COntinuing build-out and some tweaks.

Author: jackVanish

R/ato_dep_from_glatos.R

@@ -0,0 +1,123 @@
+ato_dep_from_glatos <- function(glatos_file, type = "meta") {
+  # Read in the file we've been given if we haven't been handed a dataframe.
+  if (!is.data.frame(glatos_file)) {
+    # Grab the extension.
+    extension <- tools::file_ext(otn_detections)
+    # If it's a parquet, read it in as one...
+    if (extension == "parquet") {
+      otn_file <- read_parquet(otn_detections)
+    } else if (extension == "xlsx" || extension == "xls") {
+      otn_file <- read_excel(otn_detections)
+    } else {
+      # Otherwise bring it in as a CSV.
+      otn_file <- read.csv(otn_detections, na = c("", "null", "NA"))
+    }
+  }
+  
+  # If we've been given a metadata file, we read it in as one.
+  if (type == "meta") {
+    # This we can pull directly from the metadata.
+    dep <- make_dep(
+      receiver_model = otn_file$INS_MODEL_NO,
+      receiver_serial = otn_file$INS_SERIAL_NO,
+      receiver_codeset = otn_file$CODE_SET,
+      deploy_location = otn_file$STATION_NO,
+      deploy_datetime = otn_file$DEPLOY_DATE_TIME,
+      deploy_lat = otn_file$DEPLOY_LAT,
+      deploy_lon = otn_file$DEPLOY_LON,
+      deploy_z = otn_file$BOTTOM_DEPTH,
+      recover_datetime = otn_file$RECOVER_DATE_TIME,
+      recover_lat = otn_file$RECOVER_LAT,
+      recover_lon = otn_file$RECOVER_LON,
+      transmitter = otn_file$TRANSMITTER,
+      transmitter_manufacturer = NA_character_,
+      transmitter_ping_rate = NA_character_,
+      transmitter_model = otn_file$TRANSMIT_MODEL,
+      transmitter_serial = NA_character_
+    )
+    return(dep)
+  } else if (type == "extract") {
+    # In the case where we don't have a metadata file to work with, we can use a similar setup to how we derive
+    # receiver data from detection extracts for IMOS.
+    
+    # To start, we will filter the releases out of our detections dataframe.
+    no_releases <- otn_file %>% filter(receiver != "release")
+    
+    # The first thing we need to do is gin up some inferred min and max deployment dates.
+    # We'll use the following code to do so.
+    rcvr_grouped <- NULL
+    
+    # Start by grouping the detections by station, and ordering them by date.
+    rcvr_grouped_list <- no_releases %>%
+      group_by(station) %>%
+      arrange(dateCollectedUTC, .by_group = TRUE)
+    
+    # Set min date and max date to null.
+    minDate <- NULL
+    maxDate <- NULL
+    
+    # Create a 'lead' dataframe for us to compare our current dataframe against.
+    rcvr_grouped_list_next <- lead(rcvr_grouped_list)
+    
+    # For each row in the list
+    for (i in 1:nrow(rcvr_grouped_list)) {
+      row <- rcvr_grouped_list[i, ]
+      
+      # If minDate is null, set it to the currently available date. minDate being null implies that
+      # we're just starting with this station (see where it's set to Null, below)
+      if (is.null(minDate)) {
+        minDate <- row$dateCollectedUTC
+      }
+      
+      # Get the next row from our "lead" frame.
+      nextStation <- rcvr_grouped_list_next[i, ]
+      
+      # If our next station is Null (i.e, we're at the end of the frame), or the next station is different from
+      # the current one (i.e, we've reached the end of this time chunk)...
+      if (is.na(nextStation$receiver) || nextStation$receiver != row$receiver) {
+        # Set Maxdate to our current date.
+        maxDate <- row$dateCollectedUTC
+        
+        # Add the min and max dates as entries in the row.
+        row <- row %>% mutate(
+          minDetectionDate = minDate,
+          maxDetectionDate = maxDate
+        )
+        
+        # if rcvr_group hasn't been instantiated yet, use row to create it.
+        if (is.null(rcvr_grouped)) {
+          rcvr_grouped <- row
+        }
+        # Otherwise, just add the row to the group of receivers.
+        else {
+          rcvr_grouped <- rbind(rcvr_grouped, row)
+        }
+        
+        # reset our min and max date to null so the next group will be handled properly.
+        minDate <- NULL
+        maxDate <- NULL
+      }
+    }
+    
+    dep <- make_dep(
+      receiver_model = NA_character_,
+      receiver_serial = as.integer(rcvr_grouped$receiver),
+      receiver_codeset = rcvr_grouped$codeSpace,
+      deploy_location = rcvr_grouped$station,
+      deploy_datetime = as.POSIXct(NA_real_),
+      deploy_lat = rcvr_grouped$decimalLatitude,
+      deploy_lon = rcvr_grouped$decimalLongitude,
+      recover_datetime = as.POSIXct(NA_real_),
+      recover_lat = NA_real_,
+      recover_lon = NA_real_,
+      transmitter = NA_character_,
+      transmitter_model = NA_character_,
+      transmitter_serial = NA_integer_,
+      tz = "UTC"
+    )
+    
+    return(dep)
+  } else {
+    message("Invalid type specified. Use either 'meta' (if loading from a metadata file) or 'extract' (if deriving deployment metadata from a detection extract).")
+  }
+}

R/ato_tag_from_otn.R

@@ -24,7 +24,7 @@ ato_tag_from_otn <- function(otn_file, type = "meta") {
       ping_rate = NA_real_, # ???
       ping_variation = NA_real_, # ???
       serial = otn_file$TAG_SERIAL_NUMBER,
-      transmitter = NA_character_, # ???
+      transmitter = paste(otn_file$TAG_CODE_SPACE, "-", TAG_ID_CODE)
       activation_datetime = as.POSIXct(otn_file$TAG_ACTIVATION_DATE),
       battery_life = otn_file$EST_TAG_LIFE,
       sensor_type = NA_character_, # ???