fasttime -> fast_strptime. Closes ocean-tracking-network#211.

NAMESPACE

@@ -99,7 +99,7 @@ importFrom(graphics,par)
 importFrom(graphics,points)
 importFrom(graphics,symbols)
 importFrom(graphics,text)
-importFrom(lubridate,parse_date_time)
+importFrom(lubridate,fast_strptime)
 importFrom(magrittr,"%>%")
 importFrom(stats,approx)
 importFrom(stats,dnorm)

R/load-read_glatos_detections.r

@@ -16,8 +16,8 @@
 #'   never need to set this argument (`NULL` should work).
 #'
 #' @details Data are loaded using [fread][data.table::fread] and timestamps are
-#' coerced to POSIXct using [fastPOSIXct][fasttime::fastPOSIXct]. All times must
-#' be in UTC timezone per GLATOS standard.
+#' coerced to POSIXct using [fast_strptime][lubridate::fast_strptime]. All times
+#' must be in UTC timezone per GLATOS standard.
 #'
 #' @details Column `animal_id` is considered a required column by many other
 #'   functions in this package, so it will be created if any records are `NULL`.
@@ -40,7 +40,7 @@
 #'
 #' det <- read_glatos_detections(det_file)
 #'
-#' @importFrom lubridate parse_date_time
+#' @importFrom lubridate fast_strptime
 #'
 #' @export
 read_glatos_detections <- function(det_file, version = NULL) {
@@ -84,16 +84,13 @@ read_glatos_detections <- function(det_file, version = NULL) {
       na.strings = c("", "NA")
     )
 
-    # coerce timestamps to POSIXct; note that with fastPOSIXct raw
-    #  timestamp must be in UTC; and tz argument sets the tzone attr only
-    options(lubridate.fasttime = TRUE)
+    # coerce timestamps to POSIXct
     for (j in timestamp_cols) {
       data.table::set(dtc,
         j = glatos_detection_schema[[vversion]]$name[j],
-        value = lubridate::parse_date_time(
+        value = lubridate::fast_strptime(
           dtc[[glatos_detection_schema[[vversion]]$name[j]]],
-          orders = "ymd HMS",
-          tz = "UTC"
+          format = "%Y-%m-%d %H:%M:%S", tz = "UTC", lt = FALSE
         )
       )
     }

R/load-read_glatos_receivers.r

@@ -15,7 +15,7 @@
 #'   `"1.0"`. Any other values will trigger an error.
 #'
 #' @details Data are loaded using [fread][data.table::fread] and timestamps are
-#'   coerced to POSIXct using [fastPOSIXct][fasttime::fastPOSIXct]. All
+#'   coerced to POSIXct using [fast_strptime][lubridate::fast_strptime]. All
 #'   timestamps must be 'YYYY-MM-DD HH:MM' format and in UTC timezone per GLATOS
 #'   standard.
 #'
@@ -36,7 +36,7 @@
 #'
 #' rcv <- read_glatos_receivers(rec_file)
 #'
-#' @importFrom lubridate parse_date_time
+#' @importFrom lubridate fast_strptime
 #'
 #' @export
 read_glatos_receivers <- function(rec_file, version = NULL) {
@@ -80,16 +80,13 @@ read_glatos_receivers <- function(rec_file, version = NULL) {
     # read data
     rec <- data.table::fread(rec_file, sep = ",", colClasses = col_classes)
 
-    # coerce timestamps to POSIXct; note that with fastPOSIXct raw
-    #  timestamp must be in UTC; and tz argument sets the tzone attr only
-    options(lubridate.fasttime = TRUE)
+    # coerce timestamps to POSIXct
     for (j in timestamp_cols) {
       data.table::set(rec,
         j = glatos_receivers_schema[[ver_txt]]$name[j],
-        value = lubridate::parse_date_time(
+        value = lubridate::fast_strptime(
           rec[[glatos_receivers_schema[[ver_txt]]$name[j]]],
-          orders = "ymd HMS",
-          tz = "UTC"
+          format = "%Y-%m-%d %H:%M:%S", tz = "UTC", lt = FALSE
         )
       )
     }

