| Title: | Preprocessing Pupil Size Data |
|---|---|
| Description: | Pupillometric data collected using SR Research Eyelink eye trackers requires significant preprocessing. This package contains functions for preparing pupil dilation data for visualization and statistical analysis. Specifically, it provides a pipeline of functions which aid in data validation, the removal of blinks/artifacts, downsampling, and baselining, among others. Additionally, plotting functions for creating grand average and conditional average plots are provided. See the vignette for samples of the functionality. The package is designed for handling data collected with SR Research Eyelink eye trackers using Sample Reports created in SR Research Data Viewer. |
| Authors: | Aki-Juhani Kyröläinen [aut, cre], Vincent Porretta [aut], Jacolien van Rij [ctb], Juhani Järvikivi [ctb] |
| Maintainer: | Aki-Juhani Kyröläinen <[email protected]> |
| License: | GPL-3 |
| Version: | 0.6.2 |
| Built: | 2024-07-23 06:16:57 UTC |
| Source: | CRAN |
apply_butter applies a Butterworth filter to the pupil
size data.
apply_butter(data = data, n = NULL, W = NULL, type = NULL, plane = "z")apply_butter(data = data, n = NULL, W = NULL, type = NULL, plane = "z")
data |
A data table object. |
n |
A number specifying the filter order (as described in butter). |
W |
The critical frequencies of the filter (as described in butter). W must be a scalar for low-pass or high-pass filters. W must be a two-element vector c(low, high) specifying the lower and upper bands for stop-band or band-pass filters. For digital filters, W must be between 0 and 1 where 1 is the Nyquist frequency. |
type |
The filter type (as described in butter), one of "low" for a low-pass filter, "high" for a high-pass filter, "stop" for a stop-band (band-reject) filter, or "pass" for a pass-band filter. |
plane |
A character string (as described in butter), "z" for a digital filter or "s" for an analog filter. |
# Load example data data("Pupilex5") dat <- apply_butter(Pupilex5, n = 1, W = 0.1, type = "low", plane = "z") # Please see the vignettes for detailed example usage. vignette("PupilPre_Interpolation_and_Filtering", package="PupilPre")# Load example data data("Pupilex5") dat <- apply_butter(Pupilex5, n = 1, W = 0.1, type = "low", plane = "z") # Please see the vignettes for detailed example usage. vignette("PupilPre_Interpolation_and_Filtering", package="PupilPre")
apply_cleanup_change applies to each event the user-selected
changes to the automatic cleanup based on information stored in the RDS file
using verify_cleanup_app which was created using either
blink_cleanup or artifact_cleanup.
apply_cleanup_change(data = data, LogFile = NULL)apply_cleanup_change(data = data, LogFile = NULL)
data |
A data frame object created from |
LogFile |
A character string indicating the name (and location) of the log file. |
An object of type data table as described in tibble.
if (interactive()) { # Load example data data("Pupilex3") # Ensure the log file exists by running cleanup # Writing log file to temporary folder for the example dat <- clean_blink(Pupilex3, BlinkPadding = c(100, 100), Delta = 5, MaxValueRun = 5, NAsAroundRun = c(2,2), LogFile = paste0(tempdir(),"/BlinkCleanupLog.rds")) # Read log file from temporary folder verify_cleanup_app(dat, LogFile = paste0(tempdir(),"/BlinkCleanupLog.rds")) # Make verification via the app interface # Read log file from the temporary folder dat <- apply_user_cleanup(dat, LogFile = paste0(tempdir(),"/BlinkCleanupLog.rds")) } # Please see the vignettes for detailed example usage. # vignette("PupilPre_Cleanup", package="PupilPre")if (interactive()) { # Load example data data("Pupilex3") # Ensure the log file exists by running cleanup # Writing log file to temporary folder for the example dat <- clean_blink(Pupilex3, BlinkPadding = c(100, 100), Delta = 5, MaxValueRun = 5, NAsAroundRun = c(2,2), LogFile = paste0(tempdir(),"/BlinkCleanupLog.rds")) # Read log file from temporary folder verify_cleanup_app(dat, LogFile = paste0(tempdir(),"/BlinkCleanupLog.rds")) # Make verification via the app interface # Read log file from the temporary folder dat <- apply_user_cleanup(dat, LogFile = paste0(tempdir(),"/BlinkCleanupLog.rds")) } # Please see the vignettes for detailed example usage. # vignette("PupilPre_Cleanup", package="PupilPre")
apply_user_cleanup applies to each event the manual cleanup based on
data points stored in the RDS file created using user_cleanup_app. The
Identified datapoints will be changed to NA.
apply_user_cleanup(data = data, LogFile = NULL)apply_user_cleanup(data = data, LogFile = NULL)
data |
A data frame object created from |
LogFile |
A character string indicating the name (and location) of the log file. |
An object of type data table as described in tibble.
