Added read_bonsai and light testing

Author: Mikkel Roald-Arbøl

DESCRIPTION

@@ -24,6 +24,7 @@ Imports:
     lifecycle,
     rlang,
     stringi,
+    tidyselect,
     vroom,
     zoo
 Suggests: 

NAMESPACE

@@ -7,6 +7,7 @@ export(clean_kinematics)
 export(ensure_file_has_expected_headers)
 export(ensure_file_has_headers)
 export(read_animalta)
+export(read_bonsai)
 export(read_deeplabcut)
 export(read_idtracker)
 export(read_movement)
@@ -22,6 +23,7 @@ export(validate_time)
 export(validate_trackball)
 import(circular)
 import(dplyr)
+import(tidyselect)
 importFrom(circular,circular)
 importFrom(circular,is.circular)
 importFrom(cli,cli_abort)

R/read_bonsai.R

@@ -0,0 +1,35 @@
+#' Read centroid tracking data from Bonsai
+#'
+#' @description
+#' `r lifecycle::badge('experimental')`
+#'
+#' @param path Path to a Bonsai data file
+#' @import dplyr
+#' @import tidyselect
+#' @importFrom vroom vroom
+#'
+#' @return a movement dataframe
+#' @export
+read_bonsai <- function(path) {
+  # There can be tracking from multiple ROIs at the same time
+  # We need to check everything matches expectations
+  # We should be able to use only a single timestamp (should be the same across all ROIs)
+  validate_files(path, expected_suffix = "csv")
+  data <- vroom::vroom(
+    path,
+    delim = ",",
+    show_col_types = FALSE
+    ) |>
+    suppressMessages() |>
+    dplyr::select(tidyselect::contains(c("Timestamp", "Centroid"))) |>
+    dplyr::rename(time = tidyselect::contains("Timestamp"),
+                  x = tidyselect::contains("X"),
+                  y = tidyselect::contains("Y")) |>
+    dplyr::mutate(keypoint = factor("centroid")) |>
+    dplyr::relocate("keypoint", .after = .data$time)
+
+  attributes(data)$spec <- NULL
+  attributes(data)$problems <- NULL
+
+  return(data)
+}

R/read_deeplabcut.R

@@ -3,10 +3,10 @@
 #' @description
 #' `r lifecycle::badge('experimental')`
 #'
-#' @param data A DeepLabCut data frame
+#' @param path Path to a DeepLabCut data file
 #'
 #' @return a movement dataframe
 #' @export
-read_deeplabcut <- function(data) {
+read_deeplabcut <- function(path) {
   cli::cli_abort("`read_deeplabcut` has not yet been implemented. Coming soon!")
 }

R/read_sleap.R

@@ -3,10 +3,10 @@
 #' @description
 #' `r lifecycle::badge('experimental')`
 #'
-#' @param data A SLEAP data frame
+#' @param path A SLEAP data frame
 #'
 #' @return a movement dataframe
 #' @export
-read_sleap <- function(data) {
+read_sleap <- function(path) {
   cli::cli_abort("`read_sleap` has not yet been implemented. Coming soon!")
 }

man/read_bonsai.Rd

@@ -54,6 +54,31 @@
       ],
       "Hash": "9fe98599ca456d6552421db0d6772d8f"
     },
+    "boot": {
+      "Package": "boot",
+      "Version": "1.3-30",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "graphics",
+        "stats"
+      ],
+      "Hash": "96abeed416a286d4a0f52e550b612343"
+    },
+    "circular": {
+      "Package": "circular",
+      "Version": "0.5-1",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "boot",
+        "mvtnorm",
+        "stats"
+      ],
+      "Hash": "3cf8da958fff9dcb209dd1e549a60a05"
+    },
     "cli": {
       "Package": "cli",
       "Version": "3.6.3",
@@ -207,6 +232,17 @@
       ],
       "Hash": "7ce2733a9826b3aeb1775d56fd305472"
     },
+    "mvtnorm": {
+      "Package": "mvtnorm",
+      "Version": "1.3-1",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "stats"
+      ],
+      "Hash": "77c61d51ce0f36e3c1a76e6b295aab31"
+    },
     "pillar": {
       "Package": "pillar",
       "Version": "1.9.0",
@@ -279,6 +315,19 @@
       ],
       "Hash": "3eec01f8b1dee337674b2e34ab1f9bc1"
     },
+    "stringi": {
+      "Package": "stringi",
+      "Version": "1.8.4",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "R",
+        "stats",
+        "tools",
+        "utils"
+      ],
+      "Hash": "39e1144fd75428983dc3f63aa53dfa91"
+    },
     "tibble": {
       "Package": "tibble",
       "Version": "3.2.1",