From 3f85f5bbdea466ca69181d7eda6ae7e6f9d08b80 Mon Sep 17 00:00:00 2001
From: Pieter Huybrechts <48065851+PietrH@users.noreply.github.com>
Date: Fri, 14 Jul 2023 12:04:03 +0200
Subject: [PATCH 01/40] move `check_package()` outside of zzz.R

---
 R/check_package.R | 53 ++++++++++++++++++++++++++++++++++++++++++++++
 R/zzz.R           | 54 -----------------------------------------------
 2 files changed, 53 insertions(+), 54 deletions(-)
 create mode 100644 R/check_package.R

diff --git a/R/check_package.R b/R/check_package.R
new file mode 100644
index 00000000..625d80da
--- /dev/null
+++ b/R/check_package.R
@@ -0,0 +1,53 @@
+#' Check validity camera trap data package
+#'
+#' Checks the validity of a camera trap data package.
+#' It checks whether the data package is a list containing an element called
+#' `data` with the following resources as tibble data frames:
+#' - `observations`
+#' - `multimedia`
+#' - `deployments`
+#'
+#' @param package Camera trap data package
+#' @param datapkg Deprecated. Use `package` instead.
+#' @return A camera trap data package.
+#' @noRd
+check_package <- function(package = NULL,
+                          datapkg = NULL,
+                          function_name) {
+  if (lifecycle::is_present(datapkg) & !is.null(datapkg)) {
+    lifecycle::deprecate_warn(
+      when = "0.16.0",
+      what = paste0(function_name, "(datapkg = )"),
+      with = paste0(function_name, "(package = )")
+    )
+    if (is.null(package)) {
+      package <- datapkg
+    }
+  }
+  # camera trap data package is a list
+  assertthat::assert_that(is.list(package))
+  assertthat::assert_that(!is.data.frame(package))
+  # check existence of an element called data
+  assertthat::assert_that("data" %in% names(package))
+  # check validity data element of package: does it contain all 4 elements?
+  elements <- c("deployments", "media", "observations")
+  tables_absent <- names(elements)[
+    !names(elements) %in% names(package$data)
+  ]
+  n_tables_absent <- length(tables_absent)
+  assertthat::assert_that(n_tables_absent == 0,
+                          msg = glue::glue(
+                            "Can't find {n_tables_absent} elements in data package: {tables_absent*}",
+                            .transformer = collapse_transformer(sep = ", ", last = " and ")
+                          )
+  )
+  
+  # check observations and deployments are data.frames
+  assertthat::assert_that(is.data.frame(package$data$observations))
+  assertthat::assert_that(is.data.frame(package$data$deployments))
+  # check multimedia is a data.frame (if imported, i.e. if not NULL)
+  if (!is.null(package$data$multimedia)) {
+    assertthat::assert_that(is.data.frame(package$data$multimedia))
+  }
+  package
+}
diff --git a/R/zzz.R b/R/zzz.R
index 3a772adf..c76a2746 100644
--- a/R/zzz.R
+++ b/R/zzz.R
@@ -1,57 +1,3 @@
-#' Check validity camera trap data package
-#'
-#' Checks the validity of a camera trap data package.
-#' It checks whether the data package is a list containing an element called
-#' `data` with the following resources as tibble data frames:
-#' - `observations`
-#' - `multimedia`
-#' - `deployments`
-#'
-#' @param package Camera trap data package
-#' @param datapkg Deprecated. Use `package` instead.
-#' @return A camera trap data package.
-#' @noRd
-check_package <- function(package = NULL,
-                          datapkg = NULL,
-                          function_name) {
-  if (lifecycle::is_present(datapkg) & !is.null(datapkg)) {
-    lifecycle::deprecate_warn(
-      when = "0.16.0",
-      what = paste0(function_name, "(datapkg = )"),
-      with = paste0(function_name, "(package = )")
-    )
-    if (is.null(package)) {
-      package <- datapkg
-    }
-  }
-  # camera trap data package is a list
-  assertthat::assert_that(is.list(package))
-  assertthat::assert_that(!is.data.frame(package))
-  # check existence of an element called data
-  assertthat::assert_that("data" %in% names(package))
-  # check validity data element of package: does it contain all 4 elements?
-  elements <- c("deployments", "media", "observations")
-  tables_absent <- names(elements)[
-    !names(elements) %in% names(package$data)
-  ]
-  n_tables_absent <- length(tables_absent)
-  assertthat::assert_that(n_tables_absent == 0,
-    msg = glue::glue(
-      "Can't find {n_tables_absent} elements in data package: {tables_absent*}",
-      .transformer = collapse_transformer(sep = ", ", last = " and ")
-    )
-  )
-
-  # check observations and deployments are data.frames
-  assertthat::assert_that(is.data.frame(package$data$observations))
-  assertthat::assert_that(is.data.frame(package$data$deployments))
-  # check multimedia is a data.frame (if imported, i.e. if not NULL)
-  if (!is.null(package$data$multimedia)) {
-    assertthat::assert_that(is.data.frame(package$data$multimedia))
-  }
-  package
-}
-
 #' Check input value against list of provided values
 #'
 #' Will return error message if an input value cannot be found in list of

From e871c25720d9f9e27fdde6e6b5117ae9a6425c9a Mon Sep 17 00:00:00 2001
From: Pieter Huybrechts <48065851+PietrH@users.noreply.github.com>
Date: Fri, 14 Jul 2023 12:09:07 +0200
Subject: [PATCH 02/40] rename multimedia to media

overlooked from old version, discussed with Damiano

Co-Authored-By: Damiano Oldoni <damiano.oldoni@inbo.be>
---
 R/check_package.R | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/R/check_package.R b/R/check_package.R
index 625d80da..13bb191c 100644
--- a/R/check_package.R
+++ b/R/check_package.R
@@ -4,7 +4,7 @@
 #' It checks whether the data package is a list containing an element called
 #' `data` with the following resources as tibble data frames:
 #' - `observations`
-#' - `multimedia`
+#' - `media`
 #' - `deployments`
 #'
 #' @param package Camera trap data package
@@ -45,9 +45,9 @@ check_package <- function(package = NULL,
   # check observations and deployments are data.frames
   assertthat::assert_that(is.data.frame(package$data$observations))
   assertthat::assert_that(is.data.frame(package$data$deployments))
-  # check multimedia is a data.frame (if imported, i.e. if not NULL)
-  if (!is.null(package$data$multimedia)) {
-    assertthat::assert_that(is.data.frame(package$data$multimedia))
+  # check media is a data.frame (if imported, i.e. if not NULL)
+  if (!is.null(package$data$media)) {
+    assertthat::assert_that(is.data.frame(package$data$media))
   }
   package
 }

From 06e3bfdaa2eecf94c7a8ff08b81410c99614d2d8 Mon Sep 17 00:00:00 2001
From: Pieter Huybrechts <48065851+PietrH@users.noreply.github.com>
Date: Fri, 14 Jul 2023 13:37:50 +0200
Subject: [PATCH 03/40] add comment on deprecation warning

---
 R/check_package.R | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/R/check_package.R b/R/check_package.R
index 13bb191c..cfa70904 100644
--- a/R/check_package.R
+++ b/R/check_package.R
@@ -14,6 +14,8 @@
 check_package <- function(package = NULL,
                           datapkg = NULL,
                           function_name) {
+  # Warn for usage of datapkg argument, mention (parent-) function name in error
+  # message
   if (lifecycle::is_present(datapkg) & !is.null(datapkg)) {
     lifecycle::deprecate_warn(
       when = "0.16.0",

From e16686dc6eb541d4e1ef6843abf6c1882ba3cba5 Mon Sep 17 00:00:00 2001
From: Pieter Huybrechts <48065851+PietrH@users.noreply.github.com>
Date: Fri, 14 Jul 2023 13:38:22 +0200
Subject: [PATCH 04/40] When a package is valid, return TRUE

---
 R/check_package.R | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/R/check_package.R b/R/check_package.R
index cfa70904..977a99de 100644
--- a/R/check_package.R
+++ b/R/check_package.R
@@ -51,5 +51,6 @@ check_package <- function(package = NULL,
   if (!is.null(package$data$media)) {
     assertthat::assert_that(is.data.frame(package$data$media))
   }
-  package
+  # When all is good, return TRUE
+  return(TRUE)
 }

From 4449ff6f3d7b11bcc6fb09ab52c61ed5bce5089f Mon Sep 17 00:00:00 2001
From: Pieter Huybrechts <48065851+PietrH@users.noreply.github.com>
Date: Fri, 14 Jul 2023 14:23:40 +0200
Subject: [PATCH 05/40] test deprecation warning

---
 tests/testthat/test-check_package.R | 12 ++++++++++++
 1 file changed, 12 insertions(+)
 create mode 100644 tests/testthat/test-check_package.R

diff --git a/tests/testthat/test-check_package.R b/tests/testthat/test-check_package.R
new file mode 100644
index 00000000..6bae3039
--- /dev/null
+++ b/tests/testthat/test-check_package.R
@@ -0,0 +1,12 @@
+test_that("check_package() returns depreciation warning on datapkg argument", {
+  expect_warning(
+    check_package(datapkg = mica, function_name = "function_name_here"),
+    regexp = "The `datapkg` argument of `function_name_here()` is deprecated as of camtraptor 0.16.0.",
+    fixed = TRUE
+  )
+})
+
+
+test_that("check_package() returns TRUE on valid package", {
+  expect_true(check_package(mica))
+})

From ed425774193fdd335c980e3b0fc042e17359c2f6 Mon Sep 17 00:00:00 2001
From: Pieter Huybrechts <48065851+PietrH@users.noreply.github.com>
Date: Fri, 14 Jul 2023 14:24:08 +0200
Subject: [PATCH 06/40] test package class

---
 tests/testthat/test-check_package.R | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/tests/testthat/test-check_package.R b/tests/testthat/test-check_package.R
index 6bae3039..fbc6cb5a 100644
--- a/tests/testthat/test-check_package.R
+++ b/tests/testthat/test-check_package.R
@@ -6,6 +6,19 @@ test_that("check_package() returns depreciation warning on datapkg argument", {
   )
 })
 
+test_that("check_package() returns error when package is not a list", {
+  expect_error(
+    check_package("not a list!"),
+    regexp = "package is not a list",
+    fixed = TRUE
+  )
+  expect_error(
+    check_package(data.frame(letters = c("a","b","c"), numbers = c(pi,2*pi,3*pi))),
+    regexp = "package is not a list",
+    fixed = TRUE
+  )
+})
+
 
 test_that("check_package() returns TRUE on valid package", {
   expect_true(check_package(mica))

From a541ff528351e0c74e487bc92867bc0b7dd93dd5 Mon Sep 17 00:00:00 2001
From: Pieter Huybrechts <48065851+PietrH@users.noreply.github.com>
Date: Fri, 14 Jul 2023 14:24:18 +0200
Subject: [PATCH 07/40] test for missing data elements

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

diff --git a/tests/testthat/test-check_package.R b/tests/testthat/test-check_package.R
index fbc6cb5a..9d942d89 100644
--- a/tests/testthat/test-check_package.R
+++ b/tests/testthat/test-check_package.R
@@ -19,6 +19,14 @@ test_that("check_package() returns error when package is not a list", {
   )
 })
 
+test_that("check_package() returns error on missing data", {
+  expect_error(
+    check_package(purrr::discard_at(mica,at = "data")),
+    regexp = "data element is missing from package",
+    fixed = TRUE
+  )
+})
+
 
 test_that("check_package() returns TRUE on valid package", {
   expect_true(check_package(mica))

From 2121af87d8c22a3a1db2727114d8086adf07bc1d Mon Sep 17 00:00:00 2001
From: Pieter Huybrechts <48065851+PietrH@users.noreply.github.com>
Date: Fri, 14 Jul 2023 14:24:38 +0200
Subject: [PATCH 08/40] test for number/identity of data elements

---
 tests/testthat/test-check_package.R | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/tests/testthat/test-check_package.R b/tests/testthat/test-check_package.R
index 9d942d89..f49158f1 100644
--- a/tests/testthat/test-check_package.R
+++ b/tests/testthat/test-check_package.R
@@ -27,6 +27,23 @@ test_that("check_package() returns error on missing data", {
   )
 })
 
+test_that("check_package() returns error if not all elements are present", {
+  mica_no_media <- mica
+  mica_no_media$data$media <- NULL
+  expect_error(
+    check_package(mica_no_media),
+    regexp = "Can't find 1 elements in data package: media",
+    fixed = TRUE
+  )
+  mica_no_media_no_obs <- mica_no_media
+  mica_no_media_no_obs$data$observations <- NULL
+  expect_error(
+    check_package(mica_no_media_no_obs),
+    regexp = "Can't find 2 elements in data package: media and observations",
+    fixed = TRUE
+  )
+})
+
 
 test_that("check_package() returns TRUE on valid package", {
   expect_true(check_package(mica))

From e0f2e5909509cba28c332d42f6a719fc75adee26 Mon Sep 17 00:00:00 2001
From: Pieter Huybrechts <48065851+PietrH@users.noreply.github.com>
Date: Fri, 14 Jul 2023 14:24:55 +0200
Subject: [PATCH 09/40] add error messages

---
 R/check_package.R | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/R/check_package.R b/R/check_package.R
index 977a99de..3cf13158 100644
--- a/R/check_package.R
+++ b/R/check_package.R
@@ -28,10 +28,12 @@ check_package <- function(package = NULL,
   }
   # camera trap data package is a list
   assertthat::assert_that(is.list(package))
-  assertthat::assert_that(!is.data.frame(package))
+  assertthat::assert_that(!is.data.frame(package),
+                          msg = "package is not a list")
   # check existence of an element called data
-  assertthat::assert_that("data" %in% names(package))
-  # check validity data element of package: does it contain all 4 elements?
+  assertthat::assert_that("data" %in% names(package),
+                          msg = "data element is missing from package")
+  # check validity data element of package: does it contain all 3 elements?
   elements <- c("deployments", "media", "observations")
   tables_absent <- names(elements)[
     !names(elements) %in% names(package$data)

