Rename get_cam_op()

See #239
inbo · Jul 22, 2024 · 7e44fd2 · 7e44fd2
1 parent dee8feb
commit 7e44fd2
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diff --git a/R/get_cam_op.R b/R/get_cam_op.R
@@ -35,10 +35,10 @@
 #' library(dplyr)
 #' 
 #' x <- example_dataset()
-#' get_cam_op(x)
+#' camtrapR_cameraOperation(x)
 #'
 #' # Specify column with station names
-#' get_cam_op(x, station_col = "locationID")
+#' camtrapR_cameraOperation(x, station_col = "locationID")
 #'
 #' # Specify column with session IDs
 #' x_sessions <- x
@@ -49,19 +49,19 @@
 #'       "before2020"
 #'   )
 #' )
-#' get_cam_op(x_sessions, session_col = "session")
+#' camtrapR_cameraOperation(x_sessions, session_col = "session")
 #'
 #' # Specify column with camera IDs
 #' x_cameras <- x_sessions
 #' x_cameras$data$deployments$cameraID <- c(1, 2, 3, 4)
-#' get_cam_op(x_cameras, camera_col = "cameraID")
+#' camtrapR_cameraOperation(x_cameras, camera_col = "cameraID")
 #'
 #' # Specify both session and camera IDs
-#' get_cam_op(x_cameras, camera_col = "cameraID", session_col = "session")
+#' camtrapR_cameraOperation(x_cameras, camera_col = "cameraID", session_col = "session")
 #' 
 #' # Use prefix Station as in camtrapR's camera operation matrix
-#' get_cam_op(x, use_prefix = TRUE)
-get_cam_op <- function(x,
+#' camtrapR_cameraOperation(x, use_prefix = TRUE)
+camtrapR_cameraOperation <- function(x,
                        station_col = "locationName",
                        camera_col = NULL,
                        session_col = NULL,

diff --git a/R/get_custom_effort.R b/R/get_custom_effort.R
@@ -2,7 +2,7 @@
 #'
 #' Gets the custom effort (deployment duration) for a custom time window and a
 #' specific time interval such as day, week, month or year. The custom effort is
-#' also calculated over all deployments. This function calls `get_cam_op()`
+#' also calculated over all deployments. This function calls `camtrapR_cameraOperation()`
 #' internally.
 #'
 #' @param start Start date. Default: `NULL`. If `NULL` the earliest start date
@@ -95,7 +95,7 @@ get_custom_effort <- function(x,
   deployments <- deployments(x)
 
   # Camera operation matrix with filter(s) on deployments
-  cam_op <- get_cam_op(x, station_col = "deploymentID")
+  cam_op <- camtrapR_cameraOperation(x, station_col = "deploymentID")
 
