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Pull changes from camtraptor 0.27, see #344

DESCRIPTION

@@ -35,6 +35,7 @@ BugReports: https://github.com/inbo/camtraptor/issues
 Depends: 
     R (>= 3.5.0)
 Imports:
+    activity,
     assertthat,
     camtrapdp,
     dplyr (>= 1.1.0),
@@ -45,6 +46,7 @@ Imports:
     leaflet,
     lifecycle,
     lubridate,
+    overlap,
     purrr,
     RColorBrewer,
     readr,

NEWS.md

@@ -24,6 +24,10 @@ This is a major release that updates the internal data model to Camtrap DP 1.0 a
 - Function `filter_out_timelapse()` allows to filter out timelapse observations (#306). See [`camtrapdp::filter_out_timelapse()`](https://inbo.github.io/camtrapdp/reference/filter_out_timelapse.html).
 - File `CITATION.cff` added to the package (#345).
 
+# camtraptor 0.27.0
+
+- `get_record_table()` returns now 4 new columns: `longitude`, `latitude` (deployment coordinates), `clock` (clock time of the observation in radians) and `solar` (sun time of the observation in radians) (#341).
+
 # camtraptor 0.26.0
 
 - `get_custom_effort()` returns now the effort for each deployment separately (#333). The returned data frame has two new columns: `deploymentID` and `locationName`.

R/camtrapR_recordTable.R

@@ -52,6 +52,10 @@
 #'   as defined in column `filePath` of `media`.
 #'   - `Filename`: List, file names of the images linked to the given record,
 #'   as defined in column `fileName` of `media`.
+#'   - `Latitude`: Numeric, latitude of the station, based on `deploymentID` of the observations.
+#'   - `Longitude`: Numeric, longitude of the station, based on `deploymentID` of the observations.
+#'   - `clock`: Numeric, clock time in radians.
+#'   - `solar`: Numeric, solar time in radians. Calculated using `overlap::sunTime`, which essentially uses the approach described in [Nouvellet et al. (2012)](https://doi.org/10.1111/j.1469-7998.2011.00864.x).
 #' @inheritParams n_species
 #' @family camtrapR-derived functions
 #' @export
@@ -172,6 +176,10 @@ camtrapR_recordTable <- function(x,
   )
 
   # remove observations of unidentified individuals
+  # Add coordinates to observations
+  x <- add_coordinates(x)
+
+  # Remove observations of unidentified individuals
   obs <- observations(x) %>%
     dplyr::filter(!is.na(.data$scientificName))
 
@@ -277,6 +285,18 @@ camtrapR_recordTable <- function(x,
     )) %>%
     dplyr::ungroup()
 
+  # Add clock time in radians
+  record_table <- record_table %>%
+    dplyr::mutate(clock = activity::gettime(.data$timestamp))
+  # Add solar time in radians
+  matrix_coords <- matrix(c(record_table$longitude, record_table$latitude),
+                          ncol = 2)
+  record_table <- record_table %>%
+    dplyr::mutate(solar = overlap::sunTime(.data$clock,
+                                           .data$timestamp,
+                                           matrix_coords))
+
+  # Finalize `record_table`
   record_table <- record_table %>%
     dplyr::rename(Station := !!stationCol,
       Species = "scientificName",

tests/testthat/test-camtrapR_recordTable.R

@@ -70,6 +70,14 @@ test_that("input of camtrapR_recordTable, removeDuplicateRecords, is checked pro
     removeDuplicateRecords = NA
   ))
 })
+test_that("warning is returned if some observations have no timestamp", {
+  mica_no_timestamp <- mica
+  mica_no_timestamp$data$observations$timestamp[3:5] <- NA
+  expect_warning(
+    get_record_table(mica_no_timestamp),
+    "Some observations have no timestamp and will be removed."
+  )
+})
 
 test_that("right columns are returned", {
   skip_if_offline()
@@ -88,7 +96,11 @@ test_that("right columns are returned", {
       "delta.time.hours",
       "delta.time.days",
       "Directory",
-      "FileName"
+      "FileName",
+      "latitude",
+      "longitude",
+      "clock",
+      "solar"
     )
   )
 })
@@ -201,8 +213,7 @@ test_that(
         by = "sequenceID"
       )
     expect_equal(output$len, output$n_media)
-  }
-)
+})
 
 test_that(paste(
   "removeDuplicateRecords allows removing duplicates,",
@@ -250,19 +261,31 @@ test_that(paste(
   )
 })
 
+test_that("clock is always in the range [0, 2*pi]", {
+  clock_values <- get_record_table(mica) %>%
+    dplyr::pull(clock)
+  expect_true(all(clock_values >= 0))
+  expect_true(all(clock_values <= 2 * pi))
+})
+
+test_that("solar is always in the range [0, 2*pi]", {
+  solar_values <- get_record_table(mica) %>%
+    dplyr::pull(solar)
+  expect_true(all(solar_values >= 0))
+  expect_true(all(solar_values <= 2 * pi))
+})
+
 test_that("get_record_table() is deprecated and calls camtrapR_recordTable()", {
   skip_if_offline()
   x <- example_dataset()
   lifecycle::expect_deprecated(get_record_table(x))
 })
 
 test_that(
-  "output of get_record_table() is the same as camtrapR_recordTable()",
-  {
+  "output of get_record_table() is the same as camtrapR_recordTable()", {
     skip_if_offline()
     x <- example_dataset()
     expect_identical(
       suppressWarnings(get_record_table(x)),
       camtrapR_recordTable(x))
-  }
-)
+})