Glatos otn animals

NAMESPACE

@@ -1,12 +1,14 @@
 # Generated by roxygen2: do not edit by hand
 
+export(glatos_to_ato)
 export(imos_otn_column_map)
 export(imos_to_otn_detections)
 export(imos_to_otn_receivers)
 export(imos_to_otn_tags)
 export(map_otn_file)
 export(otn_imos_column_map)
 export(otn_imos_new_style_column_map)
+export(otn_to_ato)
 export(rollup)
 importFrom(dplyr,'%>%')
 importFrom(dplyr,arrange)

R/ato_ani_from_glatos.R

@@ -0,0 +1,20 @@
+ato_ani_from_glatos <- function(glatos_file) {
+  # Load the data file we've been given- probably detections data since published glatos data will only have detections and receivers.
+  glatos_data <- load_file(glatos_file)
+
+  # We don't really have the option here to get this from an 'animal metadata' file so we're always going to be deriving.
+  ani <- make_ani(
+    animal = as.character(glatos_data$animal_id),
+    capture_location = as.character(glatos_data$capture_location),
+    capture_datetime = as.POSIXct(glatos_data$glatos_caught_date),
+    capture_lat = NA_real_,
+    capture_lon = NA_real_,
+    release_loaction = glatos_data$release_location,
+    release_datetime = as.POSIXct(glatos_data$utc_release_date_time),
+    release_lat = glatos_data$release_latitude,
+    release_lon = glatos_data$release_longitude,
+    tz = "UTC"
+  )
+
+  return(ani)
+}

R/ato_ani_from_otn.R

@@ -0,0 +1,18 @@
+ato_ani_from_otn <- function(otn_file) {
+  # Import the file we've got.
+  otn_data <- load_file(otn_file)
+
+  # OTN doesn't have a bespoke animal file so we'll take what we get from the tag file.
+  ani <- make_ani(
+    animal = otn_data$ANIMAL_ID,
+    capture_location = otn_data$CAPTURE_LOCATION,
+    capture_datetime = as.POSIXct(NA_real_),
+    capture_lat = otn_data$CAPTURE_LAT,
+    capture_lon = otn_data$CAPTURE_LON,
+    release_location = otn_data$RELEASE_LOCATION,
+    release_datetime = as.POSIXct(otn_data$UTC_RELEASE_DATE_TIME),
+    release_lat = otn_data$RELEASE_LATITUDE,
+    release_lon = otn_data$RELEASE_LONGITUDE,
+    tz = "UTC",
+  )
+}

R/glatos_to_ato.R

@@ -1,6 +1,6 @@
 ##' @title Convert GLATOS detection data to an ATO object.
 ##'
-##' @description Takes a GLATOS detection sheet and optionally receiver/tag metadata and returns an ATO object.
+##' @description Takes a GLATOS detection sheet and optionally receiver metadata and returns an ATO object.
 ##'
 ##' @param otn_detections The dataframe containing detection information.
 ##' @param otn_receivers The dataframe containing receiver information.
@@ -15,7 +15,7 @@
 ##' @export
 ##'
 
-glatos_to_ato <- function(glatos_detections, glatos_receivers = "", glatos_tags = "") {
+glatos_to_ato <- function(glatos_detections, glatos_receivers = "") {
   glatos_detections <- load_file(glatos_detections)
 
   # Now we have a dataframe we can start loading into an ATO object. Let's make an instance of the object.
@@ -34,9 +34,8 @@ glatos_to_ato <- function(glatos_detections, glatos_receivers = "", glatos_tags
   GLATOS_ATO <- add(GLATOS_ATO, det)
 
   # I used to have a 'derive' argument as in some of the original OTN-to-IMOS functions but then I realised it was safer to just
-  # automatically try to derive receiver/tag metadata from the extract if no file is supplied.
+  # automatically try to derive receiver metadata from the extract if no file is supplied.
   dep <- ""
-  tag <- ""
 
   # In both cases, if a file is supplied, we'll make the metadata objects using the information therein;
   # otherwise, we'll attempt to make approximately correct receiver/tag metadata from only what's contained in
@@ -49,15 +48,11 @@ glatos_to_ato <- function(glatos_detections, glatos_receivers = "", glatos_tags
 
   GLATOS_ATO <- add(GLATOS_ATO, dep)
 
-  # In the detection extract zip I had for reference there didn't seem to be a bespoke Tag metadata file. I'll leave this structure here in case we need to build it out further but I think it's only ever going to flop into the else.
-  # if (glatos_tags != "") {
-  #  tag <- ato_tag_from_glatos(glatos_tags, type = "meta")
+  # Tag information is not part of what's distributed in glatos publications so we can neither load it nor meaningfully derive it.
 
-  # } else {
-  #  tag <- ato_tag_from_glatos(glatos_detections, type = "extract")
-  # }
+  ani <- ato_ani_from_glatos(glatos_detections)
 
-  # GLATOS_ATO <- add(GLATOS_ATO, tag)
+  GLATOS_ATO <- add(GLATOS_ATO, ani)
 
   return(GLATOS_ATO)
 }

R/otn_to_ato.R

@@ -63,6 +63,10 @@ otn_to_ato <- function(otn_detections, otn_receivers = "", otn_tags = "") {
 
   if (otn_tags != "") {
     tag <- ato_tag_from_otn(otn_tags, type = "meta")
+    # If we have a tag metadata file, we can derive an animal object; if we don't, there's hardly enough information to bother,
+    # and if people are so inclined they can add it manually through the ATO's default functions and ATools.
+    ani <- ato_ani_from_otn(otn_tags)
+    OTN_ATO <- add(OTN_ATO, ani)
   } else {
     tag <- ato_tag_from_otn(otn_detections, type = "extract")
   }