Merge pull request #67 from roaldarbol/animalta_patch

Update animalta detailed parameter

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: animovement
 Type: Package
 Title: An R toolbox for analysing animal movement across space and time
-Version: 0.4.0
+Version: 0.4.1
 Authors@R: 
     person(
       "Mikkel", 

NEWS.md

@@ -1,3 +1,7 @@
+# animovement 0.4.1
+
+Changed parameter in `read_animalta()`.
+
 # animovement 0.4.0
 
 Added readers for AnimalTA (`read_animalta`) and idtracker.ai (`read_idtracker`).

R/read_animalta.R

@@ -1,33 +1,33 @@
 #' Read AnimalTA data
 #'
-#' @description
-#' `r lifecycle::badge('experimental')`
+#' @description `r lifecycle::badge('experimental')`
 #'
 #' @param path An AnimalTA data frame
-#' @param with_roi Were one or more ROIs used?
+#' @param detailed Animal export either raw (default) or detailed data files. We
+#'   only have limited support for detailed data.
 #'
 #' @import dplyr
 #' @import vroom
 #' @importFrom janitor clean_names
 #'
 #' @return a movement dataframe
 #' @export
-read_animalta <- function(path, with_roi = FALSE) {
+read_animalta <- function(path, detailed = FALSE) {
   # Inspect headers
-  if (with_roi == FALSE){
+  if (detailed == TRUE){
     validate_files(
       path,
       expected_suffix = "csv",
       expected_headers = c("X", "Y", "Time")
       )
-    data <- read_animalta_no_roi(path)
+    data <- read_animalta_detailed(path)
   } else {
     validate_files(
       path,
       expected_suffix = "csv",
       expected_headers = c("Time", "X_Arena0_Ind0", "Y_Arena0_Ind0")
     )
-    data <- read_animalta_with_roi(path)
+    data <- read_animalta_raw(path)
   }
   data <- data |>
     dplyr::mutate(keypoint = factor("centroid")) |>
@@ -37,7 +37,7 @@ read_animalta <- function(path, with_roi = FALSE) {
 
 #' @inheritParams read_animalta
 #' @keywords internal
-read_animalta_no_roi <- function(path){
+read_animalta_detailed <- function(path){
   data <- vroom::vroom(
     path,
     delim = ";",
@@ -57,7 +57,7 @@ read_animalta_no_roi <- function(path){
 #' @inheritParams read_animalta
 #' @import tidyr
 #' @keywords internal
-read_animalta_with_roi <- function(path){
+read_animalta_raw <- function(path){
   data <- vroom::vroom(
     path,
     delim = ";",

tests/testthat/test-read_animalta.R

@@ -1,41 +1,41 @@
 # Test arguments
 library(here)
 here::i_am("tests/testthat/test-read_animalta.R")
-path_roi <- here("tests", "data", "animalta", "single_individual_multi_arena.csv")
-path_no_roi <- here("tests", "data", "animalta", "variable_individuals_single_arena.csv")
+path_raw <- here("tests", "data", "animalta", "single_individual_multi_arena.csv")
+path_detailed <- here("tests", "data", "animalta", "variable_individuals_single_arena.csv")
 
 # File headers
 test_that("File headers", {
   expect_no_error(
-    ensure_file_has_headers(path_roi)
+    ensure_file_has_headers(path_raw)
   )
   expect_no_error(
-    ensure_file_has_headers(path_no_roi)
+    ensure_file_has_headers(path_detailed)
   )
 })
 
 
 # Read file
 test_that("Read file", {
   expect_no_error(
-    read_animalta(path_roi, with_roi = TRUE)
+    read_animalta(path_raw, detailed = FALSE)
   )
   expect_no_error(
-    read_animalta(path_no_roi, with_roi = FALSE)
+    read_animalta(path_detailed, detailed = TRUE)
   )
   expect_error(
-    read_animalta(path_roi, with_roi = FALSE)
+    read_animalta(path_raw, detailed = TRUE)
   )
   expect_error(
-    read_animalta(path_no_roi, with_roi = TRUE)
+    read_animalta(path_detailed, detailed = FALSE)
   )
   expect_contains(
-    read_animalta(path_roi, with_roi = TRUE) |>
+    read_animalta(path_raw, detailed = FALSE) |>
       names(),
     c("time", "individual", "keypoint", "x", "y")
   )
   expect_contains(
-    read_animalta(path_no_roi, with_roi = FALSE) |>
+    read_animalta(path_detailed, detailed = TRUE) |>
       names(),
     c("time", "individual", "keypoint", "x", "y")
   )