From 36871af5405e52dad80742154e1514a04e707211 Mon Sep 17 00:00:00 2001
From: Pieter Huybrechts <48065851+PietrH@users.noreply.github.com>
Date: Fri, 14 Jul 2023 14:25:55 +0200
Subject: [PATCH 10/40] refactor so it works

test was failing
---
 R/check_package.R | 19 +++++++++----------
 1 file changed, 9 insertions(+), 10 deletions(-)

diff --git a/R/check_package.R b/R/check_package.R
index 3cf13158..53e1e4a1 100644
--- a/R/check_package.R
+++ b/R/check_package.R
@@ -35,16 +35,15 @@ check_package <- function(package = NULL,
                           msg = "data element is missing from package")
   # check validity data element of package: does it contain all 3 elements?
   elements <- c("deployments", "media", "observations")
-  tables_absent <- names(elements)[
-    !names(elements) %in% names(package$data)
-  ]
-  n_tables_absent <- length(tables_absent)
-  assertthat::assert_that(n_tables_absent == 0,
-                          msg = glue::glue(
-                            "Can't find {n_tables_absent} elements in data package: {tables_absent*}",
-                            .transformer = collapse_transformer(sep = ", ", last = " and ")
-                          )
-  )
+  tables_absent <- dplyr::setdiff(elements, names(package$data))
+  assertthat::assert_that(
+    assertthat::are_equal(elements,
+                          names(package$data)),
+    msg = glue::glue(
+      "Can't find {n_tables_absent} elements in data package: {tables_absent*}",
+      .transformer = collapse_transformer(sep = ", ", last = " and "),
+      n_tables_absent = length(tables_absent)
+    ))
   
   # check observations and deployments are data.frames
   assertthat::assert_that(is.data.frame(package$data$observations))

From 81c837103e362774fdcee93e2fa00af35252b401 Mon Sep 17 00:00:00 2001
From: Pieter Huybrechts <48065851+PietrH@users.noreply.github.com>
Date: Fri, 14 Jul 2023 14:56:52 +0200
Subject: [PATCH 11/40] test for data.frame elements

---
 tests/testthat/test-check_package.R | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/tests/testthat/test-check_package.R b/tests/testthat/test-check_package.R
index f49158f1..a87597c3 100644
--- a/tests/testthat/test-check_package.R
+++ b/tests/testthat/test-check_package.R
@@ -44,6 +44,27 @@ test_that("check_package() returns error if not all elements are present", {
   )
 })
 
+test_that("check_package() returns error if observations is not a data.frame", {
+  mica_listed <- mica
+  mica_listed$data$observations <- as.list(mica_listed$data$observations)
+  
+  expect_error(
+    check_package(mica_listed),
+    regexp = "package$data$observations is not a data frame",
+    fixed = TRUE
+  )
+})
+
+test_that("check_package() returns error if deployments is not a data.frame", {
+  mica_listed <- mica
+  mica_listed$data$deployments <- as.list(mica_listed$data$deployments)
+  expect_error(
+    check_package(mica_listed),
+    regexp = "package$data$deployments is not a data frame",
+    fixed = TRUE
+  )
+})
+
 
 test_that("check_package() returns TRUE on valid package", {
   expect_true(check_package(mica))

From 9e4f5ccdd1ecda6cf7ceb3f40a9392f2a00a1c38 Mon Sep 17 00:00:00 2001
From: Pieter Huybrechts <48065851+PietrH@users.noreply.github.com>
Date: Fri, 14 Jul 2023 14:57:03 +0200
Subject: [PATCH 12/40] test for no error if media is not imported

---
 tests/testthat/test-check_package.R | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/tests/testthat/test-check_package.R b/tests/testthat/test-check_package.R
index a87597c3..556df9ea 100644
--- a/tests/testthat/test-check_package.R
+++ b/tests/testthat/test-check_package.R
@@ -65,6 +65,12 @@ test_that("check_package() returns error if deployments is not a data.frame", {
   )
 })
 
+test_that("check_package() doesn't return an error on a NULL media object", {
+  # the case when media is not imported
+  mica_null_media <- mica
+  mica_null_media$data["media"] <- list(NULL)
+  expect_true(check_package(mica_null_media))
+})
 
 test_that("check_package() returns TRUE on valid package", {
   expect_true(check_package(mica))

From efb23d3243c875f9ec14855254d64d5cb6c05929 Mon Sep 17 00:00:00 2001
From: Pieter Huybrechts <48065851+PietrH@users.noreply.github.com>
Date: Fri, 14 Jul 2023 14:57:52 +0200
Subject: [PATCH 13/40] test for error when media is not a data.frame

---
 tests/testthat/test-check_package.R | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/tests/testthat/test-check_package.R b/tests/testthat/test-check_package.R
index 556df9ea..53a17641 100644
--- a/tests/testthat/test-check_package.R
+++ b/tests/testthat/test-check_package.R
@@ -72,6 +72,16 @@ test_that("check_package() doesn't return an error on a NULL media object", {
   expect_true(check_package(mica_null_media))
 })
 
+test_that("check_package() returns error if media is not a data.frame", {
+  mica_listed <- mica
+  mica_listed$data$media <- as.list(mica_listed$data$media)
+  expect_error(
+    check_package(mica_listed),
+    regexp = "package$data$media is not a data frame",
+    fixed = TRUE
+  )
+})
+
 test_that("check_package() returns TRUE on valid package", {
   expect_true(check_package(mica))
 })

From b444abe262640ec55ac5e872f873cc3525f51f01 Mon Sep 17 00:00:00 2001
From: Pieter Huybrechts <48065851+PietrH@users.noreply.github.com>
Date: Fri, 14 Jul 2023 14:58:52 +0200
Subject: [PATCH 14/40] stylr

---
 tests/testthat/test-check_package.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tests/testthat/test-check_package.R b/tests/testthat/test-check_package.R
index 53a17641..01dedd7c 100644
--- a/tests/testthat/test-check_package.R
+++ b/tests/testthat/test-check_package.R
@@ -13,7 +13,7 @@ test_that("check_package() returns error when package is not a list", {
     fixed = TRUE
   )
   expect_error(
-    check_package(data.frame(letters = c("a","b","c"), numbers = c(pi,2*pi,3*pi))),
+    check_package(data.frame(letters = c("a", "b", "c"), numbers = c(pi, 2 * pi, 3 * pi))),
     regexp = "package is not a list",
     fixed = TRUE
   )
@@ -21,7 +21,7 @@ test_that("check_package() returns error when package is not a list", {
 
 test_that("check_package() returns error on missing data", {
   expect_error(
-    check_package(purrr::discard_at(mica,at = "data")),
+    check_package(purrr::discard_at(mica, at = "data")),
     regexp = "data element is missing from package",
     fixed = TRUE
   )
@@ -47,7 +47,7 @@ test_that("check_package() returns error if not all elements are present", {
 test_that("check_package() returns error if observations is not a data.frame", {
   mica_listed <- mica
   mica_listed$data$observations <- as.list(mica_listed$data$observations)
-  
+
   expect_error(
     check_package(mica_listed),
     regexp = "package$data$observations is not a data frame",

From 2c9e2b9a9a593215a3f0e2bf14894b8065f11c65 Mon Sep 17 00:00:00 2001
From: Pieter Huybrechts <48065851+PietrH@users.noreply.github.com>
Date: Fri, 14 Jul 2023 15:09:06 +0200
Subject: [PATCH 15/40] no longer assign check_package() to validate

---
 R/check_species.R       | 3 ++-
 R/get_cam_op.R          | 2 +-
 R/get_custom_effort.R   | 2 +-
 R/get_effort.R          | 2 +-
 R/get_n_individuals.R   | 2 +-
 R/get_n_obs.R           | 2 +-
 R/get_n_species.R       | 2 +-
 R/get_rai.R             | 4 ++--
 R/get_record_table.R    | 2 +-
 R/get_scientific_name.R | 2 +-
 R/get_species.R         | 2 +-
 R/map_dep.R             | 2 +-
 R/zzz.R                 | 2 +-
 13 files changed, 15 insertions(+), 14 deletions(-)

diff --git a/R/check_species.R b/R/check_species.R
index c7ba8181..0911399b 100644
--- a/R/check_species.R
+++ b/R/check_species.R
@@ -38,7 +38,8 @@ check_species <- function(package = NULL,
                           arg_name = "species",
                           datapkg = lifecycle::deprecated()) {
   # Check camera trap data package
-  package <- check_package(package, datapkg, "check_species")
+  check_package(package, datapkg, "check_species")
+  
   assertthat::assert_that(
     !is.null(species) & length(species) > 0,
     msg = "`species` parameter must be specified"
diff --git a/R/get_cam_op.R b/R/get_cam_op.R
index c90fa783..00ab37a5 100644
--- a/R/get_cam_op.R
+++ b/R/get_cam_op.R
@@ -49,7 +49,7 @@ get_cam_op <- function(package = NULL,
                        use_prefix = FALSE,
                        datapkg = NULL) {
   # check camera trap data package
-  package <- check_package(package, datapkg, "get_cam_op")
+  check_package(package, datapkg, "get_cam_op")
 
   # Check that station_col is one of the columns in deployments
   assertthat::assert_that(
diff --git a/R/get_custom_effort.R b/R/get_custom_effort.R
index e0041a0e..35c3a398 100644
--- a/R/get_custom_effort.R
+++ b/R/get_custom_effort.R
@@ -116,7 +116,7 @@ get_custom_effort <- function(package = NULL,
   check_value(group_by, group_bys, "group_by", null_allowed = TRUE)
 
   # check camera trap data package
-  package <- check_package(package, datapkg, "get_custom_effort")
+  check_package(package, datapkg, "get_custom_effort")
 
   # get deployments
   deployments <- package$data$deployments
diff --git a/R/get_effort.R b/R/get_effort.R
index 4165dc14..5c6f03c0 100644
--- a/R/get_effort.R
+++ b/R/get_effort.R
@@ -42,7 +42,7 @@ get_effort <- function(package = NULL,
   check_value(unit, units, "unit", null_allowed = FALSE)
 
   # check camera trap data package
-  package <- check_package(package, datapkg, "get_effort")
+  check_package(package, datapkg, "get_effort")
 
   # apply filtering
   package$data$deployments <- apply_filter_predicate(
diff --git a/R/get_n_individuals.R b/R/get_n_individuals.R
index 0cd1a27a..6874ae28 100644
--- a/R/get_n_individuals.R
+++ b/R/get_n_individuals.R
@@ -67,7 +67,7 @@ get_n_individuals <- function(package = NULL,
                               life_stage = NULL,
                               datapkg = lifecycle::deprecated()) {
   # check input data package
-  package <- check_package(package, datapkg, "get_n_individuals")
+  check_package(package, datapkg, "get_n_individuals")
 
   # avoid to call variables like column names to make life easier using filter()
   sex_value <- sex
diff --git a/R/get_n_obs.R b/R/get_n_obs.R
index 4e7e4a7d..ddf97a15 100644
--- a/R/get_n_obs.R
+++ b/R/get_n_obs.R
@@ -64,7 +64,7 @@ get_n_obs <- function(package = NULL,
                       life_stage = NULL,
                       datapkg = lifecycle::deprecated()) {
   # check input data package
-  package <- check_package(package, datapkg, "get_n_obs")
+  check_package(package, datapkg, "get_n_obs")
 
   # avoid to call variables like column names to make life easier using filter()
   sex_value <- sex
diff --git a/R/get_n_species.R b/R/get_n_species.R
index 473fd792..94349b13 100644
--- a/R/get_n_species.R
+++ b/R/get_n_species.R
@@ -23,7 +23,7 @@ get_n_species <- function(package = NULL,
                           ...,
                           datapkg = lifecycle::deprecated()) {
   # check input data package
-  package <- check_package(package, datapkg, "get_n_species")
+  check_package(package, datapkg, "get_n_species")
 
   # extract observations and deployments
   observations <- package$data$observations
diff --git a/R/get_rai.R b/R/get_rai.R
index 21c67f37..63d57e80 100644
--- a/R/get_rai.R
+++ b/R/get_rai.R
@@ -58,7 +58,7 @@ get_rai <- function(package = NULL,
                     life_stage = NULL,
                     datapkg = lifecycle::deprecated()) {
   # check camera trap data package
-  package <- check_package(package, datapkg, "get_rai")
+  check_package(package, datapkg, "get_rai")
 
   get_rai_primitive(package, ...,
     use = "n_obs",
@@ -135,7 +135,7 @@ get_rai_individuals <- function(package = NULL,
                                 life_stage = NULL,
                                 datapkg = lifecycle::deprecated()) {
   # check camera trap data package
-  package <- check_package(package, datapkg, "get_rai_individuals")
+  check_package(package, datapkg, "get_rai_individuals")
   get_rai_primitive(package, ...,
     use = "n_individuals",
     species = species,
diff --git a/R/get_record_table.R b/R/get_record_table.R
index 39b12a9f..40d014c7 100644
--- a/R/get_record_table.R
+++ b/R/get_record_table.R
@@ -102,7 +102,7 @@ get_record_table <- function(package = NULL,
                              removeDuplicateRecords = TRUE,
                              datapkg = lifecycle::deprecated()) {
   # check data package
-  package <- check_package(package, datapkg, "get_record_table")
+  check_package(package, datapkg, "get_record_table")
 
   # check stationCol is a valid column name
   assertthat::assert_that(
diff --git a/R/get_scientific_name.R b/R/get_scientific_name.R
index b79b304a..29329a47 100644
--- a/R/get_scientific_name.R
+++ b/R/get_scientific_name.R
@@ -35,7 +35,7 @@
 get_scientific_name <- function(package = NULL,
                                 vernacular_name,
                                 datapkg = lifecycle::deprecated()) {
-  package <- check_package(package, datapkg, "get_scientific_name")
+  check_package(package, datapkg, "get_scientific_name")
   all_sn_vn <- get_species(package)
 
