hotix bug in summarize_detections() where value in 'locations' output…

… column was name of input column (e.g. 'glatos_array'), rather than values from that column (e.g., 'AGR', 'BBI'); fixes #182; cherrypicked from commit db9d69a which was merged to dev

DESCRIPTION

@@ -1,53 +1,53 @@
-Package: glatos
-Type: Package
-Title: A package for the Great Lakes Acoustic Telemetry Observation System
-Description: Functions useful to members of the Great Lakes Acoustic Telemetry Observation System https://glatos.glos.us; many more broadly relevant to simulating, processing, analysing, and visualizing acoustic telemetry data.
-Version: 0.7.1
-Date: 2024-01-19
-Depends: R (>= 3.5.0)
-Imports:
-		av,
-		data.table,		
-		fasterize,
-		fasttime,
-		gdalUtilities,
-		geodist,
-		gdistance,
-		jsonlite,
-		knitr,
-		lubridate,
-		magrittr,
-		methods,
-		plotrix,
-		plyr,
-		purrr,
-		raster,
-		readxl,
-		rmarkdown,
-		sf,
-		tibble,
-		tidyr
-Suggests: 
-		gganimate,
-		gifsky,
-		GISTools,
-		png,
-		tint
-URL: https://github.com/ocean-tracking-network/glatos
-BugReports: https://github.com/ocean-tracking-network/glatos/issues
-Authors@R: c(
-    person("Christopher", "Holbrook", email = "cholbrook@usgs.gov",
-			role = c("cre", "aut")),
-    person("Todd", "Hayden", role = "aut"),
-		person("Thomas", "Binder", role = "aut"),
-		person("Jon", "Pye", role = "aut"),
-		person("Alex", "Nunes", role = "ctb"),
-		person("Angela", "Dini", role = "ctb"),
-		person("Ryan", "Gosse", role = "ctb"))
-License: GPL-2
-LazyLoad: yes
-LazyData: true
-RoxygenNote: 7.2.3
-VignetteBuilder: knitr
-Encoding: UTF-8
-Roxygen: list(markdown = TRUE)
+Package: glatos
+Type: Package
+Title: A package for the Great Lakes Acoustic Telemetry Observation System
+Description: Functions useful to members of the Great Lakes Acoustic Telemetry Observation System https://glatos.glos.us; many more broadly relevant to simulating, processing, analysing, and visualizing acoustic telemetry data.
+Version: 0.7.2
+Date: 2024-02-25
+Depends: R (>= 3.5.0)
+Imports:
+		av,
+		data.table,		
+		fasterize,
+		fasttime,
+		gdalUtilities,
+		geodist,
+		gdistance,
+		jsonlite,
+		knitr,
+		lubridate,
+		magrittr,
+		methods,
+		plotrix,
+		plyr,
+		purrr,
+		raster,
+		readxl,
+		rmarkdown,
+		sf,
+		tibble,
+		tidyr
+Suggests: 
+		gganimate,
+		gifsky,
+		GISTools,
+		png,
+		tint
+URL: https://github.com/ocean-tracking-network/glatos
+BugReports: https://github.com/ocean-tracking-network/glatos/issues
+Authors@R: c(
+    person("Christopher", "Holbrook", email = "cholbrook@usgs.gov",
+			role = c("cre", "aut")),
+    person("Todd", "Hayden", role = "aut"),
+		person("Thomas", "Binder", role = "aut"),
+		person("Jon", "Pye", role = "aut"),
+		person("Alex", "Nunes", role = "ctb"),
+		person("Angela", "Dini", role = "ctb"),
+		person("Ryan", "Gosse", role = "ctb"))
+License: GPL-2
+LazyLoad: yes
+LazyData: true
+RoxygenNote: 7.3.1
+VignetteBuilder: knitr
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)

NEWS.md

@@ -1,5 +1,21 @@
 ----
 
+# glatos 0.7.2 (2024-02-25)
+
+
+### Bug fixes
+
+
+- Fixed bug in `summarize_detections()` where value in `locations` output 
+  column was name of input column (e.g. "glatos_array"), rather than values 
+  from that column (e.g., "AGR", "BBI").
+    - fixed [issue #182](https://github.com/ocean-tracking-network/glatos/issues/182)
+    - cherry-picked from [commit 182]( https://github.com/ocean-tracking-network/glatos/commit/db9d69a3d08a97e7b8f86e0d4977aa0909776ddd)
+      which was merged with dev but not main.
+
+
+----
+
 # glatos 0.7.1 (2024-01-19)
 