if (interactive()) { # Load example data data("Pupilex4") # Ensure log file exists by using the cleanup app # Writing log file to temporary folder for the example user_cleanup_app(Pupilex4, LogFile = paste0(tempdir(),"/UserCleanupLog.rds")) # Make cleanup via the app interface # Read log file from the temporary folder dat <- apply_user_cleanup(Pupilex4, LogFile = paste0(tempdir(),"/UserCleanupLog.rds")) } # Please see the vignettes for detailed example usage. # vignette("PupilPre_Cleanup", package="PupilPre")if (interactive()) { # Load example data data("Pupilex4") # Ensure log file exists by using the cleanup app # Writing log file to temporary folder for the example user_cleanup_app(Pupilex4, LogFile = paste0(tempdir(),"/UserCleanupLog.rds")) # Make cleanup via the app interface # Read log file from the temporary folder dat <- apply_user_cleanup(Pupilex4, LogFile = paste0(tempdir(),"/UserCleanupLog.rds")) } # Please see the vignettes for detailed example usage. # vignette("PupilPre_Cleanup", package="PupilPre")
baseline calculates the average pupil value for the window of Time
provided in BaselineWindow. The baseline value is then used in one of three
different calculation types that must be specified (Subtraction, Division,
or Normalization). Baselining is carried out separately for each event.
baseline(data = data, BaselineWindow = 0, BaselineType = NULL, DiffBaseOverride = FALSE)baseline(data = data, BaselineWindow = 0, BaselineType = NULL, DiffBaseOverride = FALSE)
data |
A data frame object created from |
BaselineWindow |
A numeric vector of length 1 or 2 specifying the time points of the baseline window to be examined. Providing two values indicates the start time and the end time of the baseline, respectively. Providing a single value (i.e., time point) assumes that every preceding time point is part of the baseline (N.B. trials may vary in the size of the baseline window and will result in an error). |
BaselineType |
A character string specifying Subtraction, Division, or Normalization. Subtraction subtracts the average baseline value; Division divides by the average baseline value; and Normalization subtracts and divides by the average baseline value. |
DiffBaseOverride |
A logical value indicating whether or not to override the error produced when baseline windows differ in size. |
An object of type data table as described in tibble.
# Load example data data("Pupilex4") dat <- baseline(Pupilex4, BaselineWindow = c(-500, 0), BaselineType = "Subtraction") # Please see the vignettes for detailed example usage. vignette("PupilPre_Basic_Preprocessing", package="PupilPre")# Load example data data("Pupilex4") dat <- baseline(Pupilex4, BaselineWindow = c(-500, 0), BaselineType = "Subtraction") # Please see the vignettes for detailed example usage. vignette("PupilPre_Basic_Preprocessing", package="PupilPre")
blink_summary summarizes Eyelink marked blinks by Event, Subject, or Item.
blink_summary(data, Summary = "Event", ReturnData = FALSE)blink_summary(data, Summary = "Event", ReturnData = FALSE)
data |
A data table object output by |
Summary |
A character string indicating the type of summary. |
ReturnData |
A logical indicating whether to return a data table containing Start Time information for each event. |
Summary information
# Load example data data("Pupilex3") blink_summary(Pupilex3, Summary = "Event") # Please see the vignettes for detailed example usage. # vignette("PupilPre_Basic_Preprocessing", package="PupilPre")# Load example data data("Pupilex3") blink_summary(Pupilex3, Summary = "Event") # Please see the vignettes for detailed example usage. # vignette("PupilPre_Basic_Preprocessing", package="PupilPre")
butter_filter_app produces a plot of Butterworth filtered pupil data over the
original data to visually inspect the effect of different filter settings.
butter_filter_app(data)butter_filter_app(data)
data |
A data table object. |
if (interactive()) { # Load example data data("Pupilex5") butter_filter_app(Pupilex5) } # Please see the vignettes for detailed example usage. # vignette("PupilPre_Interpolation_and_Filtering", package="PupilPre")if (interactive()) { # Load example data data("Pupilex5") butter_filter_app(Pupilex5) } # Please see the vignettes for detailed example usage. # vignette("PupilPre_Interpolation_and_Filtering", package="PupilPre")
check_baseline examines the data in a specified baseline window.
check_baseline(data = data, BaselineWindow = NULL, ReturnData = FALSE)check_baseline(data = data, BaselineWindow = NULL, ReturnData = FALSE)
data |
A data table object output by |
BaselineWindow |
A numeric vector of length 1 or 2 specifying the time points of the baseline window to be examined. Providing two values indicates the start time and the end time of the baseline, respectively. Providing a single value (i.e., time point) assumes that every preceding time point is part of the baseline (N.B. trials may vary in the size of the baseline window and will result in an error). |
ReturnData |
A logical indicating whether to return a data table containing information for each event. |
Summary information
# Load example data data("Pupilex3") check_baseline(Pupilex3, BaselineWindow = c(-500, 0)) # Please see the vignettes for detailed example usage. # vignette("PupilPre_Basic_Preprocessing", package="PupilPre")# Load example data data("Pupilex3") check_baseline(Pupilex3, BaselineWindow = c(-500, 0)) # Please see the vignettes for detailed example usage. # vignette("PupilPre_Basic_Preprocessing", package="PupilPre")
clean_artifact performs two stage and distributional automated
clean-up of artifacts in the pupil and gaze coordinate data.
