diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index 8d60ca8..dd147dc 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.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
diff --git a/.github/workflows/style.yaml b/.github/workflows/style.yaml
index 66958a4..6f1682d 100644
--- a/.github/workflows/style.yaml
+++ b/.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
diff --git a/DESCRIPTION b/DESCRIPTION
index 87fd428..74c4848 100644
--- a/DESCRIPTION
+++ b/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"))
diff --git a/NEWS.md b/NEWS.md
index 0669ba8..9cd91cd 100644
--- a/NEWS.md
+++ b/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)
diff --git a/R/leaflet_graph.R b/R/leaflet_graph.R
index fdafec9..ac21727 100644
--- a/R/leaflet_graph.R
+++ b/R/leaflet_graph.R
@@ -1,36 +1,44 @@
#' 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 , "
",
- "PI:", df$PI, "
",
- "Detections:", df$Detections, "
",
- "detectedby:", df$detectedby, "
",
- "Individuals:", df$Individuals),
- radius = ~(df$Individuals)) |>
-
+ leaflet::addCircleMarkers(
+ lat = ~lat, lng = ~lon,
+ color = "black",
+ fillColor = ~ numPal(Detections),
+ fillOpacity = 0.7,
+ popup = paste(
+ "Station ", df$station, "
",
+ "PI:", df$PI, "
",
+ "Detections:", df$Detections, "
",
+ "detectedby:", df$detectedby, "
",
+ "Individuals:", df$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,
@@ -38,9 +46,6 @@ leaflet_graph <- function(station_spatial) {
shape = 'rect',
position = 'bottomright',
height = 20,
- width = 100)
-
-
-
+ width = 100
+ )
}
-
diff --git a/R/match_table.R b/R/match_table.R
index 6f9980d..37f3488 100644
--- a/R/match_table.R
+++ b/R/match_table.R
@@ -6,6 +6,9 @@
#'
#' @examples
#' \dontrun{
+#' td <- file.path(tempdir(), "matos_test_files")
+#' dir.create(td)
+#'
#' # Receiver
#' download.file(
#' paste0(
diff --git a/R/matched_abacus.R b/R/matched_abacus.R
index 103b164..fb5848f 100644
--- a/R/matched_abacus.R
+++ b/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(
diff --git a/R/prep_station_spatial.R b/R/prep_station_spatial.R
index 2de07ad..78cb077 100644
--- a/R/prep_station_spatial.R
+++ b/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(
diff --git a/R/remaining_transmitters.R b/R/remaining_transmitters.R
index b4944c8..4f12541 100644
--- a/R/remaining_transmitters.R
+++ b/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)
#'