Merge pull request #4 from tombeesley/develop

Merge develop to master for version 0.6.0
tombeesley · Sep 26, 2024 · 0b682df · 0b682df
2 parents 2d0df26 + 8900fff
commit 0b682df
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Showing 104 changed files with 118,378 additions and 670 deletions.
diff --git a/.Rbuildignore.rej b/.Rbuildignore.rej
diff --git a/.gitignore b/.gitignore
@@ -1,8 +1,5 @@
+**/.DS_Store
 .Rproj.user
 .Rhistory
 .RData
 .Ruserdata
-<<<<<<< .merge_file_a05752
-=======
-
->>>>>>> .merge_file_a13928
diff --git a/102_EG_dec.csv b/102_EG_dec.csv
diff --git a/102_training.csv b/102_training.csv
@@ -0,0 +1,120 @@
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+4,2,4,8,4,4,0,2,1,2,4,1,1,12227,1.3751e+15,1.3751e+15,1.3751e+15,1.3751e+15,1.3751e+15
+4,3,2,6,4,4,0,1,2,1,4,1,1,4334.7,1.3751e+15,1.3751e+15,1.3751e+15,1.3751e+15,1.3751e+15
+4,4,1,5,3,3,0,1,2,2,3,1,1,2457.2,1.3751e+15,1.3751e+15,1.3751e+15,1.3751e+15,1.3751e+15
+5,1,2,6,4,4,0,1,2,1,4,1,1,3976.1,1.3751e+15,1.3751e+15,1.3751e+15,1.3751e+15,1.3751e+15
+5,2,1,5,3,3,0,1,1,2,3,1,1,2544.3,1.3751e+15,1.3751e+15,1.3751e+15,1.3751e+15,1.3751e+15
+5,3,4,8,4,4,0,2,1,2,4,1,1,6234.9,1.3751e+15,1.3751e+15,1.3751e+15,1.3751e+15,1.3751e+15
+5,4,3,7,3,3,0,2,1,1,3,1,1,3650.3,1.3751e+15,1.3751e+15,1.3751e+15,1.3751e+15,1.3751e+15
+6,1,2,6,4,4,0,1,1,2,4,1,1,3014.3,1.3751e+15,1.3751e+15,1.3751e+15,1.3751e+15,1.3751e+15
+6,2,1,5,3,3,0,1,2,2,3,1,1,1671,1.3751e+15,1.3751e+15,1.3751e+15,1.3751e+15,1.3751e+15
+6,3,4,8,4,4,0,2,2,1,4,1,1,2717.2,1.3751e+15,1.3751e+15,1.3751e+15,1.3751e+15,1.3751e+15
+6,4,3,7,3,3,0,2,2,1,3,1,1,2945.3,1.3751e+15,1.3751e+15,1.3751e+15,1.3751e+15,1.3751e+15
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,9 +1,10 @@
 Type: Package
 Package: eyetools
 Title: Tools for eye data analysis
-Version: 0.5.1
-Author: Tom Beesley
-Maintainer: Tom Beesley <t.beesley@lancaster.ac.uk>
+Version: 0.6.0
+Authors@R: c(
+    person("Beesley", "Tom", email = "t.beesley@lancaster.ac.uk", role = c("aut", "cre")),
+    person("Ivory", "Matthew", email = "matthew.ivory@lancaster.ac.uk", role = "aut"))
 Description: A set of tools for eye data processing. The intended flow is
     from data processing, to fixation analysis, to data visualisation and
     trial level summaries.
@@ -15,6 +16,7 @@ Imports:
     ggforce,
     ggplot2,
     glue,
+    hdf5r,
     lifecycle,
     magick,
     magrittr,
@@ -26,11 +28,12 @@ Imports:
     zoo
 Suggests: 
     knitr,
-    rmarkdown
-VignetteBuilder: 
-    knitr
+    rmarkdown,
+    testthat (>= 3.0.0)
+VignetteBuilder: knitr
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.2
+RoxygenNote: 7.3.1
 URL: https://tombeesley.github.io/eyetools/
+Config/testthat/edition: 3
diff --git a/NAMESPACE b/NAMESPACE
@@ -1,33 +1,44 @@
 # Generated by roxygen2: do not edit by hand
 