   # Sum effort over all deployments for each day  (in day units)
   sum_effort <- colSums(cam_op, na.rm = TRUE, dims = 1)

diff --git a/tests/testthat/test-get_cam_op.R b/tests/testthat/test-get_cam_op.R
@@ -2,22 +2,22 @@ test_that("input camtrap dp is checked properly", {
   skip_if_offline()
   x <- example_dataset()
   # Character instead of datapackage
-  expect_error(get_cam_op("aaa"))
+  expect_error(camtrapR_cameraOperation("aaa"))
   # Numeric instead of datapackage
-  expect_error(get_cam_op(1))
+  expect_error(camtrapR_cameraOperation(1))
   # Station_col is not NA
   expect_error(
-    get_cam_op(x, station_col = NA),
+    camtrapR_cameraOperation(x, station_col = NA),
     "station_col is not a string (a length one character vector).",
     fixed = TRUE)
   # Station_col is length 1
   expect_error(
-    get_cam_op(x, station_col = c("locationID","locationName")),
+    camtrapR_cameraOperation(x, station_col = c("locationID","locationName")),
     "station_col is not a string (a length one character vector).",
     fixed = TRUE)
   # Station_col value is not a column of deployments
   expect_error(
-    get_cam_op(x, station_col = "bla"),
+    camtrapR_cameraOperation(x, station_col = "bla"),
     paste0(
       "Station column name (`bla`) is not valid: ", 
       "it must be one of the deployments column names."
@@ -27,22 +27,22 @@ test_that("input camtrap dp is checked properly", {
   # Column specified by station_col contains empty values
   x_empty_location_name <- x
   x_empty_location_name$data$deployments$locationName[2:3] <- NA
-  expect_error(get_cam_op(x_empty_location_name),
+  expect_error(camtrapR_cameraOperation(x_empty_location_name),
                "Column `locationName` must be non-empty: 2 NAs found."
   )
   # Camera_col is not NA
   expect_error(
-    get_cam_op(x, camera_col = NA),
+    camtrapR_cameraOperation(x, camera_col = NA),
     "camera_col is not a string (a length one character vector).",
     fixed = TRUE)
   # Camera_col is length 1
   expect_error(
-    get_cam_op(x, camera_col = c("locationID","locationName")),
+    camtrapR_cameraOperation(x, camera_col = c("locationID","locationName")),
     "camera_col is not a string (a length one character vector).",
     fixed = TRUE)
   # Station_col value is not a column of deployments
   expect_error(
-    get_cam_op(x, camera_col = "bla"),
+    camtrapR_cameraOperation(x, camera_col = "bla"),
     paste0(
       "Camera column name (`bla`) is not valid: ", 
       "it must be one of the deployments column names."
@@ -51,39 +51,39 @@ test_that("input camtrap dp is checked properly", {
   )
   # Session_col is not NA
   expect_error(
-    get_cam_op(x, session_col = NA),
+    camtrapR_cameraOperation(x, session_col = NA),
     "session_col is not a string (a length one character vector).",
     fixed = TRUE)
   # Session_col is length 1
   expect_error(
-    get_cam_op(x, session_col = c("locationID","locationName")),
+    camtrapR_cameraOperation(x, session_col = c("locationID","locationName")),
     "session_col is not a string (a length one character vector).",
     fixed = TRUE)
   # Session_col value is not a column of deployments
   expect_error(
-    get_cam_op(x, session_col = "bla"),
+    camtrapR_cameraOperation(x, session_col = "bla"),
     paste0(
       "Session column name (`bla`) is not valid: ", 
       "it must be one of the deployments column names."
     ),
     fixed = TRUE
   )
   # use_prefix must be TRUE or FALSE
-  expect_error(get_cam_op(x, use_prefix = "bla"))
-  expect_error(get_cam_op(x, use_prefix = NA))
+  expect_error(camtrapR_cameraOperation(x, use_prefix = "bla"))
+  expect_error(camtrapR_cameraOperation(x, use_prefix = NA))
 })
 
 test_that("output is a matrix", {
   skip_if_offline()
   x <- example_dataset()
-  cam_op_matrix <- get_cam_op(x)
+  cam_op_matrix <- camtrapR_cameraOperation(x)
   expect_true(is.matrix(cam_op_matrix))
 })
 