   # get vernacular names for check
diff --git a/R/get_species.R b/R/get_species.R
index 924d068a..3ee20b3d 100644
--- a/R/get_species.R
+++ b/R/get_species.R
@@ -14,7 +14,7 @@
 #' get_species(mica)
 get_species <- function(package = NULL, datapkg = lifecycle::deprecated()) {
   # Check camera trap data package
-  package <- check_package(package, datapkg, "get_species")
+  check_package(package, datapkg, "get_species")
 
   # Get taxonomic information from package metadata
   if (!"taxonomic" %in% names(package)) {
diff --git a/R/map_dep.R b/R/map_dep.R
index 5027c5a9..606424df 100644
--- a/R/map_dep.R
+++ b/R/map_dep.R
@@ -317,7 +317,7 @@ map_dep <- function(package = NULL,
                     datapkg = lifecycle::deprecated()) {
 
   # check camera trap data package
-  package <- check_package(package, datapkg, "map_dep")
+  check_package(package, datapkg, "map_dep")
 
   # define possible feature values
   features <- c(
diff --git a/R/zzz.R b/R/zzz.R
index c76a2746..5430ce9a 100644
--- a/R/zzz.R
+++ b/R/zzz.R
@@ -154,7 +154,7 @@ get_dep_no_obs <- function(package = NULL,
                            datapkg = lifecycle::deprecated()) {
 
   # check input camera trap data package
-  package <- check_package(package, datapkg, "get_dep_no_obs")
+  check_package(package, datapkg, "get_dep_no_obs")
 
   # extract observations and deployments
   observations <- package$data$observations

From 80432181fb80f4bd63ccd193aa990139a3c6e123 Mon Sep 17 00:00:00 2001
From: Pieter Huybrechts <48065851+PietrH@users.noreply.github.com>
Date: Fri, 14 Jul 2023 15:22:27 +0200
Subject: [PATCH 16/40] silence messages during testing

---
 tests/testthat/test-check_species.R | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tests/testthat/test-check_species.R b/tests/testthat/test-check_species.R
index 155b4ae2..45445da3 100644
--- a/tests/testthat/test-check_species.R
+++ b/tests/testthat/test-check_species.R
@@ -40,19 +40,19 @@ test_that("Multiput scientific names are allowed", {
 
 test_that("Function works with vernacular names", {
   vn_names <- c("beech marten", "mallard")
-  species <- check_species(mica, vn_names)
+  species <- suppressMessages(check_species(mica, vn_names))
   testthat::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 <- check_species(mica, vn_names)
+  species <- suppressMessages(check_species(mica, vn_names))
   testthat::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 <- check_species(mica, mixed_names)
+  species <- suppressMessages(check_species(mica, mixed_names))
   testthat::expect_equal(
     species,
     c(
@@ -69,7 +69,7 @@ test_that("Taxon IDs are not allowed", {
 })
 
 test_that("Functions works case insensitively", {
-  vn_name <- check_species(mica, c("MallARD"))
+  vn_name <- suppressMessages(check_species(mica, c("MallARD")))
   species <- check_species(mica, vn_name)
   testthat::expect_equal(species, "Anas platyrhynchos")
 })

From 7e6a4397db8213100fc84d1502fe40be812f31fa Mon Sep 17 00:00:00 2001
From: Pieter Huybrechts <48065851+PietrH@users.noreply.github.com>
Date: Fri, 14 Jul 2023 16:18:29 +0200
Subject: [PATCH 17/40] remove test covered by test-check_package.R

---
 tests/testthat/test-check_species.R | 9 ---------
 1 file changed, 9 deletions(-)

diff --git a/tests/testthat/test-check_species.R b/tests/testthat/test-check_species.R
index 45445da3..74bff7d1 100644
--- a/tests/testthat/test-check_species.R
+++ b/tests/testthat/test-check_species.R
@@ -73,12 +73,3 @@ test_that("Functions works case insensitively", {
   species <- check_species(mica, vn_name)
   testthat::expect_equal(species, "Anas platyrhynchos")
 })
-
-test_that("Argument datapkg is deprecated: warning returned", {
-  testthat::expect_warning(
-    rlang::with_options(
-      lifecycle_verbosity = "warning",
-      check_species(datapkg = mica, species = "Anas strepera")
-    )
-  )
-})

From 390f95dde3910775155a323ea8413e22ad13712a Mon Sep 17 00:00:00 2001
From: Pieter Huybrechts <48065851+PietrH@users.noreply.github.com>
Date: Fri, 14 Jul 2023 16:18:29 +0200
Subject: [PATCH 18/40] remove test covered by test-check_package.R

The usage of the `datapkg` argument is tested in test-check_package.R, I don't think it needs to be tested for every function individually.
---
 tests/testthat/test-check_species.R       | 9 ---------
 tests/testthat/test-get_cam_op.R          | 9 ---------
 tests/testthat/test-get_custom_effort.R   | 9 ---------
 tests/testthat/test-get_effort.R          | 9 ---------
 tests/testthat/test-get_n_individuals.R   | 9 ---------
 tests/testthat/test-get_n_obs.R           | 9 ---------
 tests/testthat/test-get_n_species.R       | 9 ---------
 tests/testthat/test-get_rai.R             | 9 ---------
 tests/testthat/test-get_rai_individuals.R | 9 ---------
 tests/testthat/test-get_record_table.R    | 9 ---------
 tests/testthat/test-get_scientific_name.R | 9 ---------
 11 files changed, 99 deletions(-)

diff --git a/tests/testthat/test-check_species.R b/tests/testthat/test-check_species.R
index 45445da3..74bff7d1 100644
--- a/tests/testthat/test-check_species.R
+++ b/tests/testthat/test-check_species.R
@@ -73,12 +73,3 @@ test_that("Functions works case insensitively", {
   species <- check_species(mica, vn_name)
   testthat::expect_equal(species, "Anas platyrhynchos")
 })
-
-test_that("Argument datapkg is deprecated: warning returned", {
-  testthat::expect_warning(
-    rlang::with_options(
-      lifecycle_verbosity = "warning",
-      check_species(datapkg = mica, species = "Anas strepera")
-    )
-  )
-})
diff --git a/tests/testthat/test-get_cam_op.R b/tests/testthat/test-get_cam_op.R
index 3bd2c88a..a8800b5b 100644
--- a/tests/testthat/test-get_cam_op.R
+++ b/tests/testthat/test-get_cam_op.R
@@ -143,12 +143,3 @@ test_that("filtering predicates are allowed and work well", {
   filtered_cam_op_matrix <- get_cam_op(mica, pred_lt("longitude", 4.0))
   expect_equal(rownames(filtered_cam_op_matrix), "Mica Viane")
 })
-
-test_that("Argument datapkg is deprecated: warning returned", {
-  expect_warning(
-    rlang::with_options(
-      lifecycle_verbosity = "warning",
-      get_cam_op(datapkg = mica)
-    )
-  )
-})
diff --git a/tests/testthat/test-get_custom_effort.R b/tests/testthat/test-get_custom_effort.R
index a83aea15..acdbb284 100644
--- a/tests/testthat/test-get_custom_effort.R
+++ b/tests/testthat/test-get_custom_effort.R
@@ -178,12 +178,3 @@ test_that("check effort and unit values", {
   # unit value is equal to day if unit value is set to "day"
   expect_equal(unique(tot_effort_days$unit), "day")
 })
-
-test_that("Argument datapkg is deprecated: warning returned", {
-  expect_warning(
-    rlang::with_options(
-      lifecycle_verbosity = "warning",
-      get_custom_effort(datapkg = mica)
-    )
-  )
-})
diff --git a/tests/testthat/test-get_effort.R b/tests/testthat/test-get_effort.R
index 572b90a9..c9af3cab 100644
--- a/tests/testthat/test-get_effort.R
+++ b/tests/testthat/test-get_effort.R
@@ -75,12 +75,3 @@ testthat::test_that("get_effort returns the right number of rows", {
     n_all_deployments
   )
 })
-
-testthat::test_that("Argument datapkg is deprecated: warning returned", {
-  testthat::expect_warning(
-    rlang::with_options(
-      lifecycle_verbosity = "warning",
-      get_effort(datapkg = mica)
-    )
-  )
-})
diff --git a/tests/testthat/test-get_n_individuals.R b/tests/testthat/test-get_n_individuals.R
index ee7e4ad0..ff66adc1 100644
--- a/tests/testthat/test-get_n_individuals.R
+++ b/tests/testthat/test-get_n_individuals.R
@@ -244,12 +244,3 @@ test_that("error returned if life stage or sex is not present", {
   expect_error(get_n_individuals(mica, life_stage = "bad"))
   expect_error(get_n_individuals(mica, sex = "bad"))
 })
-
-test_that("Argument datapkg is deprecated: warning returned", {
-  expect_warning(
-    rlang::with_options(
-      lifecycle_verbosity = "warning",
-      get_n_individuals(datapkg = mica)
-    )
-  )
-})
diff --git a/tests/testthat/test-get_n_obs.R b/tests/testthat/test-get_n_obs.R
index e7d51b1b..4cde9c3f 100644
--- a/tests/testthat/test-get_n_obs.R
+++ b/tests/testthat/test-get_n_obs.R
@@ -243,15 +243,6 @@ test_that(paste(
   expect_true(all(species_value %in% n_obs$scientificName))
 })
 
-test_that("Argument datapkg is deprecated: warning returned", {
-  expect_warning(
-    rlang::with_options(
-      lifecycle_verbosity = "warning",
-      get_n_obs(datapkg = mica)
-    )
-  )
-})
-
 test_that("Filter by date of deployments via predicates works correctly", {
   end_date <- as.Date("2021-01-01", format = "%Y-%m-%d")
   mica_with_obs_filtered_manually <- mica
diff --git a/tests/testthat/test-get_n_species.R b/tests/testthat/test-get_n_species.R
index d2638c77..54b2adf6 100644
--- a/tests/testthat/test-get_n_species.R
+++ b/tests/testthat/test-get_n_species.R
@@ -19,12 +19,3 @@ test_that("get_n_species returns the right dataframe", {
     )
   )
 })
-
-test_that("Argument datapkg is deprecated: warning returned", {
-  expect_warning(
-    rlang::with_options(
-      lifecycle_verbosity = "warning",
-      get_n_species(datapkg = mica)
-    )
-  )
-})
diff --git a/tests/testthat/test-get_rai.R b/tests/testthat/test-get_rai.R
index 8e43fd49..851991ae 100644
--- a/tests/testthat/test-get_rai.R
+++ b/tests/testthat/test-get_rai.R
@@ -94,12 +94,3 @@ test_that("life_stage filters data correctly", {
     ignore_attr = TRUE
   )
 })
-
-test_that("Argument datapkg is deprecated: warning returned", {
-  expect_warning(
-    rlang::with_options(
-      lifecycle_verbosity = "warning",
-      get_rai(datapkg = mica)
-    )
-  )
-})
diff --git a/tests/testthat/test-get_rai_individuals.R b/tests/testthat/test-get_rai_individuals.R
index a3380024..b6df1be4 100644
--- a/tests/testthat/test-get_rai_individuals.R
+++ b/tests/testthat/test-get_rai_individuals.R
@@ -94,12 +94,3 @@ test_that("life_stage filters data correctly", {
     ignore_attr = TRUE
   )
 })
-
-test_that("Argument datapkg is deprecated: warning returned", {
-  expect_warning(
-    rlang::with_options(
-      lifecycle_verbosity = "warning",
-      get_rai_individuals(datapkg = mica)
-    )
-  )
-})
diff --git a/tests/testthat/test-get_record_table.R b/tests/testthat/test-get_record_table.R
index cb07270e..a39f725d 100644
--- a/tests/testthat/test-get_record_table.R
+++ b/tests/testthat/test-get_record_table.R
@@ -191,12 +191,3 @@ test_that("filtering predicates are allowed and work well", {
     dplyr::pull(locationName)
   testthat::expect_identical(stations, stations_calculate)
 })
-
-test_that("Argument datapkg is deprecated: warning returned", {
-  expect_warning(
-    rlang::with_options(
-      lifecycle_verbosity = "warning",
-      get_record_table(datapkg = mica)
-    )
-  )
-})
diff --git a/tests/testthat/test-get_scientific_name.R b/tests/testthat/test-get_scientific_name.R
index b4d9aec9..43ed331b 100644
--- a/tests/testthat/test-get_scientific_name.R
+++ b/tests/testthat/test-get_scientific_name.R
@@ -18,12 +18,3 @@ test_that("Functions works case insensitively", {
   sc_names <- get_scientific_name(mica, c("beeCH MArten"))
   expect_equal(sc_names, c("Martes foina"))
 })
-
-test_that("Argument datapkg is deprecated: warning returned", {
-  expect_warning(
-    rlang::with_options(
-      lifecycle_verbosity = "warning",
-      get_scientific_name(datapkg = mica, vernacular_name = "beech marten")
-    )
-  )
-})

From 9aa6cf06e96818c844a0f87f3fb9bcb6d148cedd Mon Sep 17 00:00:00 2001
From: Pieter Huybrechts <48065851+PietrH@users.noreply.github.com>
Date: Fri, 14 Jul 2023 16:25:38 +0200
Subject: [PATCH 19/40] `check_package()` now returns TRUE on a valid package

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

diff --git a/tests/testthat/test-read_wi.R b/tests/testthat/test-read_wi.R
index 90a69e82..9d170803 100644
--- a/tests/testthat/test-read_wi.R
+++ b/tests/testthat/test-read_wi.R
@@ -6,5 +6,5 @@ test_that("read_wi() returns error when files are not found", {
 })
 
 test_that("read_wi() returns a valid package", {
-  expect_type(camtraptor:::check_package(read_wi("data")), "list")
+  expect_true(camtraptor:::check_package(read_wi("data")))
 })

