From 201737e8ae77f768db308e65ecb8394603add1b2 Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Wed, 8 Nov 2023 16:45:12 +0100
Subject: [PATCH 01/35] Fix #279

---
 R/get_record_table.R | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/R/get_record_table.R b/R/get_record_table.R
index 13c06024..ac808915 100644
--- a/R/get_record_table.R
+++ b/R/get_record_table.R
@@ -265,11 +265,13 @@ get_record_table <- function(package = NULL,
       Species = "scientificName",
       DateTimeOriginal = "timestamp",
       Directory = "filePath",
-      FileName = "fileName"
+      FileName = "fileName",
+      n = "count"
     ) %>%
     dplyr::select(
       "Station",
       "Species",
+      "n",
       "DateTimeOriginal",
       "Date",
       "Time",

From d58f547fb1acef02e5a4e1270e56017da19534fb Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Wed, 8 Nov 2023 16:45:44 +0100
Subject: [PATCH 02/35] Add test about expected columns returned

---
 tests/testthat/test-get_record_table.R | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/tests/testthat/test-get_record_table.R b/tests/testthat/test-get_record_table.R
index 9e0193f8..2d84638f 100644
--- a/tests/testthat/test-get_record_table.R
+++ b/tests/testthat/test-get_record_table.R
@@ -57,6 +57,24 @@ test_that("input of get_record_table, removeDuplicateRecords, is checked properl
   ))
 })
 
+test_that("right columns are returned", {
+  record_table <- get_record_table(mica)
+  expected_colnames <- c("Station",
+                         "Species",
+                         "n",
+                          "DateTimeOriginal",
+                         "Date",
+                         "Time",
+                         "delta.time.secs",
+                         "delta.time.mins",
+                         "delta.time.hours",
+                         "delta.time.days",
+                         "Directory",
+                         "FileName"
+  )
+  testthat::expect_identical(names(record_table), expected_colnames)
+})
+
 test_that("nrows = n obs of identified individuals if minDeltaTime is 0", {
   nrow_output <- get_record_table(mica, minDeltaTime = 0) %>% nrow()
   testthat::expect_equal(

From 22eda4461e21d0b75bcd931efac583aff9b271cb Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Wed, 8 Nov 2023 16:47:35 +0100
Subject: [PATCH 03/35] Creates meaningful examples of using minDeltaTime

The new mica datapackage example requires some changes to make meaningful example of setting minDeltaTime to remove not independent observations.
---
 R/get_record_table.R | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/R/get_record_table.R b/R/get_record_table.R
index ac808915..45502821 100644
--- a/R/get_record_table.R
+++ b/R/get_record_table.R
@@ -66,8 +66,10 @@
 #'
 #' # Set a minDeltaTime of 20 minutes from last independent record for filtering
 #' # out not independent observations
+#' mica_dependent <- mica
+#' mica_dependent$data$observations[4,"timestamp"] <- lubridate::as_datetime("2020-07-29 05:55:00")
 #' get_record_table(
-#'   mica,
+#'   mica_dependent,
 #'   minDeltaTime = 20,
 #'   deltaTimeComparedTo = "lastIndependentRecord"
 #' )
@@ -75,7 +77,7 @@
 #' # Set a minDeltaTime of 20 minutes from last record for filtering out not
 #' # independent observations
 #' get_record_table(
-#'   mica,
+#'   mica_dependent,
 #'   minDeltaTime = 20,
 #'   deltaTimeComparedTo = "lastRecord"
 #' )

From 3dbd53b85ad94ef92a28cbcd22768307aec49e1e Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Wed, 8 Nov 2023 16:47:56 +0100
Subject: [PATCH 04/35] Update species in example comment

---
 R/get_record_table.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/get_record_table.R b/R/get_record_table.R
index 45502821..de270b8e 100644
--- a/R/get_record_table.R
+++ b/R/get_record_table.R
@@ -82,7 +82,7 @@
 #'   deltaTimeComparedTo = "lastRecord"
 #' )
 #'
-#' # Exclude observations of brown rat
+#' # Exclude observations of mallard
 #' # Exclude is case insensitive and vernacular names are allowed
 #' get_record_table(mica, exclude = "wilde eend")
 #'

From f2aabf5a78041ab9a898bc56c82dd71c2bd27e8b Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Wed, 8 Nov 2023 16:49:10 +0100
Subject: [PATCH 05/35] Update a test after adding column n

Column added in 201737e8ae77f768db308e65ecb8394603add1b2
---
 tests/testthat/test-get_record_table.R | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/tests/testthat/test-get_record_table.R b/tests/testthat/test-get_record_table.R
index 2d84638f..8a49d669 100644
--- a/tests/testthat/test-get_record_table.R
+++ b/tests/testthat/test-get_record_table.R
@@ -169,12 +169,13 @@ test_that(
     n_media <-
       mica$data$media %>%
       dplyr::group_by(.data$sequenceID) %>%
-      dplyr::count()
+      dplyr::count() %>%
+      dplyr::rename(n_media = n)
     output <- output %>%
       dplyr::left_join(n_media,
         by = "sequenceID"
       )
-    testthat::expect_equal(output$len, output$n)
+    testthat::expect_equal(output$len, output$n_media)
   }
 )
 

From 88f7641d8532e3d92414e3b539535b130eda3a3c Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Wed, 8 Nov 2023 16:50:08 +0100
Subject: [PATCH 06/35] Adjust threshold for removing not independent obs

Multiply by ten actually or in character terms adding a zero
---
 tests/testthat/test-get_record_table.R | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/tests/testthat/test-get_record_table.R b/tests/testthat/test-get_record_table.R
index 8a49d669..70b0a840 100644
--- a/tests/testthat/test-get_record_table.R
+++ b/tests/testthat/test-get_record_table.R
@@ -106,18 +106,18 @@ test_that("nrows = n obs of red foxes if all other species are excluded", {
 
 test_that("Higher minDeltaTime means less rows returned", {
   nrow_delta_0 <- get_record_table(mica) %>% nrow()
-  nrow_delta_1000 <- get_record_table(mica,
-    minDeltaTime = 1000,
-    deltaTimeComparedTo = "lastRecord"
-  ) %>%
-    nrow()
   nrow_delta_10000 <- suppressMessages(get_record_table(mica,
     minDeltaTime = 10000,
     deltaTimeComparedTo = "lastRecord"
   )) %>%
     nrow()
-  testthat::expect_true(nrow_delta_1000 <= nrow_delta_0)
-  testthat::expect_true(nrow_delta_10000 <= nrow_delta_1000)
+  nrow_delta_100000 <- suppressMessages(get_record_table(mica,
+    minDeltaTime = 100000,
+    deltaTimeComparedTo = "lastRecord"
+  )) %>%
+    nrow()
+  testthat::expect_true(nrow_delta_10000 < nrow_delta_0)
+  testthat::expect_true(nrow_delta_100000 < nrow_delta_10000)
 })
 
 test_that("stations names are equal to values in column passed to StationCOl", {

From 7be7555c4791b9c76ba7de404ffaa779acc555fa Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Wed, 8 Nov 2023 16:58:51 +0100
Subject: [PATCH 07/35] Add line in news about solving #279

---
 NEWS.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/NEWS.md b/NEWS.md
index 8330eae0..8f9e1963 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -6,3 +6,4 @@
   0.1.6 which is currently used as internal data model for camtraptor.
 - `get_custom_effort()` now calculates per calendar month/week (#219).
 - `write_dwc()` has an updated mapping for dwc_audubon.csv (#274).
+- `get_record_table()` returns the number of observed individuals (#279).

From 553bf1cc47730a5db42a2ec668da373f79870fdf Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Thu, 9 Nov 2023 10:16:07 +0100
Subject: [PATCH 08/35] Add new column to vignette

---
 vignettes/record-table.Rmd | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/vignettes/record-table.Rmd b/vignettes/record-table.Rmd
index 03aec8a1..3f352eb7 100644
--- a/vignettes/record-table.Rmd
+++ b/vignettes/record-table.Rmd
@@ -44,12 +44,13 @@ If we consider that all observations are independent, then, it will be sufficien
 get_record_table(mica)
 ```
 
-The function returns the same columns as the camtrapR's function `recordTable()`. The following mapping is applied:
+The function returns the same columns as the camtrapR's function `recordTable()` except for column `n`. The following mapping is applied:
 
 column name output | description
 --- | ---
 `Station` | the station name as provided by argument `stationCol` (default: `locationName`). It has to be a column of `deployments`
 `Species` |  `scientific_name` column in `observations`
+`n` | `count` column in `observations` (number of individuals)
 `DateTimeOriginal` | the `timestamp` column in `observations`
 `Date` | the date from `timestamp`
 `Time` | the time part from `timestamp`
@@ -106,20 +107,19 @@ get_record_table(mica, stationCol = "locationID")
 
 It can happen that "duplicates" occur, e.g. when two distinct observations of the same species are made based on the same sequence of images, e.g. same species but different `lifeStage` or `sex`. You can decide what to do with these duplicates by using the argument `removeDuplicateRecords`: by default it is equal to `TRUE`. The duplicates are therefore removed.  To not remove them, set `removeDuplicateRecords` equal to `FALSE`.
 
-Let's create an easy example with duplicates based on `mica` datapackage:
+Let's create an easy example with a duplicate based on `mica` datapackage:
 
 ```{r dummy_data_with_duplicates}
 mica_dup <- mica
-  mica_dup$observations$sequenceID <- mica_dup$observations$sequenceID[1]
-  mica_dup$observations$deploymentID <- mica_dup$observations$deploymentID[1]
-  mica_dup$observations$timestamp <- mica_dup$observations$timestamp[1]
-  mica_dup$observations$scientificName <- "Anas strepera"
+# create a duplicate at 2020-07-29 05:46:48, location: B_DL_val 5_beek kleine vijver
+mica_dup$data$observations[4,"sequenceID"] <- mica_dup$data$observations$sequenceID[3]
+mica_dup$data$observations[4, "deploymentID"] <- mica_dup$data$observations$deploymentID[3]
+mica_dup$data$observations[4, "timestamp"] <- mica_dup$data$observations$timestamp[3]
 ```
 
 Record table without duplicates:
 