clean_artifact(data = data, MADWindow = 100, MADConstant = 2, MADPadding = c(200, 200), MahaConstant = 2, Method = "Robust", XandY = TRUE, Second = TRUE, MaxValueRun = 5, NAsAroundRun = c(2, 2), LogFile = NULL)clean_artifact(data = data, MADWindow = 100, MADConstant = 2, MADPadding = c(200, 200), MahaConstant = 2, Method = "Robust", XandY = TRUE, Second = TRUE, MaxValueRun = 5, NAsAroundRun = c(2, 2), LogFile = NULL)
data |
A data frame object created from |
MADWindow |
A numeric value specifying the window size (in msec) to use for the MAD calculation. |
MADConstant |
A numeric value specifying the constant (a multiplier for the third quartile) when determining MAD outlier status. |
MADPadding |
A numeric vector of length two containing values (in msec) to pad the identified artifact creating a window within which to operate the cleanup. |
MahaConstant |
A numeric value specifying the constant (a multiplier for the third quartile) when determining Mahalanobis outlier status. |
Method |
A character string ("Basic" or "Robust") indicating
which method to use for the distance calculation. Basic is a standard
Mahalanobis distance calculation based on covariance. Robust is also a
Mahalanobis distance, however, it is based on Minimum Covariance
Determinant (Rousseeuw and van Driessen, 1999) with reweighted covariance
(Pison et al., 2002). For more details, see |
XandY |
A logical value specifying whether to also use horizontal velocity and acceleration in outlier detection. |
Second |
A logical value specifying whether secondary cleaning should be applied. |
MaxValueRun |
A numeric value specifying the maximal run of existing values flanked by NAs that could be targeted for removal. |
NAsAroundRun |
A numeric vector of length two containing values (in number of subsequent NA) to be used to identify straggler runs of data that could be removed. |
LogFile |
A character string indicating the file name (with extension) of the log file to be created/written. The file keeps track of which events have been cleaned. We suggest "ArtifactCleanupLog.rds". |
An object of type data table as described in tibble.
Rousseeuw, P. J. and van Driessen, K. (1999) A fast algorithm for the minimum covariance determinant estimator. Technometrics 41, 212–223.
Pison, G., Van Aelst, S., and Willems, G. (2002) Small Sample Corrections for LTS and MCD, Metrika 55, 111–123.
# Load example data data("Pupilex4") # Writing log file to temporary folder for the example dat <- clean_artifact(Pupilex4, MADWindow = 100, MADConstant = 2, MADPadding = c(200, 200), MahaConstant = 2, Method = "Robust", XandY = TRUE, Second = TRUE, MaxValueRun = 5, NAsAroundRun = c(2,2), LogFile = paste0(tempdir(),"/ArtifactCleanupLog.rds")) # Please see the vignettes for detailed example usage. # vignette("PupilPre_Cleanup", package="PupilPre")# Load example data data("Pupilex4") # Writing log file to temporary folder for the example dat <- clean_artifact(Pupilex4, MADWindow = 100, MADConstant = 2, MADPadding = c(200, 200), MahaConstant = 2, Method = "Robust", XandY = TRUE, Second = TRUE, MaxValueRun = 5, NAsAroundRun = c(2,2), LogFile = paste0(tempdir(),"/ArtifactCleanupLog.rds")) # Please see the vignettes for detailed example usage. # vignette("PupilPre_Cleanup", package="PupilPre")
clean_blink performs two stage automated clean-up of blinks
in the pupil and gaze coordinate data.
clean_blink(data = data, BlinkPadding = c(100, 100), Delta = NA, MaxValueRun = 5, NAsAroundRun = c(2, 2), LogFile = NULL)clean_blink(data = data, BlinkPadding = c(100, 100), Delta = NA, MaxValueRun = 5, NAsAroundRun = c(2, 2), LogFile = NULL)
data |
A data frame object created from |
BlinkPadding |
A numeric vector of length two containing values (in msec) to pad the marked blink creating a window within which to operate the cleanup. |
Delta |
A numeric value specifying the maximal difference between subsequent pupil values in order to mark greater differences for removal. If NA, the delta will be estimated from the data using the 95th percentile value. |
MaxValueRun |
A numeric value specifying the maximal run of existing values flanked by NAs that could be targeted for removal. |
NAsAroundRun |
A numeric vector of length two containing values (in number of subsequent NA) to be used to identify straggler runs of data that could be removed. |
LogFile |
A character string indicating the file name (with extension) of the log file to be created/written. The file keeps track of which events have been cleaned. We suggest "BlinkCleanupLog.rds". |
An object of type data table as described in tibble.
