Improve gam visualization

.github/workflows/update-citation-cff.yaml

@@ -0,0 +1,58 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# The action runs when:
+# - A new release is published
+# - The DESCRIPTION or inst/CITATION are modified
+# - Can be run manually
+# For customizing the triggers, visit https://docs.github.com/en/actions/learn-github-actions/events-that-trigger-workflows
+on:
+  release:
+    types: [published]
+  push:
+    branches: [master, main]
+    paths:
+      - DESCRIPTION
+      - inst/CITATION
+  workflow_dispatch:
+
+name: Update CITATION.cff
+
+jobs:
+  update-citation-cff:
+    runs-on: macos-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v3
+      - uses: r-lib/actions/setup-r@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: |
+            any::cffr
+            any::V8
+
+      - name: Update CITATION.cff
+        run: |
+
+          library(cffr)
+
+          # Customize with your own code
+          # See https://docs.ropensci.org/cffr/articles/cffr.html
+
+          # Write your own keys
+          mykeys <- list()
+
+          # Create your CITATION.cff file
+          cff_write(keys = mykeys)
+
+        shell: Rscript {0}
+
+      - name: Commit results
+        run: |
+          git config --local user.name "github-actions[bot]"
+          git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com"
+          git add CITATION.cff
+          git commit -m 'Update CITATION.cff' || echo "No changes to commit"
+          git push origin || echo "No changes to commit"
+
+
+

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: trias
 Title: Process Data for the Project Tracking Invasive Alien Species
     (TrIAS)
-Version: 3.0.1
+Version: 3.0.2
 Authors@R: c(
     person("Damiano", "Oldoni", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-3445-7562")),

NEWS.md

@@ -1,3 +1,9 @@
+# trias 3.0.2
+
+- Improve `apply_gam()` to avoid emerging status change for negligible near zero values (#150).
+- Show all emerging status values in the legend of the plots returned by `apply_gam()` (#152).
+- `CITATION.cff` is updated automatically via GitHub Actions (#151).
+
 # trias 3.0.1
 
 - Function `get_cred()` is not exported anymore (#146). Internally used only.

R/apply_gam.R

@@ -668,19 +668,19 @@ apply_gam <- function(df,
           deriv1 %>%
           dplyr::filter(!is.na(!!dplyr::sym(year))) %>%
           dplyr::mutate(em1 = dplyr::case_when(
-            .data$lower_ci < 0 & .data$upper_ci <= 0 ~ -1,
-            .data$lower_ci < 0 & .data$upper_ci > 0 ~ 0,
-            .data$lower_ci >= 0 & .data$upper_ci > 0 ~ 1
+            .data$lower_ci < 0 & .data$upper_ci <= - 0.01 ~ -1,
+            .data$lower_ci < 0.01 & .data$upper_ci > - 0.01 ~ 0,
+            .data$lower_ci >= 0.01 & .data$upper_ci > 0 ~ 1
           )) %>%
           dplyr::select(!!dplyr::sym(year), "em1") %>%
           dplyr::mutate(!!dplyr::sym(year) := round(!!dplyr::sym(year)))
 
         em2 <- deriv2 %>%
           dplyr::filter(!is.na(!!dplyr::sym(year))) %>%
           dplyr::mutate(em2 = dplyr::case_when(
-            .data$lower_ci < 0 & .data$upper_ci <= 0 ~ -1,
-            .data$lower_ci < 0 & .data$upper_ci > 0 ~ 0,
-            .data$lower_ci >= 0 & .data$upper_ci > 0 ~ 1
+            .data$lower_ci < 0 & .data$upper_ci <= - 0.01 ~ -1,
+            .data$lower_ci < 0.01 & .data$upper_ci > - 0.01 ~ 0,
+            .data$lower_ci >= 0.01 & .data$upper_ci > 0 ~ 1
           )) %>%
           dplyr::select(!!dplyr::sym(year), "em2") %>%
           dplyr::mutate(!!dplyr::sym(year) := round(!!dplyr::sym(year)))
@@ -824,6 +824,7 @@ apply_gam <- function(df,
 #'   are returned. Default: \code{FALSE}.
 #' @return a ggplot2 plot object.
 #' @importFrom dplyr .data %>%
+#' @noRd
 plot_ribbon_em <- function(df_plot,
                            x_axis = "year",
                            y_axis = "obs",
@@ -862,17 +863,22 @@ plot_ribbon_em <- function(df_plot,
       ) +
       ggplot2::geom_line(ggplot2::aes(x = .data$year, y = .data$fit),
                          color = "grey50") +
-      ggplot2::geom_point(ggplot2::aes(
-        x = .data$year,
-        y = .data$fit,
-        color = factor(.data$em_status)
-      ),
-      size = 2
-      ) +
+      ggplot2::geom_point(
+        mapping = ggplot2::aes(
+          x = .data$year,
+          y = .data$fit,
+          color = factor(
+            .data$em_status, 
+            levels = names(colors_em)
+          )
+        ),
+        size = 2,
+        show.legend = TRUE) +
       ggplot2::scale_colour_manual(
         values = colors_em,
         labels = labels_em,
-        name = "Emerging status"
+        name = "Emerging status",
+        drop = FALSE
       ) +
       ggplot2::theme(plot.title = ggplot2::element_text(size = 10))
   } else {
@@ -889,7 +895,7 @@ plot_ribbon_em <- function(df_plot,
 
 #' Add annotation when status cannot be assessed
 #'
-#' Internal function to be used when GAM cannot be applied to it doesn't
+#' Internal function to be used when GAM cannot be applied as it doesn't
 #' converge.
 #'
 #' @param plot_obs ggplot2 plot object showing the observations.