 ```{r no_duplicates}
-# equivalent of get_record_table(mica, removeDuplicateRecords = TRUE)
 get_record_table(mica_dup)
 ```
 

From 2710a3c23ec43b1f22ded69e41af48cf9f9bbfd2 Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Thu, 9 Nov 2023 10:16:28 +0100
Subject: [PATCH 09/35] Add examples about duplicate removel in examples

---
 R/get_record_table.R | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/R/get_record_table.R b/R/get_record_table.R
index de270b8e..1c1e9610 100644
--- a/R/get_record_table.R
+++ b/R/get_record_table.R
@@ -93,6 +93,20 @@
 #'   minDeltaTime = 20,
 #'   deltaTimeComparedTo = "lastRecord"
 #' )
+#' 
+#' # How to deal with duplicates
+#' mica_dup <- mica
+#' # create a duplicate at 2020-07-29 05:46:48, location: B_DL_val 5_beek kleine vijver
+#' mica_dup$data$observations[4,"sequenceID"] <- mica_dup$data$observations$sequenceID[3]
+#' mica_dup$data$observations[4, "deploymentID"] <- mica_dup$data$observations$deploymentID[3]
+#' mica_dup$data$observations[4, "timestamp"] <- mica_dup$data$observations$timestamp[3]
+#'
+#' # duplicate removed
+#' get_record_table(mica_dup)
+#' 
+#' # duplicate not removed
+#' get_record_table(mica_dup, removeDuplicateRecords = FALSE)
+#' 
 #' # Applying filter(s) on deployments, e.g. deployments with latitude >= 51.18
 #' get_record_table(mica, pred_gte("latitude", 51.18))
 get_record_table <- function(package = NULL,

From fc60b6f0fdf9115ad0356b76f94529c24a1e1efe Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Thu, 9 Nov 2023 10:17:50 +0100
Subject: [PATCH 10/35] Update chunks about duplicates based on new mica
 dataset

---
 vignettes/record-table.Rmd | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/vignettes/record-table.Rmd b/vignettes/record-table.Rmd
index 3f352eb7..772c3235 100644
--- a/vignettes/record-table.Rmd
+++ b/vignettes/record-table.Rmd
@@ -73,16 +73,18 @@ As described in [Chapter 3](https://jniedballa.github.io/camtrapR/articles/camtr
 Again, as for `recordTable()`, we provide an argument, `deltaTimeComparedTo`, to further control how independence between records is assessed. Setting it to `“lastRecord”` returns only records taken `minDeltaTime` minutes after the last record, i.e. `minDeltaTime` minutes after `timestamp` of the last recorded media file. Example with  `minDeltaTime = 60` (1 hour):
 
 ```{r example_lastRecord}
-get_record_table(mica, 
-                 minDeltaTime = 60, 
+mica_dependent <- mica
+mica_dependent$data$observations[4,"timestamp"] <- lubridate::as_datetime("2020-07-29 05:55:00")
+get_record_table(mica_dependent, 
+                 minDeltaTime = 10, 
                  deltaTimeComparedTo = "lastRecord")
 ```
 
 Setting `deltaTimeComparedTo` to `“lastIndependentRecord”` returns only records taken `minDeltaTime` minutes after the last independent record, i.e. `minDeltaTime` minutes after `timestamp` of the last observation. Example with  `minDeltaTime = 60` (1 hour):
 
