Merge branch 'dev' into main

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

@@ -6,6 +6,10 @@ on:
   pull_request:
     branches: [main, dev]
 
+concurrency:
+  group: rcmdcheck-${{ github.ref }}
+  cancel-in-progress: true
+
 name: R-CMD-check
 
 jobs:
@@ -46,4 +50,5 @@ jobs:
 
       - uses: r-lib/actions/check-r-package@v2
         with:
+          error-on: '"note"'
           upload-snapshots: true

.github/workflows/style.yaml

@@ -3,6 +3,8 @@
 on:
   push:
     paths: ["**.[rR]", "**.[qrR]md", "**.[rR]markdown", "**.[rR]nw", "**.[rR]profile"]
+  pull_request:
+    paths: ["**.[rR]", "**.[qrR]md", "**.[rR]markdown", "**.[rR]nw", "**.[rR]profile"]
 
 name: Style
 

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: otndo
 Title: Understand your OTN data
-Version: 0.2.2
+Version: 0.2.3.9000
 Authors@R: 
     person("Michael", "O'Brien", , "mike@obrien.page", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-1420-6395"))

NEWS.md

@@ -1,4 +1,7 @@
 ## otndo 0.2
+### v 0.2.3
+* Switched from using the `mapview` package for interactive maps to `leaflet` and `leaflet_legend`. Thanks to [@joyliujoyliu](https://github.com/joyliujoyliu) for their work here!
+
 ### v 0.2.2
 * Fixed behavior where `clean_otn_deployment` would return different columns if there was no internal transmitter logged. [Issue #10](https://github.com/mhpob/otndo/issues/10); [d58e2d4](https://github.com/mhpob/otndo/pull/31/commits/d58e2d46e05aed7ba4acc08b8d02672b28d79804)
 * Add internal function (`convert_times`) that checks for Excel-formatted date-times and converts accordingly [f13f360](https://github.com/mhpob/otndo/pull/31/commits/f13f360fe5e4438b6ba668039a6c94f04eeafe60)

R/leaflet_graph.R

@@ -1,46 +1,51 @@
 #' Plot the leaflet graphs for detection and individual
-#' @param   station_spatial is created by prep_station_spatial,which is a spatial object with the geometry
+#'
+#' @param station_spatial sf spatial data/frame created by prep_station_spatial
+#'
 #' @export
 
 leaflet_graph <- function(station_spatial) {
-  geometry<- NULL
-  df <- station_spatial |> tidyr::extract(geometry, c('lon', 'lat'), '\\((.*), (.*)\\)', convert = TRUE)
-  numPal <- leaflet::colorNumeric('viridis', df $Detections)
+  geometry <- NULL
+  df <- station_spatial |> tidyr::extract(geometry, c("lon", "lat"), "\\((.*), (.*)\\)", convert = TRUE)
+  numPal <- leaflet::colorNumeric("viridis", df$Detections)
   leaflet::leaflet(data = df) |>
     leaflet::addTiles() |>
-    leaflet::addCircleMarkers( lat = ~lat, lng = ~lon,
-                      color= 'black', fillColor = ~numPal(df$Detections),fillOpacity = 0.7,
-                      popup =  paste("Station ", df$station , "<br>",
-                                     "PI:", df$PI, "<br>",
-                                    "Detections:", df$Detections, "<br>",
-                                    "detectedby:", df$detectedby, "<br>",
-                                    "Individuals:", df$Individuals),
-                      radius = ~(df$Individuals)) |>
-
+    leaflet::addCircleMarkers(
+      lat = ~lat, lng = ~lon,
+      color = "black",
+      fillColor = ~ numPal(Detections),
+      fillOpacity = 0.7,
+      popup = paste(
+        "Station ", df$station, "<br>",
+        "PI:", df$PI, "<br>",
+        "Detections:", df$Detections, "<br>",
+        "detectedby:", df$detectedby, "<br>",
+        "Individuals:", df$Individuals
+      ),
+      radius = ~ Individuals
+    ) |>
     leaflegend::addLegendSize(
-      values = df $Individuals,
+      values = df$Individuals,
       baseSize = 5,
-      color = 'black',
-      title = 'Individual',
-      shape = 'circle',
-      orientation = 'horizontal',
-      opacity = .5,
+      color = "black",
+      title = "Individual",
+      shape = "circle",
+      orientation = "horizontal",
+      opacity = 0.5,
       fillOpacity = 0,
       breaks = 5,
-      position = 'bottomright') |>
+      position = "bottomright"
+    ) |>
     leaflegend::addLegendNumeric(
       pal = numPal,
-      title = 'Matched Detection',
+      title = 'Matched Detections',
       values = df$Detections,
       fillOpacity = .5,
       decreasing = FALSE,
       orientation = 'horizontal',
       shape = 'rect',
       position = 'bottomright',
       height = 20,
-      width = 100)
-
-
-
+      width = 100
+    )
 }
-

R/match_table.R

@@ -6,6 +6,9 @@
 #'
 #' @examples
 #' \dontrun{
+#' td <- file.path(tempdir(), "matos_test_files")
+#' dir.create(td)
+#'
 #' # Receiver
 #' download.file(
 #'   paste0(

R/matched_abacus.R

@@ -6,6 +6,9 @@
 #'
 #' @examples
 #' \dontrun{
+#' td <- file.path(tempdir(), "matos_test_files")
+#' dir.create(td)
+#'
 #' # Get a detection file
 #' download.file(
 #'   paste0(

R/prep_station_spatial.R

@@ -5,6 +5,9 @@
 #'
 #' @examples
 #' \dontrun{
+#' td <- file.path(tempdir(), "matos_test_files")
+#' dir.create(td)
+#'
 #' # Get an extract file
 #' download.file(
 #'   paste0(

R/remaining_transmitters.R

@@ -13,7 +13,7 @@
 #'
 #' @examples
 #' \dontrun{
-#' #' # Set up example data
+#' # Set up example data
 #' td <- file.path(tempdir(), "otndo_example")
 #' dir.create(td)
 #'