Merge pull request #33 from joyliujoyliu/main

mapview to leaflet

DESCRIPTION

@@ -24,7 +24,10 @@ Imports:
     quarto,
     readxl,
     rmarkdown,
-    utils
+    utils,
+    leaflet,
+    leaflegend,
+    tidyr
 Suggests: 
     curl,
     knitr,

NAMESPACE

@@ -1,6 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
 export(deployment_gantt)
+export(leaflet_graph)
 export(make_receiver_push_summary)
 export(make_tag_push_summary)
 export(match_map)

R/leaflet_graph.R

@@ -0,0 +1,43 @@
+#' 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
+#' @export
+
+leaflet_graph <- function(station_spatial) {
+  geometry<- NULL
+  df <- station_spatial |> tidyr::extract(geometry, c('lon', 'lat'), '\\((.*), (.*)\\)', convert = TRUE)
+  numPal <- leaflet::colorNumeric('viridis', df $Detections)
+  leaflet::leaflet(data = df) |>
+    leaflet::addTiles() |>
+    leaflet::addCircleMarkers( lat = ~lat, lng = ~lon,
+                      color= ~numPal(Detections), fillColor = ~numPal(Detections),fillOpacity = 0.7,
+                      popup =  paste("Station ", df$station , "<br>",
+                                     "PI:", df$PI, "<br>",
+                                    "Detections:", df$Detections, "<br>",
+                                    "detectedby:", df$detectedby, "<br>",
+                                    "Individuals:", df$Individuals),
+                      radius = ~Individuals) |>
+
+    leaflegend::addLegendSize(
+      values = df $Individuals,
+      baseSize = 1,
+      color = 'black',
+      title = 'Individual',
+      shape = 'circle',
+      orientation = 'horizontal',
+      opacity = .5,
+      fillOpacity = 0,
+      breaks = 5,
+      position = 'bottomright') |>
+    leaflegend::addLegendNumeric(
+      pal = numPal,
+      title = 'Matched Detection',
+      shape = 'stadium',
+      values = df $Detections,
+      fillOpacity = .5,
+      decreasing = TRUE,
+      position = 'bottomright')
+
+
+
+}
+

inst/qmd_template/make_tag_push_summary.qmd

@@ -23,10 +23,8 @@ knitr::opts_chunk$set(
 ```{r}
 #| label: packages
 #| message: false
-
-library(otndo)
 library(data.table)
-library(mapview)
+library(otndo)
 library(reactable)
 ```
 
@@ -226,18 +224,15 @@ reactable(new_station_summary)
 
 ```{r}
 #| label: new-detection-map-leaflet
-#| fig-cap: Figure 7. Number of newly-added detections per receiver. Points represent receiver locations, while size and color reflect the number of detections at that location.
+#| fig-cap: Figure 7. Number of newly-added detections per receiver. Points represent receiver locations, where color reflects the number of detections  and size  reflects the number of fish at that location.
 #| eval: !expr "nrow(new_matches) > 0"
 
-new_station_spatial <- prep_station_spatial(new_matches, type = "tag")
-
-mapview::mapview(new_station_spatial,
-  zcol = "Detections",
-  cex = "Individuals",
-  layer.name = "Matched detections"
-)
+leaflet_graph(station_spatial)
 ```
 
+
+
+
 ```{r results='asis', echo=FALSE}
 if (is.null(params$since)) {
   cat("-->")