 ```{r example_lastIndependentRecord}
-get_record_table(mica, 
-                 minDeltaTime = 60, 
+get_record_table(mica_dependent, 
+                 minDeltaTime = 10, 
                  deltaTimeComparedTo = "lastIndependentRecord")
 ```
 

From f37ef07e532e72dd713ec01310afa5d1e2ca0252 Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Thu, 9 Nov 2023 10:19:11 +0100
Subject: [PATCH 11/35] Use mica_dup instead of mica_duplicates

---
 tests/testthat/test-get_record_table.R | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/tests/testthat/test-get_record_table.R b/tests/testthat/test-get_record_table.R
index 70b0a840..9b7392d0 100644
--- a/tests/testthat/test-get_record_table.R
+++ b/tests/testthat/test-get_record_table.R
@@ -183,13 +183,15 @@ test_that(paste(
   "removeDuplicateRecords allows removing duplicates,",
   "but structure output remains the same"
 ), {
-  mica_duplicates <- mica
-  mica_duplicates$data$observations$sequenceID <- mica_duplicates$data$observations$sequenceID[1]
-  mica_duplicates$data$observations$deploymentID <- mica_duplicates$data$observations$deploymentID[1]
-  mica_duplicates$data$observations$timestamp <- mica_duplicates$data$observations$timestamp[1]
-  mica_duplicates$data$observations$scientificName <- "Anas strepera"
-  rec_table <- get_record_table(mica_duplicates)
-  rec_table_dup <- get_record_table(mica_duplicates,
+  mica_dup <- mica
+  # create duplicates at 2020-07-29 05:46:48, location: B_DL_val 5_beek kleine vijver
+  mica_dup$data$observations[,"sequenceID"] <- mica_dup$data$observations$sequenceID[3]
+  mica_dup$data$observations[, "deploymentID"] <- mica_dup$data$observations$deploymentID[3]
+  mica_dup$data$observations[, "timestamp"] <- mica_dup$data$observations$timestamp[3]
+  mica_dup$data$observations[, "scientificName"] <- mica_dup$data$observations$scientificName[3]
+  
+  rec_table <- get_record_table(mica_dup)
+  rec_table_dup <- get_record_table(mica_dup,
     removeDuplicateRecords = FALSE
   )
   testthat::expect_equal(nrow(rec_table), 1)

From d8dc12537b72804a685a74fdc8256d90349b2054 Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Thu, 9 Nov 2023 10:22:13 +0100
Subject: [PATCH 12/35] Explain why using 3rd obs as template for mica_dup

---
 tests/testthat/test-get_record_table.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/testthat/test-get_record_table.R b/tests/testthat/test-get_record_table.R
index 9b7392d0..f11cf036 100644
--- a/tests/testthat/test-get_record_table.R
+++ b/tests/testthat/test-get_record_table.R
@@ -185,6 +185,7 @@ test_that(paste(
 ), {
   mica_dup <- mica
   # create duplicates at 2020-07-29 05:46:48, location: B_DL_val 5_beek kleine vijver
+  # use 3rd observation as the first two are unknown or blank (= no animal)
   mica_dup$data$observations[,"sequenceID"] <- mica_dup$data$observations$sequenceID[3]
   mica_dup$data$observations[, "deploymentID"] <- mica_dup$data$observations$deploymentID[3]
   mica_dup$data$observations[, "timestamp"] <- mica_dup$data$observations$timestamp[3]

From c2b320f49bcd0583aeadb9b4e7ec4a276fdf7fff Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Thu, 9 Nov 2023 10:22:31 +0100
Subject: [PATCH 13/35] Use 3rd timestamp in test

---
 tests/testthat/test-get_record_table.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/testthat/test-get_record_table.R b/tests/testthat/test-get_record_table.R
index f11cf036..ba022d1e 100644
--- a/tests/testthat/test-get_record_table.R
+++ b/tests/testthat/test-get_record_table.R
@@ -197,7 +197,7 @@ test_that(paste(
   )
   testthat::expect_equal(nrow(rec_table), 1)
   testthat::expect_equal(
-    rec_table$DateTimeOriginal, mica$data$observations$timestamp[1]
+    rec_table$DateTimeOriginal, mica$data$observations$timestamp[3]
   )
   testthat::expect_equal(rec_table$delta.time.secs, 0)
   testthat::expect_equal(names(rec_table_dup), names(rec_table))

From 1ea3aea85cf11e6d7b75818d5d78067bb8070b13 Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Thu, 9 Nov 2023 10:23:26 +0100
Subject: [PATCH 14/35] Use mica_dup instead of mica_duplicates

Same as f37ef07
---
 tests/testthat/test-get_record_table.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/testthat/test-get_record_table.R b/tests/testthat/test-get_record_table.R
index ba022d1e..88a44701 100644
--- a/tests/testthat/test-get_record_table.R
+++ b/tests/testthat/test-get_record_table.R
@@ -203,7 +203,7 @@ test_that(paste(
   testthat::expect_equal(names(rec_table_dup), names(rec_table))
   testthat::expect_equal(
     nrow(rec_table_dup),
-    nrow(mica_duplicates$data$observations)
+    nrow(mica_dup$data$observations)
   )
 })
 

From ba7eb71b09246ff69433885cc78cc2cfb731bb44 Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Thu, 9 Nov 2023 12:34:07 +0100
Subject: [PATCH 15/35] Fix #288

Examples updated as well
---
 R/get_cam_op.R | 116 +++++++++++++++++++++++++++++++++++++++++--------
 1 file changed, 99 insertions(+), 17 deletions(-)

diff --git a/R/get_cam_op.R b/R/get_cam_op.R
index d366c1a1..18ab83d1 100644
--- a/R/get_cam_op.R
+++ b/R/get_cam_op.R
@@ -6,9 +6,8 @@
 #' https://jniedballa.github.io/camtrapR/reference/cameraOperation.html).
 #'
 #' The deployment data are by default grouped by `locationName` (station ID in
-#' camtrapR jargon) or another column specified by the user.
-#' If multiple deployments are linked to same location, daily efforts higher
-#' than 1 occur.
+#' camtrapR jargon) or another column specified by the user. If multiple
+#' deployments are linked to same location, daily efforts higher than 1 occur.
 #'
 #' Partially active days, e.g. the first or the last day of a deployment, result
 #' in decimal effort values as in [camtrapR::cameraOperation()](
@@ -16,19 +15,22 @@
 #'
 #' @param package Camera trap data package object, as returned by
 #'   `read_camtrap_dp()`.
-#' @param station_col Column name to use for identifying the stations.
-#'   Default: `"locationName"`.
-#' @param use_prefix Logical (`TRUE`or `FALSE`).
-#'   If `TRUE` the returned row names will start with prefix `"Station"` as
-#'   returned by [camtrapR::cameraOperation()](
+#' @param station_col Column name to use for identifying the stations. Default:
+#'   `"locationName"`.
+#' @param camera_col Column name of the column specifying Camera ID. Default:
+#'   `NULL`.
+#' @param session_col Column name to use for identifying the session. Default:
+#'   `NULL`. Use it for creating multi-session / multi-season detection
+#'   histories.
+#' @param use_prefix Logical (`TRUE`or `FALSE`). If `TRUE` the returned row
+#'   names will start with prefix `"Station"` as returned by
+#'   [camtrapR::cameraOperation()](
 #'   https://jniedballa.github.io/camtrapR/reference/cameraOperation.html).
 #'   Default: `FALSE`.
-#' @param datapkg Deprecated.
-#'   Use `package` instead.
+#' @param datapkg Deprecated. Use `package` instead.
 #' @param ... filter predicates for filtering on deployments.
-#' @return A matrix.
-#'   Row names always indicate the station ID.
-#'   Column names are dates.
+#' @return A matrix. Row names always indicate the station ID. Column names are
+#'   dates.
 #' @family exploration functions
 #' @importFrom dplyr %>% .data
 #' @export
@@ -41,11 +43,32 @@
 #' # Specify column with station names
 #' get_cam_op(mica, station_col = "locationID")
 #'
+#' # Specify column with session IDs
+#' mica_sessions <- mica
+#' mica_sessions$data$deployments <- mica_sessions$data$deployments %>%
+#'   dplyr::mutate(session = ifelse(
+#'     stringr::str_starts(.data$locationName, "B_DL_"),
+#'       "after2020",
+#'       "before2020"
+#'   )
+#' )
+#' get_cam_op(mica_sessions, session_col = "session")
+#'
+#' # Specify column with camera IDs
+#' mica_cameras <- mica_sessions
+#' mica_cameras$data$deployments$cameraID <- c(1, 2, 3, 4)
+#' get_cam_op(mica_cameras, camera_col = "cameraID")
+#'
+#' # Specify both session and camera IDs
+#' get_cam_op(mica_cameras, camera_col = "cameraID", session_col = "session")
+#' 
 #' # Use prefix Station as in camtrapR's camera operation matrix
 #' get_cam_op(mica, use_prefix = TRUE)
 get_cam_op <- function(package = NULL,
                        ...,
                        station_col = "locationName",
+                       camera_col = NULL,
+                       session_col = NULL,
                        use_prefix = FALSE,
                        datapkg = lifecycle::deprecated()) {
   # check camera trap data package
@@ -65,7 +88,7 @@ get_cam_op <- function(package = NULL,
     )
   )
   
-  # Check that station_col doesn't contain empty values (NA)
+  # Check that `station_col` doesn't contain empty values (NA)
   n_na <- package$data$deployments %>%
     dplyr::filter(is.na(.data[[station_col]])) %>%
     nrow()
@@ -76,7 +99,48 @@ get_cam_op <- function(package = NULL,
       "{n_na} NAs found."
     )
   )
-
+  
+  # Check that `session_col` exists in deployments, if defined
+  if (!is.null(session_col)) {
+    assertthat::assert_that(assertthat::is.string(session_col))
+    assertthat::assert_that(
+      session_col %in% names(package$data$deployments),
+      msg = glue::glue(
+        "Session column name (`{session_col}`) is not valid: ",
+        "it must be one of the deployments column names."
+      )
+    )
+    assertthat::assert_that(
+      all(!stringr::str_detect(string = package$data$deployments[[session_col]],
+                           pattern = "__SESS_|__CAM_")),
+      msg = glue::glue(
+        "Session column name (`{session_col}`) must not contain any of the ",
+        "reserved words: \"__SESS_\", \"__CAM_\"."
+      )
+    )
+  }
+  
+  # Check that `camera_col` exists in deployments, if defined, and that its
+  # values do not contain the reserved words "__SESS_" and "__CAM_"
+  if (!is.null(camera_col)) {
+    assertthat::assert_that(assertthat::is.string(camera_col))
+    assertthat::assert_that(
+      camera_col %in% names(package$data$deployments),
+      msg = glue::glue(
+        "Camera column name (`{camera_col}`) is not valid: ",
+        "it must be one of the deployments column names."
+      )
+    )
+    assertthat::assert_that(
+      all(!stringr::str_detect(string = package$data$deployments[[camera_col]],
+                           pattern = "__SESS_|__CAM_")),
+      msg = glue::glue(
+        "Camera column name (`{camera_col}`) must not contain any of the ",
+        "reserved words: \"__SESS_\", \"__CAM_\"."
+      )
+    )
+  }
+  
   assertthat::assert_that(
     use_prefix %in% c(TRUE, FALSE),
     msg = "use_prefix must be TRUE or FALSE."
@@ -140,8 +204,26 @@ get_cam_op <- function(package = NULL,
     }
   )
   names(deployment_operational) <- deploys$deploymentID
-
-  # get for each location which days a deployment was active
+  
+  # add session to station names
+  if (!is.null(session_col)) {
+    deploys <- deploys %>%
+      dplyr::mutate(!!station_col := paste(.data[[station_col]], 
+                                         .data[[session_col]],
+                                         sep = "__SESS_")
+      )
+  }
+  
+  # add camera to column names
+  if (!is.null(camera_col)) {
+    deploys <- deploys %>%
+      dplyr::mutate(!!station_col := paste(.data[[station_col]], 
+                                           .data[[camera_col]],
+                                           sep = "__CAM_")
+      )
+  }
+  
+  # get for each station_col which days a deployment was active
   camOps <- purrr::map_dfc(
     unique(deploys[[station_col]]),
     function(loc_name) {

From 0c01da0b4eca4820044b602d8ba6b225460ca312 Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Thu, 9 Nov 2023 12:34:37 +0100
Subject: [PATCH 16/35] Run devtools::document

---
 man/get_cam_op.Rd       | 51 ++++++++++++++++++++++++++++++-----------
 man/get_record_table.Rd | 22 +++++++++++++++---
 2 files changed, 57 insertions(+), 16 deletions(-)

diff --git a/man/get_cam_op.Rd b/man/get_cam_op.Rd
index 83c57185..5f7b935e 100644
--- a/man/get_cam_op.Rd
+++ b/man/get_cam_op.Rd
@@ -8,6 +8,8 @@ get_cam_op(
   package = NULL,
   ...,
   station_col = "locationName",
+  camera_col = NULL,
+  session_col = NULL,
   use_prefix = FALSE,
   datapkg = lifecycle::deprecated()
 )
@@ -18,21 +20,26 @@ get_cam_op(
 
 \item{...}{filter predicates for filtering on deployments.}
 
-\item{station_col}{Column name to use for identifying the stations.
-Default: \code{"locationName"}.}
+\item{station_col}{Column name to use for identifying the stations. Default:
+\code{"locationName"}.}
 
-\item{use_prefix}{Logical (\code{TRUE}or \code{FALSE}).
-If \code{TRUE} the returned row names will start with prefix \code{"Station"} as
-returned by \href{https://jniedballa.github.io/camtrapR/reference/cameraOperation.html}{camtrapR::cameraOperation()}.
+\item{camera_col}{Column name of the column specifying Camera ID. Default:
+\code{NULL}.}
+
+\item{session_col}{Column name to use for identifying the session. Default:
+\code{NULL}. Use it for creating multi-session / multi-season detection
+histories.}
+
+\item{use_prefix}{Logical (\code{TRUE}or \code{FALSE}). If \code{TRUE} the returned row
+names will start with prefix \code{"Station"} as returned by
+\href{https://jniedballa.github.io/camtrapR/reference/cameraOperation.html}{camtrapR::cameraOperation()}.
 Default: \code{FALSE}.}
 
-\item{datapkg}{Deprecated.
-Use \code{package} instead.}
+\item{datapkg}{Deprecated. Use \code{package} instead.}
 }
 \value{
-A matrix.
-Row names always indicate the station ID.
-Column names are dates.
+A matrix. Row names always indicate the station ID. Column names are
+dates.
 }
 \description{
 Returns the \href{https://jniedballa.github.io/camtrapR/reference/cameraOperation.html}{camera operation matrix} as
@@ -40,9 +47,8 @@ returned by \href{https://jniedballa.github.io/camtrapR/reference/cameraOperatio
 }
 \details{
 The deployment data are by default grouped by \code{locationName} (station ID in
-camtrapR jargon) or another column specified by the user.
-If multiple deployments are linked to same location, daily efforts higher
-than 1 occur.
+camtrapR jargon) or another column specified by the user. If multiple
+deployments are linked to same location, daily efforts higher than 1 occur.
 
 Partially active days, e.g. the first or the last day of a deployment, result
 in decimal effort values as in \href{https://jniedballa.github.io/camtrapR/reference/cameraOperation.html}{camtrapR::cameraOperation()}.
@@ -56,6 +62,25 @@ get_cam_op(mica, pred_gte("latitude", 51.18))
 # Specify column with station names
 get_cam_op(mica, station_col = "locationID")
 
+# Specify column with session IDs
+mica_sessions <- mica
+mica_sessions$data$deployments <- mica_sessions$data$deployments \%>\%
+  dplyr::mutate(session = ifelse(
+    stringr::str_starts(.data$locationName, "B_DL_"),
+      "after2020",
+      "before2020"
+  )
+)
+get_cam_op(mica_sessions, session_col = "session")
+
+# Specify column with camera IDs
+mica_cameras <- mica_sessions