 test_that("output matrix has locations as rownames", {
   skip_if_offline()
   x <- example_dataset()
-  cam_op_matrix <- get_cam_op(x)
+  cam_op_matrix <- camtrapR_cameraOperation(x)
   locations <- deployments(x)$locationName
   n_locations <- length(deployments(x)$locationName)
   expect_identical(nrow(cam_op_matrix), n_locations)
@@ -101,7 +101,7 @@ test_that("output matrix has sessions addded to locations as rownames", {
       "before2020"
    )
   )
-  cam_op_matrix <- get_cam_op(x_sessions, session_col = "session")
+  cam_op_matrix <- camtrapR_cameraOperation(x_sessions, session_col = "session")
   locations_sessions <- paste(deployments(x_sessions)$locationName,
                               deployments(x_sessions)$session,
                               sep = "__SESS_"
@@ -116,7 +116,7 @@ test_that("output matrix has camera IDs addded to locations as rownames", {
   x <- example_dataset()
   x_cameras <- x
   x_cameras$data$deployments$cameraID <- c(1, 2, 3, 4)
-  cam_op_matrix <- get_cam_op(x_cameras, camera_col = "cameraID")
+  cam_op_matrix <- camtrapR_cameraOperation(x_cameras, camera_col = "cameraID")
   locations_cameras <- paste(deployments(x_sessions)$locationName,
                              deployments(x_sessions)$cameraID,
                              sep = "__CAM_"
@@ -133,7 +133,7 @@ test_that(
     x_sess_cam <- x
     x_sess_cam$data$deployments$cameraID <- c(1, 2, 3, 4)
     x_sess_cam$data$deployments$session <- c(1, 2, 3, 4)
-    cam_op_matrix <- get_cam_op(x_sess_cam, 
+    cam_op_matrix <- camtrapR_cameraOperation(x_sess_cam, 
                                 camera_col = "cameraID", 
                                 session_col = "session"
     )
@@ -157,14 +157,14 @@ test_that(
     x <- example_dataset()
     x_sess <- x
     x_sess$data$deployments$session <- c("1__SESS_1")
-    expect_error(get_cam_op(x_sess, session_col = "session"),
+    expect_error(camtrapR_cameraOperation(x_sess, session_col = "session"),
                  paste0("Session column name (`session`) must not contain any ",
                         "of the reserved words: \"__SESS_\", \"__CAM_\"."),
                  fixed = TRUE
     )
     x_sess <- x
     x_sess$data$deployments$cameraID <- paste0(c(1,2,3,4), "__SESS_")
-    expect_error(get_cam_op(x_sess, camera_col = "cameraID"),
+    expect_error(camtrapR_cameraOperation(x_sess, camera_col = "cameraID"),
                  paste0("Camera column name (`cameraID`) must not contain any ",
                         "of the reserved words: \"__SESS_\", \"__CAM_\"."),
                  fixed = TRUE
@@ -175,7 +175,7 @@ test_that(
       deployments(x_sess)$locationName[1]
     )
     expect_error(
-      get_cam_op(x_sess),
+      camtrapR_cameraOperation(x_sess),
       paste0("Station column name (`locationName`) must not contain any ",
              "of the reserved words: \"__SESS_\", \"__CAM_\"."),
       fixed = TRUE
@@ -190,14 +190,14 @@ test_that(
     x <- example_dataset()
     x_cam <- x
     x_cam$data$deployments$session[1] <- c("1__CAM_1")
-    expect_error(get_cam_op(x_cam, session_col = "session"),
+    expect_error(camtrapR_cameraOperation(x_cam, session_col = "session"),
                  paste0("Session column name (`session`) must not contain any ",
                         "of the reserved words: \"__SESS_\", \"__CAM_\"."),
                  fixed = TRUE
     )
     x_cam <- x
     x_cam$data$deployments$cameraID <- paste0(c(1,2,3,4), "__CAM_")
-    expect_error(get_cam_op(x_cam, camera_col = "cameraID"),
+    expect_error(camtrapR_cameraOperation(x_cam, camera_col = "cameraID"),
                  paste0("Camera column name (`cameraID`) must not contain any ",
                         "of the reserved words: \"__SESS_\", \"__CAM_\"."),
                  fixed = TRUE
@@ -208,7 +208,7 @@ test_that(
       deployments(x_cam)$locationName[1]
     )
     expect_error(
-      get_cam_op(x_cam),
+      camtrapR_cameraOperation(x_cam),
       paste0("Station column name (`locationName`) must not contain any ",
              "of the reserved words: \"__SESS_\", \"__CAM_\"."),
       fixed = TRUE
@@ -219,7 +219,7 @@ test_that(
 test_that("output matrix has Station prefix in rownames", {
   skip_if_offline()
   x <- example_dataset()
-  cam_op_matrix <- get_cam_op(x, use_prefix = TRUE)
+  cam_op_matrix <- camtrapR_cameraOperation(x, use_prefix = TRUE)
   locations <- paste0("Station", deployments(x)$locationName)
   n_locations <- length(deployments(x)$locationName)
   expect_identical(nrow(cam_op_matrix), n_locations)
@@ -229,7 +229,7 @@ test_that("output matrix has Station prefix in rownames", {
 test_that("output matrix has specified location column as rownames", {
   skip_if_offline()
   x <- example_dataset()
-  cam_op_matrix <- get_cam_op(x, station_col = "locationID")
+  cam_op_matrix <- camtrapR_cameraOperation(x, station_col = "locationID")
   locations <- deployments(x)$locationID
   n_locations <- length(deployments(x)$locationID)
   expect_identical(nrow(cam_op_matrix), n_locations)
@@ -240,7 +240,7 @@ test_that("output matrix has specified location column as rownames", {
 test_that("output matrix has all deployment days as colnames", {
   skip_if_offline()
   x <- example_dataset()
-  cam_op_matrix <- get_cam_op(x)
+  cam_op_matrix <- camtrapR_cameraOperation(x)
   days_activity <- seq(as.Date(min(deployments(x)$start)),
     as.Date(max(deployments(x)$end)),
     by = "days"
@@ -254,7 +254,7 @@ test_that("output matrix has all deployment days as colnames", {
 test_that("daily effort is > 0 for fully active days, NA for inactive days", {
   skip_if_offline()
   x <- example_dataset()
-  cam_op_matrix <- get_cam_op(x)
+  cam_op_matrix <- camtrapR_cameraOperation(x)
   location <- deployments(x)$locationName[4]
   deployment_start <- deployments(x) %>%
     dplyr::filter(locationName == location) %>%
@@ -280,7 +280,7 @@ test_that("daily effort is > 0 for fully active days, NA for inactive days", {
 test_that("daily effort is > 0 and < 1 for partial active days (start/end)", {
   skip_if_offline()
   x <- example_dataset()
-  cam_op_matrix <- get_cam_op(x)
+  cam_op_matrix <- camtrapR_cameraOperation(x)
   location <- deployments(x)$locationName[4]
   start <- as.character(as.Date(deployments(x)$start[4]))
   end <- as.character(as.Date(deployments(x)$end[4]))
@@ -299,7 +299,7 @@ test_that(
     x1$data$deployments$start[2] <- lubridate::as_datetime("2020-07-30 21:00:00")
     x1$data$deployments$end[2] <- lubridate::as_datetime("2020-08-07 21:00:00")
     x1$data$deployments$locationName[2] <- deployments(x1)$locationName[1]
-    cam_op_matrix <- get_cam_op(x1)
+    cam_op_matrix <- camtrapR_cameraOperation(x1)
 
