Improved code and added README

roaldarbol · Mar 17, 2024 · 2cd48ea · 2cd48ea
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -2,3 +2,5 @@
 ^renv\.lock$
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^codecov\.yml$
+^LICENSE\.md$
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -6,6 +6,9 @@ Author: Who wrote it
 Maintainer: The package maintainer <yourself@somewhere.net>
 Description: More about what it does (maybe more than one line)
     Use four spaces when indenting paragraphs within the Description.
-License: What license is it under?
+License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
+Suggests: 
+    testthat (>= 3.0.0)
+Config/testthat/edition: 3
diff --git a/LICENSE b/LICENSE
@@ -0,0 +1,2 @@
+YEAR: 2024
+COPYRIGHT HOLDER: trackballr authors
diff --git a/LICENSE.md b/LICENSE.md
@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) 2024 trackballr authors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
diff --git a/R/augment_trackball.R b/R/augment_trackball.R
@@ -3,44 +3,49 @@
 #' @param data
 #' @param x
 #' @param y
+#' @param time Which variable contains time. If no column includes time, use sampling_rate.
 #' @param sampling_rate
 #' @param rollmean_k
 #' @param mouse_dcpm
 #'
 #' @return
 #' @export
+#' @import dplyr
+#' @importFrom tidyr replace_na
+#' @importFrom zoo rollmean
 #'
 #' @examples
 augment_trackball <- function(
     data,
-    x,
-    y,
+    x = y_Right,
+    y = y_Left,
+    time = NULL,
     sampling_rate = 125,
     rollmean_k = 30,
     mouse_dcpm = 394
     ) {
-  data <- data %>%
+  data <- data |>
     mutate(row = row_number(),
            time = row / sampling_rate,
            x = y_Right,
            x = zoo::rollmean(x, k = rollmean_k, fill = NA),
            y = y_Left,
            y = zoo::rollmean(y, k = rollmean_k, fill = NA),
            cum_x = 0,
-           cum_y = 0) %>%
-    select(!c(1:4)) %>%
+           cum_y = 0) |>
+    select(!c(1:4)) |>
     mutate(distance = sqrt(x^2 + y^2) / mouse_dpcm,
            v_translation = distance * sampling_rate,
            direction = atan2(y,x),
            rotation = if_else(abs(x) > 1 & abs(y) > 1,
                               abs(lag(direction) - direction),
                               0),
            rotation = if_else(rotation > pi, 2*pi - rotation, rotation),
-           v_rotation = rotation * sampling_rate) %>%
+           v_rotation = rotation * sampling_rate) |>
     mutate(
-      x = replace_na(x, 0),
-      y = replace_na(y, 0))
-  # filter(distance < 1000) # Filters away trials covering less than 1000 pixels
+      x = tidyr::replace_na(x, 0),
+      y = tidyr::replace_na(y, 0))
+
   data$cum_x <- cumsum(data$x)
   data$cum_y <- cumsum(data$y)
   return(data)

diff --git a/R/mode.R b/R/mode.R
@@ -1,4 +1,4 @@
-#' Title
+#' Mode
 #'
 #' @param x A vector of numbers
 #'
@@ -7,5 +7,6 @@
 #'
 #' @examples
 mode <- function(x){
-  which.max(tabulate(x))
+  y <- tabulate(x)
+  which(y == max(y, na.rm = TRUE))
 }
diff --git a/R/read_data.R b/R/read_data.R
@@ -7,9 +7,12 @@
 #' @export
 #'
 #' @examples
-read_trackball_from_rdata <- function(
-    data,
-    sensor_names = c("Left", "Right")
+read_trackball_data <- function(
+    folder_path,
+    sensor_names = c("Left", "Right"),
+    format = "RDS"
 ){
 
