-efh/product-requests/issues). +All of the rasters used for the EFH 2023 Five-Year Review are stored on a shared drive at NOAA. For the purposes of the following example, the datasets are embedded in the package. For additional rasters and datasets, contact the package developers or submit a data [product request](https://github.com/alaska-groundfish-efh/product-requests/issues). -For example purposes, we will used only the last years of data and only a few covariates. *Note that this means that the map you produce will look different from the final map produced in the 2022 EFH 5-year Review.* +For example purposes, we will used only the last years of data and only a few covariates. *Note that this means that the map you produce will look different from the final map produced in the 2023 EFH 5-year Review.* ### Load EFHSDM ```r @@ -116,7 +118,8 @@ region.data$sponge <- as.integer(region.data$sponge > 0) region.data$logarea <- log(region.data$area) -raster.stack <- raster_stack +raster.stack <- terra::rast(terra::unwrap(raster_stack)) +#raster.stack <- raster::raster(raster.stack) # option to turn this spatraster stack into a regular raster stack (only works if you don't crop ) ``` ### Next we will fit a basic Poisson model and generate an abundance map