     first_full_day_two_deps <- as.character(
       as.Date(deployments(x1)$start[2]) + lubridate::ddays(1)
@@ -323,8 +323,8 @@ test_that(
     x <- example_dataset()
     x1 <- x
     x1$data$deployments$locationName[2] <- deployments(x1)$locationName[1]
-    cam_op_matrix1 <- get_cam_op(x1)
-    cam_op_matrix <- get_cam_op(x)
+    cam_op_matrix1 <- camtrapR_cameraOperation(x1)
+    cam_op_matrix <- camtrapR_cameraOperation(x)
     start_date1 <- as.character(as.Date(deployments(x)$start[1]))
     start_date2 <- as.character(as.Date(deployments(x)$start[2]))
     end_date1 <- as.character(as.Date(deployments(x)$end[1]))
@@ -353,9 +353,9 @@ test_that("Argument datapkg is deprecated: warning returned", {
   expect_warning(
     rlang::with_options(
       lifecycle_verbosity = "warning",
-      get_cam_op(datapkg = x)
+      camtrapR_cameraOperation(datapkg = x)
     ),
-    paste0("The `datapkg` argument of `get_cam_op()` is deprecated ",
+    paste0("The `datapkg` argument of `camtrapR_cameraOperation()` is deprecated ",
            "as of camtraptor 0.16.0."
     ),
     fixed = TRUE

diff --git a/vignettes/camera-operation-matrix.Rmd b/vignettes/camera-operation-matrix.Rmd
@@ -42,7 +42,7 @@ It contains camera trap data about musk rat and coypu. We will use this variable
 You can create a camera operation matrix by passing a camera trap data package:
 
 ```{r basic_usage}
-get_cam_op(x)
+camtrapR_cameraOperation(x)
 ```
 
