detection and deployment load-in are more or less working, though I think I can squeeze more data out of them.

Author: jackVanish

R/ato_dep_from_glatos.R

@@ -3,7 +3,7 @@ ato_dep_from_glatos <- function(glatos_file, glatos_detection_data = "", type =
   glatos_data <- load_file(glatos_file)
 
   #Detection data is an optional pass-through but if we have it, we can join it to the receiver dataframe to get additional transmitter data. 
-  if (glatos_detection_data != "" && is.data.frame(glatos_detection_data) {
+  if (glatos_detection_data != "" && is.data.frame(glatos_detection_data)) {
     #TODO: Join the two dataframes to get transmitter data passed through.
   }
 
@@ -15,16 +15,17 @@ ato_dep_from_glatos <- function(glatos_file, glatos_detection_data = "", type =
       receiver_serial = glatos_data$ins_serial_no,
       receiver_codeset = glatos_data$code_map,
       deploy_location = glatos_data$station,
-      deploy_datetime = glatos_data$deploy_date_time,
+      deploy_datetime = as.POSIXct(glatos_data$deploy_date_time),
+      tz = "UTC", 
       deploy_lat = glatos_data$deploy_lat,
       deploy_lon = glatos_data$deploy_long,
       deploy_z = glatos_data$bottom_depth,
-      recover_datetime = glatos_data$recover_date_time, # ??? We might be able to get this from another part of the sheet
+      recover_datetime = as.POSIXct(glatos_data$recover_date_time),
       recover_lat = glatos_data$recover_lat,
       recover_lon = glatos_data$recover_long,
       transmitter = NA_character_, # ???
       transmitter_manufacturer = NA_character_, # ???
-      transmitter_ping_rate = NA_character_, # ???
+      transmitter_ping_rate = as.numeric(glatos_data$glatos_ins_frequency), #is this accurate? I think this mapping is right.
       transmitter_model = NA_character_, # ???
       transmitter_serial = NA_integer_
     )
@@ -97,13 +98,13 @@ ato_dep_from_glatos <- function(glatos_file, glatos_detection_data = "", type =
       receiver_serial = as.integer(rcvr_grouped$receiver_sn),
       receiver_codeset = NA_character_,
       deploy_location = rcvr_grouped$station,
-      deploy_datetime = rcvr_grouped$minDetectionDate,
+      deploy_datetime = as.POSIXct(rcvr_grouped$minDetectionDate),
       deploy_lat = rcvr_grouped$deploy_lat,
-      deploy_lon = rcvr_grouped$deploy_lon,
-      recover_datetime = rcvr_grouped$maxDetectionDate,
+      deploy_lon = rcvr_grouped$deploy_long,
+      recover_datetime = as.POSIXct(rcvr_grouped$maxDetectionDate),
       recover_lat = NA_real_,
       recover_lon = NA_real_,
-      transmitter = paste(rcvr_grouped$transmitter_code_space, "-", rcvr_grouped$transmitter_id),
+      transmitter = paste(rcvr_grouped$transmitter_codespace, "-", rcvr_grouped$transmitter_id, sep=""),
       transmitter_model = NA_character_,
       transmitter_serial = rcvr_grouped$transmitter_id,
       tz = "UTC"

R/glatos_to_ato.R

@@ -26,7 +26,7 @@ glatos_to_ato <- function(glatos_detections, glatos_receivers = "", glatos_tags
     datetime = as.POSIXct(glatos_detections$detection_timestamp_utc),
     frac_second = NA_real_,
     receiver_serial = as.integer(glatos_detections$receiver_sn),
-    transmitter = NA_character_ #Might have to synthesize this from other fields
+    transmitter = paste(glatos_detections$transmitter_codespace, "-", glatos_detections$transmitter_id, sep=""), #Might have to synthesize this from other fields
     sensor_value = as.numeric(glatos_detections$sensor_value),
     tz = "UTC"
   )
@@ -50,14 +50,14 @@ 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")
+  #if (glatos_tags != "") {
+  #  tag <- ato_tag_from_glatos(glatos_tags, type = "meta")
 
-  } else {
-    tag <- ato_tag_from_glatos(glatos_detections, type = "extract")
-  }
+  #} else {
+  #  tag <- ato_tag_from_glatos(glatos_detections, type = "extract")
+  #}
 
-  GLATOS_ATO <- add(GLATOS_ATO, tag)
+  #GLATOS_ATO <- add(GLATOS_ATO, tag)
 
   return(GLATOS_ATO)
 }