From 1d40a023af29c874ea0d401efd089179366d9965 Mon Sep 17 00:00:00 2001
From: Pieter Huybrechts <48065851+PietrH@users.noreply.github.com>
Date: Fri, 14 Jul 2023 16:52:49 +0200
Subject: [PATCH 20/40] silence messages in testing output

---
 tests/testthat/test-get_cam_op.R          |  4 +-
 tests/testthat/test-get_custom_effort.R   |  8 +--
 tests/testthat/test-get_n_individuals.R   | 45 ++++++++--------
 tests/testthat/test-get_n_obs.R           | 66 ++++++++++++++---------
 tests/testthat/test-get_rai.R             | 26 ++++++---
 tests/testthat/test-get_rai_individuals.R | 30 ++++++++---
 tests/testthat/test-get_record_table.R    | 37 +++++++------
 7 files changed, 134 insertions(+), 82 deletions(-)

diff --git a/tests/testthat/test-get_cam_op.R b/tests/testthat/test-get_cam_op.R
index a8800b5b..1c0afa65 100644
--- a/tests/testthat/test-get_cam_op.R
+++ b/tests/testthat/test-get_cam_op.R
@@ -140,6 +140,8 @@ test_that(
 )
 
 test_that("filtering predicates are allowed and work well", {
-  filtered_cam_op_matrix <- get_cam_op(mica, pred_lt("longitude", 4.0))
+  filtered_cam_op_matrix <- suppressMessages(
+    get_cam_op(mica, pred_lt("longitude", 4.0))
+  )
   expect_equal(rownames(filtered_cam_op_matrix), "Mica Viane")
 })
diff --git a/tests/testthat/test-get_custom_effort.R b/tests/testthat/test-get_custom_effort.R
index acdbb284..b6470b31 100644
--- a/tests/testthat/test-get_custom_effort.R
+++ b/tests/testthat/test-get_custom_effort.R
@@ -163,9 +163,11 @@ test_that("right columns, cols types, right relative number of rows", {
 test_that("check effort and unit values", {
   tot_effort <- get_custom_effort(mica)
   # filtering deployments reduces effort value
-  filter_deploys <- get_custom_effort(mica,
-    pred_gte("latitude", 51.18),
-    group_by = "year"
+  filter_deploys <- suppressMessages(
+    get_custom_effort(mica,
+      pred_gte("latitude", 51.18),
+      group_by = "year"
+    )
   )
   expect_lt(filter_deploys$effort, tot_effort$effort)
 
diff --git a/tests/testthat/test-get_n_individuals.R b/tests/testthat/test-get_n_individuals.R
index ff66adc1..ee12f289 100644
--- a/tests/testthat/test-get_n_individuals.R
+++ b/tests/testthat/test-get_n_individuals.R
@@ -1,9 +1,8 @@
 test_that("get_n_individuals returns the right structure of dataframe", {
-
   # species arg specified
-  output_anas_platyrhyncos <- get_n_individuals(mica,
+  output_anas_platyrhyncos <- suppressMessages(get_n_individuals(mica,
     species = "Anas platyrhynchos"
-  )
+  ))
 
   # type list
   expect_type(output_anas_platyrhyncos, "list")
@@ -64,9 +63,9 @@ test_that(paste(
   n_deployments <- length(deployments)
 
   # calculate get_n_individuals for a species undetected in one deployment
-  output_martes_foina <- get_n_individuals(mica,
+  output_martes_foina <- suppressMessages(get_n_individuals(mica,
     species = "Martes foina"
-  )
+  ))
 
   # number of rows should be equal to number of deployments
   expect_equal(nrow(output_martes_foina), n_deployments)
@@ -104,8 +103,8 @@ test_that("species = 'all' returns the same of using a vector with all species",
 
 test_that("species is case insensitive", {
   expect_equal(
-    get_n_individuals(mica, species = "Anas platyrhynchos"),
-    get_n_individuals(mica, species = toupper("Anas platyrhynchos"))
+    suppressMessages(get_n_individuals(mica, species = "Anas platyrhynchos")),
+    suppressMessages(get_n_individuals(mica, species = toupper("Anas platyrhynchos")))
   )
 })
 
@@ -113,15 +112,14 @@ test_that(paste(
   "species accepts use of common names and return",
   "the same as using scientic name"
 ), {
-
   # define scientific name
   scn <- "Anas platyrhynchos"
   # define correspondent vernacular name
   vn <- "Mallard"
 
   # get number of individuals for both cases
-  output_anas_platyrhyncos <- get_n_individuals(mica, species = scn)
-  output_mallard <- get_n_individuals(mica, species = vn)
+  output_anas_platyrhyncos <- suppressMessages(get_n_individuals(mica, species = scn))
+  output_mallard <- suppressMessages(get_n_individuals(mica, species = vn))
 
   # same outputs
   expect_equal(output_anas_platyrhyncos, output_mallard)
@@ -129,9 +127,9 @@ test_that(paste(
 
 test_that("if subset of species is specified, less individuals are returned", {
   output_all_species <- get_n_individuals(mica)
-  output_anas_platyrhyncos <- get_n_individuals(mica,
+  output_anas_platyrhyncos <- suppressMessages(get_n_individuals(mica,
     species = "Anas platyrhynchos"
-  )
+  ))
 
   expect_true(sum(output_all_species$n) >= sum(output_anas_platyrhyncos$n))
 })
@@ -166,10 +164,10 @@ test_that("number of individuals is equal to sum of counts", {
     dplyr::filter(scientificName == species) %>%
     dplyr::pull(count) %>%
     sum()
-  n_individuals <- get_n_individuals(mica,
+  n_individuals <- suppressMessages(get_n_individuals(mica,
     species = "Mallard",
     pred("deploymentID", deploy_id)
-  )
+  ))
   expect_equal(n_individuals$n, n_individuals_via_count)
 })
 
@@ -180,7 +178,8 @@ test_that("sex filters data correctly", {
     dplyr::filter(sex == sex_value) %>%
     dplyr::pull(count) %>%
     sum()
-  n_individuals_females <- get_n_individuals(mica, species = NULL, sex = sex_value)
+  n_individuals_females <-
+    suppressMessages(get_n_individuals(mica, species = NULL, sex = sex_value))
   tot_n_individuals_females <- sum(n_individuals_females$n)
   expect_equal(tot_n_individuals_females, n_individuals_via_count)
   expect_equal(nrow(n_individuals_females), nrow(mica$data$deployments))
@@ -193,10 +192,10 @@ test_that("multiple sex values allowed", {
     dplyr::filter(sex %in% sex_value) %>%
     dplyr::pull(count) %>%
     sum()
-  n_individuals_females_undefined <- get_n_individuals(mica,
+  n_individuals_females_undefined <- suppressMessages(get_n_individuals(mica,
     species = NULL,
     sex = sex_value
-  )
+  ))
   tot_n_individuals_females_undefined <- sum(n_individuals_females_undefined$n)
   expect_equal(
     tot_n_individuals_females_undefined,
@@ -215,7 +214,9 @@ test_that("life stage filters data correctly", {
     dplyr::filter(lifeStage == life_stage_value) %>%
     dplyr::pull(count) %>%
     sum()
-  n_individuals_juvenile <- get_n_individuals(mica, species = NULL, life_stage = life_stage_value)
+  n_individuals_juvenile <- suppressMessages(
+    get_n_individuals(mica, species = NULL, life_stage = life_stage_value)
+  )
   tot_n_individuals_juvenile <- sum(n_individuals_juvenile$n)
   expect_equal(tot_n_individuals_juvenile, n_individuals_juvenile_via_count)
   expect_equal(nrow(n_individuals_juvenile), nrow(mica$data$deployments))
@@ -228,9 +229,11 @@ test_that("multiple age values allowed", {
     dplyr::filter(lifeStage %in% life_stage_value) %>%
     dplyr::pull(count) %>%
     sum()
-  n_individuals_juvenile_adult <- get_n_individuals(mica,
-    species = NULL,
-    life_stage = life_stage_value
+  n_individuals_juvenile_adult <- suppressMessages(
+    get_n_individuals(mica,
+      species = NULL,
+      life_stage = life_stage_value
+    )
   )
   tot_n_individuals_juvenile_adult <- sum(n_individuals_juvenile_adult$n)
   expect_equal(
diff --git a/tests/testthat/test-get_n_obs.R b/tests/testthat/test-get_n_obs.R
index 4cde9c3f..6629aeea 100644
--- a/tests/testthat/test-get_n_obs.R
+++ b/tests/testthat/test-get_n_obs.R
@@ -1,8 +1,9 @@
 test_that("get_n_obs returns the right structure of dataframe", {
-
   # species arg specified
-  output_anas_platyrhyncos <- get_n_obs(mica,
-    species = "Anas platyrhynchos"
+  output_anas_platyrhyncos <- suppressMessages(
+    get_n_obs(mica,
+      species = "Anas platyrhynchos"
+    )
   )
 
   # type list
@@ -64,8 +65,10 @@ test_that(paste(
   n_deployments <- length(deployments)
 
   # calculate get_n_obs for a species undetected in one deployment
-  output_ondatra_zibethicus <- get_n_obs(mica,
-    species = "Anas strepera"
+  output_ondatra_zibethicus <- suppressMessages(
+    get_n_obs(mica,
+      species = "Anas strepera"
+    )
   )
 
   # number of rows should be equal to number of deployments
@@ -104,8 +107,10 @@ test_that("species = 'all' returns the same of using a vector with all species",
 
 test_that("species is case insensitive", {
   expect_equal(
-    get_n_obs(mica, species = "Anas platyrhynchos"),
-    get_n_obs(mica, species = toupper("ANAS platYrhyncHOS"))
+    suppressMessages(
+      get_n_obs(mica, species = "Anas platyrhynchos")
+    ),
+    suppressMessages(get_n_obs(mica, species = toupper("ANAS platYrhyncHOS")))
   )
 })
 
@@ -113,15 +118,14 @@ test_that(paste(
   "species accepts use of common names and return",
   "the same as using scientic name"
 ), {
-
   # define scientific name
   scn <- "Anas platyrhynchos"
   # define correspondent vernacular name
   vn <- "Mallard"
 
   # get number of observations for both cases
-  output_anas_platyrhyncos <- get_n_obs(mica, species = scn)
-  output_mallard <- get_n_obs(mica, species = vn)
+  output_anas_platyrhyncos <- suppressMessages(get_n_obs(mica, species = scn))
+  output_mallard <- suppressMessages(get_n_obs(mica, species = vn))
 
   # same outputs
   expect_equal(output_anas_platyrhyncos, output_mallard)
@@ -129,8 +133,10 @@ test_that(paste(
 
 test_that("if subset of species is specified, less observations are returned", {
   output_all_species <- get_n_obs(mica)
-  output_anas_platyrhyncos <- get_n_obs(mica,
-    species = "Anas platyrhynchos"
+  output_anas_platyrhyncos <- suppressMessages(
+    get_n_obs(mica,
+      species = "Anas platyrhynchos"
+    )
   )
 
   expect_true(sum(output_all_species$n) >= sum(output_anas_platyrhyncos$n))
@@ -170,16 +176,18 @@ test_that(paste(
     dplyr::pull(.data$sequenceID) %>%
     dplyr::n_distinct()
   # one sequenceID  linked to two observations (different age, sex and count)
-  n_obs <- get_n_obs(mica,
+  n_obs <- suppressMessages(get_n_obs(mica,
     species = "Mallard",
     pred("deploymentID", deploy_id)
-  )
+  ))
   expect_equal(n_obs$n, n_obs_via_sequence_id)
 })
 
 test_that("sex filters data correctly", {
   sex_value <- "female"
-  n_obs_females <- get_n_obs(mica, species = NULL, sex = sex_value)
+  n_obs_females <- suppressMessages(
+    get_n_obs(mica, species = NULL, sex = sex_value)
+  )
   tot_n_obs_females <- sum(n_obs_females$n)
   expect_equal(tot_n_obs_females, 1)
   expect_equal(nrow(n_obs_females), nrow(mica$data$deployments))
@@ -187,10 +195,10 @@ test_that("sex filters data correctly", {
 
 test_that("multiple sex values allowed", {
   sex_value <- c("female", "unknown")
-  n_obs_females_unknown <- get_n_obs(mica,
+  n_obs_females_unknown <- suppressMessages(get_n_obs(mica,
     species = NULL,
     sex = sex_value
-  )
+  ))
   tot_n_obs_females_unknown <- sum(n_obs_females_unknown$n)
   expect_equal(
     tot_n_obs_females_unknown,
@@ -209,7 +217,9 @@ test_that("life_stage filters data correctly", {
     dplyr::filter(.data$lifeStage %in% life_stage_value) %>%
     dplyr::distinct(.data$sequenceID) %>%
     nrow()
-  n_obs_subadult <- get_n_obs(mica, species = NULL, life_stage = life_stage_value)
+  n_obs_subadult <- suppressMessages(
+    get_n_obs(mica, species = NULL, life_stage = life_stage_value)
+  )
   tot_n_obs_subadult <- sum(n_obs_subadult$n)
   expect_equal(tot_n_obs_subadult, n_obs_subadult_via_distinct)
   expect_equal(nrow(n_obs_subadult), nrow(mica$data$deployments))
@@ -217,7 +227,9 @@ test_that("life_stage filters data correctly", {
 
 test_that("multiple age values allowed", {
   life_stage_value <- c("subadult", "adult")
-  n_obs_subadult_adult <- get_n_obs(mica, species = NULL, life_stage = life_stage_value)
+  n_obs_subadult_adult <- suppressMessages(
+    get_n_obs(mica, species = NULL, life_stage = life_stage_value)
+  )
   tot_n_obs_subadult_adult <- sum(n_obs_subadult_adult$n)
   n_obs_subadult_adult_calculate <-
     mica$data$observations %>%
@@ -238,7 +250,9 @@ test_that(paste(
 ), {
   species_value <- "Anas platyrhynchos"
   sex_value <- "female"
-  n_obs <- get_n_obs(mica, species = species_value, sex = sex_value)
+  n_obs <- suppressMessages(
+    get_n_obs(mica, species = species_value, sex = sex_value)
+  )
   expect_true(all(n_obs$scientificName %in% species_value))
   expect_true(all(species_value %in% n_obs$scientificName))
 })
@@ -255,10 +269,14 @@ test_that("Filter by date of deployments via predicates works correctly", {
   mica_with_obs_filtered_manually$data$observations <-
     mica_with_obs_filtered_manually$data$observations %>%
     dplyr::filter(.data$deploymentID %in% deploys_filtered)
-  obs_filtered_man <- get_n_obs(mica_with_obs_filtered_manually, 
-                                pred_lt(arg = "end", value = end_date)) %>%
+  obs_filtered_man <- suppressMessages(get_n_obs(
+    mica_with_obs_filtered_manually,
+    pred_lt(arg = "end", value = end_date)
+  )) %>%
     dplyr::arrange(deploymentID, scientificName)
-  obs_filtered <- get_n_obs(mica, pred_lt(arg = "end", value = end_date)) %>%
+  obs_filtered <- suppressMessages(
+    get_n_obs(mica, pred_lt(arg = "end", value = end_date))
+  ) %>%
     dplyr::arrange(deploymentID, scientificName)
   expect_equal(obs_filtered, obs_filtered_man)
-})
\ No newline at end of file
+})
diff --git a/tests/testthat/test-get_rai.R b/tests/testthat/test-get_rai.R
index 851991ae..52844f55 100644
--- a/tests/testthat/test-get_rai.R
+++ b/tests/testthat/test-get_rai.R
@@ -4,8 +4,10 @@ test_that("get_rai returns error if no species is specified", {
 })
 
 test_that("get_rai returns the right dataframe", {
-  output_anas_platyrhyncos <- get_rai(mica,
-    species = "Anas platyrhynchos"
+  output_anas_platyrhyncos <- suppressMessages(
+    get_rai(mica,
+      species = "Anas platyrhynchos"
+    )
   )
 
