Merge pull request #31 from mhpob/issue-10

Deal with Excel date-times in deployment data sheets

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: otndo
 Title: Understand your OTN data
-Version: 0.2.1
+Version: 0.2.2
 Authors@R: 
     person("Michael", "O'Brien", , "mike@obrien.page", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-1420-6395"))

NEWS.md

@@ -1,4 +1,8 @@
 ## otndo 0.2
+### v 0.2.2
+* Fixed behavior where `clean_otn_deployment` would return different columns if there was no internal transmitter logged. [Issue #10](https://github.com/mhpob/otndo/issues/10); [d58e2d4](https://github.com/mhpob/otndo/pull/31/commits/d58e2d46e05aed7ba4acc08b8d02672b28d79804)
+* Add internal function (`convert_times`) that checks for Excel-formatted date-times and converts accordingly [f13f360](https://github.com/mhpob/otndo/pull/31/commits/f13f360fe5e4438b6ba668039a6c94f04eeafe60)
+
 ### v 0.2.1
 
 * Fleshes out tests to get to 100% coverage (for now!). Note that this is an overestimate as I can't actually get into the QMD files to test.

R/utilities_make.R

@@ -5,7 +5,7 @@
 #' @param files Character. File paths of files to be unzipped or written to a directory
 #' @param temp_dir Character. File path of temporary directory
 #' @param detection_file Character. File path of detections.
-#'
+#' @param date_time Character or numeric. Date-time to convert.
 #'
 #' @name utilities-make
 #' @keywords internal
@@ -59,22 +59,8 @@ clean_otn_deployment <- function(deployment) {
   deployment <- deployment[!is.na(deployment$deploy_date_time), ]
   deployment <- deployment[!deployment$recovered %in% c("l", "failed", NA), ]
 
-  deployment$deploy_date_time <- as.POSIXct(
-    deployment$deploy_date_time,
-    tz = "UTC",
-    tryFormats = c(
-      "%Y-%m-%dT%H:%M:%S",
-      "%Y-%m-%d %H:%M:%S"
-    )
-  )
-  deployment$recover_date_time <- as.POSIXct(
-    deployment$recover_date_time,
-    tz = "UTC",
-    tryFormats = c(
-      "%Y-%m-%dT%H:%M:%S",
-      "%Y-%m-%d %H:%M:%S"
-    )
-  )
+  deployment$deploy_date_time <- convert_times(deployment$deploy_date_time)
+  deployment$recover_date_time <- convert_times(deployment$recover_date_time)
 
   deployment <- deployment[!is.na(deployment$deploy_date_time) &
     !is.na(deployment$recover_date_time), ]
@@ -86,23 +72,45 @@ clean_otn_deployment <- function(deployment) {
 
   if ("transmitter" %in% names(deployment)) {
     deployment$internal_transmitter <- deployment$transmitter
-    deployment[, c(
-      "stationname", "receiver", "internal_transmitter",
-      "deploy_date_time", "deploy_lat", "deploy_long",
-      "recover_date_time"
-    )]
   } else {
-    (
-      deployment[, c(
-        "stationname", "receiver",
-        "deploy_date_time", "deploy_lat", "deploy_long",
-        "recover_date_time"
-      )]
-    )
+    deployment$internal_transmitter <- NA
   }
+
+  deployment[, c(
+    "stationname", "receiver", "internal_transmitter",
+    "deploy_date_time", "deploy_lat", "deploy_long",
+    "recover_date_time"
+  )]
 }
 
 
+#' @rdname utilities-make
+#' @keywords internal
+convert_times <- function(date_time) {
+  check_times <- function(x) {
+    # check if Excel format
+    #   Assumes that it starts with 5 numbers
+    if (grepl("^\\d{5}", x)) {
+      as.POSIXct(
+        as.numeric(x) * (60 * 60 * 24),
+        tz = "UTC",
+        origin = "1899-12-30"
+      )
+    } else {
+      as.POSIXct(
+        x,
+        tz = "UTC",
+        tryFormats = c(
+          "%Y-%m-%dT%H:%M:%S",
+          "%Y-%m-%d %H:%M:%S"
+        )
+      )
+    }
+  }
+
+  do.call("c", lapply(date_time, check_times))
+}
+
 #' @rdname utilities-make
 #' @keywords internal
 provided_file_unzip <- function(files, temp_dir) {

tests/testthat/test-clean_otn_deployment.R

@@ -190,7 +190,8 @@ test_that("Correct names when no internal transmitter columns", {
   expect_named(
     clean_otn_deployment(deployment_sheet1),
     c(
-      "stationname", "receiver", "deploy_date_time", "deploy_lat", "deploy_long",
+      "stationname", "receiver", "internal_transmitter",
+      "deploy_date_time", "deploy_lat", "deploy_long",
       "recover_date_time"
     )
   )

tests/testthat/test-convert_times.R

@@ -0,0 +1,54 @@
+test_datetime <- as.POSIXct("2020-04-09T11:04:59",
+  tz = "UTC",
+  format = "%Y-%m-%dT%H:%M:%S"
+)
+
+test_that("converts ISO 8601", {
+  expect_equal(
+    convert_times("2020-04-09T11:04:59"),
+    test_datetime
+  )
+})
+
+
+
+
+test_that("converts space-separated date-times", {
+  expect_equal(
+    convert_times("2020-04-09 11:04:59"),
+    test_datetime
+  )
+})
+
+
+
+
+test_that("converts Excel numeric", {
+  expect_equal(
+    convert_times(43930.461793981),
+    test_datetime
+  )
+})
+
+
+
+
+test_that("converts Excel character", {
+  expect_equal(
+    convert_times("43930.461793981"),
+    test_datetime
+  )
+})
+
+
+
+
+test_that("works with vectors", {
+  expect_equal(
+    convert_times(c(
+      "2020-04-09T11:04:59", "2020-04-09 11:04:59",
+      "43930.461793981", 43930.461793981
+    )),
+    rep(test_datetime, 4)
+  )
+})