+mica_cameras$data$deployments$cameraID <- c(1, 2, 3, 4)
+get_cam_op(mica_cameras, camera_col = "cameraID")
+
+# Specify both session and camera IDs
+get_cam_op(mica_cameras, camera_col = "cameraID", session_col = "session")
+
 # Use prefix Station as in camtrapR's camera operation matrix
 get_cam_op(mica, use_prefix = TRUE)
 }
diff --git a/man/get_record_table.Rd b/man/get_record_table.Rd
index 48ceae1c..62d4a141 100644
--- a/man/get_record_table.Rd
+++ b/man/get_record_table.Rd
@@ -88,8 +88,10 @@ get_record_table(mica)
 
 # Set a minDeltaTime of 20 minutes from last independent record for filtering
 # out not independent observations
+mica_dependent <- mica
+mica_dependent$data$observations[4,"timestamp"] <- lubridate::as_datetime("2020-07-29 05:55:00")
 get_record_table(
-  mica,
+  mica_dependent,
   minDeltaTime = 20,
   deltaTimeComparedTo = "lastIndependentRecord"
 )
@@ -97,12 +99,12 @@ get_record_table(
 # Set a minDeltaTime of 20 minutes from last record for filtering out not
 # independent observations
 get_record_table(
-  mica,
+  mica_dependent,
   minDeltaTime = 20,
   deltaTimeComparedTo = "lastRecord"
 )
 
-# Exclude observations of brown rat
+# Exclude observations of mallard
 # Exclude is case insensitive and vernacular names are allowed
 get_record_table(mica, exclude = "wilde eend")
 
@@ -113,6 +115,20 @@ get_record_table(
   minDeltaTime = 20,
   deltaTimeComparedTo = "lastRecord"
 )
+
+# How to deal with duplicates
+mica_dup <- mica
+# create a duplicate at 2020-07-29 05:46:48, location: B_DL_val 5_beek kleine vijver
+mica_dup$data$observations[4,"sequenceID"] <- mica_dup$data$observations$sequenceID[3]
+mica_dup$data$observations[4, "deploymentID"] <- mica_dup$data$observations$deploymentID[3]
+mica_dup$data$observations[4, "timestamp"] <- mica_dup$data$observations$timestamp[3]
+
+# duplicate removed
+get_record_table(mica_dup)
+
+# duplicate not removed
+get_record_table(mica_dup, removeDuplicateRecords = FALSE)
+
 # Applying filter(s) on deployments, e.g. deployments with latitude >= 51.18
 get_record_table(mica, pred_gte("latitude", 51.18))
 }

From 6e1fef409e7e973759447844fd0312ec09c2a7d2 Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Thu, 9 Nov 2023 15:18:03 +0100
Subject: [PATCH 17/35] Add check reserved words in station column

---
 R/get_cam_op.R | 15 ++++++++++++++-
 1 file changed, 14 insertions(+), 1 deletion(-)

diff --git a/R/get_cam_op.R b/R/get_cam_op.R
index 18ab83d1..479eb207 100644
--- a/R/get_cam_op.R
+++ b/R/get_cam_op.R
@@ -100,7 +100,20 @@ get_cam_op <- function(package = NULL,
     )
   )
   
-  # Check that `session_col` exists in deployments, if defined
+  # Check that `station_col` do not contain the reserved words "__SESS_" and
+  # "__CAM_" (no need to remove NAs beforehand as station_col must not contain
+  # any NA, see previous check)
+  assertthat::assert_that(
+    all(!stringr::str_detect(string = package$data$deployments[[station_col]],
+                             pattern = "__SESS_|__CAM_")),
+    msg = glue::glue(
+      "Station column name (`{station_col}`) must not contain any of the ",
+      "reserved words: \"__SESS_\", \"__CAM_\"."
+    )
+  )
+  
+  # Check that `session_col` exists in deployments, if defined, and that its
+  # values do not contain the reserved words "__SESS_" and "__CAM_"
   if (!is.null(session_col)) {
     assertthat::assert_that(assertthat::is.string(session_col))
     assertthat::assert_that(

From 9e101f848e3114202835db96342537583ca86aea Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Thu, 9 Nov 2023 15:18:58 +0100
Subject: [PATCH 18/35] Remove NAs before checking presence reserved words

---
 R/get_cam_op.R | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/R/get_cam_op.R b/R/get_cam_op.R
index 479eb207..9dcc34aa 100644
--- a/R/get_cam_op.R
+++ b/R/get_cam_op.R
@@ -123,9 +123,11 @@ get_cam_op <- function(package = NULL,
         "it must be one of the deployments column names."
       )
     )
+    session_values <- package$data$deployments[[session_col]]
+    session_values <- session_values[!is.na(session_values)]
     assertthat::assert_that(
-      all(!stringr::str_detect(string = package$data$deployments[[session_col]],
-                           pattern = "__SESS_|__CAM_")),
+      all(!stringr::str_detect(string = session_values,
+                               pattern = "__SESS_|__CAM_")),
       msg = glue::glue(
         "Session column name (`{session_col}`) must not contain any of the ",
         "reserved words: \"__SESS_\", \"__CAM_\"."
@@ -144,8 +146,10 @@ get_cam_op <- function(package = NULL,
         "it must be one of the deployments column names."
       )
     )
+    camera_values <- package$data$deployments[[session_col]]
+    camera_values <- camera_values[!is.na(camera_values)]
     assertthat::assert_that(
-      all(!stringr::str_detect(string = package$data$deployments[[camera_col]],
+      all(!stringr::str_detect(string = camera_values,
                            pattern = "__SESS_|__CAM_")),
       msg = glue::glue(
         "Camera column name (`{camera_col}`) must not contain any of the ",

From d208521c8cfe029109ef2dbf72bb3d1713d20fa4 Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Thu, 9 Nov 2023 15:19:36 +0100
Subject: [PATCH 19/35] Add tests of new features

---
 tests/testthat/test-get_cam_op.R | 159 ++++++++++++++++++++++++++++++-
 1 file changed, 158 insertions(+), 1 deletion(-)

diff --git a/tests/testthat/test-get_cam_op.R b/tests/testthat/test-get_cam_op.R
index 60dda148..48a9588e 100644
--- a/tests/testthat/test-get_cam_op.R
+++ b/tests/testthat/test-get_cam_op.R
@@ -28,6 +28,44 @@ test_that("input camtrap dp is checked properly", {
   expect_error(get_cam_op(mica_empty_location_name),
                "Column `locationName` must be non-empty: 2 NAs found."
   )
+  # camera_col is not NA
+  expect_error(
+    get_cam_op(mica, camera_col = NA),
+    "camera_col is not a string (a length one character vector).",
+    fixed = TRUE)
+  # camera_col is length 1
+  expect_error(
+    get_cam_op(mica, camera_col = c("locationID","locationName")),
+    "camera_col is not a string (a length one character vector).",
+    fixed = TRUE)
+  # station_col value is not a column of deployments
+  expect_error(
+    get_cam_op(mica, camera_col = "bla"),
+    paste0(
+      "Camera column name (`bla`) is not valid: ", 
+      "it must be one of the deployments column names."
+    ),
+    fixed = TRUE
+  )
+  # session_col is not NA
+  expect_error(
+    get_cam_op(mica, session_col = NA),
+    "session_col is not a string (a length one character vector).",
+    fixed = TRUE)
+  # session_col is length 1
+  expect_error(
+    get_cam_op(mica, session_col = c("locationID","locationName")),
+    "session_col is not a string (a length one character vector).",
+    fixed = TRUE)
+  # session_col value is not a column of deployments
+  expect_error(
+    get_cam_op(mica, session_col = "bla"),
+    paste0(
+      "Session column name (`bla`) is not valid: ", 
+      "it must be one of the deployments column names."
+    ),
+    fixed = TRUE
+  )
   # use_prefix must be TRUE or FALSE
   expect_error(get_cam_op(mica, use_prefix = "bla"))
   expect_error(get_cam_op(mica, use_prefix = NA))
@@ -46,6 +84,122 @@ test_that("output matrix has locations as rownames", {
   expect_equal(row.names(cam_op_matrix), locations)
 })
 
+test_that("output matrix has sessions addded to locations as rownames", {
+  mica_sessions <- mica
+  mica_sessions$data$deployments <- mica_sessions$data$deployments %>%
+    dplyr::mutate(session = ifelse(
+      stringr::str_starts(.data$locationName, "B_DL_"),
+      "after2020",
+      "before2020"
+   )
+  )
+  cam_op_matrix <- get_cam_op(mica_sessions, session_col = "session")
+  locations_sessions <- paste(mica_sessions$data$deployments$locationName,
+                              mica_sessions$data$deployments$session,
+                              sep = "__SESS_"
+  )
+  n_locations <- length(mica_sessions$data$deployments$locationName)
+  expect_equal(nrow(cam_op_matrix), n_locations)
+  expect_identical(row.names(cam_op_matrix), locations_sessions)
+})
+
+test_that("output matrix has camera IDs addded to locations as rownames", {
+  mica_cameras <- mica
+  mica_cameras$data$deployments$cameraID <- c(1, 2, 3, 4)
+  cam_op_matrix <- get_cam_op(mica_cameras, camera_col = "cameraID")
+  locations_cameras <- paste(mica_cameras$data$deployments$locationName,
+                             mica_cameras$data$deployments$cameraID,
+                             sep = "__CAM_"
+  )
+  n_locations <- length(mica_cameras$data$deployments$locationName)
+  expect_equal(nrow(cam_op_matrix), n_locations)
+  expect_identical(row.names(cam_op_matrix), locations_cameras)
+})
+
+test_that(
+  "output matrix has sessions and cameras addded to locations as rownames", {
+    mica_sess_cam <- mica
+    mica_sess_cam$data$deployments$cameraID <- c(1, 2, 3, 4)
+    mica_sess_cam$data$deployments$session <- c(1, 2, 3, 4)
+    cam_op_matrix <- get_cam_op(mica_sess_cam, 
+                                camera_col = "cameraID", 
+                                session_col = "session"
+    )
+    locations_sess_cam <- paste(mica_sess_cam$data$deployments$locationName,
+                                mica_sess_cam$data$deployments$session,
+                               sep = "__SESS_"
+    )
+    locations_sess_cam <- paste(locations_sess_cam,
+                                mica_sess_cam$data$deployments$cameraID,
+                                sep = "__CAM_"
+    )
+    n_locations <- length(mica_sess_cam$data$deployments$locationName)
+    expect_equal(nrow(cam_op_matrix), n_locations)
+    expect_identical(row.names(cam_op_matrix), locations_sess_cam)
+})
+
+test_that(
+  "__SESS_ is a reserved word not used in station, session and camera columns",
+  {
+    mica__sess <- mica
+    mica__sess$data$deployments$session <- c("1__SESS_1")
+    expect_error(get_cam_op(mica__sess, session_col = "session"),
+                 paste0("Session column name (`session`) must not contain any ",
+                        "of the reserved words: \"__SESS_\", \"__CAM_\"."),
+                 fixed = TRUE
+    )
+    mica__sess <- mica
+    mica__sess$data$deployments$cameraID <- paste0(c(1,2,3,4), "__SESS_")
+    expect_error(get_cam_op(mica__sess, camera_col = "cameraID"),
+                 paste0("Camera column name (`cameraID`) must not contain any ",
+                        "of the reserved words: \"__SESS_\", \"__CAM_\"."),
+                 fixed = TRUE
+    )
+    mica__sess <- mica
+    mica__sess$data$deployments$locationName[1] <- paste0(
+      "__SESS_",
+      mica__sess$data$deployments$locationName[1]
+    )
+    expect_error(
+      get_cam_op(mica__sess),
+      paste0("Station column name (`locationName`) must not contain any ",
+             "of the reserved words: \"__SESS_\", \"__CAM_\"."),
+      fixed = TRUE
+    )
+  }
+)
+
+test_that(
+  "__CAM_ is a reserved word not used in station, session and camera columns",
+  {
+    mica__cam <- mica
+    mica__cam$data$deployments$session[1] <- c("1__CAM_1")
+    expect_error(get_cam_op(mica__cam, session_col = "session"),
+                 paste0("Session column name (`session`) must not contain any ",
+                        "of the reserved words: \"__SESS_\", \"__CAM_\"."),
+                 fixed = TRUE
+    )
+    mica__cam <- mica
+    mica__cam$data$deployments$cameraID <- paste0(c(1,2,3,4), "__CAM_")
+    expect_error(get_cam_op(mica__cam, camera_col = "cameraID"),
+                 paste0("Camera column name (`cameraID`) must not contain any ",
+                        "of the reserved words: \"__SESS_\", \"__CAM_\"."),
+                 fixed = TRUE
+    )
+    mica__cam <- mica
+    mica__cam$data$deployments$locationName[1] <- paste0(
+      "__CAM_",
+      mica__cam$data$deployments$locationName[1]
+    )
+    expect_error(
+      get_cam_op(mica__cam),
+      paste0("Station column name (`locationName`) must not contain any ",
+             "of the reserved words: \"__SESS_\", \"__CAM_\"."),
+      fixed = TRUE
+    )
+  }
+)
+
 test_that("output matrix has Station prefix in rownames", {
   cam_op_matrix <- get_cam_op(mica, use_prefix = TRUE)
   locations <- paste0("Station", mica$data$deployments$locationName)
@@ -62,6 +216,7 @@ test_that("output matrix has specified location column as rownames", {
   expect_equal(row.names(cam_op_matrix), locations)
 })
 
+
 test_that("output matrix has all deployment days as colnames", {
   cam_op_matrix <- get_cam_op(mica)
   days_activity <- seq(as.Date(min(mica$data$deployments$start)),
@@ -175,7 +330,9 @@ test_that("Argument datapkg is deprecated: warning returned", {
       lifecycle_verbosity = "warning",
       get_cam_op(datapkg = mica)
     ),
-    "The `datapkg` argument of `get_cam_op()` is deprecated as of camtraptor 0.16.0.",
+    paste0("The `datapkg` argument of `get_cam_op()` is deprecated ",
+           "as of camtraptor 0.16.0."
+    ),
     fixed = TRUE
   )
 })

From 9f5d48419813632a4c86353b8d3b8b513fa4c23c Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Thu, 9 Nov 2023 15:20:00 +0100
Subject: [PATCH 20/35] Update vignette describing new features

---
 vignettes/camera-operation-matrix.Rmd | 32 +++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

diff --git a/vignettes/camera-operation-matrix.Rmd b/vignettes/camera-operation-matrix.Rmd
index 20a6044f..03fa0759 100644
--- a/vignettes/camera-operation-matrix.Rmd
+++ b/vignettes/camera-operation-matrix.Rmd
@@ -90,3 +90,35 @@ You can also decide to use prefix `"Station"` in the station names as done by ca
 cam_op_with_prefix <- get_cam_op(mica, use_prefix = TRUE)
 cam_op_with_prefix[1:4,1:2]
 ```
+
+### Session and camera IDs
+
+You can specify the column containing the camera IDs to be added to the station names following the camtrapR's convention: `Station__CAM_CameraID`. Only the row names are shown:
+
+```{r add_camera_IDs}
+mica_cameras <- mica
+mica_cameras$data$deployments$cameraID <- c(1, 2, 3, 4)
+cam_op_with_camera_ids <- get_cam_op(mica_cameras, camera_col = "cameraID")
+row.names(cam_op_with_camera_ids)
+```
+
+You cans also add the session IDs using `session_col` argument, following the camtrapR's convention: `Station__SESS_sessionID`:
+
+```{r add_session_IDs}
+mica_sessions <- mica
+mica_sessions$data$deployments$session <- c(1, 2, 3, 4)
+cam_op_with_session_ids <- get_cam_op(mica_sessions, session_col = "session")
+row.names(cam_op_with_session_ids)
+```
+
+To use both camera and session IDs, the camtrapR's convention `Station__SESS_SessionID__CAM_CameraID` is followed:
+
+```{r add_session_camera_IDs}
+mica_sessions$data$deployments$cameraID <- c(1, 2, 3, 4)
+cam_op_with_session_and_camera_ids <- get_cam_op(
+  mica_sessions, 
+  camera_col = "cameraID",
+  session_col = "session"
+)
+row.names(cam_op_with_session_and_camera_ids)
+```

