update

NAMESPACE

@@ -1,6 +1,5 @@
 # Generated by roxygen2: do not edit by hand
 
-export(calculate_angle)
 export(calculate_angles_for_track)
 export(plot_degrees)
 export(plot_motion)

R/angles.R

@@ -1,22 +1,3 @@
-#' @title Calculate Angle Between Two Vectors
-#' @name calculate_angle
-#'
-#' @param u Numeric vector representing the first vector.
-#' @param v Numeric vector representing the second vector.
-#'
-#' @return Numeric value representing the angle in degrees.
-#'
-#' @export
-
-calculate_angle <- function(u, v) {
-  dot_product <- sum(u * v)
-  magnitude_u <- sqrt(sum(u^2))
-  magnitude_v <- sqrt(sum(v^2))
-  cos_theta <- dot_product / (magnitude_u * magnitude_v)
-  angle <- acos(cos_theta) * 180 / pi
-  return(angle)
-}
-
 #' @title Calculate Angles for a Track
 #' @name calculate_angles_for_track
 #'
@@ -29,17 +10,39 @@ calculate_angle <- function(u, v) {
 #' @export
 
 calculate_angles_for_track <- function(track_data, x, y) {
+  # Check for valid input data
+  if (!is.data.frame(track_data)) stop("track_data must be a data frame")
+  if (!(x %in% names(track_data) && y %in% names(track_data))) stop("x and y must be valid column names in track_data")
+  if (nrow(track_data) < 3) return(rep(NA, nrow(track_data)))  # Not enough points to calculate angles
+
   n <- nrow(track_data)
-  angles <- numeric(n)
-  for (i in 2:(n - 1)) {
-    p1 <- track_data[i - 1, c(x, y)]
-    p2 <- track_data[i, c(x, y)]
-    p3 <- track_data[i + 1, c(x, y)]
+  angles <- rep(NA, n)  # Pre-allocate the angles vector
+
+  # Extract coordinates
+  x_coords <- track_data[[x]]
+  y_coords <- track_data[[y]]
+
+  # Calculate differences between consecutive points
+  dx <- diff(x_coords)
+  dy <- diff(y_coords)
+
+  # Calculate vectors for points 1:(n-2), 2:(n-1), and 3:n
+  u_x <- dx[1:(n-2)]
+  u_y <- dy[1:(n-2)]
+  v_x <- dx[2:(n-1)]
+  v_y <- dy[2:(n-1)]
 
-    u <- as.numeric(p2 - p1)
-    v <- as.numeric(p3 - p2)
+  # Calculate dot products and magnitudes
+  dot_products <- u_x * v_x + u_y * v_y
+  magnitudes_u <- sqrt(u_x^2 + u_y^2)
+  magnitudes_v <- sqrt(v_x^2 + v_y^2)
+
+  # Calculate cosine of angles, handle numerical issues
+  cos_theta <- pmin(1, pmax(-1, dot_products / (magnitudes_u * magnitudes_v)))
+
+  # Calculate angles in degrees
+  angles[2:(n - 1)] <- acos(cos_theta) * 180 / pi
 
-    angles[i] <- calculate_angle(u, v)
-  }
   return(angles)
 }
+

R/plot-motion.R

@@ -36,22 +36,28 @@ plot_motion <- function(data, x, y, frames) {
 
 plot_degrees <- function(data, x, y, joint_ids, frames, plot = TRUE) {
 
+  angle <- NULL
+
   data$angle <- NA
   x_var <- deparse(substitute(x))
   y_var <- deparse(substitute(y))
   joint_var <- deparse(substitute(joint_ids))
   frame_var <- deparse(substitute(frames))
 
-  unique_tids <- unique(data[[frame_var]])
+  unique_frames <- unique(data[[frame_var]])
 
-  for (tid in unique_tids) {
-    data[data[[frame_var]] == tid, "angle"] <- calculate_angles_for_track(data[data[[frame_var]] == tid,], x_var, y_var)
+  for (one_frame in unique_frames) {
+    ind <- data[[frame_var]] == one_frame
+    data[ind, "angle"] <- calculate_angles_for_track(data[ind,], x_var, y_var)
   }
 
-  if(!plot) return(data)
+  if(!plot) {
+    out_data <- data[,c(joint_var, frame_var, x_var, y_var, "angle")]
+    return(out_data)
+  }
 
