Merge pull request #22 from alaska-groundfish-efh/dev

Update for terra dependencies, fix bugs

Author: MargaretSiple-NOAA

.Rbuildignore

@@ -2,3 +2,6 @@
 ^\.Rproj\.user$
 ^dev$
 ^R/Meatgrinder5\.R$
+^LICENSE\.md$
+^doc$
+^Meta$

.github/workflows/r-cmd-check.yml

@@ -0,0 +1,80 @@
+# R-CMD-Check
+
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+  schedule:
+    - cron: "0 0 1 * *"
+
+name: r-cmd-check
+
+jobs:
+
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: windows-latest, r: 'release'}
+          - {os: macOS-latest, r: 'release'}
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        if: runner.os != 'Windows'
+        uses: actions/cache@v2
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+
+      - name: Install dependencies
+        run: |
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("rcmdcheck")
+        shell: Rscript {0}
+
+      - name: Check
+        env:
+          _R_CHECK_CRAN_INCOMING_REMOTE_: false
+        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "error", check_dir = "check")
+        shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@main
+        with:
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check

.github/workflows/secretScan.yml

@@ -0,0 +1,13 @@
+name: gitleaks
+
+on: [push, pull_request]
+
+jobs:
+  gitleaks:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: '0'
+      - name: gitleaks-action
+        uses: gitleaks/gitleaks-action@v1.6.0

.gitignore

@@ -42,3 +42,5 @@ vignettes/*.pdf
 *.html
 .Rproj.user
 inst/doc
+/doc/
+/Meta/

DESCRIPTION

@@ -14,39 +14,32 @@ Authors@R:
            comment = c(ORCID = "0000-0002-4260-9856"))     
            )
 Description: This package fits species distribution models (SDMs) to groundfish and crab data from the Eastern Bering Sea, Aleutian Islands, and Gulf of Alaska. These SDMs were used in the 2022 EFH 5-Year Review. 
-License: `use_mit_license()`
+License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.2
+RoxygenNote: 7.3.2
 Suggests: 
     knitr,
     rmarkdown,
+    gridExtra
 VignetteBuilder: knitr
 Imports: 
     ggplot2,
-    akgfmaps (>= 1.7.4),
+    akgfmaps,
     viridis,
     stars,
     sf,
-    gridExtra,
-    patchwork,
-    MASS,
     scales,
-    labeling,
     mgcv,
     raster,
     PresenceAbsence,
-    gstat,
     maxnet,
-    ENMeval,
     xtable,
-    XML,
     magrittr,
     terra,
     tidyterra
-Remotes: 
-    git::https://github.com/afsc-gap-products/akgfmaps.git@master
+Remotes: afsc-gap-products/akgfmaps
 Depends: 
     R (>= 3.5.0)
 LazyData: 
-    true
+    false

LICENSE

@@ -0,0 +1,2 @@
+YEAR: 2024
+COPYRIGHT HOLDER: EFHSDM authors

LICENSE.md

@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) 2024 EFHSDM authors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

NAMESPACE

@@ -33,3 +33,10 @@ export(RMSE)
 export(ValidateEnsemble)
 importFrom(akgfmaps,get_base_layers)
 importFrom(magrittr,"%>%")
+importFrom(stats,aggregate)
+importFrom(stats,density)
+importFrom(stats,var)
+importFrom(terra,classify)
+importFrom(terra,extract)
+importFrom(terra,setValues)
+importFrom(terra,values)

R/Functions_Ensemble.R

@@ -266,6 +266,7 @@ GetEnsembleVariance<-function(model.weights,variance.list,abund.list,ensemble.ab
 #' @param model.weights vector of numeric weights for each model, must match order of effects.list
 #' @param vars character; vector of desired term names or "all"
 #' @param scale character; should effects be in "log" or "abund" scale
+#' @importFrom stats var
 #'
 #' @return list of data frames containing the estimated covariate effects in the ensemble
 #' @export

R/Functions_GamModel.R

@@ -1,21 +1,3 @@
-# This script includes functions for fitting GAM and HGAM models
-
-# Setting lists of required packages & installing it
-# rpackages <- c("mgcv", "raster", "PresenceAbsence")
-#
-# # rJava, rgeos, maps
-# which_not_installed <- which(rpackages %in% rownames(installed.packages()) == FALSE)
-#
-# if (length(which_not_installed) > 1) {
-#   install.packages(rpackages[which_not_installed], dep = TRUE)
-# }
-# rm(rpackages, which_not_installed)
-#
-# require(mgcv)
-# require(raster)
-# require(PresenceAbsence)
-
-
 #' Make a GAM formula
 #'
 #' @description Improved version designed to use the tables produced by the Autodetect functions
@@ -27,7 +9,6 @@
 #' @return Returns a formula object, or list of formulas for hgam
 #' @export
 #'
-#'
 #' @examples
 AssembleGAMFormula <- function(yvar, gam.table, hgam = F) {
 
@@ -123,6 +104,13 @@ AssembleGAMFormula <- function(yvar, gam.table, hgam = F) {
 #' @export
 #'
 #' @examples
+#' gam.form <- formula("a_atf ~ s(lon,lat,bs = 'ds',m=c(1,.5), k=10) + s(bdepth, bs='tp',m=1,k=4) + s(btemp, bs='tp',m=1,k=4) + s(slope, bs='tp',m=1,k=4) + offset(logarea)")
+#' data("region_data_all")
+#' region_data_all$sponge <- as.integer(region_data_all$sponge > 0)
+#' region_data_all$logarea <- log(region_data_all$area)
+#'
+#' poisson.model <- FitGAM(gam.formula = gam.form, data = region_data_all, family.gam = "poisson")
+
 FitGAM <- function(data,
                    gam.formula = NULL,
                    reduce = F,
@@ -496,7 +484,7 @@ AutodetectGAMTerms <- function(model, hgam = "all") {
 #' @param model a GAM model object
 #' @param data a data frame; usually the same one used to fit the GAM model
 #'
-#' @return a named vector of decimal values indicating the percent contribution
+#' @return a named vector of decimal values indicating the percent contribution to deviance explained
 #' @export
 #'
 #' @examples
@@ -560,7 +548,7 @@ GAMStats <- function(model, # a gam model
       # update progress bar
       utils::setTxtProgressBar(pb, i)
     } else {
-      utils::setTxtProgressBar(pb, length(gam.terms))
+      utils::setTxtProgressBar(pb, length(gam.terms)) # maybe change this to just 'terms'?
       print("Deviance could not be estimated for model; returning NAs")
       break
     }