From 2a1181e3bfde8e7fad85c745441d5ccd02481a9d Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Thu, 9 Nov 2023 15:20:29 +0100
Subject: [PATCH 21/35] Report new features of get_cam_op in NEWS.md

---
 NEWS.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/NEWS.md b/NEWS.md
index 8f9e1963..733e8ee3 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -7,3 +7,4 @@
 - `get_custom_effort()` now calculates per calendar month/week (#219).
 - `write_dwc()` has an updated mapping for dwc_audubon.csv (#274).
 - `get_record_table()` returns the number of observed individuals (#279).
+- `get_cam_op()` allows to add session and camera IDs to station names output (#288)

From 387086968dd53f545d1957e16ccb18fc3ad46dcd Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Thu, 9 Nov 2023 15:21:35 +0100
Subject: [PATCH 22/35] Remove typo

---
 R/get_cam_op.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/get_cam_op.R b/R/get_cam_op.R
index 9dcc34aa..7308c339 100644
--- a/R/get_cam_op.R
+++ b/R/get_cam_op.R
@@ -146,7 +146,7 @@ get_cam_op <- function(package = NULL,
         "it must be one of the deployments column names."
       )
     )
-    camera_values <- package$data$deployments[[session_col]]
+    camera_values <- package$data$deployments[[camera_col]]
     camera_values <- camera_values[!is.na(camera_values)]
     assertthat::assert_that(
       all(!stringr::str_detect(string = camera_values,

From ac380cdd7cfa32f9401241c98387206620048bb9 Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Thu, 9 Nov 2023 15:29:22 +0100
Subject: [PATCH 23/35] Load dplyr in examples to use %>%

---
 R/get_cam_op.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/R/get_cam_op.R b/R/get_cam_op.R
index 7308c339..be03c80e 100644
--- a/R/get_cam_op.R
+++ b/R/get_cam_op.R
@@ -35,6 +35,7 @@
 #' @importFrom dplyr %>% .data
 #' @export
 #' @examples
+#' library(dplyr)
 #' get_cam_op(mica)
 #'
 #' # Applying filter(s) on deployments, e.g. deployments with latitude >= 51.18

From a5938395679d836a260088a4a106d7a8107e7138 Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Thu, 9 Nov 2023 15:48:45 +0100
Subject: [PATCH 24/35] Add importFrom for rlang symbols !! and :=

---
 R/get_cam_op.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/R/get_cam_op.R b/R/get_cam_op.R
index be03c80e..efb9d188 100644
--- a/R/get_cam_op.R
+++ b/R/get_cam_op.R
@@ -33,6 +33,7 @@
 #'   dates.
 #' @family exploration functions
 #' @importFrom dplyr %>% .data
+#' @importFrom rlang !! :=
 #' @export
 #' @examples
 #' library(dplyr)

From bf093322ca178567d55ca905f2f3348a830ed984 Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Thu, 9 Nov 2023 15:49:32 +0100
Subject: [PATCH 25/35] Run devtools::document()

---
 man/get_cam_op.Rd | 1 +
 1 file changed, 1 insertion(+)

diff --git a/man/get_cam_op.Rd b/man/get_cam_op.Rd
index 5f7b935e..8f83da99 100644
--- a/man/get_cam_op.Rd
+++ b/man/get_cam_op.Rd
@@ -54,6 +54,7 @@ Partially active days, e.g. the first or the last day of a deployment, result
 in decimal effort values as in \href{https://jniedballa.github.io/camtrapR/reference/cameraOperation.html}{camtrapR::cameraOperation()}.
 }
 \examples{
+library(dplyr)
 get_cam_op(mica)
 
 # Applying filter(s) on deployments, e.g. deployments with latitude >= 51.18

From 8eccfa2a75581d12d3f6525619bf2a35e30c3ca8 Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Thu, 9 Nov 2023 16:00:52 +0100
Subject: [PATCH 26/35] Improve grammar

Co-Authored-By: Peter Desmet <peter.desmet@inbo.be>
---
 NEWS.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/NEWS.md b/NEWS.md
index 733e8ee3..d832c816 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -7,4 +7,4 @@
 - `get_custom_effort()` now calculates per calendar month/week (#219).
 - `write_dwc()` has an updated mapping for dwc_audubon.csv (#274).
 - `get_record_table()` returns the number of observed individuals (#279).
-- `get_cam_op()` allows to add session and camera IDs to station names output (#288)
+- `get_cam_op()` allows to add session and camera IDs to the station names output (#288).

From 5a81082d2c6b6ca5cd1ca9f6c74af79cc3ae5e7a Mon Sep 17 00:00:00 2001
From: Pieter Huybrechts <48065851+PietrH@users.noreply.github.com>
Date: Fri, 10 Nov 2023 10:13:09 +0100
Subject: [PATCH 27/35] use `testthat::expect_named()` instead of
 `expect_identical(colnames( ...`

---
 tests/testthat/test-get_record_table.R | 30 ++++++++++++++------------
 1 file changed, 16 insertions(+), 14 deletions(-)

diff --git a/tests/testthat/test-get_record_table.R b/tests/testthat/test-get_record_table.R
index 88a44701..49d0874b 100644
--- a/tests/testthat/test-get_record_table.R
+++ b/tests/testthat/test-get_record_table.R
@@ -58,21 +58,23 @@ test_that("input of get_record_table, removeDuplicateRecords, is checked properl
 })
 
 test_that("right columns are returned", {
-  record_table <- get_record_table(mica)
-  expected_colnames <- c("Station",
-                         "Species",
-                         "n",
-                          "DateTimeOriginal",
-                         "Date",
-                         "Time",
-                         "delta.time.secs",
-                         "delta.time.mins",
-                         "delta.time.hours",
-                         "delta.time.days",
-                         "Directory",
-                         "FileName"
+  expect_named(
+    get_record_table(mica),
+    c(
+      "Station",
+      "Species",
+      "n",
+      "DateTimeOriginal",
+      "Date",
+      "Time",
+      "delta.time.secs",
+      "delta.time.mins",
+      "delta.time.hours",
+      "delta.time.days",
+      "Directory",
+      "FileName"
+    )
   )
-  testthat::expect_identical(names(record_table), expected_colnames)
 })
 
 test_that("nrows = n obs of identified individuals if minDeltaTime is 0", {

From 55d1ebab25012198853f5dcae6d7f49d4e855a1c Mon Sep 17 00:00:00 2001
From: Pieter Huybrechts <48065851+PietrH@users.noreply.github.com>
Date: Fri, 10 Nov 2023 10:28:46 +0100
Subject: [PATCH 28/35] add missing space in documentation

---
 R/get_cam_op.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/get_cam_op.R b/R/get_cam_op.R
index efb9d188..d3f3358f 100644
--- a/R/get_cam_op.R
+++ b/R/get_cam_op.R
@@ -22,7 +22,7 @@
 #' @param session_col Column name to use for identifying the session. Default:
 #'   `NULL`. Use it for creating multi-session / multi-season detection
 #'   histories.
-#' @param use_prefix Logical (`TRUE`or `FALSE`). If `TRUE` the returned row
+#' @param use_prefix Logical (`TRUE` or `FALSE`). If `TRUE` the returned row
 #'   names will start with prefix `"Station"` as returned by
 #'   [camtrapR::cameraOperation()](
 #'   https://jniedballa.github.io/camtrapR/reference/cameraOperation.html).

