App update

.Rbuildignore

@@ -11,3 +11,16 @@
 ^tmp$
 ^notes\.md$
 ^\.vscode$
+^.*\.Rproj$
+^\.Rproj\.user$
+^data-raw$
+dev_history.R
+^dev$
+$run_dev.*
+^manifest\.json$
+^app\.R$
+^\.rscignore$
+^doc$
+^Meta$
+^\.github$
+^\.renvignore$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/R-CMD-check.yaml

@@ -1,10 +1,13 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
     branches: main
   pull_request:
-    branches: main
 
-name: R CMD Check
+name: R-CMD-check.yaml
+
+permissions: read-all
 
 jobs:
   R-CMD-check:
@@ -16,30 +19,32 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          #- {os: macOS-latest, r: 'release'}
+          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
-          - {os: ubuntu-latest, r: 'devel'}
-          - {os: ubuntu-latest, r: 'release'}
-          - {os: ubuntu-latest, r: 'oldrel'}
+          # - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
 
     env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      _R_CHECK_DONTTEST_EXAMPLES_: false
-      CRAN: ${{ matrix.config.cran }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v6
 
       - uses: r-lib/actions/setup-pandoc@v2
 
       - uses: r-lib/actions/setup-r@v2
         with:
-          use-public-rspm: true
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: any::rcmdcheck
           needs: check
 
       - uses: r-lib/actions/check-r-package@v2
-
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/pkgdown.yaml

@@ -2,7 +2,7 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master]
+    branches: main
   pull_request:
   release:
     types: [published]
@@ -23,13 +23,11 @@ jobs:
     permissions:
       contents: write
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
       - 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:
@@ -42,8 +40,8 @@ jobs:
 
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'pull_request'
-        uses: JamesIves/github-pages-deploy-action@v4.5.0
+        uses: JamesIves/github-pages-deploy-action@d92aa235d04922e8f08b40ce78cc5442fcfbfa2f # v4.8.0
         with:
           clean: false
           branch: gh-pages
-          folder: docs
+          folder: docs

.gitignore

@@ -1,7 +1,7 @@
 # Project-specific files
 fetchR
 tmp
-
+inst/extdata/polygons/Great_Lakes_High_Resolution_Shorelines_
 
 # vscode
 .vscode
@@ -47,4 +47,6 @@ vignettes/*.pdf
 .Renviron
 inst/doc
 docs
-.DS_Store
+.DS_Store
+/doc/
+/Meta/

.renvignore

@@ -0,0 +1 @@
+tmp/

.rscignore

@@ -0,0 +1,24 @@
+# macOS files ----
+.DS_Store
+
+# History files ----
+.Rhistory
+.Rapp.history
+
+# Session Data files ----
+.RData
+.Ruserdata
+
+# RStudio files ----
+*.Rproj
+.Rproj.user
+
+# R Environment Variables ----
+.Renviron
+
+# User-specific files ----
+README.html
+inst/doc
+
+# temporary files ----
+tmp

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: SAVM
 Title: Submerged aquatic vegetation model
-Version: 0.0.1.9005
-Date: 2025-08-12
+Version: 0.1.1
+Date: 2025-10-09
 Authors@R: c(
     person(given = "Kevin",
            family = "Cazelles",
@@ -27,16 +27,31 @@ License: GPL-3
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-Depends: 
+Depends:
     R (>= 4.2),
     randomForest (>= 4.7-1.2)
-Imports: 
+Imports:
+    bs4Dash,
     cli (>= 3.6.4),
+    config,
+    DT,
     dplyr (>= 1.1.4),
     ggplot2 (>= 3.5.1),
+    glue,
+    golem,
+    leaflet,
+    mapedit,
+    leafpm,
+    lme4,
+    lmerTest,
+    mgcv,
     patchwork (>= 1.3.0),
     rlang (>= 1.1.5),
     sf (>= 1.0-19),
+    shiny,
+    shinyjs,
+    shinycssloaders,
+    shinyWidgets,
     stats,
     tmap (>= 4.0),
     tools,
@@ -50,6 +65,6 @@ Suggests:
     stars,
     vdiffr,
     withr
-RoxygenNote: 7.3.2
 VignetteBuilder: knitr
 Config/testthat/edition: 3
+Config/roxygen2/version: 8.0.0