# Load example data data("Pupilex3") # Writing log file to temporary folder for the example dat <- clean_blink(Pupilex3, BlinkPadding = c(100, 100), Delta = 5, MaxValueRun = 5, NAsAroundRun = c(2,2), LogFile = paste0(tempdir(),"/BlinkCleanupLog.rds")) # Please see the vignettes for detailed example usage. # vignette("PupilPre_Cleanup", package="PupilPre")# Load example data data("Pupilex3") # Writing log file to temporary folder for the example dat <- clean_blink(Pupilex3, BlinkPadding = c(100, 100), Delta = 5, MaxValueRun = 5, NAsAroundRun = c(2,2), LogFile = paste0(tempdir(),"/BlinkCleanupLog.rds")) # Please see the vignettes for detailed example usage. # vignette("PupilPre_Cleanup", package="PupilPre")
compare_summary is a utility function to compare pupil size data
before and after applying the cleanup and summarizes a comparison between
Pupil and Pupil_Previous by Event
compare_summary(data, ReturnData = FALSE)compare_summary(data, ReturnData = FALSE)
data |
A data table object output by |
ReturnData |
A logical indicating whether to return a data table containing the summary information. |
Summary information.
# Load example data data("Pupilex4") compare_summary(Pupilex4) # Please see the vignettes for detailed example usage. # vignette("PupilPre_Basic_Preprocessing", package="PupilPre")# Load example data data("Pupilex4") compare_summary(Pupilex4) # Please see the vignettes for detailed example usage. # vignette("PupilPre_Basic_Preprocessing", package="PupilPre")
downsample reduces the sampling rate using median values for the
Pupil and gaze coordinates.
downsample(data, SamplingRate = NULL, NewRate = NULL)downsample(data, SamplingRate = NULL, NewRate = NULL)
data |
A data frame object created from |
SamplingRate |
A postive integer specifying the current sampling rate. |
NewRate |
A postive integer specifying the desired downsampled rate. |
An object of type data table as described in tibble.
# Load example data data("Pupilex4") dat <- downsample(Pupilex4, SamplingRate = 250, NewRate = 25) # Please see the vignettes for detailed example usage. vignette("PupilPre_Basic_Preprocessing", package="PupilPre")# Load example data data("Pupilex4") dat <- downsample(Pupilex4, SamplingRate = 250, NewRate = 25) # Please see the vignettes for detailed example usage. vignette("PupilPre_Basic_Preprocessing", package="PupilPre")
interpolate_NAs performs interpolation of missing data for
the pupil and gaze coordinates (if desired).
interpolate_NAs(data = data, Method = "linear", XandY = TRUE, MinData = 2)interpolate_NAs(data = data, Method = "linear", XandY = TRUE, MinData = 2)
data |
A data frame object created from |
Method |
A character string indicating type of interpolation ("linear" or "spline") as implemented in na.approx. |
XandY |
A logical specifying if interpolation should also be done on gaze coordinates |
MinData |
A number indicating the minimum number of data points required in order for interpolation to be applied to the event. |
An object of type data table as described in tibble.
# Load example data data("Pupilex4") dat <- interpolate_NAs(Pupilex4, Method = "linear", XandY = TRUE, MinData = 2) # Please see the vignettes for detailed example usage. # vignette("PupilPre_Interpolation_and_Filtering", package="PupilPre")# Load example data data("Pupilex4") dat <- interpolate_NAs(Pupilex4, Method = "linear", XandY = TRUE, MinData = 2) # Please see the vignettes for detailed example usage. # vignette("PupilPre_Interpolation_and_Filtering", package="PupilPre")
NA_summary summarizes missing data by Event, Subject, or Item.
NA_summary(data, Summary = "Event", PupilColumn = NULL, ReturnData = FALSE)NA_summary(data, Summary = "Event", PupilColumn = NULL, ReturnData = FALSE)
data |
A data table object output by |
Summary |
A character string indicating the type of summary. |
PupilColumn |
A character string indicating which column to use for the summary. |
ReturnData |
A logical indicating whether to return a data table containing the summary information. |
Summary information.