 

R/summ-summarize_detections.r

@@ -182,6 +182,8 @@
 #' 
 #' @export
 
+
+
 summarize_detections <- function(det, location_col = "glatos_array", 
                                  receiver_locs = NULL, animals = NULL, 
                                  summ_type = "animal"){
@@ -190,8 +192,8 @@ summarize_detections <- function(det, location_col = "glatos_array",
   dtc <- data.table::as.data.table(det)
 
   #check 'summ_type'
-  if(!(summ_type %in% c("animal", "location", "both"))) stop(paste0("invalid ",
-     "summary type ('summ_type'); must be 'animal', 'location', or 'both'."))
+  if(!(summ_type %in% c("animal", "location", "both"))) stop(paste0("invalid",
+     "summary type ('summ_type'); must be 'animal', 'location', or 'both'."))
 
   #check that required columns exist in detections
   missing_cols <- setdiff(c("animal_id", "detection_timestamp_utc"), names(dtc))
@@ -211,26 +213,26 @@ summarize_detections <- function(det, location_col = "glatos_array",
     stop("Column 'detection_timestamp_utc' in 'dtc' must be of class POSIXct.")
   }  
 
-  if(!is.null(receiver_locs)){
-
-    #check that location_col exists in receiver locations
-    if(!(location_col %in% names(receiver_locs))){
-      stop(paste0("Column ", location_col, " is missing in 'receiver_locs'.\n",
-        "Double check input argument 'location_col'."))
-    } 
-    rcv <- data.table::as.data.table(receiver_locs)
-
-    #get mean receiver locations from receiver_locs
-    mean_locs <- rcv[ , list(mean_lat = mean(deploy_lat), 
-                            mean_lon = mean(deploy_long)), 
-                            by = location_col]
-  } else {
+  if(!is.null(receiver_locs)){
+
+    #check that location_col exists in receiver locations
+    if(!(location_col %in% names(receiver_locs))){
+      stop(paste0("Column ", location_col, " is missing in 'receiver_locs'.\n",
+        "Double check input argument 'location_col'."))
+    } 
+    rcv <- data.table::as.data.table(receiver_locs)
+
+    #get mean receiver locations from receiver_locs
+    mean_locs <- rcv[ , list(mean_lat = mean(deploy_lat),
+                            mean_lon = mean(deploy_long)),
+                            by = location_col]
+  } else {
     #get mean receiver locations from dtc
-    mean_locs <- dtc[ , list(mean_lat = mean(deploy_lat), 
-      mean_lon = mean(deploy_long)), 
-      by = location_col]    
-  }
-
+    mean_locs <- dtc[ , list(mean_lat = mean(deploy_lat),
+      mean_lon = mean(deploy_long)), 
+      by = location_col]
+  }
+
   if(!is.null(animals)){
 
     #read animal_id vector from data frame if passed as data frame
@@ -263,15 +265,15 @@ summarize_detections <- function(det, location_col = "glatos_array",
     det_sum <- loc_summary
   } 
 
-  if(summ_type == "animal"){
-    #summarize fish detections
-    anim_summary <- dtc[ , list(num_locs = data.table::uniqueN(location_col), 
-                                num_dets = .N,
-      first_det = min(detection_timestamp_utc),
-      last_det = max(detection_timestamp_utc),
-      locations = paste(sort(unique(location_col)), collapse = " ")),
-      by = animal_id]
-
+  if(summ_type == "animal"){
+    #summarize fish detections
+    anim_summary <- dtc[ , list(num_locs = data.table::uniqueN(location_col),
+                                num_dets = .N,
+      first_det = min(detection_timestamp_utc),
+      last_det = max(detection_timestamp_utc),
+      locations = paste(sort(unique(dtc[[location_col]])), collapse = " ")),
+      by = animal_id]
+
     #add animals not detected
     anim_summary <- merge(anim_summary, 
        data.table::data.table(animal_id = animals), by = "animal_id", all.y = TRUE)