   # Plot the data using ggplot2
-  ggplot2::ggplot(data = data[data$angle != 0,],
+  ggplot2::ggplot(data = data[!is.na(data$angle),],
                   mapping = ggplot2::aes(x = .data[[frame_var]]/max(.data[[frame_var]]), y = angle, col = .data[[frame_var]])) +
     ggplot2::facet_grid(ggplot2::vars(.data[[joint_var]]), scales = "free_y") +
     ggplot2::geom_point(na.rm = T) +

README.Rmd

@@ -37,6 +37,59 @@ devtools::install_github("matcasti/kinemov")
 
 You can try using the example dataset `gait` this way:
 
-```r
-plot_motion(gait, x_coord, y_coord, frame)
+```{r}
+library(kinemov)
+
+plot_motion(gait, x_coord, y_coord, frame) 
+```
+
+You can also plot the degrees between joints in this way:
+
+```{r}
+fig <- plot_degrees(gait, x_coord, y_coord, joint, frame)
+fig
+```
+
+As it is a ggplot object, you can further customize the output object:
+
+```{r}
+library(ggplot2)
+library(scales)
+
+fig + 
+  labs(title = "Gait Arthrokinematics",
+       subtitle = "Assessed through manual motion capture with ImageJ",
+       caption = "Source: Own elaboration") +
+  scale_color_viridis_c(option = "C") + 
+  scale_x_continuous(labels = label_percent()) + 
+  theme(plot.background = element_rect(fill = "black"),
+        panel.background = element_rect(fill = "black"),
+        strip.background = element_rect(fill = "black"),
+        legend.background = element_rect(fill = "black"),
+        panel.grid = element_blank(),
+        text = element_text(colour = "white"),
+        axis.text = element_text(colour = "white"))
+```
+
+And from the `plot_degrees()` function, you can also only extract the degrees by specifying `plot = FALSE`:
+
+```{r}
+out <- plot_degrees(gait, x_coord, y_coord, joint, frame, plot = FALSE)
+
+subset(out, !is.na(angle)) |> head()
+```
+
+One can further process the output data.frame to better describe the angles for each joint and for each frame:
+
+```{r}
+library(data.table)
+
+out <- as.data.table(out)
+out[i = !is.na(angle), 
+    j = list(min = min(angle), 
+             mean = mean(angle),
+             median = median(angle),
+             max = max(angle)) |> 
+      lapply(round),
+    by = joint]
 ```

README.md

@@ -31,5 +31,79 @@ devtools::install_github("matcasti/kinemov")
 You can try using the example dataset `gait` this way:
 