# Load example data data("Pupilex3") NA_summary(Pupilex3, Summary = "Event", PupilColumn = "Pupil") # Please see the vignettes for detailed example usage. # vignette("PupilPre_Basic_Preprocessing", package="PupilPre")# Load example data data("Pupilex3") NA_summary(Pupilex3, Summary = "Event", PupilColumn = "Pupil") # Please see the vignettes for detailed example usage. # vignette("PupilPre_Basic_Preprocessing", package="PupilPre")
plot_compare_app produces a comparison plot of Pupil and
Pupil_Previous by event to visual changes.
plot_compare_app(data)plot_compare_app(data)
data |
A data table object. |
if (interactive()) { # Load example data data("Pupilex4") plot_compare_app(Pupilex4) } # Please see the vignettes for detailed example usage. # vignette("PupilPre_Basic_Preprocessing", package="PupilPre")if (interactive()) { # Load example data data("Pupilex4") plot_compare_app(Pupilex4) } # Please see the vignettes for detailed example usage. # vignette("PupilPre_Basic_Preprocessing", package="PupilPre")
plot_events plots each event in a group as a multi-panel plot and
saves it into specified directory.
plot_events(data = data, Column = NULL, Grouping = "Subject", Nrow = 1, Ncol = 1, Device = "pdf", ...)plot_events(data = data, Column = NULL, Grouping = "Subject", Nrow = 1, Ncol = 1, Device = "pdf", ...)
data |
A data table object output by
|
Column |
A character string indicating the column to plot. |
Grouping |
A character string indicating the column to serve as the grouping. For example, "Subject" will use the subject identifier, producing one image per subject containing all the events for that subject. |
Nrow |
= A number specifying how many rows per page. |
Ncol |
= A number specifying how many columns per page. |
Device |
A character string indicating device type passed to
|
... |
Arguments to be passed to |
Files containing plots.
# Load example data data("Pupilex3") # Writing files to temporary folder for the example plot_events(Pupilex3, Column = "Pupil", Device = "pdf", Grouping = "Subject", path = paste0(tempdir(),"/Figs"), Nrow = 1, Ncol = 1, width = 11, height = 8.5) # Please see the vignettes for detailed example usage. # vignette("PupilPre_Plotting", package="PupilPre")# Load example data data("Pupilex3") # Writing files to temporary folder for the example plot_events(Pupilex3, Column = "Pupil", Device = "pdf", Grouping = "Subject", path = paste0(tempdir(),"/Figs"), Nrow = 1, Ncol = 1, width = 11, height = 8.5) # Please see the vignettes for detailed example usage. # vignette("PupilPre_Plotting", package="PupilPre")
plot_summary_app plots summary of a given subject or item.
plot_summary_app(data)plot_summary_app(data)
data |
A data table object. |
if (interactive()) { # Load example data data("Pupilex4") plot_summary_app(Pupilex4) } # Please see the vignettes for detailed example usage. # vignette("PupilPre_Basic_Preprocessing", package="PupilPre")if (interactive()) { # Load example data data("Pupilex4") plot_summary_app(Pupilex4) } # Please see the vignettes for detailed example usage. # vignette("PupilPre_Basic_Preprocessing", package="PupilPre")
ppl_check_eye_recording quickly checks which eyes contain gaze data
either using the EYE_TRACKED column (if available) or the Right and
Left interest area columns. It prints a summary and
suggests which setting to use for the Recording parameter in the
function ppl_select_recorded_eye.
ppl_check_eye_recording(data)ppl_check_eye_recording(data)
data |
A data table object output by |
Text feedback and instruction.
# Load example data data("Pupilex2") ppl_check_eye_recording(data = Pupilex2) # Please see the vignettes for detailed example usage. # vignette("PupilPre_Basic_Preprocessing", package="PupilPre")# Load example data data("Pupilex2") ppl_check_eye_recording(data = Pupilex2) # Please see the vignettes for detailed example usage. # vignette("PupilPre_Basic_Preprocessing", package="PupilPre")
ppl_plot_avg calculates the grand or conditional averages with
standard error. It then plots the results.
N.B.: This function will work for data with a maximum of 2 conditions.