 The function will read the `deployments` slot of the data package to create the matrix.
@@ -58,7 +58,7 @@ x1 <- x
 x1$data$deployments$locationName <- deployments(x1)$locationName[1]
 x1$data$deployments$start <- deployments(x1)$start[1]
 x1$data$deployments$end <- deployments(x1)$deployments$end[1]
-multiple_deploys_matrix <- get_cam_op(x1)
+multiple_deploys_matrix <- camtrapR_cameraOperation(x1)
 multiple_deploys_matrix
 ```
 
@@ -75,7 +75,7 @@ deployments(x2) %>% dplyr::select(locationName, start, end)
 This results in the following camera operation matrix:
 
 ```{r camOp_two_deploys_two_periods}
-two_deploys_two_periods_matrix <- get_cam_op(x2)
+two_deploys_two_periods_matrix <- camtrapR_cameraOperation(x2)
 days_to_show <- seq(as.Date(deployments(x2)$start[3]),
                     as.Date(deployments(x2)$end[4]),
                     by = "days")
@@ -87,14 +87,14 @@ two_deploys_two_periods_matrix[3,as.character(days_to_show)]
 You can specify the column containing the station names instead of using the default `locationName`. In the example below we use the column `locationID`. A small preview of the matrix is shown:
 
 ```{r cam_op_with_locationID}
-cam_op_with_locationID <- get_cam_op(x, station_col = "locationID")
+cam_op_with_locationID <- camtrapR_cameraOperation(x, station_col = "locationID")
 cam_op_with_locationID[1:4, 1:2]
 ```
 
 You can also decide to use prefix `"Station"` in the station names as done by camtrapR's `cameraOperation()` by setting `use_prefix = TRUE`. A small preview of the entire matrix is shown:
 
 ```{r use_prefix}
-cam_op_with_prefix <- get_cam_op(x, use_prefix = TRUE)
+cam_op_with_prefix <- camtrapR_cameraOperation(x, use_prefix = TRUE)
 cam_op_with_prefix[1:4,1:2]
 ```
 
@@ -105,7 +105,7 @@ You can specify the column containing the camera IDs to be added to the station
 ```{r add_camera_IDs}
 x_cameras <- x
 x_cameras$data$deployments$cameraID <- c(1, 2, 3, 4)
-cam_op_with_camera_ids <- get_cam_op(x_cameras, camera_col = "cameraID")
+cam_op_with_camera_ids <- camtrapR_cameraOperation(x_cameras, camera_col = "cameraID")
 row.names(cam_op_with_camera_ids)
 ```
 
@@ -114,15 +114,15 @@ You cans also add the session IDs using `session_col` argument, following the ca
 ```{r add_session_IDs}
 x_sessions <- x
 x_sessions$data$deployments$session <- c(1, 2, 3, 4)
-cam_op_with_session_ids <- get_cam_op(x_sessions, session_col = "session")
+cam_op_with_session_ids <- camtrapR_cameraOperation(x_sessions, session_col = "session")
 row.names(cam_op_with_session_ids)
 ```
 
 To use both camera and session IDs, the camtrapR's convention `Station__SESS_SessionID__CAM_CameraID` is followed:
 
 ```{r add_session_camera_IDs}
 x_sessions$data$deployments$cameraID <- c(1, 2, 3, 4)
-cam_op_with_session_and_camera_ids <- get_cam_op(
+cam_op_with_session_and_camera_ids <- camtrapR_cameraOperation(
   x_sessions, 
   camera_col = "cameraID",
   session_col = "session"