 ``` r
-plot_motion(gait, x_coord, y_coord, frame)
+library(kinemov)
+
+plot_motion(gait, x_coord, y_coord, frame) 
+```
+
+<img src="man/figures/README-unnamed-chunk-2-1.png" width="100%" />
+
+You can also plot the degrees between joints in this way:
+
+``` r
+fig <- plot_degrees(gait, x_coord, y_coord, joint, frame)
+fig
+```
+
+<img src="man/figures/README-unnamed-chunk-3-1.png" width="100%" />
+
+As it is a ggplot object, you can further customize the output object:
+
+``` r
+library(ggplot2)
+library(scales)
+
+fig + 
+  labs(title = "Gait Arthrokinematics",
+       subtitle = "Assessed through manual motion capture with ImageJ",
+       caption = "Source: Own elaboration") +
+  scale_color_viridis_c(option = "C") + 
+  scale_x_continuous(labels = label_percent()) + 
+  theme(plot.background = element_rect(fill = "black"),
+        panel.background = element_rect(fill = "black"),
+        strip.background = element_rect(fill = "black"),
+        legend.background = element_rect(fill = "black"),
+        panel.grid = element_blank(),
+        text = element_text(colour = "white"),
+        axis.text = element_text(colour = "white"))
+```
+
+<img src="man/figures/README-unnamed-chunk-4-1.png" width="100%" />
+
+And from the `plot_degrees()` function, you can also only extract the
+degrees by specifying `plot = FALSE`:
+
+``` r
+out <- plot_degrees(gait, x_coord, y_coord, joint, frame, plot = FALSE)
+
+subset(out, !is.na(angle)) |> head()
+#>    joint frame x_coord y_coord    angle
+#> 29     2     1   123.0   340.0 125.0958
+#> 30     2     2   123.0   339.0 133.8656
+#> 31     2     3   122.5   338.0 136.2633
+#> 32     2     4   123.5   337.0 126.2360
+#> 33     2     5   123.5   337.5 121.2637
+#> 34     2     6   124.0   336.0 119.3529
+```
+
+One can further process the output data.frame to better describe the
+angles for each joint and for each frame:
+
+``` r
+library(data.table)
+
+out <- as.data.table(out)
+out[i = !is.na(angle), 
+    j = list(min = min(angle), 
+             mean = mean(angle),
+             median = median(angle),
+             max = max(angle)) |> 
+      lapply(round),
+    by = joint]
+#>    joint   min  mean median   max
+#>    <int> <num> <num>  <num> <num>
+#> 1:     2   119   130    129   144
+#> 2:     3    15    39     38    56
+#> 3:     4     6    28     19    74
+#> 4:     5     1    18     17    40
 ```

tests/testthat.R

@@ -6,7 +6,7 @@
 # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
 # * https://testthat.r-lib.org/articles/special-files.html
 
-# library(testthat)
-# library(kinemov)
-#
-# test_check("kinemov")
+library(testthat)
+library(kinemov)
+
+test_check("kinemov")

tests/testthat/test-angles.R

@@ -0,0 +1,30 @@
+test_that("calculate_angles_for_track works correctly", {
+  # Create sample data
+  track_data <- data.frame(
+    x = c(1, 2, 3, 4, 5),
+    y = c(1, 2, 1, 2, 1)
+  )
+
+  # Calculate angles
+  angles <- calculate_angles_for_track(track_data, "x", "y")
+
+  # Expected results
+  expected_angles <- c(NA, 90, 90, 90, NA)
+
+  # Check if the angles are as expected (within a tolerance)
+  expect_equal(angles, expected_angles, tolerance = 1e-6)
+
+  # Test with insufficient points
+  track_data_insufficient <- data.frame(
+    x = c(1, 2),
+    y = c(1, 2)
+  )
+  angles_insufficient <- calculate_angles_for_track(track_data_insufficient, "x", "y")
+  expect_equal(angles_insufficient, c(NA, NA))
+
+  # Test with missing column names
+  expect_error(calculate_angles_for_track(track_data, "a", "b"), "x and y must be valid column names in track_data")
+
+  # Test with incorrect data type
+  expect_error(calculate_angles_for_track(list(a = 1, b = 2), "x", "y"), "track_data must be a data frame")
+})

tests/testthat/test-plot_motion.R

@@ -0,0 +1,58 @@
+test_that("plot_motion generates a ggplot object", {
+  # Create sample data
+  sample_data <- data.frame(
+    x = c(1, 2, 3, 4, 5, 1+1, 2+2, 3+3, 4+4, 5+5),
+    y = c(1, 1, 1, 1, 1, 2, 2, 2, 2, 2),
+    frames = rep(1:5, 2)
+  )
+
+  # Generate the plot
+  plot <- plot_motion(sample_data, x, y, frames)
+
+  # Check if the output is a ggplot object
+  expect_s3_class(plot, "ggplot")
+})
+
+test_that("plot_degrees generates a ggplot object and calculates angles correctly", {
+  # Create sample data
+  sample_data <- data.frame(
+    x = c(1, 2, 3, 4, 5, 1+1, 2+2, 3+3, 4+4, 5+5, 1, 2, 3, 4, 5),
+    y = c(1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3),
+    joint_ids = rep(1:3, each = 5),
+    frames = rep(1:5, 3)
+  )
+
+  # Generate the plot
+  plot <- plot_degrees(sample_data, x, y, joint_ids, frames)
+
+  # Check if the output is a ggplot object
+  expect_s3_class(plot, "ggplot")
+
+  # Check if the angles are calculated correctly
+  angle_data <- plot_degrees(sample_data, x, y, joint_ids, frames, plot = FALSE)
+  expect_true("angle" %in% names(angle_data))
+
+  # Check the angle values
+  expected_angles <- c(NA, NA, NA, NA, NA, 90, 126.8, 143.1,
+                       151.9, 157.3, NA, NA, NA, NA, NA)
+  expect_equal(angle_data$angle, expected_angles, tolerance = 1e-3)
+})
+
+test_that("plot_degrees returns data with angle measurements when plot is FALSE", {
+  # Create sample data
+  sample_data <- data.frame(
+    x = c(1, 2, 3, 4, 5, 1+1, 2+2, 3+3, 4+4, 5+5, 1, 2, 3, 4, 5),
+    y = c(1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3),
+    joint_ids = rep(1:3, each = 5),
+    frames = rep(1:5, 3)
+  )
+
+  # Get the angle data
+  angle_data <- plot_degrees(sample_data, x, y, joint_ids, frames, plot = FALSE)
+
+  # Check if the output is a data frame
+  expect_s3_class(angle_data, "data.frame")
+
+  # Check if the angle column exists
+  expect_true("angle" %in% names(angle_data))
+})