ppl_plot_avg(data, xlim = NA, Column = NULL, Averaging = "Event", Condition1 = NULL, Condition2 = NULL, Cond1Labels = NA, Cond2Labels = NA, ErrorBar = TRUE, PupilPreTheme = TRUE, ConfLev = 95, CItype = "simultaneous", ErrorBand = FALSE, ErrorType = "SE")ppl_plot_avg(data, xlim = NA, Column = NULL, Averaging = "Event", Condition1 = NULL, Condition2 = NULL, Cond1Labels = NA, Cond2Labels = NA, ErrorBar = TRUE, PupilPreTheme = TRUE, ConfLev = 95, CItype = "simultaneous", ErrorBand = FALSE, ErrorType = "SE")
data |
A data table object output after having executed
|
xlim |
A vector of two integers specifying the limits of the x-axis. |
Column |
A character string specifying the desired column. |
Averaging |
A character string indicating how the averaging should be done. "Event" (default) will produce the overall mean in the data, while "Subject" or "Item" (or, in principle, any other column name) will calculate the grand mean by that factor. |
Condition1 |
A string containing the column name corresponding to the first condition, if available. |
Condition2 |
A string containing the column name corresponding to the second condition, if available. |
Cond1Labels |
A named character vector specifying the desired custom labels of the levels of the first condition. |
Cond2Labels |
A named character vector specifying the desired custom labels of the levels of the second condition. |
ErrorBar |
A logical indicating whether error bars should be included in the plot. |
PupilPreTheme |
A logical indicating whether the theme included with the function should be applied, or ggplot2's base theme (to which any other custom theme could be added).. |
ConfLev |
A number indicating the confidence level of the CI. |
CItype |
A string indicating "simultaneous" or "pointwise". Simultaneous performs a Bonferroni correction for the interval. |
ErrorBand |
A logical indicating whether error bands should be included in the plot. |
ErrorType |
A string indicating "SE" (Standard Error) or "CI" (Confidence Interval). |
# Load example data data("Pupilex7") ppl_plot_avg(data = Pupilex7, xlim = c(0, 1900), Column = "Pupil", Condition1 = NULL, Condition2 = NULL, Cond1Labels = NA, Cond2Labels = NA, ErrorBar = TRUE, PupilPreTheme = TRUE) # Please see the vignettes for detailed example usage. # vignette("PupilPre_Plotting", package="PupilPre")# Load example data data("Pupilex7") ppl_plot_avg(data = Pupilex7, xlim = c(0, 1900), Column = "Pupil", Condition1 = NULL, Condition2 = NULL, Cond1Labels = NA, Cond2Labels = NA, ErrorBar = TRUE, PupilPreTheme = TRUE) # Please see the vignettes for detailed example usage. # vignette("PupilPre_Plotting", package="PupilPre")
ppl_plot_avg_cdiff calculates the average of differences between
two specified conditions along with standard error and then plots the
results.
ppl_plot_avg_cdiff(data, Column = NULL, xlim = NA, Averaging = "Subject", Condition = NULL, CondLabels = NA, ErrorBar = TRUE, PupilPreTheme = TRUE, ConfLev = 95, CItype = "simultaneous", ErrorBand = FALSE, ErrorType = "SE")ppl_plot_avg_cdiff(data, Column = NULL, xlim = NA, Averaging = "Subject", Condition = NULL, CondLabels = NA, ErrorBar = TRUE, PupilPreTheme = TRUE, ConfLev = 95, CItype = "simultaneous", ErrorBand = FALSE, ErrorType = "SE")
data |
A data table object. |
Column |
A character vector specifying the desired column. |
xlim |
A vector of two integers specifying the limits of the x-axis. |
Averaging |
A character string indicating how the averaging should be done. "Subject" (default) will produce the grand mean in the data, while "Item" (or, in principle, any other column name) will calculate the grand mean by that factor. |
Condition |
A list containing the column name corresponding to the condition and factor levels to be used for calculating the difference. |
CondLabels |
A named character vector specifying the desired labels of the levels of the condition. |
ErrorBar |
A logical indicating whether error bars should be included in the plot. |
PupilPreTheme |
A logical indicating whether the theme included with the function should be applied, or ggplot2's base theme (to which any other custom theme could be added). |
ConfLev |
A number indicating the confidence level of the CI. |
CItype |
A string indicating "simultaneous" or "pointwise". Simultaneous performs a Bonferroni correction for the interval. |
ErrorBand |
A logical indicating whether error bands should be included in the plot. |
ErrorType |
A string indicating "SE" or "CI". |
# Load example data data("Pupilex7") ppl_plot_avg_cdiff(data = Pupilex7, Column = "Pupil", Condition = list(talker = c("EN3", "CH1")), ErrorBar = TRUE, PupilPreTheme = TRUE) # Please see the vignettes for detailed example usage. # vignette("PupilPre_Plotting", package="PupilPre")# Load example data data("Pupilex7") ppl_plot_avg_cdiff(data = Pupilex7, Column = "Pupil", Condition = list(talker = c("EN3", "CH1")), ErrorBar = TRUE, PupilPreTheme = TRUE) # Please see the vignettes for detailed example usage. # vignette("PupilPre_Plotting", package="PupilPre")
ppl_plot_avg_contour calculates the conditional average of pupil
size by Time and a specified continuous variable. It then applies a 3D smooth
(derived using gam) over the surface and plots the
results as a contour plot.