From 68f591cf9f832b1e637d150d72f9fdd2fbfaceb0 Mon Sep 17 00:00:00 2001
From: Pieter Huybrechts <48065851+PietrH@users.noreply.github.com>
Date: Fri, 10 Nov 2023 10:38:12 +0100
Subject: [PATCH 29/35] use `is.matrix()` for a slightly better failure message

---
 tests/testthat/test-get_cam_op.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/testthat/test-get_cam_op.R b/tests/testthat/test-get_cam_op.R
index 48a9588e..f7748193 100644
--- a/tests/testthat/test-get_cam_op.R
+++ b/tests/testthat/test-get_cam_op.R
@@ -73,7 +73,7 @@ test_that("input camtrap dp is checked properly", {
 
 test_that("output is a matrix", {
   cam_op_matrix <- get_cam_op(mica)
-  expect_true("matrix" %in% class(cam_op_matrix))
+  expect_true(is.matrix(cam_op_matrix))
 })
 
 test_that("output matrix has locations as rownames", {

From 3af4488f32880f83aeea986917e1d58bc56044e6 Mon Sep 17 00:00:00 2001
From: Pieter Huybrechts <48065851+PietrH@users.noreply.github.com>
Date: Fri, 10 Nov 2023 10:38:37 +0100
Subject: [PATCH 30/35] Mention the specific argument needed to specify

---
 R/get_cam_op.R    | 5 +++--
 man/get_cam_op.Rd | 7 ++++---
 2 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/R/get_cam_op.R b/R/get_cam_op.R
index d3f3358f..b9a8e395 100644
--- a/R/get_cam_op.R
+++ b/R/get_cam_op.R
@@ -6,8 +6,9 @@
 #' https://jniedballa.github.io/camtrapR/reference/cameraOperation.html).
 #'
 #' The deployment data are by default grouped by `locationName` (station ID in
-#' camtrapR jargon) or another column specified by the user. If multiple
-#' deployments are linked to same location, daily efforts higher than 1 occur.
+#' camtrapR jargon) or another column specified by the user via the 
+#' `station_col` argument. If multiple deployments are linked to same location, 
+#' daily efforts higher than 1 occur.
 #'
 #' Partially active days, e.g. the first or the last day of a deployment, result
 #' in decimal effort values as in [camtrapR::cameraOperation()](
diff --git a/man/get_cam_op.Rd b/man/get_cam_op.Rd
index 8f83da99..81f01f45 100644
--- a/man/get_cam_op.Rd
+++ b/man/get_cam_op.Rd
@@ -30,7 +30,7 @@ get_cam_op(
 \code{NULL}. Use it for creating multi-session / multi-season detection
 histories.}
 
-\item{use_prefix}{Logical (\code{TRUE}or \code{FALSE}). If \code{TRUE} the returned row
+\item{use_prefix}{Logical (\code{TRUE} or \code{FALSE}). If \code{TRUE} the returned row
 names will start with prefix \code{"Station"} as returned by
 \href{https://jniedballa.github.io/camtrapR/reference/cameraOperation.html}{camtrapR::cameraOperation()}.
 Default: \code{FALSE}.}
@@ -47,8 +47,9 @@ returned by \href{https://jniedballa.github.io/camtrapR/reference/cameraOperatio
 }
 \details{
 The deployment data are by default grouped by \code{locationName} (station ID in
-camtrapR jargon) or another column specified by the user. If multiple
-deployments are linked to same location, daily efforts higher than 1 occur.
+camtrapR jargon) or another column specified by the user via the
+\code{station_col} argument. If multiple deployments are linked to same location,
+daily efforts higher than 1 occur.
 
 Partially active days, e.g. the first or the last day of a deployment, result
 in decimal effort values as in \href{https://jniedballa.github.io/camtrapR/reference/cameraOperation.html}{camtrapR::cameraOperation()}.

From e7d99ad5ab1619a09a4bac561089579fda82b732 Mon Sep 17 00:00:00 2001
From: Pieter Huybrechts <48065851+PietrH@users.noreply.github.com>
Date: Fri, 10 Nov 2023 11:04:25 +0100
Subject: [PATCH 31/35] Reduce numerical tolerance, increase strictness

---
 tests/testthat/test-get_cam_op.R | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/tests/testthat/test-get_cam_op.R b/tests/testthat/test-get_cam_op.R
index f7748193..3c1febdd 100644
--- a/tests/testthat/test-get_cam_op.R
+++ b/tests/testthat/test-get_cam_op.R
@@ -80,8 +80,8 @@ test_that("output matrix has locations as rownames", {
   cam_op_matrix <- get_cam_op(mica)
   locations <- mica$data$deployments$locationName
   n_locations <- length(mica$data$deployments$locationName)
-  expect_equal(nrow(cam_op_matrix), n_locations)
-  expect_equal(row.names(cam_op_matrix), locations)
+  expect_identical(nrow(cam_op_matrix), n_locations)
+  expect_identical(row.names(cam_op_matrix), locations)
 })
 
 test_that("output matrix has sessions addded to locations as rownames", {
@@ -99,7 +99,7 @@ test_that("output matrix has sessions addded to locations as rownames", {
                               sep = "__SESS_"
   )
   n_locations <- length(mica_sessions$data$deployments$locationName)
-  expect_equal(nrow(cam_op_matrix), n_locations)
+  expect_identical(nrow(cam_op_matrix), n_locations)
   expect_identical(row.names(cam_op_matrix), locations_sessions)
 })
 
@@ -112,7 +112,7 @@ test_that("output matrix has camera IDs addded to locations as rownames", {
                              sep = "__CAM_"
   )
   n_locations <- length(mica_cameras$data$deployments$locationName)
-  expect_equal(nrow(cam_op_matrix), n_locations)
+  expect_identical(nrow(cam_op_matrix), n_locations)
   expect_identical(row.names(cam_op_matrix), locations_cameras)
 })
 
@@ -134,7 +134,7 @@ test_that(
                                 sep = "__CAM_"
     )
     n_locations <- length(mica_sess_cam$data$deployments$locationName)
-    expect_equal(nrow(cam_op_matrix), n_locations)
+    expect_identical(nrow(cam_op_matrix), n_locations)
     expect_identical(row.names(cam_op_matrix), locations_sess_cam)
 })
 
@@ -204,16 +204,16 @@ test_that("output matrix has Station prefix in rownames", {
   cam_op_matrix <- get_cam_op(mica, use_prefix = TRUE)
   locations <- paste0("Station", mica$data$deployments$locationName)
   n_locations <- length(mica$data$deployments$locationName)
-  expect_equal(nrow(cam_op_matrix), n_locations)
-  expect_equal(row.names(cam_op_matrix), locations)
+  expect_identical(nrow(cam_op_matrix), n_locations)
+  expect_identical(row.names(cam_op_matrix), locations)
 })
 
 test_that("output matrix has specified location column as rownames", {
   cam_op_matrix <- get_cam_op(mica, station_col = "locationID")
   locations <- mica$data$deployments$locationID
   n_locations <- length(mica$data$deployments$locationID)
-  expect_equal(nrow(cam_op_matrix), n_locations)
-  expect_equal(row.names(cam_op_matrix), locations)
+  expect_identical(nrow(cam_op_matrix), n_locations)
+  expect_identical(row.names(cam_op_matrix), locations)
 })
 
 
@@ -225,8 +225,8 @@ test_that("output matrix has all deployment days as colnames", {
   )
   days_activity <- as.character(days_activity)
   n_days <- length(days_activity)
-  expect_equal(ncol(cam_op_matrix), n_days)
-  expect_equal(colnames(cam_op_matrix), days_activity)
+  expect_identical(ncol(cam_op_matrix), n_days)
+  expect_identical(colnames(cam_op_matrix), days_activity)
 })
 
 test_that("daily effort is > 0 for fully active days, NA for inactive days", {
@@ -321,7 +321,7 @@ test_that("filtering predicates are allowed and work well", {
   filtered_cam_op_matrix <- suppressMessages(
     get_cam_op(mica, pred_lt("longitude", 4.0))
   )
-  expect_equal(rownames(filtered_cam_op_matrix), "Mica Viane")
+  expect_identical(rownames(filtered_cam_op_matrix), "Mica Viane")
 })
 
 test_that("Argument datapkg is deprecated: warning returned", {

From a31614dbef6a1a15eaafd3fe1a8dee66e949ad8e Mon Sep 17 00:00:00 2001
From: Pieter Huybrechts <48065851+PietrH@users.noreply.github.com>
Date: Fri, 10 Nov 2023 11:09:31 +0100
Subject: [PATCH 32/35] use comparison expectations for better failure messages

---
 tests/testthat/test-get_cam_op.R       | 12 ++++++------
 tests/testthat/test-get_record_table.R |  4 ++--
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/tests/testthat/test-get_cam_op.R b/tests/testthat/test-get_cam_op.R
index 3c1febdd..948f6cf0 100644
--- a/tests/testthat/test-get_cam_op.R
+++ b/tests/testthat/test-get_cam_op.R
@@ -258,10 +258,10 @@ test_that("daily effort is > 0 and < 1 for partial active days (start/end)", {
   location <- mica$data$deployments$locationName[4]
   start <- as.character(as.Date(mica$data$deployments$start[4]))
   end <- as.character(as.Date(mica$data$deployments$end[4]))
-  expect_true(cam_op_matrix[4, start] > 0)
-  expect_true(cam_op_matrix[4, start] < 1)
-  expect_true(cam_op_matrix[4, end] > 0)
-  expect_true(cam_op_matrix[4, end] < 1)
+  expect_gt(cam_op_matrix[4, start], 0)
+  expect_lt(cam_op_matrix[4, start],1)
+  expect_gt(cam_op_matrix[4, end], 0)
+  expect_lt(cam_op_matrix[4, end], 1)
 })
 
 test_that(
@@ -283,8 +283,8 @@ test_that(
     expect_true(
       nrow(cam_op_matrix) == length(unique(mica1$data$deployments$locationName))
     )
-    expect_true(cam_op_matrix[1, first_full_day_two_deps] > 1)
-    expect_true(cam_op_matrix[1, last_full_day_two_deps] > 1)
+    expect_gt(cam_op_matrix[1, first_full_day_two_deps], 1)
+    expect_gt(cam_op_matrix[1, last_full_day_two_deps], 1)
   }
 )
 
diff --git a/tests/testthat/test-get_record_table.R b/tests/testthat/test-get_record_table.R
index 49d0874b..7e5f62bf 100644
--- a/tests/testthat/test-get_record_table.R
+++ b/tests/testthat/test-get_record_table.R
@@ -118,8 +118,8 @@ test_that("Higher minDeltaTime means less rows returned", {
     deltaTimeComparedTo = "lastRecord"
   )) %>%
     nrow()
-  testthat::expect_true(nrow_delta_10000 < nrow_delta_0)
-  testthat::expect_true(nrow_delta_100000 < nrow_delta_10000)
+  expect_lt(nrow_delta_10000, nrow_delta_0)
+  expect_lt(nrow_delta_100000, nrow_delta_10000)
 })
 
 test_that("stations names are equal to values in column passed to StationCOl", {

From 4dcdd6564465d90808737dc320985d83ea8e9571 Mon Sep 17 00:00:00 2001
From: Pieter Huybrechts <48065851+PietrH@users.noreply.github.com>
Date: Fri, 10 Nov 2023 11:37:01 +0100
Subject: [PATCH 33/35] increase test strictness by removing tolerance