-export("%>%")
 export(AOI_seq)
 export(AOI_time)
-export(VTI_saccade)
 export(combine_eyes)
+export(compare_algorithms)
+export(conditional_transform)
 export(dist_to_visual_angle)
-export(fix_dispersion)
+export(fixation_VTI)
+export(fixation_dispersion)
+export(hdf5_to_csv)
 export(interpolate)
-export(seq_plot)
+export(plot_seq)
+export(plot_spatial)
+export(saccade_VTI)
 export(smoother)
-export(spatial_plot)
 import(dplyr)
 import(ggforce)
 import(ggplot2)
+import(hdf5r)
 import(rlang)
-importFrom(dplyr,between)
 importFrom(glue,glue)
 importFrom(lifecycle,deprecated)
 importFrom(magick,image_read)
 importFrom(magrittr,"%>%")
 importFrom(pbapply,pblapply)
 importFrom(rlang,.data)
 importFrom(stats,aggregate)
+importFrom(stats,complete.cases)
+importFrom(stats,cor.test)
 importFrom(stats,dist)
 importFrom(stats,loess)
+importFrom(stats,median)
 importFrom(stats,na.exclude)
+importFrom(stats,na.omit)
 importFrom(stats,predict)
+importFrom(stats,reshape)
+importFrom(stats,setNames)
+importFrom(stats,time)
+importFrom(utils,head)
+importFrom(utils,stack)
 importFrom(utils,tail)
 importFrom(zoo,na.approx)
 importFrom(zoo,na.spline)
-importFrom(zoo,na.trim)
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,5 @@
+# eyetools 0.6.0
+
 # eyetools 0.5.1
 
 # eyetools 0.5.0

diff --git a/R/AOI_seq.R b/R/AOI_seq.R
@@ -6,21 +6,22 @@
 #' @param AOIs A dataframe of areas of interest (AOIs), with one row per AOI (x, y, width_radius, height).
 #' @param AOI_names An optional vector of AOI names to replace the default "AOI_1", "AOI_2", etc.
 #' @param sample_rate Optional sample rate of the eye-tracker (Hz) for use with raw_data. If not supplied, the sample rate will be estimated from the time column and the number of samples.
-#'
-#' @return a dataframe containing the sequence of entries into AOIs on each trial
+#' @param long Whether to return the AOI fixations in long or wide format. Defaults to long
+#' @return a long format dataframe containing the sequence of entries into AOIs on each trial
 #' @export
 #'
 #' @examples
-#' fix_d <- fix_dispersion(eyetools::example_raw_WM)
-#' AOI_seq(fix_d, eyetools::AOIs_WM)
-#'
-#' @importFrom dplyr between
+#' fix_d <- fixation_dispersion(example_raw_WM)
+#' AOI_seq(fix_d, AOIs_WM)
 #'
+#' @importFrom stats setNames complete.cases
+#' @importFrom utils stack
 
 AOI_seq <- function(data,
                     AOIs,
                     AOI_names = NULL,
-                    sample_rate = NULL) {
+                    sample_rate = NULL,
+                    long = TRUE) {
 
   # split data by trial
   proc_data <- sapply(split(data, data$trial),
@@ -31,6 +32,29 @@ AOI_seq <- function(data,
   data <- data.frame(trial = unique(data$trial),
                      AOI_entry_seq = proc_data)
 
+  if (long == TRUE) {
+
+    split_list <- strsplit(data$AOI_entry_seq,';')
+
+    split_list_names <- setNames(split_list, data$trial)
+
+    data <- stack(split_list_names)
+
+    data <- data.frame(trial = as.numeric(data$ind),
+           AOI = as.numeric(data$value))
+
+# add in entry_n by way of indexing each trial
+get_row_n <- function(i) {
+  store <- data[data$trial == i,]
+  store$entry_n <- 1:nrow(store)
+
+  store
+}
+
+    data <- do.call(rbind.data.frame, lapply(1:max(data$trial), get_row_n))
+
+  }
+
 
   return(data)
 