   # type list
@@ -66,15 +68,19 @@ test_that("get_rai returns the same if 'all' is used instead of vector with all
 
 test_that("species is case insensitive", {
   expect_equal(
-    get_rai(mica, species = "Anas platyrhynchos"),
-    get_rai(mica, species = toupper("Anas platyrhynchos"))
+    suppressMessages(get_rai(mica, species = "Anas platyrhynchos")),
+    suppressMessages(get_rai(mica, species = toupper("Anas platyrhynchos")))
   )
 })
 
 test_that("sex filters data correctly", {
   sex_value <- "female"
-  n_obs_females <- get_n_obs(mica, species = "Mallard", sex = sex_value)
-  rai_females <- get_rai(mica, species = "Mallard", sex = sex_value)
+  n_obs_females <- suppressMessages(
+    get_n_obs(mica, species = "Mallard", sex = sex_value)
+  )
+  rai_females <- suppressMessages(
+    get_rai(mica, species = "Mallard", sex = sex_value)
+  )
   # same first two cols as in get_n_obs
   expect_equal(names(n_obs_females)[1:2], names(rai_females)[1:2])
   expect_equal(nrow(n_obs_females), nrow(rai_females))
@@ -85,8 +91,12 @@ test_that("sex filters data correctly", {
 
 test_that("life_stage filters data correctly", {
   life_stage_value <- "subadult"
-  n_obs_subadult <- get_n_obs(mica, species = "Mallard", life_stage = life_stage_value)
-  rai_subadult <- get_rai(mica, species = "Mallard", life_stage = life_stage_value)
+  n_obs_subadult <- suppressMessages(
+    get_n_obs(mica, species = "Mallard", life_stage = life_stage_value)
+  )
+  rai_subadult <- suppressMessages(
+    get_rai(mica, species = "Mallard", life_stage = life_stage_value)
+  )
   # same first two cols as in get_n_obs
   expect_equal(names(n_obs_subadult)[1:2], names(rai_subadult)[1:2])
   expect_equal(nrow(n_obs_subadult), nrow(rai_subadult))
diff --git a/tests/testthat/test-get_rai_individuals.R b/tests/testthat/test-get_rai_individuals.R
index b6df1be4..601f5649 100644
--- a/tests/testthat/test-get_rai_individuals.R
+++ b/tests/testthat/test-get_rai_individuals.R
@@ -4,8 +4,10 @@ test_that("get_rai_individuals returns error if no species is specified", {
 })
 
 test_that("get_rai_individuals returns the right dataframe", {
-  output_anas_platyrhyncos <- get_rai_individuals(mica,
-    species = "Anas platyrhynchos"
+  output_anas_platyrhyncos <- suppressMessages(
+    get_rai_individuals(mica,
+      species = "Anas platyrhynchos"
+    )
   )
 
   # type list
@@ -66,15 +68,23 @@ test_that("get_rai_individuals returns the same if 'all' is used instead of vect
 
 test_that("species is case insensitive", {
   expect_equal(
-    get_rai_individuals(mica, species = "Anas platyrhynchos"),
-    get_rai_individuals(mica, species = toupper("Anas platyrhynchos"))
+    suppressMessages(
+      get_rai_individuals(mica, species = "Anas platyrhynchos")
+    ),
+    suppressMessages(
+      get_rai_individuals(mica, species = toupper("Anas platyrhynchos"))
+    )
   )
 })
 
 test_that("sex filters data correctly", {
   sex_value <- "female"
-  n_obs_females <- get_n_obs(mica, species = "Mallard", sex = sex_value)
-  rai_females <- get_rai_individuals(mica, species = "Mallard", sex = sex_value)
+  n_obs_females <- suppressMessages(
+    get_n_obs(mica, species = "Mallard", sex = sex_value)
+  )
+  rai_females <- suppressMessages(
+    get_rai_individuals(mica, species = "Mallard", sex = sex_value)
+  )
   # same first two cols as in get_n_obs
   expect_equal(names(n_obs_females)[1:2], names(rai_females)[1:2])
   expect_equal(nrow(n_obs_females), nrow(rai_females))
@@ -85,8 +95,12 @@ test_that("sex filters data correctly", {
 
 test_that("life_stage filters data correctly", {
   life_stage_value <- "subadult"
-  n_obs_subadult <- get_n_obs(mica, species = "Mallard", life_stage = life_stage_value)
-  rai_subadult <- get_rai_individuals(mica, species = "Mallard", life_stage = life_stage_value)
+  n_obs_subadult <- suppressMessages(
+    get_n_obs(mica, species = "Mallard", life_stage = life_stage_value)
+  )
+  rai_subadult <- suppressMessages(
+    get_rai_individuals(mica, species = "Mallard", life_stage = life_stage_value)
+  )
   # same first two cols as in get_n_obs
   expect_equal(names(n_obs_subadult)[1:2], names(rai_subadult)[1:2])
   expect_equal(nrow(n_obs_subadult), nrow(rai_subadult))
diff --git a/tests/testthat/test-get_record_table.R b/tests/testthat/test-get_record_table.R
index a39f725d..d6dc6adf 100644
--- a/tests/testthat/test-get_record_table.R
+++ b/tests/testthat/test-get_record_table.R
@@ -38,9 +38,11 @@ test_that("if not integer, minDeltaTime is set to integer (floor)", {
     minDeltaTime = 1000,
     deltaTimeComparedTo = "lastRecord"
   )
-  record_table_dec <- get_record_table(mica,
-    minDeltaTime = 1000.7,
-    deltaTimeComparedTo = "lastRecord"
+  record_table_dec <- suppressMessages(
+    get_record_table(mica,
+      minDeltaTime = 1000.7,
+      deltaTimeComparedTo = "lastRecord"
+    )
   )
   testthat::expect_equal(record_table_int, record_table_dec)
 })
@@ -91,10 +93,10 @@ test_that("Higher minDeltaTime means less rows returned", {
     deltaTimeComparedTo = "lastRecord"
   ) %>%
     nrow()
-  nrow_delta_10000 <- get_record_table(mica,
+  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)
@@ -133,17 +135,18 @@ test_that(
     # add n media, observationID and sequenceID to record table
     output <- output %>%
       dplyr::mutate(len = purrr::map_dbl(Directory, function(x) length(x))) %>%
-      dplyr::left_join(mica$data$observations %>%
-        dplyr::select(
-          observationID,
-          timestamp,
-          scientificName,
-          sequenceID
-        ),
-      by = c(
-        "DateTimeOriginal" = "timestamp",
-        "Species" = "scientificName"
-      )
+      dplyr::left_join(
+        mica$data$observations %>%
+          dplyr::select(
+            observationID,
+            timestamp,
+            scientificName,
+            sequenceID
+          ),
+        by = c(
+          "DateTimeOriginal" = "timestamp",
+          "Species" = "scientificName"
+        )
       )
     n_media <-
       mica$data$media %>%
@@ -184,7 +187,7 @@ test_that(paste(
 
 test_that("filtering predicates are allowed and work well", {
   stations <- unique(
-    get_record_table(mica, pred_lt("longitude", 4.0))$Station
+    suppressMessages(get_record_table(mica, pred_lt("longitude", 4.0)))$Station
   )
   stations_calculate <- mica$data$deployments %>%
     dplyr::filter(longitude < 4.0) %>%

From 46ab17a97409adf25394a57a0184233758cb0e8d Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Mon, 24 Jul 2023 14:17:36 +0200
Subject: [PATCH 21/40] Adap read function to new output check_package

---
 R/read_camtrap_dp.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/read_camtrap_dp.R b/R/read_camtrap_dp.R
index d98bca53..aea7e58b 100644
--- a/R/read_camtrap_dp.R
+++ b/R/read_camtrap_dp.R
@@ -147,7 +147,7 @@ read_camtrap_dp <- function(file = NULL,
   }
  
   package$data <- data
-  package <- check_package(package, media = media)
+  check_package(package, media = media)
   
   package <- add_taxonomic_info(package)
   
@@ -165,7 +165,7 @@ read_camtrap_dp <- function(file = NULL,
     package$data$media <- order_cols_media(package$data$media)
   }
   
-  package <- check_package(package, media = media)
+  check_package(package, media = media)
   
   # Inherit parsing issues from reading
   attr(package$data$observations, which = "problems") <- issues_observations

From 15d971cee378a2af76aa219f38fdddbbdc9284cb Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Mon, 24 Jul 2023 14:18:05 +0200
Subject: [PATCH 22/40] Avoid returning TRUE explicitly

---
 R/check_package.R | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/R/check_package.R b/R/check_package.R
index bcd3f66b..882d3003 100644
--- a/R/check_package.R
+++ b/R/check_package.R
@@ -46,11 +46,12 @@ check_package <- function(package = NULL,
   tables_absent <- elements[
     !elements %in% names(package$data)
   ]
-  assertthat::assert_that(length(tables_absent) == 0,
-                          msg = glue::glue(
-                            "Can't find {tables_absent} elements in data package: {tables_absent*}",
-                            .transformer = collapse_transformer(sep = ", ", last = " and ")
-                          )
+  assertthat::assert_that(
+    length(tables_absent) == 0,
+    msg = glue::glue(
+      "Can't find {tables_absent} elements in data package: {tables_absent*}",
+      .transformer = collapse_transformer(sep = ", ", last = " and ")
+    )
   )
   if (media) {
     assertthat::assert_that(
@@ -65,6 +66,5 @@ check_package <- function(package = NULL,
   if (!is.null(package$data$media)) {
     assertthat::assert_that(is.data.frame(package$data$media))
   }
-  # When all is good, return TRUE
-  return(TRUE)
+  # When all is good, nothing
 }

From 36404cad32875481c9549429c96b9476bfc778b8 Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Mon, 24 Jul 2023 14:18:49 +0200
Subject: [PATCH 23/40] Improve documentation about returned object

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

diff --git a/R/check_package.R b/R/check_package.R
index 882d3003..3e78a289 100644
--- a/R/check_package.R
+++ b/R/check_package.R
@@ -11,7 +11,7 @@
 #' @param datapkg Deprecated. Use `package` instead.
 #' @param media Has the `media` resource been loaded while reading the data
 #'   package? Default: `FALSE`.
-#' @return A camera trap data package.
+#' @return `TRUE` or error.
 #' @noRd
 check_package <- function(package = NULL,
                           datapkg = NULL,

From ada3a0d6ab45271756d7decf34fccf9078b52e7d Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Mon, 24 Jul 2023 14:18:59 +0200
Subject: [PATCH 24/40] Run devtools::document()

---
 man/write_dwc.Rd | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/man/write_dwc.Rd b/man/write_dwc.Rd
index 4642e94e..13e8310b 100644
--- a/man/write_dwc.Rd
+++ b/man/write_dwc.Rd
@@ -15,13 +15,13 @@ useful for extending/adapting the Darwin Core mapping before writing with
 \code{\link[readr:write_delim]{readr::write_csv()}}.}
 }
 \value{
-CSV file(s) written to disk or list of data frames when
-\code{directory = NULL}.
+CSV and \code{meta.xml} files written to disk or a list of data
+frames when \code{directory = NULL}.
 }
 \description{
 Transforms data from a \href{https://tdwg.github.io/camtrap-dp/}{Camera Trap Data Package} to \href{https://dwc.tdwg.org/}{Darwin Core}.
-The resulting CSV file(s) can be uploaded to an \href{https://www.gbif.org/ipt}{IPT} for publication to GBIF.
-A \code{meta.xml} file is not created.
+The resulting CSV files can be uploaded to an \href{https://www.gbif.org/ipt}{IPT} for publication to GBIF.
+A \code{meta.xml} file is included as well.
 See \code{write_eml()} to create an \code{eml.xml} file.
 }
 \section{Transformation details}{

From ca26d97b9006ed4964e77ec9bec4c90c3eee34df Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Mon, 24 Jul 2023 18:00:32 +0200
Subject: [PATCH 25/40] Add/ improve messages in assertions