---
 tests/testthat/test-get_record_table.R | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/tests/testthat/test-get_record_table.R b/tests/testthat/test-get_record_table.R
index 7e5f62bf..3761fbb3 100644
--- a/tests/testthat/test-get_record_table.R
+++ b/tests/testthat/test-get_record_table.R
@@ -44,7 +44,7 @@ test_that("if not integer, minDeltaTime is set to integer (floor)", {
       deltaTimeComparedTo = "lastRecord"
     )
   )
-  testthat::expect_equal(record_table_int, record_table_dec)
+  testthat::expect_identical(record_table_int, record_table_dec)
 })
 
 test_that("input of get_record_table, removeDuplicateRecords, is checked properly", {
@@ -79,7 +79,7 @@ test_that("right columns are returned", {
 
 test_that("nrows = n obs of identified individuals if minDeltaTime is 0", {
   nrow_output <- get_record_table(mica, minDeltaTime = 0) %>% nrow()
-  testthat::expect_equal(
+  testthat::expect_identical(
     nrow_output,
     mica$data$observations %>%
       dplyr::filter(!is.na(scientificName)) %>% nrow()
@@ -99,7 +99,7 @@ test_that("nrows = n obs of red foxes if all other species are excluded", {
   )
   nrow_foxes <- get_record_table(mica, exclude = species_to_exclude) %>%
     nrow()
-  testthat::expect_equal(
+  testthat::expect_identical(
     nrow_foxes,
     mica$data$observations %>%
       dplyr::filter(scientificName == "Vulpes vulpes") %>% nrow()
@@ -197,13 +197,13 @@ test_that(paste(
   rec_table_dup <- get_record_table(mica_dup,
     removeDuplicateRecords = FALSE
   )
-  testthat::expect_equal(nrow(rec_table), 1)
-  testthat::expect_equal(
+  testthat::expect_identical(nrow(rec_table), 1L)
+  testthat::expect_identical(
     rec_table$DateTimeOriginal, mica$data$observations$timestamp[3]
   )
-  testthat::expect_equal(rec_table$delta.time.secs, 0)
-  testthat::expect_equal(names(rec_table_dup), names(rec_table))
-  testthat::expect_equal(
+  testthat::expect_identical(rec_table$delta.time.secs, 0)
+  testthat::expect_identical(names(rec_table_dup), names(rec_table))
+  testthat::expect_identical(
     nrow(rec_table_dup),
     nrow(mica_dup$data$observations)
   )

From c264ebafa5b3cb27388ff7028b1bbb998f3d4351 Mon Sep 17 00:00:00 2001
From: Pieter Huybrechts <48065851+PietrH@users.noreply.github.com>
Date: Fri, 10 Nov 2023 11:40:36 +0100
Subject: [PATCH 34/35] No need to announce testthat namespace in tests

easier to read and slight performance benefit
---
 tests/testthat/test-calc_animal_pos.R  | 38 ++++++++++----------
 tests/testthat/test-check_species.R    | 20 +++++------
 tests/testthat/test-get_effort.R       | 36 +++++++++----------
 tests/testthat/test-get_record_table.R | 48 +++++++++++++-------------
 4 files changed, 71 insertions(+), 71 deletions(-)

diff --git a/tests/testthat/test-calc_animal_pos.R b/tests/testthat/test-calc_animal_pos.R
index 02d603d1..b86fdddf 100644
--- a/tests/testthat/test-calc_animal_pos.R
+++ b/tests/testthat/test-calc_animal_pos.R
@@ -1,10 +1,10 @@
-testthat::test_that(
+test_that(
   "calc_animal_pos returns errors if animal_pos is not valid",
   {
     # animal_pos is not a dataframe
-    testthat::expect_error(calc_animal_pos(1, list(a = "a")))
+    expect_error(calc_animal_pos(1, list(a = "a")))
     # x, y and sequenceID columns missing
-    testthat::expect_error(
+    expect_error(
       calc_animal_pos(
         dplyr::tibble(
           deploymentID = "A",
@@ -16,7 +16,7 @@ testthat::test_that(
       "Columns `sequenceID`, `x` and `y` not found in `animal_pos`."
     )
     # imageWidth, imageHeight and deploymentID columns missing
-    testthat::expect_error(
+    expect_error(
       calc_animal_pos(
         dplyr::tibble(
           width = 5,
@@ -31,7 +31,7 @@ testthat::test_that(
   }
 )
 
-testthat::test_that(
+test_that(
   "calc_animal_post returns errors if calib_models is not valid",
   {
     df <- dplyr::tibble(
@@ -44,18 +44,18 @@ testthat::test_that(
       deployment = 2
     )
     # calib_models is not a (named) list
-    testthat::expect_error(calc_animal_pos(df, calib_models = 2))
-    testthat::expect_error(
+    expect_error(calc_animal_pos(df, calib_models = 2))
+    expect_error(
       calc_animal_pos(df, calib_models = list(2)),
       "`calib_models` must be a named list."
     )
   }
 )
 
-testthat::test_that("Deployments with no matching calibration model", {
+test_that("Deployments with no matching calibration model", {
   missing_calib_model <- dep_calib_models
   missing_calib_model$S01 <- NULL
-  testthat::expect_warning(
+  expect_warning(
     calc_animal_pos(animal_positions, missing_calib_model),
     paste(
       "Some deployments have no matching calibration model",
@@ -64,11 +64,11 @@ testthat::test_that("Deployments with no matching calibration model", {
   )
 })
 
-testthat::test_that("Deploys with multiple values for image width/height", {
+test_that("Deploys with multiple values for image width/height", {
   multi_pixel_dim <- animal_positions
   multi_pixel_dim$imageWidth[1] <- 4096
   multi_pixel_dim$imageHeight[20] <- 3072
-  testthat::expect_warning(
+  expect_warning(
     calc_animal_pos(multi_pixel_dim, dep_calib_models),
     paste(
       "There is more than one unique value per deployment for `imageWidth`",
@@ -78,27 +78,27 @@ testthat::test_that("Deploys with multiple values for image width/height", {
   )
 })
 
-testthat::test_that("Right output", {
+test_that("Right output", {
   output <- calc_animal_pos(animal_positions, dep_calib_models)
   # right class
-  testthat::expect_true(inherits(output, c("tbl_df", "tbl", "data.frame")))
+  expect_true(inherits(output, c("tbl_df", "tbl", "data.frame")))
   # right number of rows
-  testthat::expect_true(nrow(output) == nrow(animal_positions))
+  expect_true(nrow(output) == nrow(animal_positions))
   # right number of columns
-  testthat::expect_true(ncol(output) == ncol(animal_positions) + 3)
+  expect_true(ncol(output) == ncol(animal_positions) + 3)
   # new columns have right names
-  testthat::expect_true(
+  expect_true(
     all(c("radius", "angle", "frame_count") %in% names(output))
   )
   # output is exactly the same as animal_positions except for the new columns
-  testthat::expect_equal(
+  expect_equal(
     output %>%
       dplyr::select(-c(radius, angle, frame_count)),
     animal_positions
   )
 })
 
-testthat::test_that("Right output with non default column names", {
+test_that("Right output with non default column names", {
   output_default <- calc_animal_pos(animal_positions, dep_calib_models)
   animal_positions_non_default <- dplyr::rename(
     animal_positions,
@@ -121,5 +121,5 @@ testthat::test_that("Right output with non default column names", {
   # content is the same (column names are different)
   names(output) <- as.character(1:length(names(output)))
   names(output_default) <- as.character(1:length(names(output_default)))
-  testthat::expect_equal(output, output_default)
+  expect_equal(output, output_default)
 })
diff --git a/tests/testthat/test-check_species.R b/tests/testthat/test-check_species.R
index e60681c6..a4079a15 100644
--- a/tests/testthat/test-check_species.R
+++ b/tests/testthat/test-check_species.R
@@ -1,10 +1,10 @@
 test_that("Error is returned if species is NULL or of length 0", {
-  testthat::expect_error(check_species(mica, NULL))
-  testthat::expect_error(check_species(mica, character(0)))
+  expect_error(check_species(mica, NULL))
+  expect_error(check_species(mica, character(0)))
 })
 
 test_that("Error is returned if one or more species are invalid", {
-  testthat::expect_error(
+  expect_error(
     check_species(
       mica,
       c(
@@ -30,31 +30,31 @@ test_that("Error is returned if one or more species are invalid", {
 test_that("If input is a scientific name, the result is equal to input", {
   sc_name <- "Anas strepera"
   species <- check_species(mica, sc_name)
-  testthat::expect_equal(species, sc_name)
+  expect_equal(species, sc_name)
 })
 
 test_that("Multiput scientific names are allowed", {
   sc_names <- c("Anas strepera", "Ardea cinerea")
   species <- check_species(mica, sc_names)
-  testthat::expect_equal(species, sc_names)
+  expect_equal(species, sc_names)
 })
 
 test_that("Function works with vernacular names", {
   vn_names <- c("beech marten", "mallard")
   species <- suppressMessages(check_species(mica, vn_names))
-  testthat::expect_equal(species, c("Martes foina", "Anas platyrhynchos"))
+  expect_equal(species, c("Martes foina", "Anas platyrhynchos"))
 })
 
 test_that("Functions works well with vernacular names of different languages", {
   vn_names <- c("beech marten", "wilde eend")
   species <- suppressMessages(check_species(mica, vn_names))
-  testthat::expect_equal(species, c("Martes foina", "Anas platyrhynchos"))
+  expect_equal(species, c("Martes foina", "Anas platyrhynchos"))
 })
 
 test_that("Functions works with a mix of scientific and vernacular names", {
   mixed_names <- c("mallard", "steenmarter", "Castor fiber")
   species <- suppressMessages(check_species(mica, mixed_names))
-  testthat::expect_equal(
+  expect_equal(
     species,
     c(
       "Anas platyrhynchos",
@@ -66,11 +66,11 @@ test_that("Functions works with a mix of scientific and vernacular names", {
 
 test_that("Taxon IDs are not allowed", {
   taxon_id <- mica$taxonomic[[1]]$taxonID
-  testthat::expect_error(check_species(mica, taxon_id))
+  expect_error(check_species(mica, taxon_id))
 })
 
 test_that("Functions works case insensitively", {
   vn_name <- suppressMessages(check_species(mica, c("MallARD")))
   species <- check_species(mica, vn_name)
-  testthat::expect_equal(species, "Anas platyrhynchos")
+  expect_equal(species, "Anas platyrhynchos")
 })
diff --git a/tests/testthat/test-get_effort.R b/tests/testthat/test-get_effort.R
index 86de9ad1..3f7e3c9b 100644
--- a/tests/testthat/test-get_effort.R
+++ b/tests/testthat/test-get_effort.R
@@ -1,5 +1,5 @@
-testthat::test_that("get_effort returns error for invalid effort units", {
-  testthat::expect_error(
+test_that("get_effort returns error for invalid effort units", {
+  expect_error(
     get_effort(mica, unit = "bad_unit"),
     paste0(
       "Invalid value for unit parameter: bad_unit.\n",
@@ -7,7 +7,7 @@ testthat::test_that("get_effort returns error for invalid effort units", {
     ),
     fixed = TRUE
   )
-  testthat::expect_error(
+  expect_error(
     get_effort(mica, unit = NULL),
     paste0(
       "Invalid value for unit parameter: NULL.\n",
@@ -17,50 +17,50 @@ testthat::test_that("get_effort returns error for invalid effort units", {
   )
 })
 