+
+
 }
diff --git a/README.md b/README.md
@@ -0,0 +1,67 @@
+# trackballr
+
+<!-- badges: start -->
+[![Codecov test coverage](https://codecov.io/gh/roaldarbol/trackballr/branch/main/graph/badge.svg)](https://app.codecov.io/gh/roaldarbol/trackballr?branch=main)
+<!-- badges: end -->
+
+The goal of {trackballr} is to make analysis of trackball data easy-
+
+## Installation
+
+You can install the development version of trackballr from [GitHub](https://github.com/) with:
+
+``` r
+# install.packages("devtools")
+devtools::install_github("roaldarbol/trackballr")
+```
+or from my -universe:
+```
+install.packages("trackballr", repos = c("https://roaldarbol.r-universe.dev", "https://cran.r-project.org"))
+```
+
+## Example
+
+This is a basic example which shows you how to solve a common problem:
+
+``` r
+library(trackballr)
+
+## Read all files into list
+data_list <- read_trackball_data(folder_path, sensors = c("Right", "Left"))
+
+# Augment all data in list
+data_list <- lapply(data_list, beetle_augment)
+
+# Bind list into single data frame
+data_df <- bind_rows(sensor_data_temp)
+```
+
+Once the data has been pre-processed, it can then easily generate useful summaries - here are some examples.
+```r
+# Compute translational summary
+sensor_summary <- sensor_data_df |> 
+  na.omit()  |> 
+  group_by(id, date) |> 
+  filter(abs(x) > 0 | abs(y) > 0) |> # Only keep rows containing movement
+  summarise(total_translation = sum(distance),
+            v_translation_mean = mean(v_translation),
+            v_translation_sd = sd(v_translation),
+            sinuosity = sqrt(last(cum_x)^2 + last(cum_y)^2)/sum(distance)
+            ) |> 
+  mutate(trial = if_else(date <= min(date), "first", "second")) |> # Each animal has been on the trackball on two days - here we assign which day/trial
+  slice(1:2) |> 
+  filter(total_translation > 0) |> # Filter away trials with no translation
+  filter(n() == 2) # Keep only observations where both trials are present
+
+# Compute rotational summary
+# Here wa are also filtering out trials with a faulty sensor/no data for one sensor
+rotation_summary <- sensor_data_df |> 
+  na.omit() |>
+  group_by(id, date) |> 
+  filter(v_rotation > 0) |>
+  summarise(total_rotation = sum(rotation, na.rm = TRUE),
+            v_rotation_mean = mean(v_rotation, na.rm = TRUE)) |>
+  mutate(trial = if_else(date <= min(date), "first", "second")) |> 
+  slice(1:2) |>
+  filter(n() == 2)
+```
diff --git a/codecov.yml b/codecov.yml
@@ -0,0 +1,14 @@
+comment: false
+
+coverage:
+  status:
+    project:
+      default:
+        target: auto
+        threshold: 1%
+        informational: true
+    patch:
+      default:
+        target: auto
+        threshold: 1%
+        informational: true
diff --git a/tests/testthat.R b/tests/testthat.R
@@ -0,0 +1,12 @@
+# This file is part of the standard setup for testthat.
+# It is recommended that you do not modify it.
+#
+# Where should you do additional test configuration?
+# Learn more about the roles of various files in:
+# * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
+# * https://testthat.r-lib.org/articles/special-files.html
+
+library(testthat)
+library(trackballr)
+
+test_check("trackballr")
diff --git a/tests/testthat/test-mode.R b/tests/testthat/test-mode.R
@@ -0,0 +1,14 @@
+test_that("Mode works!", {
+
+  # Single outcome
+  my_single_vector <- c(1,2,3,3,4,5)
+  expect_equal(trackballr::mode(my_single_vector), 3)
+
+  # Multiple outcomes
+  my_multi_vector <- c(1,2,3,3,4,5,5)
+  expect_equal(trackballr::mode(my_multi_vector), 3)
+
+  # Removes NA
+  my_na_vector <- c(1,2,3,3,NA,5)
+  expect_equal(trackballr::mode(my_na_vector), 3)
+})
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		YEAR: 2024
		COPYRIGHT HOLDER: trackballr authors