Probably removed while merging from main?
---
 R/check_package.R                   | 9 ++++++---
 tests/testthat/test-check_package.R | 7 ++++---
 2 files changed, 10 insertions(+), 6 deletions(-)

diff --git a/R/check_package.R b/R/check_package.R
index 3e78a289..242c7986 100644
--- a/R/check_package.R
+++ b/R/check_package.R
@@ -33,10 +33,13 @@ check_package <- function(package = NULL,
     msg = "`media` must be a logical: TRUE or FALSE"
   )
   # camera trap data package is a list
-  assertthat::assert_that(is.list(package))
-  assertthat::assert_that(!is.data.frame(package))
+  assertthat::assert_that(is.list(package),
+                          msg = "package is not a list.")
+  assertthat::assert_that(!is.data.frame(package),
+                          msg = "package is not a list.")
   # check existence of an element called data
-  assertthat::assert_that("data" %in% names(package))
+  assertthat::assert_that("data" %in% names(package),
+                          msg = "data element is missing from package")
   # check validity data element of package: does it contain deployments and
   # observations?
   elements <- c("deployments", "observations")
diff --git a/tests/testthat/test-check_package.R b/tests/testthat/test-check_package.R
index 01dedd7c..49e012ae 100644
--- a/tests/testthat/test-check_package.R
+++ b/tests/testthat/test-check_package.R
@@ -9,12 +9,13 @@ test_that("check_package() returns depreciation warning on datapkg argument", {
 test_that("check_package() returns error when package is not a list", {
   expect_error(
     check_package("not a list!"),
-    regexp = "package is not a list",
+    regexp = "package is not a list.",
     fixed = TRUE
   )
   expect_error(
-    check_package(data.frame(letters = c("a", "b", "c"), numbers = c(pi, 2 * pi, 3 * pi))),
-    regexp = "package is not a list",
+    check_package(data.frame(letters = c("a", "b", "c"), 
+                             numbers = c(pi, 2 * pi, 3 * pi))),
+    regexp = "package is not a list.",
     fixed = TRUE
   )
 })

From 0c748eb4bba7c21d2020be4785410ccd61a67008 Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Mon, 24 Jul 2023 18:01:22 +0200
Subject: [PATCH 26/40] Remove typo while forming the message

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

diff --git a/R/check_package.R b/R/check_package.R
index 242c7986..1ae7029e 100644
--- a/R/check_package.R
+++ b/R/check_package.R
@@ -52,7 +52,7 @@ check_package <- function(package = NULL,
   assertthat::assert_that(
     length(tables_absent) == 0,
     msg = glue::glue(
-      "Can't find {tables_absent} elements in data package: {tables_absent*}",
+      "Can't find {length(tables_absent)} elements in data package: {tables_absent*}",
       .transformer = collapse_transformer(sep = ", ", last = " and ")
     )
   )

From 819fdce4a2a879af07ef7849f67c4c43d8dd540b Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Mon, 24 Jul 2023 18:01:48 +0200
Subject: [PATCH 27/40] Add return(TRUE) back at the end of function

---
 R/check_package.R | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/R/check_package.R b/R/check_package.R
index 1ae7029e..aeebf8e8 100644
--- a/R/check_package.R
+++ b/R/check_package.R
@@ -69,5 +69,6 @@ check_package <- function(package = NULL,
   if (!is.null(package$data$media)) {
     assertthat::assert_that(is.data.frame(package$data$media))
   }
-  # When all is good, nothing
+  # If no errors are encountered, TRUE is returned
+  return(TRUE)
 }

From 0fbdda24d7a58fc6a12d2c7e619edfc448352087 Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Mon, 24 Jul 2023 18:02:46 +0200
Subject: [PATCH 28/40] Avoid using media element while testing missing element
 in data

This because check_package() has been improved by adding media = FALSE by default.
---
 tests/testthat/test-check_package.R | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/tests/testthat/test-check_package.R b/tests/testthat/test-check_package.R
index 49e012ae..93cd1fd2 100644
--- a/tests/testthat/test-check_package.R
+++ b/tests/testthat/test-check_package.R
@@ -29,18 +29,18 @@ test_that("check_package() returns error on missing data", {
 })
 
 test_that("check_package() returns error if not all elements are present", {
-  mica_no_media <- mica
-  mica_no_media$data$media <- NULL
+  mica_no_dep <- mica
+  mica_no_dep$data$deployments <- NULL
   expect_error(
-    check_package(mica_no_media),
-    regexp = "Can't find 1 elements in data package: media",
+    check_package(mica_no_dep, media = TRUE),
+    regexp = "Can't find 1 elements in data package: deployments",
     fixed = TRUE
   )
-  mica_no_media_no_obs <- mica_no_media
-  mica_no_media_no_obs$data$observations <- NULL
+  mica_no_dep_no_obs <- mica_no_dep
+  mica_no_dep_no_obs$data$observations <- NULL
   expect_error(
-    check_package(mica_no_media_no_obs),
-    regexp = "Can't find 2 elements in data package: media and observations",
+    check_package(mica_no_dep_no_obs),
+    regexp = "Can't find 2 elements in data package: deployments and observations",
     fixed = TRUE
   )
 })

From 353a18cd51de872eb18cabafc08c98bffda0dfc9 Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Mon, 24 Jul 2023 18:04:47 +0200
Subject: [PATCH 29/40] Add test about media flag argument

---
 tests/testthat/test-check_package.R | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/tests/testthat/test-check_package.R b/tests/testthat/test-check_package.R
index 93cd1fd2..38e01e51 100644
--- a/tests/testthat/test-check_package.R
+++ b/tests/testthat/test-check_package.R
@@ -45,10 +45,21 @@ test_that("check_package() returns error if not all elements are present", {
   )
 })
 
+test_that(
+  "check_package() returns an error when media element is NULL only if media flag is TRUE", {
+    mica_no_media <- mica
+    mica_no_media$data$media <- NULL
+    expect_error(
+      check_package(mica_no_media, media = TRUE),
+      regexp = "Can't find 1 elements in data package: media",
+      fixed = TRUE
+    )
+    expect_true(check_package(mica_no_media))
+})
+
 test_that("check_package() returns error if observations is not a data.frame", {
   mica_listed <- mica
   mica_listed$data$observations <- as.list(mica_listed$data$observations)
-
   expect_error(
     check_package(mica_listed),
     regexp = "package$data$observations is not a data frame",

From 366d81c33042891805c23e0b99207bb07683ccbc Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Mon, 24 Jul 2023 18:05:09 +0200
Subject: [PATCH 30/40] Improve test definition back

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

diff --git a/tests/testthat/test-check_package.R b/tests/testthat/test-check_package.R
index 38e01e51..207117ff 100644
--- a/tests/testthat/test-check_package.R
+++ b/tests/testthat/test-check_package.R
@@ -94,6 +94,6 @@ test_that("check_package() returns error if media is not a data.frame", {
   )
 })
 
-test_that("check_package() returns TRUE on valid package", {
+test_that("check_package() returns nothing on valid package", {
   expect_true(check_package(mica))
 })

From 7c21229157a1759e2cb99be174a454f6710f2f43 Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Mon, 24 Jul 2023 18:05:19 +0200
Subject: [PATCH 31/40] Run devtools::document()

---
 man/map_dep.Rd | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/man/map_dep.Rd b/man/map_dep.Rd
index f3af4cfa..c8994adc 100644
--- a/man/map_dep.Rd
+++ b/man/map_dep.Rd
@@ -326,6 +326,25 @@ map_dep(
   zero_values_icon_url = "https://img.icons8.com/ios-glyphs/30/2ECC71/futurama-fry.png"
 )
 
+# Same behavior for the icon visualizing NA values (`"n_species"` feature)
+unknown_species_vs_no_obs <- mica
+unknown_species_vs_no_obs$data$observations <- 
+  unknown_species_vs_no_obs$data$observations \%>\% 
+  # a deployment has detected only unknown species
+  filter(is.na(.data$scientificName) | 
+           .data$scientificName != "Homo sapiens") \%>\%
+  # a deployment has no observations
+  filter(deploymentID != "62c200a9-0e03-4495-bcd8-032944f6f5a1")
+# create new map
+map_dep(
+  unknown_species_vs_no_obs,
+  feature = "n_species",
+  zero_values_icon_url = "https://img.icons8.com/ios-glyphs/30/2ECC71/futurama-fry.png",
+  zero_values_icon_size = 60,
+  na_values_icon_url = "https://img.icons8.com/ios-glyphs/30/E74C3C/futurama-fry.png",
+  na_values_icon_size = 60
+)
+
 # Set size of the icon for zero values deployments
 map_dep(
   mica,

From 3e4a077cafc1e20c093d0c3f837e7297d80ad901 Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Mon, 24 Jul 2023 21:57:11 +0200
Subject: [PATCH 32/40] Transfer deprecated datapkg arg to package

---
 R/get_cam_op.R          | 5 ++++-
 R/get_custom_effort.R   | 5 ++++-
 R/get_effort.R          | 5 ++++-
 R/get_n_individuals.R   | 5 ++++-
 R/get_n_obs.R           | 5 ++++-
 R/get_n_species.R       | 4 +++-
 R/get_rai.R             | 5 ++++-
 R/get_record_table.R    | 5 ++++-
 R/get_scientific_name.R | 4 ++++
 R/get_species.R         | 5 ++++-
 R/map_dep.R             | 5 ++++-
 11 files changed, 43 insertions(+), 10 deletions(-)

diff --git a/R/get_cam_op.R b/R/get_cam_op.R
index 5569d528..caecfcb5 100644
--- a/R/get_cam_op.R
+++ b/R/get_cam_op.R
@@ -50,7 +50,10 @@ get_cam_op <- function(package = NULL,
                        datapkg = NULL) {
   # check camera trap data package
   check_package(package, datapkg, "get_cam_op")
-
+  if (is.null(package) & !is.name(datapkg)) {
+    package <- datapkg
+  }
+  
   # Check that station_col is a single string
   assertthat::assert_that(assertthat::is.string(station_col))
   # Check that station_col is one of the columns in deployments
diff --git a/R/get_custom_effort.R b/R/get_custom_effort.R
index 315b78ad..74c2b69c 100644
--- a/R/get_custom_effort.R
+++ b/R/get_custom_effort.R
@@ -117,7 +117,10 @@ get_custom_effort <- function(package = NULL,
 
   # check camera trap data package
   check_package(package, datapkg, "get_custom_effort")
-
+  if (is.null(package) & !is.name(datapkg)) {
+    package <- datapkg
+  }
+  
   # get deployments
   deployments <- package$data$deployments
 
diff --git a/R/get_effort.R b/R/get_effort.R
index 5c6f03c0..0ef6616c 100644
--- a/R/get_effort.R
+++ b/R/get_effort.R
@@ -43,7 +43,10 @@ get_effort <- function(package = NULL,
 
   # check camera trap data package
   check_package(package, datapkg, "get_effort")
-
+  if (is.null(package) & !is.name(datapkg)) {
+    package <- datapkg
+  }
+  
   # apply filtering
   package$data$deployments <- apply_filter_predicate(
     df = package$data$deployments,
diff --git a/R/get_n_individuals.R b/R/get_n_individuals.R
index 6874ae28..d982dfe1 100644
--- a/R/get_n_individuals.R
+++ b/R/get_n_individuals.R
@@ -68,7 +68,10 @@ get_n_individuals <- function(package = NULL,
                               datapkg = lifecycle::deprecated()) {
   # check input data package
   check_package(package, datapkg, "get_n_individuals")
-
+  if (is.null(package) & !is.name(datapkg)) {
+    package <- datapkg
+  }
+  
   # avoid to call variables like column names to make life easier using filter()
   sex_value <- sex
 
diff --git a/R/get_n_obs.R b/R/get_n_obs.R
index ddf97a15..8d3187f7 100644
--- a/R/get_n_obs.R
+++ b/R/get_n_obs.R
@@ -65,7 +65,10 @@ get_n_obs <- function(package = NULL,
                       datapkg = lifecycle::deprecated()) {
   # check input data package
   check_package(package, datapkg, "get_n_obs")
-
+  if (is.null(package) & !is.name(datapkg)) {
+    package <- datapkg
+  }
+  
   # avoid to call variables like column names to make life easier using filter()
   sex_value <- sex
 
diff --git a/R/get_n_species.R b/R/get_n_species.R
index 94349b13..dc7167c2 100644
--- a/R/get_n_species.R
+++ b/R/get_n_species.R
@@ -24,7 +24,9 @@ get_n_species <- function(package = NULL,
                           datapkg = lifecycle::deprecated()) {
   # check input data package
   check_package(package, datapkg, "get_n_species")
-
+  if (is.null(package) & !is.name(datapkg)) {
+    package <- datapkg
+  }
   # extract observations and deployments
   observations <- package$data$observations
   deployments <- package$data$deployments
diff --git a/R/get_rai.R b/R/get_rai.R
index 63d57e80..c8f1318a 100644
--- a/R/get_rai.R
+++ b/R/get_rai.R
@@ -59,7 +59,10 @@ get_rai <- function(package = NULL,
                     datapkg = lifecycle::deprecated()) {
   # check camera trap data package
   check_package(package, datapkg, "get_rai")
-
+  if (is.null(package) & !is.name(datapkg)) {
+    package <- datapkg
+  }
+  
   get_rai_primitive(package, ...,
     use = "n_obs",
     species = species,
diff --git a/R/get_record_table.R b/R/get_record_table.R
index 1a2101aa..13c06024 100644
--- a/R/get_record_table.R
+++ b/R/get_record_table.R
@@ -103,7 +103,10 @@ get_record_table <- function(package = NULL,
                              datapkg = lifecycle::deprecated()) {
   # check data package
   check_package(package, datapkg, "get_record_table", media = TRUE)
-
+  if (is.null(package) & !is.name(datapkg)) {
+    package <- datapkg
+  }
+  
   # check stationCol is a valid column name
   assertthat::assert_that(
     stationCol %in% names(package$data$deployments),
diff --git a/R/get_scientific_name.R b/R/get_scientific_name.R
index 29329a47..6030ad30 100644
--- a/R/get_scientific_name.R
+++ b/R/get_scientific_name.R
@@ -36,6 +36,10 @@ get_scientific_name <- function(package = NULL,
                                 vernacular_name,
                                 datapkg = lifecycle::deprecated()) {
   check_package(package, datapkg, "get_scientific_name")
+  if (is.null(package) & !is.name(datapkg)) {
+    package <- datapkg
+  }
+  
   all_sn_vn <- get_species(package)
 