ppl_plot_avg_contour(data, Column = NULL, Var = NULL, Averaging = "Event", VarLabel = NULL, xlim = NA, PupilPreTheme = TRUE, Colors = c("gray20", "gray90"))ppl_plot_avg_contour(data, Column = NULL, Var = NULL, Averaging = "Event", VarLabel = NULL, xlim = NA, PupilPreTheme = TRUE, Colors = c("gray20", "gray90"))
data |
A data table object output by either |
Column |
A string specifying the column to use. |
Var |
A string containing the column name corresponding to the continuous variable. |
Averaging |
A character string indicating how the averaging should be done. "Event" (default) will produce the overall mean in the data, while "Subject" or "Item" (or, in principle, any other column name) will calculate the grand mean by that factor. |
VarLabel |
A string specifying the axis label to use for |
xlim |
A vector of two integers specifying the limits of the x-axis. |
PupilPreTheme |
A logical indicating whether the theme included with the function, or ggplot2's base theme (which any other custom theme could be added). |
Colors |
A vector of two strings specifying the colrs of the contour shading - The default values represent grayscale. |
# Load example data data("Pupilex7") ppl_plot_avg_contour(data = Pupilex7, Column = "Pupil", Var = "TRIAL_INDEX", VarLabel = "Trial", xlim = c(0,2000), PupilPreTheme = TRUE, Colors = c("gray20", "gray90")) # Please see the vignettes for detailed example usage. # vignette("PupilPre_Plotting", package="PupilPre")# Load example data data("Pupilex7") ppl_plot_avg_contour(data = Pupilex7, Column = "Pupil", Var = "TRIAL_INDEX", VarLabel = "Trial", xlim = c(0,2000), PupilPreTheme = TRUE, Colors = c("gray20", "gray90")) # Please see the vignettes for detailed example usage. # vignette("PupilPre_Plotting", package="PupilPre")
ppl_prep_data checks for necessary columns and converts the class
if needed.
ppl_prep_data(data, Subject = NULL, Item = NA, EventColumns = c("Subject", "TRIAL_INDEX"))ppl_prep_data(data, Subject = NULL, Item = NA, EventColumns = c("Subject", "TRIAL_INDEX"))
data |
A data frame object created from an Eyelink Sample Report. |
Subject |
An obligatory string containing the column name corresponding to the subject identifier. |
Item |
An optional string containing the column name corresponding to the item identifier; by default, NA. |
EventColumns |
A vector specifying the columns which will be used for creating the Event variable; by default, Subject and TRIAL_INDEX. |
An object of type data table as described in tibble.
# Load example data data("Pupilex1") dat <- ppl_prep_data(Pupilex1, Subject = "RECORDING_SESSION_LABEL", Item = "item", EventColumns = c("Subject","TRIAL_INDEX")) # Please see the vignettes for detailed example usage. # vignette("PupilPre_Basic_Preprocessing", package="PupilPre")# Load example data data("Pupilex1") dat <- ppl_prep_data(Pupilex1, Subject = "RECORDING_SESSION_LABEL", Item = "item", EventColumns = c("Subject","TRIAL_INDEX")) # Please see the vignettes for detailed example usage. # vignette("PupilPre_Basic_Preprocessing", package="PupilPre")
ppl_rm_extra_DVcols checks for unnecessary DataViewer output columns and
removes them, unless specified.
ppl_rm_extra_DVcols(data, Keep = NULL)ppl_rm_extra_DVcols(data, Keep = NULL)
data |
A data frame object created from an Eyelink Sample Report. |
Keep |
An optional string or character vector containing the column names of SR Research sample report columns the user would like to keep in the data set. |
An object of type data table as described in tibble.
# Load example data data("Pupilex1") dat <- ppl_rm_extra_DVcols(Pupilex1, Keep = NULL) # Please see the vignettes for detailed example usage. # vignette("PupilPre_Basic_Preprocessing", package="PupilPre")# Load example data data("Pupilex1") dat <- ppl_rm_extra_DVcols(Pupilex1, Keep = NULL) # Please see the vignettes for detailed example usage. # vignette("PupilPre_Basic_Preprocessing", package="PupilPre")
ppl_select_recorded_eye examines each event and determines which
eye contains interest area information, based on the Recording
parameter (which can be determined using ppl_check_eye_recording).
This function then selects the data from the recorded eye and copies it to
new columns (Pupil, Gaze_X, Gaze_Y, Velocity_X, Velocity_Y, Acceleration_X,
Acceleration_Y, In_Blink, In_Saccade). The function prints a summary of the output.
ppl_select_recorded_eye(data, Recording = NULL, WhenLandR = NA)ppl_select_recorded_eye(data, Recording = NULL, WhenLandR = NA)
data |
A data table object output by |
Recording |
A string indicating which eyes were used for recording gaze data ("R" when only right eye recording is present, "L" when only left eye recording is present, "LorR" when either the left or the right eye was recorded, "LandR" when both the left and the right eyes were recorded). |
WhenLandR |
A string indicating which eye ("Right" or "Left) to use if gaze data is available for both eyes (i.e., Recording = "LandR"). |
A data table with 11 additional columns added to data.