R/load-read_otn_deployments.R

@@ -18,7 +18,7 @@
 #'
 #' @details
 #' Data are loaded using [data.table::fread()] package and timestamps
-#' are coerced to POSIXct using the [fasttime::fastPOSIXct()]. All
+#' are coerced to POSIXct using [lubridate::fast_strptime()]. All
 #' times must be in UTC timezone per GLATOS standard.
 #'
 #' @details
@@ -39,7 +39,7 @@
 #' dep <- read_otn_deployments(deployment_file)
 #' }
 #'
-#' @importFrom lubridate parse_date_time
+#' @importFrom lubridate fast_strptime
 #' @importFrom tidyr extract
 #' @importFrom dplyr mutate
 #' @importFrom magrittr "%>%"
@@ -60,8 +60,7 @@ read_otn_deployments <- function(deployment_file,
     na.strings = c("", "NA")
   )
 
-  # coerce timestamps to POSIXct; note that with fastPOSIXct raw
-  #  timestamp must be in UTC; and tz argument sets the tzone attr only
+  # coerce timestamps to POSIXct
   dtc <- dtc %>% tidyr::extract(deploy_date_col, into = "deploy_date", regex = "(\\d+-\\d+-\\d+)")
   dtc <- dtc %>% tidyr::extract(recovery_date_col, into = "recovery_date", regex = "(\\d+-\\d+-\\d+)")
   dtc <- dtc %>% tidyr::extract(last_download_col, into = "last_download", regex = "(\\d+-\\d+-\\d+)")
@@ -70,7 +69,9 @@ read_otn_deployments <- function(deployment_file,
   for (j in timestamp_cols) {
     data.table::set(dtc,
       j = otn_deployments_schema$name[j],
-      value = lubridate::parse_date_time(dtc[[otn_deployments_schema$name[j]]], orders = "ymd", tz = "UTC")
+      value = lubridate::fast_strptime(
+        dtc[[otn_deployments_schema$name[j]]],
+        format = "%Y-%m-%d %H:%M:%S", tz = "UTC", lt = FALSE)
     )
   }
   # coerce dates to date

R/load-read_otn_detections.r

@@ -9,7 +9,7 @@
 #'
 #' @details
 #' Data are loaded using [data.table::fread()] package and timestamps
-#' are coerced to POSIXct using the [fasttime::fastPOSIXct()]. All
+#' are coerced to POSIXct using [lubridate::fast_strptime()]. All
 #' times must be in UTC timezone per GLATOS standard.
 #'
 #' @details
@@ -28,7 +28,7 @@
 #' )
 #' det <- read_otn_detections(det_file)
 #'
-#' @importFrom lubridate parse_date_time
+#' @importFrom lubridate fast_strptime
 #'
 #' @export
 read_otn_detections <- function(det_file) {
@@ -38,11 +38,11 @@ read_otn_detections <- function(det_file) {
   timestamp_cols <- which(col_classes == "POSIXct")
   date_cols <- which(col_classes == "Date")
   col_classes[c(timestamp_cols, date_cols)] <- "character"
-
+  
   # read data, suppressWarnings because some columns could be missing
   dtc <- suppressWarnings(data.table::fread(det_file,
-    sep = ",", colClasses = col_classes,
-    na.strings = c("", "NA")
+                                            sep = ",", colClasses = col_classes,
+                                            na.strings = c("", "NA")
   ))
   # This check is for non-matched detection extracts. They are missing some required columns, this attempts to create them.
   # More info on OTN detection extracts here: https://members.oceantrack.org/data/otn-detection-extract-documentation-matched-to-animals
@@ -53,13 +53,14 @@ read_otn_detections <- function(det_file) {
     dtc$tagname <- dtc$fieldnumber
     dtc$codespace <- purrr::map(dtc$fieldnumber, get_codemap)
   }
-  # coerce timestamps to POSIXct; note that with fastPOSIXct raw
-  #  timestamp must be in UTC; and tz argument sets the tzone attr only
-  options(lubridate.fasttime = TRUE)
+  # coerce timestamps to POSIXct
   for (j in timestamp_cols) {
     data.table::set(dtc,
-      j = otn_detection_schema$name[j],
-      value = lubridate::parse_date_time(dtc[[otn_detection_schema$name[j]]], orders = "ymd HMS", tz = "UTC")
+                    j = otn_detection_schema$name[j],
+                    value = lubridate::fast_strptime(
+                      dtc[[otn_detection_schema$name[j]]], 
+                      format = "%Y-%m-%d %H:%M:%S", tz = "UTC", lt = FALSE
+                    )
     )
   }
   # coerce dates to date