   # get vernacular names for check
diff --git a/R/get_species.R b/R/get_species.R
index a48be1ef..ffc26825 100644
--- a/R/get_species.R
+++ b/R/get_species.R
@@ -15,7 +15,10 @@
 get_species <- function(package = NULL, datapkg = lifecycle::deprecated()) {
   # Check camera trap data package
   check_package(package, datapkg, "get_species", media = FALSE)
-
+  if (is.null(package) & !is.name(datapkg)) {
+    package <- datapkg
+  }
+  
   # Get taxonomic information from package metadata
   if (!"taxonomic" %in% names(package)) {
     return(NULL)
diff --git a/R/map_dep.R b/R/map_dep.R
index bf18c279..d82582e2 100644
--- a/R/map_dep.R
+++ b/R/map_dep.R
@@ -353,7 +353,10 @@ map_dep <- function(package = NULL,
 
   # check camera trap data package
   check_package(package, datapkg, "map_dep")
-
+  if (is.null(package) & !is.name(datapkg)) {
+    package <- datapkg
+  }
+  
   # define possible feature values
   features <- c(
     "n_species",

From efa45682ac80e331de633ef905bfab512c319f9e Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Mon, 24 Jul 2023 22:07:09 +0200
Subject: [PATCH 33/40] Add tests about deprecation datapkg

---
 tests/testthat/test-get_cam_op.R          | 9 +++++++++
 tests/testthat/test-get_custom_effort.R   | 9 +++++++++
 tests/testthat/test-get_effort.R          | 9 +++++++++
 tests/testthat/test-get_n_individuals.R   | 9 +++++++++
 tests/testthat/test-get_n_obs.R           | 9 +++++++++
 tests/testthat/test-get_rai.R             | 9 +++++++++
 tests/testthat/test-get_rai_individuals.R | 9 +++++++++
 tests/testthat/test-get_record_table.R    | 9 +++++++++
 tests/testthat/test-get_scientific_name.R | 9 +++++++++
 tests/testthat/test-map_dep.R             | 9 +++++++++
 10 files changed, 90 insertions(+)

diff --git a/tests/testthat/test-get_cam_op.R b/tests/testthat/test-get_cam_op.R
index 902141a3..53584c24 100644
--- a/tests/testthat/test-get_cam_op.R
+++ b/tests/testthat/test-get_cam_op.R
@@ -166,3 +166,12 @@ test_that("filtering predicates are allowed and work well", {
   )
   expect_equal(rownames(filtered_cam_op_matrix), "Mica Viane")
 })
+
+test_that("Argument datapkg is deprecated: warning returned", {
+  expect_warning(
+    rlang::with_options(
+      lifecycle_verbosity = "warning",
+      get_cam_op(datapkg = mica)
+    )
+  )
+})
diff --git a/tests/testthat/test-get_custom_effort.R b/tests/testthat/test-get_custom_effort.R
index b6470b31..60c31423 100644
--- a/tests/testthat/test-get_custom_effort.R
+++ b/tests/testthat/test-get_custom_effort.R
@@ -180,3 +180,12 @@ test_that("check effort and unit values", {
   # unit value is equal to day if unit value is set to "day"
   expect_equal(unique(tot_effort_days$unit), "day")
 })
+
+test_that("Argument datapkg is deprecated: warning returned", {
+  expect_warning(
+    rlang::with_options(
+      lifecycle_verbosity = "warning",
+      get_custom_effort(datapkg = mica)
+    )
+  )
+})
\ No newline at end of file
diff --git a/tests/testthat/test-get_effort.R b/tests/testthat/test-get_effort.R
index c9af3cab..117e35f1 100644
--- a/tests/testthat/test-get_effort.R
+++ b/tests/testthat/test-get_effort.R
@@ -75,3 +75,12 @@ testthat::test_that("get_effort returns the right number of rows", {
     n_all_deployments
   )
 })
+
+test_that("Argument datapkg is deprecated: warning returned", {
+  expect_warning(
+    rlang::with_options(
+      lifecycle_verbosity = "warning",
+      get_effort(datapkg = mica)
+    )
+  )
+})
\ No newline at end of file
diff --git a/tests/testthat/test-get_n_individuals.R b/tests/testthat/test-get_n_individuals.R
index ee12f289..d724af26 100644
--- a/tests/testthat/test-get_n_individuals.R
+++ b/tests/testthat/test-get_n_individuals.R
@@ -247,3 +247,12 @@ test_that("error returned if life stage or sex is not present", {
   expect_error(get_n_individuals(mica, life_stage = "bad"))
   expect_error(get_n_individuals(mica, sex = "bad"))
 })
+
+test_that("Argument datapkg is deprecated: warning returned", {
+  expect_warning(
+    rlang::with_options(
+      lifecycle_verbosity = "warning",
+      get_n_individuals(datapkg = mica)
+    )
+  )
+})
diff --git a/tests/testthat/test-get_n_obs.R b/tests/testthat/test-get_n_obs.R
index 6629aeea..2a876320 100644
--- a/tests/testthat/test-get_n_obs.R
+++ b/tests/testthat/test-get_n_obs.R
@@ -280,3 +280,12 @@ test_that("Filter by date of deployments via predicates works correctly", {
     dplyr::arrange(deploymentID, scientificName)
   expect_equal(obs_filtered, obs_filtered_man)
 })
+
+test_that("Argument datapkg is deprecated: warning returned", {
+  expect_warning(
+    rlang::with_options(
+      lifecycle_verbosity = "warning",
+      get_n_obs(datapkg = mica)
+    )
+  )
+})
diff --git a/tests/testthat/test-get_rai.R b/tests/testthat/test-get_rai.R
index 52844f55..6da186d6 100644
--- a/tests/testthat/test-get_rai.R
+++ b/tests/testthat/test-get_rai.R
@@ -104,3 +104,12 @@ test_that("life_stage filters data correctly", {
     ignore_attr = TRUE
   )
 })
+
+test_that("Argument datapkg is deprecated: warning returned", {
+  expect_warning(
+    rlang::with_options(
+      lifecycle_verbosity = "warning",
+      get_rai(datapkg = mica)
+    )
+  )
+})
\ No newline at end of file
diff --git a/tests/testthat/test-get_rai_individuals.R b/tests/testthat/test-get_rai_individuals.R
index 601f5649..2fd4bc62 100644
--- a/tests/testthat/test-get_rai_individuals.R
+++ b/tests/testthat/test-get_rai_individuals.R
@@ -108,3 +108,12 @@ test_that("life_stage filters data correctly", {
     ignore_attr = TRUE
   )
 })
+
+test_that("Argument datapkg is deprecated: warning returned", {
+  expect_warning(
+    rlang::with_options(
+      lifecycle_verbosity = "warning",
+      get_rai_individuals(datapkg = mica)
+    )
+  )
+})
\ No newline at end of file
diff --git a/tests/testthat/test-get_record_table.R b/tests/testthat/test-get_record_table.R
index d6dc6adf..64dcc440 100644
--- a/tests/testthat/test-get_record_table.R
+++ b/tests/testthat/test-get_record_table.R
@@ -194,3 +194,12 @@ test_that("filtering predicates are allowed and work well", {
     dplyr::pull(locationName)
   testthat::expect_identical(stations, stations_calculate)
 })
+
+test_that("Argument datapkg is deprecated: warning returned", {
+  expect_warning(
+    rlang::with_options(
+      lifecycle_verbosity = "warning",
+      get_record_table(datapkg = mica)
+    )
+  )
+})
\ No newline at end of file
diff --git a/tests/testthat/test-get_scientific_name.R b/tests/testthat/test-get_scientific_name.R
index 43ed331b..8513eca8 100644
--- a/tests/testthat/test-get_scientific_name.R
+++ b/tests/testthat/test-get_scientific_name.R
@@ -18,3 +18,12 @@ test_that("Functions works case insensitively", {
   sc_names <- get_scientific_name(mica, c("beeCH MArten"))
   expect_equal(sc_names, c("Martes foina"))
 })
+
+test_that("Argument datapkg is deprecated: warning returned", {
+  expect_warning(
+    rlang::with_options(
+      lifecycle_verbosity = "warning",
+      get_scientific_name(datapkg = mica, vernacular_name = "beech marten")
+    )
+  )
+})
\ No newline at end of file
diff --git a/tests/testthat/test-map_dep.R b/tests/testthat/test-map_dep.R
index ebc06d0e..39746413 100644
--- a/tests/testthat/test-map_dep.R
+++ b/tests/testthat/test-map_dep.R
@@ -226,3 +226,12 @@ test_that("map_dep() returns a leaflet", {
   expect_no_error(map_dep(mica, feature = "n_species"))
   expect_no_message(map_dep(mica, feature = "n_species"))
 })
+
+test_that("Argument datapkg is deprecated: warning returned", {
+  expect_warning(
+    rlang::with_options(
+      lifecycle_verbosity = "warning",
+      map_dep(datapkg = mica, feature = "n_obs")
+    )
+  )
+})

From 31b35e945d9c58cbcc1e98d0e5d4801f323d2da2 Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Tue, 25 Jul 2023 10:07:22 +0200
Subject: [PATCH 34/40] Add deprecation to datapkg where forgotten

---
 R/get_cam_op.R        | 2 +-
 R/get_custom_effort.R | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/get_cam_op.R b/R/get_cam_op.R
index caecfcb5..d366c1a1 100644
--- a/R/get_cam_op.R
+++ b/R/get_cam_op.R
@@ -47,7 +47,7 @@ get_cam_op <- function(package = NULL,
                        ...,
                        station_col = "locationName",
                        use_prefix = FALSE,
-                       datapkg = NULL) {
+                       datapkg = lifecycle::deprecated()) {
   # check camera trap data package
   check_package(package, datapkg, "get_cam_op")
   if (is.null(package) & !is.name(datapkg)) {
diff --git a/R/get_custom_effort.R b/R/get_custom_effort.R
index 74c2b69c..8c52a40c 100644
--- a/R/get_custom_effort.R
+++ b/R/get_custom_effort.R
@@ -91,7 +91,7 @@ get_custom_effort <- function(package = NULL,
                               end = NULL,
                               group_by = NULL,
                               unit = "hour",
-                              datapkg = NULL) {
+                              datapkg = lifecycle::deprecated()) {
   # define possible unit values
   units <- c("hour", "day")
 

From a4d6a1066a49415ed1c3015f9d9fda984d1a0ba8 Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Tue, 25 Jul 2023 10:11:54 +0200
Subject: [PATCH 35/40] Apply devtools::document()

---
 man/get_cam_op.Rd                 |  2 +-
 man/get_custom_effort.Rd          |  2 +-
 tests/testthat/test-get_species.R | 16 +++++++++++++++-
 3 files changed, 17 insertions(+), 3 deletions(-)

diff --git a/man/get_cam_op.Rd b/man/get_cam_op.Rd
index 86d8dfe3..83c57185 100644
--- a/man/get_cam_op.Rd
+++ b/man/get_cam_op.Rd
@@ -9,7 +9,7 @@ get_cam_op(
   ...,
   station_col = "locationName",
   use_prefix = FALSE,
-  datapkg = NULL
+  datapkg = lifecycle::deprecated()
 )
 }
 \arguments{
diff --git a/man/get_custom_effort.Rd b/man/get_custom_effort.Rd
index 47bade10..2dc4e92a 100644
--- a/man/get_custom_effort.Rd
+++ b/man/get_custom_effort.Rd
@@ -11,7 +11,7 @@ get_custom_effort(
   end = NULL,
   group_by = NULL,
   unit = "hour",
-  datapkg = NULL
+  datapkg = lifecycle::deprecated()
 )
 }
 \arguments{
diff --git a/tests/testthat/test-get_species.R b/tests/testthat/test-get_species.R
index bdadf78e..e03c8847 100644
--- a/tests/testthat/test-get_species.R
+++ b/tests/testthat/test-get_species.R
@@ -77,6 +77,20 @@ test_that("Argument datapkg is deprecated: warning returned", {
     rlang::with_options(
       lifecycle_verbosity = "warning",
       get_species(datapkg = mica)
-    )
+    ),
+    paste0("\033[38;5;232mThe `datapkg` argument of `get_species()` is ",
+           "deprecated as of camtraptor 0.16.0.\n\033[36mℹ\033[38;5;232m Please",
+           " use the `package` argument instead.\n\033[36mℹ\033[38;5;232m The",
+           " deprecated feature was likely used in the ",
+           "\033[34mcamtraptor\033[38;5;232m package.\n  ",
+           "Please report the issue at \033[3m\033[34m<\033]8;;",
+           "https://github.com/inbo/camtraptor/issues\a",
+           "https://github.com/inbo/camtraptor/issues\033]8;;",
+           "\a>\033[38;5;232m\033[23m.\n\033[90mThis warning is displayed ",
+           "once every 8 hours.\033[38;5;232m\n\033[90mCall ",
+           "`lifecycle::last_lifecycle_warnings()` to see where this warning ",
+           "was generated.\033[38;5;232m\033[39m"
+    ),
+    fixed = TRUE
   )
 })

From 1a4363984fe23207e451ea3a8b6f636b491c8cab Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Tue, 25 Jul 2023 10:14:23 +0200
Subject: [PATCH 36/40] Support deprecation in get_rai_individuals as well