@@ -47,13 +71,14 @@ AOI_seq_trial_process <- function(trial_data, AOIs, AOI_names) {
 
     if (sum(!is.na(AOIs[a,])) == 4) {
       # square AOI
-      aoi_entries[,a] <- (between(trial_data$x, AOIs[a,1]-AOIs[a,3]/2, AOIs[a,1]+AOIs[a,3]/2) &
-                    between(trial_data$y, AOIs[a,2]-AOIs[a,4]/2, AOIs[a,2]+AOIs[a,4]/2))
-    } else if (sum(!is.na(AOIs[a,])) == 3) {
+      aoi_entries[,a] <- ((trial_data$x >= AOIs[a,1]-AOIs[a,3]/2 & trial_data$x <= AOIs[a,1]+AOIs[a,3]/2) &
+                            (trial_data$y >= AOIs[a,2]-AOIs[a,4]/2 & trial_data$y <= AOIs[a,2]+AOIs[a,4]/2))
+      } else if (sum(!is.na(AOIs[a,])) == 3) {
       # circle AOI
       aoi_entries[,a] <- sqrt((AOIs[a,1]-trial_data$x)^2+(AOIs[a,2]-trial_data$y)^2) < AOIs[a,3]
     } else {
       # report error message of bad AOI definition
+      stop("bad definition of AOI. Cannot identify AOI region")
 
     }
   }
@@ -71,7 +96,6 @@ AOI_seq_trial_process <- function(trial_data, AOIs, AOI_names) {
   } else {
     aoi_seq <- paste0(aoi_seq, collapse = ";")
   }
-
   return(aoi_seq)
 
 }

diff --git a/R/AOI_time.R b/R/AOI_time.R
@@ -12,11 +12,9 @@
 #' @export
 #'
 #' @examples
-#' fix_d <- fix_dispersion(eyetools::example_raw_WM)
-#' AOI_time(fix_data = fix_d, AOIs = eyetools::AOIs_WM)
-#' AOI_time(raw_data = eyetools::example_raw_WM, AOIs = eyetools::AOIs_WM, sample_rate = 120)
-#'
-#'#' @importFrom dplyr between
+#' fix_d <- fixation_dispersion(example_raw_WM)
+#' AOI_time(fix_data = fix_d, AOIs = AOIs_WM)
+#' AOI_time(raw_data = example_raw_WM, AOIs = AOIs_WM, sample_rate = 120)
 #'
 
 AOI_time <- function(fix_data = NULL, raw_data = NULL, AOIs, AOI_names = NULL, sample_rate = NULL) {
@@ -58,6 +56,15 @@ AOI_time <- function(fix_data = NULL, raw_data = NULL, AOIs, AOI_names = NULL, s
   }
 
   colnames(data) <- c("trial", AOI_name_text)
+
+  data <- do.call(cbind.data.frame, lapply(1:length(colnames(data)), function(i) {
+
+    data[,i] <- as.numeric(data[,i])
+
+  }))
+
+  colnames(data) <- c("trial", AOI_name_text)
+
   return(data.frame(data))
 
 }
@@ -107,8 +114,8 @@ AOI_time_trial_process_raw <- function(trial_data, AOIs, sample_rate) {
 
     if (sum(!is.na(AOIs[a,])) == 4) {
       # square AOI
-      xy_hits <- (between(trial_data$x, AOIs[a,1]-AOIs[a,3]/2, AOIs[a,1]+AOIs[a,3]/2) &
-                    between(trial_data$y, AOIs[a,2]-AOIs[a,4]/2, AOIs[a,2]+AOIs[a,4]/2))
+      xy_hits <- ((trial_data$x >= AOIs[a,1]-AOIs[a,3]/2 & trial_data$x <= AOIs[a,1]+AOIs[a,3]/2) &
+                    (trial_data$y >= AOIs[a,2]-AOIs[a,4]/2 & trial_data$y <= AOIs[a,2]+AOIs[a,4]/2))
     } else if (sum(!is.na(AOIs[a,])) == 3) {
       # circle AOI
       xy_hits <- sqrt((AOIs[a,1]-trial_data$x)^2+(AOIs[a,2]-trial_data$y)^2) < AOIs[a,3]

diff --git a/R/combine_eyes.R b/R/combine_eyes.R
@@ -8,7 +8,7 @@
 #' @param data raw data with columns time, left_x, left_y, right_x, right_y, and trial
 #' @param method either "average" or "best_eye" - see description.
 #'
-#' @return
+#' @return a dataframe of form c("time", "x", "y", "trial")
 #' @export
 #'
 #' @examples combine_eyes(example_raw_binocular, method = "average")