-testthat::test_that("get_effort returns error for invalid datapackage", {
-  testthat::expect_error(get_effort(mica$data$deployments))
+test_that("get_effort returns error for invalid datapackage", {
+  expect_error(get_effort(mica$data$deployments))
 })
 
 
-testthat::test_that("values in column unit are all the same", {
+test_that("values in column unit are all the same", {
   effort_df <- get_effort(mica)
   distinct_efffort_unit_values <- unique(effort_df$unit)
-  testthat::expect_equal(length(distinct_efffort_unit_values), 1)
+  expect_equal(length(distinct_efffort_unit_values), 1)
 })
 
-testthat::test_that("column effort_duration is of class 'Duration'", {
+test_that("column effort_duration is of class 'Duration'", {
   effort_df <- get_effort(mica)
-  testthat::expect_equal(class(effort_df$effort_duration)[1], "Duration")
-  testthat::expect_equal(
+  expect_equal(class(effort_df$effort_duration)[1], "Duration")
+  expect_equal(
     attr(class(effort_df$effort_duration), which = "package"),
     "lubridate"
   )
 })
 
-testthat::test_that("column unit is always equal to argument unit", {
+test_that("column unit is always equal to argument unit", {
   unit_to_test <- c("second", "minute", "hour", "day", "month", "year")
   for (chosen_unit in unit_to_test) {
     effort_df <- get_effort(mica, unit = chosen_unit)
     efffort_unit_value <- unique(effort_df$unit)
-    testthat::expect_equal(efffort_unit_value, chosen_unit)
+    expect_equal(efffort_unit_value, chosen_unit)
   }
 })
 
 
-testthat::test_that("get_effort returns the right dataframe", {
+test_that("get_effort returns the right dataframe", {
   effort_df <- get_effort(mica)
 
   # type list
-  testthat::expect_type(effort_df, "list")
+  expect_type(effort_df, "list")
 
   # class tibble data.frame
-  testthat::expect_equal(
+  expect_equal(
     class(effort_df),
     c("tbl_df", "tbl", "data.frame")
   )
 
   # columns deploymentID, effort, unit and effort_duration only
-  testthat::expect_equal(
+  expect_equal(
     names(effort_df),
     c(
       "deploymentID",
@@ -72,13 +72,13 @@ testthat::test_that("get_effort returns the right dataframe", {
 })
 
 
-testthat::test_that("get_effort returns the right number of rows", {
+test_that("get_effort returns the right number of rows", {
   effort_df <- get_effort(mica)
   all_deployments <- unique(mica$data$deployments$deploymentID)
   n_all_deployments <- length(all_deployments)
 
   # number of rows should be equal to number of deployments
-  testthat::expect_equal(
+  expect_equal(
     nrow(effort_df),
     n_all_deployments
   )
diff --git a/tests/testthat/test-get_record_table.R b/tests/testthat/test-get_record_table.R
index 3761fbb3..75a12015 100644
--- a/tests/testthat/test-get_record_table.R
+++ b/tests/testthat/test-get_record_table.R
@@ -1,33 +1,33 @@
 test_that("input of get_record_table, camtrap dp, is checked properly", {
-  testthat::expect_error(get_record_table("aaa"))
-  testthat::expect_error(get_record_table(1))
+  expect_error(get_record_table("aaa"))
+  expect_error(get_record_table(1))
 })
 
 test_that("input of get_record_table, stationCol, is checked properly", {
-  testthat::expect_error(get_record_table(mica, stationCol = "aaa"))
+  expect_error(get_record_table(mica, stationCol = "aaa"))
 })
 
 test_that("input of get_record_table, exclude, is checked properly", {
-  testthat::expect_error(get_record_table(mica, exclude = "rattus not existing"))
+  expect_error(get_record_table(mica, exclude = "rattus not existing"))
 })
 
 test_that("input of get_record_table, minDeltaTime, is checked properly", {
-  testthat::expect_error(
+  expect_error(
     get_record_table(mica, minDeltaTime = "1"),
     "`minDeltaTime` must be a number greater or equal to 0."
   )
-  testthat::expect_error(
+  expect_error(
     get_record_table(mica, minDeltaTime = -10),
     "`minDeltaTime` must be a number greater or equal to 0."
   )
 })
 
 test_that("input of get_record_table, deltaTimeComparedTo, is checked properly", {
-  testthat::expect_error(get_record_table(mica,
+  expect_error(get_record_table(mica,
     minDeltaTime = 100,
     deltaTimeComparedTo = NULL
   ))
-  testthat::expect_error(get_record_table(mica,
+  expect_error(get_record_table(mica,
     minDeltaTime = 100,
     deltaTimeComparedTo = "not valid"
   ))
@@ -44,15 +44,15 @@ test_that("if not integer, minDeltaTime is set to integer (floor)", {
       deltaTimeComparedTo = "lastRecord"
     )
   )
-  testthat::expect_identical(record_table_int, record_table_dec)
+  expect_identical(record_table_int, record_table_dec)
 })
 
 test_that("input of get_record_table, removeDuplicateRecords, is checked properly", {
   # only TRUE or FALSE are allowed
-  testthat::expect_error(get_record_table(mica,
+  expect_error(get_record_table(mica,
     removeDuplicateRecords = 5
   ))
-  testthat::expect_error(get_record_table(mica,
+  expect_error(get_record_table(mica,
     removeDuplicateRecords = NA
   ))
 })
@@ -79,7 +79,7 @@ test_that("right columns are returned", {
 
 test_that("nrows = n obs of identified individuals if minDeltaTime is 0", {
   nrow_output <- get_record_table(mica, minDeltaTime = 0) %>% nrow()
-  testthat::expect_identical(
+  expect_identical(
     nrow_output,
     mica$data$observations %>%
       dplyr::filter(!is.na(scientificName)) %>% nrow()
@@ -99,7 +99,7 @@ test_that("nrows = n obs of red foxes if all other species are excluded", {
   )
   nrow_foxes <- get_record_table(mica, exclude = species_to_exclude) %>%
     nrow()
-  testthat::expect_identical(
+  expect_identical(
     nrow_foxes,
     mica$data$observations %>%
       dplyr::filter(scientificName == "Vulpes vulpes") %>% nrow()
@@ -128,21 +128,21 @@ test_that("stations names are equal to values in column passed to StationCOl", {
     dplyr::distinct(Station) %>%
     dplyr::pull()
   location_names <- unique(mica$data$deployments$locationName)
-  testthat::expect_true(all(stations %in% location_names))
+  expect_true(all(stations %in% location_names))
 
   # use locationID as Station
   stations <- get_record_table(mica, stationCol = "locationID") %>%
     dplyr::distinct(Station) %>%
     dplyr::pull()
   location_ids <- unique(mica$data$deployments$locationID)
-  testthat::expect_true(all(stations %in% location_ids))
+  expect_true(all(stations %in% location_ids))
 })
 
 test_that("Directory and Filename columns are lists", {
   file_values <- get_record_table(mica) %>%
     dplyr::select(Directory, FileName)
-  testthat::expect_true(class(file_values$Directory) == "list")
-  testthat::expect_true(class(file_values$FileName) == "list")
+  expect_true(class(file_values$Directory) == "list")
+  expect_true(class(file_values$FileName) == "list")
 })
 
 test_that(
@@ -177,7 +177,7 @@ test_that(
       dplyr::left_join(n_media,
         by = "sequenceID"
       )
-    testthat::expect_equal(output$len, output$n_media)
+    expect_equal(output$len, output$n_media)
   }
 )
 
@@ -197,13 +197,13 @@ test_that(paste(
   rec_table_dup <- get_record_table(mica_dup,
     removeDuplicateRecords = FALSE
   )
-  testthat::expect_identical(nrow(rec_table), 1L)
-  testthat::expect_identical(
+  expect_identical(nrow(rec_table), 1L)
+  expect_identical(
     rec_table$DateTimeOriginal, mica$data$observations$timestamp[3]
   )
-  testthat::expect_identical(rec_table$delta.time.secs, 0)
-  testthat::expect_identical(names(rec_table_dup), names(rec_table))
-  testthat::expect_identical(
+  expect_identical(rec_table$delta.time.secs, 0)
+  expect_identical(names(rec_table_dup), names(rec_table))
+  expect_identical(
     nrow(rec_table_dup),
     nrow(mica_dup$data$observations)
   )
@@ -216,7 +216,7 @@ test_that("filtering predicates are allowed and work well", {
   stations_calculate <- mica$data$deployments %>%
     dplyr::filter(longitude < 4.0) %>%
     dplyr::pull(locationName)
-  testthat::expect_identical(stations, stations_calculate)
+  expect_identical(stations, stations_calculate)
 })
 
 test_that("Argument datapkg is deprecated: warning returned", {

From 41afe9af1c2140cad48c998a94dade55568a57dc Mon Sep 17 00:00:00 2001
From: Pieter Huybrechts <48065851+PietrH@users.noreply.github.com>
Date: Fri, 10 Nov 2023 11:48:50 +0100
Subject: [PATCH 35/35] clarify default behaviour

---
 R/get_record_table.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/get_record_table.R b/R/get_record_table.R
index 1c1e9610..0f3f6235 100644
--- a/R/get_record_table.R
+++ b/R/get_record_table.R
@@ -101,7 +101,7 @@
 #' mica_dup$data$observations[4, "deploymentID"] <- mica_dup$data$observations$deploymentID[3]
 #' mica_dup$data$observations[4, "timestamp"] <- mica_dup$data$observations$timestamp[3]
 #'
-#' # duplicate removed
+#' # duplicates are removed by default by get_record_table()
 #' get_record_table(mica_dup)
 #' 
 #' # duplicate not removed