---
 R/get_rai.R | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/R/get_rai.R b/R/get_rai.R
index c8f1318a..0a6de37e 100644
--- a/R/get_rai.R
+++ b/R/get_rai.R
@@ -139,6 +139,10 @@ get_rai_individuals <- function(package = NULL,
                                 datapkg = lifecycle::deprecated()) {
   # check camera trap data package
   check_package(package, datapkg, "get_rai_individuals")
+  if (is.null(package) & !is.name(datapkg)) {
+    package <- datapkg
+  }
+  
   get_rai_primitive(package, ...,
     use = "n_individuals",
     species = species,

From 5439c232493e8261cf93bacdf4d9a6774e5c1c2a Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Tue, 25 Jul 2023 10:42:10 +0200
Subject: [PATCH 37/40] Use dplyr::func_name() syntax in test

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

diff --git a/tests/testthat/test-get_n_species.R b/tests/testthat/test-get_n_species.R
index fd534791..9d15878e 100644
--- a/tests/testthat/test-get_n_species.R
+++ b/tests/testthat/test-get_n_species.R
@@ -27,7 +27,7 @@ test_that("get_n_species returns 0 for obs without recognized species", {
   unknown_species$data$observations <- 
     unknown_species$data$observations %>% 
     # a deployment has detected only unknown species
-    filter(is.na(.data$scientificName) | 
+    dplyr::filter(is.na(.data$scientificName) | 
              .data$scientificName != "Homo sapiens")
   n_species <- get_n_species(package = unknown_species)
   expect_equal(n_species[n_species$n == 0,]$n, 0)

From 5155d10ff6ad41c7b14e8271cc8df4ff012573fa Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Tue, 25 Jul 2023 10:42:44 +0200
Subject: [PATCH 38/40] Add suppressMessages() to better read output tests

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

diff --git a/tests/testthat/test-get_n_species.R b/tests/testthat/test-get_n_species.R
index 9d15878e..9f7edc9b 100644
--- a/tests/testthat/test-get_n_species.R
+++ b/tests/testthat/test-get_n_species.R
@@ -41,7 +41,7 @@ test_that("get_n_species returns NA for deployments without observations", {
   dep_no_obs <- "29b7d356-4bb4-4ec4-b792-2af5cc32efa8"
   obs <- obs[obs$deploymentID != dep_no_obs,]
   no_obs$data$observations <- obs
-  n_species <- get_n_species(package = no_obs)
+  n_species <- suppressMessages(get_n_species(package = no_obs))
   expect_true(is.na(n_species[n_species$deploymentID == dep_no_obs,]$n))
 })
 

From db8e01a4b7efc14fa93f4ac0bc096a61ce219633 Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Tue, 25 Jul 2023 10:43:43 +0200
Subject: [PATCH 39/40] Add suppressMessages in test for read_ function

---
 tests/testthat/test-read_camtrap_dp.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/testthat/test-read_camtrap_dp.R b/tests/testthat/test-read_camtrap_dp.R
index 60046226..48cd60c8 100644
--- a/tests/testthat/test-read_camtrap_dp.R
+++ b/tests/testthat/test-read_camtrap_dp.R
@@ -21,12 +21,12 @@ test_that("file can be an URL", {
 
 test_that("only DP versions 1.0-rc.1 and dp 0.1.6 are supported", {
   expect_error(
-    read_camtrap_dp("https://raw.githubusercontent.com/tdwg/camtrap-dp/bb046c85a55bef2ced709357c0047f0136df8326/example/datapackage.json"),
+    suppressMessages(read_camtrap_dp("https://raw.githubusercontent.com/tdwg/camtrap-dp/bb046c85a55bef2ced709357c0047f0136df8326/example/datapackage.json")),
     "Version https://raw.githubusercontent.com/tdwg/camtrap-dp/0.5/camtrap-dp-profile.json is not supported. Supported versions: 0.1.6 and 1.0-rc.1."
   )
   
   expect_error(
-    read_camtrap_dp("https://raw.githubusercontent.com/tdwg/dwc-for-biologging/403f57db105982dc05b70f3cf66fd2b5591798db/derived/camtrap-dp/data/raw/datapackage.json"),
+    suppressMessages(read_camtrap_dp("https://raw.githubusercontent.com/tdwg/dwc-for-biologging/403f57db105982dc05b70f3cf66fd2b5591798db/derived/camtrap-dp/data/raw/datapackage.json")),
     "Version tabular-data-package is not supported. Supported versions: 0.1.6 and 1.0-rc.1."
   )
 })

From a51a3965b1d748d7bf8f0020c0be7fe47e1e067f Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Tue, 25 Jul 2023 12:38:23 +0200
Subject: [PATCH 40/40] Add tests for deprecated arg datapkg

---
 tests/testthat/test-get_cam_op.R          |  4 +++-
 tests/testthat/test-get_custom_effort.R   |  6 ++++--
 tests/testthat/test-get_effort.R          |  4 +++-
 tests/testthat/test-get_n_individuals.R   |  4 +++-
 tests/testthat/test-get_n_obs.R           |  4 +++-
 tests/testthat/test-get_n_species.R       |  4 +++-
 tests/testthat/test-get_rai.R             |  4 +++-
 tests/testthat/test-get_rai_individuals.R |  6 ++++--
 tests/testthat/test-get_record_table.R    |  6 ++++--
 tests/testthat/test-get_scientific_name.R |  6 ++++--
 tests/testthat/test-get_species.R         | 14 +-------------
 tests/testthat/test-map_dep.R             |  4 +++-
 12 files changed, 38 insertions(+), 28 deletions(-)

diff --git a/tests/testthat/test-get_cam_op.R b/tests/testthat/test-get_cam_op.R
index 53584c24..e5726572 100644
--- a/tests/testthat/test-get_cam_op.R
+++ b/tests/testthat/test-get_cam_op.R
@@ -172,6 +172,8 @@ test_that("Argument datapkg is deprecated: warning returned", {
     rlang::with_options(
       lifecycle_verbosity = "warning",
       get_cam_op(datapkg = mica)
-    )
+    ),
+    regexp = "The `datapkg` argument of `get_cam_op()` is deprecated as of camtraptor 0.16.0.",
+    fixed = TRUE
   )
 })
diff --git a/tests/testthat/test-get_custom_effort.R b/tests/testthat/test-get_custom_effort.R
index 60c31423..1efb2d05 100644
--- a/tests/testthat/test-get_custom_effort.R
+++ b/tests/testthat/test-get_custom_effort.R
@@ -186,6 +186,8 @@ test_that("Argument datapkg is deprecated: warning returned", {
     rlang::with_options(
       lifecycle_verbosity = "warning",
       get_custom_effort(datapkg = mica)
-    )
+    ),
+    regexp = "The `datapkg` argument of `get_custom_effort()` is deprecated as of camtraptor 0.16.0.",
+    fixed = TRUE
   )
-})
\ No newline at end of file
+})
diff --git a/tests/testthat/test-get_effort.R b/tests/testthat/test-get_effort.R
index 117e35f1..1df1a113 100644
--- a/tests/testthat/test-get_effort.R
+++ b/tests/testthat/test-get_effort.R
@@ -81,6 +81,8 @@ test_that("Argument datapkg is deprecated: warning returned", {
     rlang::with_options(
       lifecycle_verbosity = "warning",
       get_effort(datapkg = mica)
-    )
+    ),
+    regexp = "The `datapkg` argument of `get_effort()` is deprecated as of camtraptor 0.16.0.",
+    fixed = TRUE
   )
 })
\ No newline at end of file
diff --git a/tests/testthat/test-get_n_individuals.R b/tests/testthat/test-get_n_individuals.R
index d724af26..c2ff521e 100644
--- a/tests/testthat/test-get_n_individuals.R
+++ b/tests/testthat/test-get_n_individuals.R
@@ -253,6 +253,8 @@ test_that("Argument datapkg is deprecated: warning returned", {
     rlang::with_options(
       lifecycle_verbosity = "warning",
       get_n_individuals(datapkg = mica)
-    )
+    ),
+    regexp = "The `datapkg` argument of `get_n_individuals()` is deprecated as of camtraptor 0.16.0.",
+    fixed = TRUE
   )
 })
diff --git a/tests/testthat/test-get_n_obs.R b/tests/testthat/test-get_n_obs.R
index 2a876320..0b4befd3 100644
--- a/tests/testthat/test-get_n_obs.R
+++ b/tests/testthat/test-get_n_obs.R
@@ -286,6 +286,8 @@ test_that("Argument datapkg is deprecated: warning returned", {
     rlang::with_options(
       lifecycle_verbosity = "warning",
       get_n_obs(datapkg = mica)
-    )
+    ),
+    regexp = "The `datapkg` argument of `get_n_obs()` is deprecated as of camtraptor 0.16.0.",
+    fixed = TRUE
   )
 })
diff --git a/tests/testthat/test-get_n_species.R b/tests/testthat/test-get_n_species.R
index 9f7edc9b..19c27ef3 100644
--- a/tests/testthat/test-get_n_species.R
+++ b/tests/testthat/test-get_n_species.R
@@ -50,6 +50,8 @@ test_that("Argument datapkg is deprecated: warning returned", {
     rlang::with_options(
       lifecycle_verbosity = "warning",
       get_n_species(datapkg = mica)
-    )
+    ),
+    regexp = "The `datapkg` argument of `get_n_species()` is deprecated as of camtraptor 0.16.0.",
+    fixed = TRUE
   )
 })
diff --git a/tests/testthat/test-get_rai.R b/tests/testthat/test-get_rai.R
index 6da186d6..dd3056df 100644
--- a/tests/testthat/test-get_rai.R
+++ b/tests/testthat/test-get_rai.R
@@ -110,6 +110,8 @@ test_that("Argument datapkg is deprecated: warning returned", {
     rlang::with_options(
       lifecycle_verbosity = "warning",
       get_rai(datapkg = mica)
-    )
+    ),
+    regexp = "The `datapkg` argument of `get_rai()` is deprecated as of camtraptor 0.16.0.",
+    fixed = TRUE
   )
 })
\ No newline at end of file
diff --git a/tests/testthat/test-get_rai_individuals.R b/tests/testthat/test-get_rai_individuals.R
index 2fd4bc62..0d59c2f8 100644
--- a/tests/testthat/test-get_rai_individuals.R
+++ b/tests/testthat/test-get_rai_individuals.R
@@ -114,6 +114,8 @@ test_that("Argument datapkg is deprecated: warning returned", {
     rlang::with_options(
       lifecycle_verbosity = "warning",
       get_rai_individuals(datapkg = mica)
-    )
+    ),
+    regexp = "The `datapkg` argument of `get_rai_individuals()` is deprecated as of camtraptor 0.16.0.",
+    fixed = TRUE
   )
-})
\ No newline at end of file
+})
diff --git a/tests/testthat/test-get_record_table.R b/tests/testthat/test-get_record_table.R
index 64dcc440..79772aa7 100644
--- a/tests/testthat/test-get_record_table.R
+++ b/tests/testthat/test-get_record_table.R
@@ -200,6 +200,8 @@ test_that("Argument datapkg is deprecated: warning returned", {
     rlang::with_options(
       lifecycle_verbosity = "warning",
       get_record_table(datapkg = mica)
-    )
+    ),
+    regexp = "The `datapkg` argument of `get_record_table()` is deprecated as of camtraptor 0.16.0.",
+    fixed = TRUE
   )
-})
\ No newline at end of file
+})
diff --git a/tests/testthat/test-get_scientific_name.R b/tests/testthat/test-get_scientific_name.R
index 8513eca8..415ad934 100644
--- a/tests/testthat/test-get_scientific_name.R
+++ b/tests/testthat/test-get_scientific_name.R
@@ -24,6 +24,8 @@ test_that("Argument datapkg is deprecated: warning returned", {
     rlang::with_options(
       lifecycle_verbosity = "warning",
       get_scientific_name(datapkg = mica, vernacular_name = "beech marten")
-    )
+    ),
+    regexp = "The `datapkg` argument of `get_scientific_name()` is deprecated as of camtraptor 0.16.0.",
+    fixed = TRUE
   )
-})
\ No newline at end of file
+})
diff --git a/tests/testthat/test-get_species.R b/tests/testthat/test-get_species.R
index e03c8847..fcfb0408 100644
--- a/tests/testthat/test-get_species.R
+++ b/tests/testthat/test-get_species.R
@@ -78,19 +78,7 @@ test_that("Argument datapkg is deprecated: warning returned", {
       lifecycle_verbosity = "warning",
       get_species(datapkg = mica)
     ),
-    paste0("\033[38;5;232mThe `datapkg` argument of `get_species()` is ",
-           "deprecated as of camtraptor 0.16.0.\n\033[36mℹ\033[38;5;232m Please",
-           " use the `package` argument instead.\n\033[36mℹ\033[38;5;232m The",
-           " deprecated feature was likely used in the ",
-           "\033[34mcamtraptor\033[38;5;232m package.\n  ",
-           "Please report the issue at \033[3m\033[34m<\033]8;;",
-           "https://github.com/inbo/camtraptor/issues\a",
-           "https://github.com/inbo/camtraptor/issues\033]8;;",
-           "\a>\033[38;5;232m\033[23m.\n\033[90mThis warning is displayed ",
-           "once every 8 hours.\033[38;5;232m\n\033[90mCall ",
-           "`lifecycle::last_lifecycle_warnings()` to see where this warning ",
-           "was generated.\033[38;5;232m\033[39m"
-    ),
+    regexp = "The `datapkg` argument of `get_species()` is deprecated as of camtraptor 0.16.0.",
     fixed = TRUE
   )
 })
diff --git a/tests/testthat/test-map_dep.R b/tests/testthat/test-map_dep.R
index 39746413..f882984e 100644
--- a/tests/testthat/test-map_dep.R
+++ b/tests/testthat/test-map_dep.R
@@ -232,6 +232,8 @@ test_that("Argument datapkg is deprecated: warning returned", {
     rlang::with_options(
       lifecycle_verbosity = "warning",
       map_dep(datapkg = mica, feature = "n_obs")
-    )
+    ),
+    regexp = "The `datapkg` argument of `map_dep()` is deprecated as of camtraptor 0.16.0.",
+    fixed = TRUE
   )
 })