Lasso

.github/workflows/pkgdown.yaml

@@ -1,54 +1,53 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
-# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
-on:
-  push:
-    branches: [main, master]
-  pull_request:
-    branches: [main, master]
-  release:
-    types: [published]
-
-name: pkgdown
-
-jobs:
-  pkgdown:
-    runs-on: ubuntu-latest
-    env:
-      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-    steps:
-      - uses: actions/checkout@v3
-
-      - uses: r-lib/actions/setup-pandoc@v2
-
-      - uses: r-lib/actions/setup-r@v2
-        with:
-          use-public-rspm: true
-
-      - uses: r-lib/actions/setup-r-dependencies@v2
-        with:
-          extra-packages: any::pkgdown, local::.
-          needs: website
-
-      - name: Install R dependencies not on CRAN
-        run: |
-          install.packages('remotes')
-          remotes::install_github("cran/RandomFieldsUtils")
-          remotes::install_github("cran/RandomFields")
-          remotes::install_github("ropensci/NLMR")
-          remotes::install_github("MoBiodiv/mobsim")
-        shell: Rscript {0}
-
-      - name: Install GRASS GIS and other dependencies
-        run: |
-          sudo apt-get update -qq
-          sudo apt-get install -y -qq grass grass-dev grass-doc wget
-
-      - name: Build site
-        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
-        shell: Rscript {0}
-
-      - name: Deploy to GitHub pages
-        run: |
-          git config --local user.name "$GITHUB_ACTOR"
-          git config --local user.email "[email protected]"
-          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'
+# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+  release:
+    types: [published]
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v4
+      - uses: r-lib/actions/setup-pandoc@v2
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          install-quarto: true
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Install R dependencies not on CRAN
+        run: |
+          install.packages('remotes')
+          remotes::install_github("cran/RandomFieldsUtils")
+          remotes::install_github("cran/RandomFields")
+          remotes::install_github("ropensci/NLMR")
+          remotes::install_github("MoBiodiv/mobsim")
+        shell: Rscript {0}
+
+      - name: Install GRASS GIS and other dependencies
+        run: |
+          sudo apt-get update -qq
+          sudo apt-get install -y -qq grass grass-dev grass-doc wget
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "[email protected]"
+          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'

DESCRIPTION

@@ -8,6 +8,8 @@ Authors@R: c(
         role = c("aut", "cre"), comment = c(ORCID = "0000-0002-0453-315X")),
     person("Manuela", "Panzacchi", email = "[email protected]",
         role = "aut"),
+    person("Neri", "Thorsen", email = "[email protected]",
+        role = "ctb"),
     person("Bram", "van Moorter", email = "[email protected]",
         role = "aut", comment = c(ORCID = "0000-0002-3196-1993")))
 Description: The package presents a set of tools to assess cumulative impacts
@@ -21,28 +23,31 @@ Depends:
 Imports: 
     dplyr, 
     tibble, 
-    purrr, 
+    purrr,
+    tidyr,
     rgrass, 
-    terra, 
-    sf, 
+    glmnet,
+    survival,
     ggplot2, 
-    scales
-Suggests:
-    raster,
-    landscapetools,
-    smoothie,
+    scales,
+    DescTools,
+    pROC,
+    terra, 
+    sf
+Suggests: 
+    foreach,
+    amt,
+    maxnet,
     knitr,
-    rmarkdown,
-    mobsim,
-    NLMR
+    rmarkdown
 Remotes:
     MoBiodiv/mobsim,
     ropensci/NLMR
 License: GPL-3
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
 URL: https://github.com/NINAnor/oneimpact,
      https://ninanor.github.io/oneimpact/
 BugReports: https://github.com/NINAnor/oneimpact/issues

NAMESPACE

@@ -2,30 +2,84 @@
 
 S3method(bartlett_decay,SpatRaster)
 S3method(bartlett_decay,numeric)
+S3method(plot_response,bag)
+S3method(rescale_coefficients,bag)
+S3method(rescale_coefficients,coxph)
+S3method(rescale_coefficients,glm)
+S3method(rescale_coefficients,lm)
 S3method(threshold_decay,SpatRaster)
 S3method(threshold_decay,numeric)
+export(AUC)
+export(Cindex)
+export(add_zoi_formula)
+export(add_zoi_layers)
+export(bag_fit_net_clogit)
+export(bag_fit_net_logit)
+export(bag_load_models)
+export(bag_models)
+export(bag_predict)
+export(bag_predict_spat)
+export(bag_predict_spat_vars)
 export(bartlett_decay)
 export(calc_zoi)
 export(calc_zoi_cumulative)
 export(calc_zoi_nearest)
+export(calc_zoi_sql)
+export(conditionalAUC)
+export(conditionalBoyce)
+export(conditionalSomersD)
+export(conditional_maxnet)
+export(coxnet.deviance)
+export(create_resamples)
+export(data_summary)
+export(data_summary_char)
 export(dist_decay)
 export(exp_decay)
+export(explore_blocks)
+export(explore_blocks_pre)
+export(extract_response_strata)
 export(filter_create)
+export(filter_na_strata)
 export(filter_save)
+export(fit_net_clogit)
+export(fit_net_issf)
+export(fit_net_logit)
+export(fit_net_rsf)
+export(fit_net_ssf)
+export(from_std)
 export(gaussian_decay)
 export(grass_binarize)
 export(grass_find_layer)
 export(grass_v2rast_count)
 export(half_norm_decay)
+export(hypothesis_func)
 export(isolation)
+export(kernel_prediction)
 export(linear_decay)
 export(mean_isolation)
+export(net_clogit)
+export(net_issf)
+export(net_logit)
+export(net_rsf)
+export(net_ssf)
+export(plot_coef)
+export(plot_importance)
+export(plot_response)
 export(plot_zoi1d)
 export(raster_rescale)
 export(rescale_coefficients)
+export(score2weight_invmean)
+export(score2weight_mean)
+export(score2weight_min_invmean)
+export(score2weight_min_mean)
 export(set_points)
 export(set_points_from_raster)
 export(set_points_sample)
+export(spat_strat)
 export(step_decay)
 export(tent_decay)
 export(threshold_decay)
+export(to_std)
+export(variable_importance)
+export(w_strech_max_squared)
+export(w_strech_maxmin_squared)