NAMESPACE

@@ -2,7 +2,6 @@
 
 S3method(preview_grid,sav_data)
 export(compute_fetch)
-export(identify_outsiders)
 export(invert_polygon)
 export(plot_sav_density)
 export(plot_sav_distribution)
@@ -12,5 +11,13 @@ export(read_sav)
 export(read_sav_aoi)
 export(read_sav_csv)
 export(read_sav_pts)
+export(run_app)
+export(sav_load_model)
 export(sav_model)
+export(visualize_outsiders)
 import(randomForest)
+import(shiny)
+importFrom(golem,activate_js)
+importFrom(golem,add_resource_path)
+importFrom(golem,bundle_resources)
+importFrom(golem,favicon)

NEWS.md

@@ -1,4 +1,32 @@
-# SAVM (devel)
+# SAVM 0.1.1
+
+* Notify users when predictor values are all NAs.
+* Drop empty columns from user input data. 
+* Add SAVM version in the top left of the navbar.  
+
+
+# SAVM 0.1.0
+
+* Fix problematic conversion to one-column matrix.
+* Lint code. 
+* CI update + manifest update.
+
+
+# SAVM 0.0.2
+
+* New shiny app that exposes the package capacities.
+* `compute_fetch()` gains argument `land_polygon` to work with land polygons.
+* Bearings are oriented properly and the element `transect_lines` of the object returned by `compute_fetch()` gains a column `cardinal_direction` (see #15).
+* Argument `remove_outsiders` has been removed from `compute_fetch()`, instead
+a column `outsider` which identifies outsiders has been added.  
+* `identify_outsiders()` has been renamed `visualize_outsiders()`.
+* `sav_load_model()` is now exposed and the vignette "SAV Prediction Models" details the model available.
+* Only models using both fetch and depth are supported, therefore argument 
+`type` has been dropped from `sav_model()`.
+* New `glmm` and `gam` models available.
+
+
+# SAVM 0.0.1
 
 * `compute_fetch()` has a new argument `remove_outsider` to remove points falling outside the polygon. Also, `identify_outsiders()` helps visualize outsiders (see #13).
 * Model and plot functions have been adjusted to handle `sf` objects (see #11).
@@ -8,4 +36,4 @@
 * `invert_polygon()` has been added to invert polygon (see #6).
 * `compute_fetch()` has a new argument `n_bearings` that provides the number of bearings, it replaces `n_quad_seg` (see #4 and #5). 
 * `compute_fetch()` only compute the mean fetch for all bearings, columns with 
-suffix `_all` where therefore removed (see #4).
+suffix `_all` where therefore removed (see #4).

R/app_config.R

@@ -0,0 +1,44 @@
+#' Access files in the current app
+#'
+#' NOTE: If you manually change your package name in the DESCRIPTION,
+#' don't forget to change it here too, and in the config file.
+#' For a safer name change mechanism, use the `golem::set_golem_name()` function.
+#'
+#' @param ... character vectors, specifying subdirectory and file(s)
+#' within your package. The default, none, returns the root of the app.
+#'
+#' @noRd
+app_sys <- function(...) {
+  system.file(..., package = "SAVM")
+}
+
+
+#' Read App Config
+#'
+#' @param value Value to retrieve from the config file.
+#' @param config GOLEM_CONFIG_ACTIVE value. If unset, R_CONFIG_ACTIVE.
+#' If unset, "default".
+#' @param use_parent Logical, scan the parent directory for config file.
+#' @param file Location of the config file
+#'
+#' @noRd
+get_golem_config <- function(
+  value,
+  config = Sys.getenv(
+    "GOLEM_CONFIG_ACTIVE",
+    Sys.getenv(
+      "R_CONFIG_ACTIVE",
+      "default"
+    )
+  ),
+  use_parent = TRUE,
+  # Modify this if your config file is somewhere else
+  file = app_sys("golem-config.yml")
+) {
+  config::get(
+    value = value,
+    config = config,
+    file = file,
+    use_parent = use_parent
+  )
+}