# Load example data data("Pupilex2") dat <- ppl_select_recorded_eye(data = Pupilex2, Recording = "R", WhenLandR = "Right") # Please see the vignettes for detailed example usage. # vignette("PupilPre_Basic_Preprocessing", package="PupilPre")# Load example data data("Pupilex2") dat <- ppl_select_recorded_eye(data = Pupilex2, Recording = "R", WhenLandR = "Right") # Please see the vignettes for detailed example usage. # vignette("PupilPre_Basic_Preprocessing", package="PupilPre")
This is a sample pupil size dataset included in the package
Aki Kyröläinen
This is an example dataset to illustrate certain functionality
Aki Kyröläinen
This is an example dataset to illustrate certain functionality
Aki Kyröläinen
This is an example dataset to illustrate certain functionality
Aki Kyröläinen
This is an example dataset to illustrate certain functionality
Aki Kyröläinen
This is an example dataset to illustrate certain functionality
Aki Kyröläinen
This is an example dataset to illustrate certain functionality
Aki Kyröläinen
This is an example dataset to illustrate certain functionality
Aki Kyröläinen
The PupilPre package provides a set of functions for preparing pupil size data collected with SR Research Eyelink eye trackers.
The function ppl_prep_data returns a data table with
correctly assigned classes for important columns.
The function ppl_select_recorded_eye returns a data table
with data from the the recorded eye in new columns (IA_ID and IA_LABEL).
The function recode_off_screen recodes samples with NA if
gaze coordinates indicate that the sample was taken while the pupil was
off-screen.
The function ppl_rm_extra_DVcols removes DataViewer coumns
that are not necessary for preprocessing with this package.
The function clean_blink returns a data table
for which blinks have been removed based on the parameters provided.
The function clean_artifact returns a data table
for which artifacts have been removed based on the parameters provided.
The function apply_cleanup_change applies user-selected
changes to the automatic cleanup.
The function apply_user_cleanup returns a data table
for which the manually selected artifacts have been removed.
The function rm_sparse_events removes events
that do not contain enough data in the baseline and/or critical windows,
as specified by the user.
The function interpolate_NAs returns a data table in which
NAs have been replaced using linear interpolation.
The function apply_butter applies a Butterworth
filter to the pupil size data.
The function trim_filtered removes a specified number
of milliseconds from the beginning and the end of each filtered event, as
to remove artifacts created by the filter.
The function downsample returns a data table for which
the data have been downsampled using the specified sampling rate.
The function baseline returns a data table for which
the pupil data have been baselined using the specified method.
The function ppl_check_eye_recording returns a summary
of whether or not the dataset contains gaze data in both the Right and
Left interest area columns.
The function blink_summary returns a summary of
Eyelink marked blinks by Event, Subject, or Item.
The function NA_summary returns a summary of missing
data by Event, Subject, or Item.
The function check_baseline examines the data within
a specified baseline window.
The function compare_summary returns a summary of
comparison between the columns Pupil and Pupil_Previous.
The function ppl_plot_avg returns a plot of the grand
or conditional averages of pupil dilation along with error bars.
The function ppl_plot_avg_contour returns a contour plot of
the conditional average of pupil dilation over Time and a specified continuous variable.
The function ppl_plot_avg_cdiff returns a plot of the
average difference between two conditions for pupil dilation with error bars.
The function plot_events returns image files containing
plots for each event by a group and saves into a specified directory.
The function user_cleanup_app opens a Shiny app
for identifying and marking datapoints associated with artifacts.
The function plot_summary_app opens a Shiny app for
inspecting by-subject or by-item averages within a specified time window.
The function plot_compare_app opens a Shiny app for
inspecting events for comparing the current pupil column to the
previous pupil column.
The function verify_cleanup_app plots the data
points changed during the previously completed auto cleanup, allowing the
user to reject the cleanup for specific events.
The function butter_filter_app produces a plot of
filtered pupil data over the original data to visually inspect the effect
of different filter settings.
The vignettes are available via browseVignettes(package = "PupilPre").
A list of all available functions is provided in
help(package = "PupilPre").
This package can be cited using the information obtained from
citation("PupilPre") or print(citation("PupilPre"), bibtex = TRUE)
Aki-Juhani Kyröläinen, Vincent Porretta, Jacolien van Rij, Juhani Järvikivi
Maintainer: Aki-Juhani Kyröläinen, ([email protected])
McMaster University, Canada
recode_off_screen checks samples falling outside the bounds of
the screen and marks them with NA
recode_off_screen(data = data, ScreenSize = NULL, PlotData = FALSE)recode_off_screen(data = data, ScreenSize = NULL, PlotData = FALSE)
data |
A data frame object created from an Eyelink Sample Report. |
ScreenSize |
A numeric vector specifying (in pixels) the dimensions of the x and y of the screen used during the experiment. |
PlotData |
A logical indicating whether or not to output a visualization of the result. |
An object of type data table as described in tibble.
# Load example data data("Pupilex3") dat <- recode_off_screen(data = Pupilex3, ScreenSize = c(1920, 1080), PlotData = FALSE) # Please see the vignettes for detailed example usage. # vignette("PupilPre_Basic_Preprocessing", package="PupilPre")# Load example data data("Pupilex3") dat <- recode_off_screen(data = Pupilex3, ScreenSize = c(1920, 1080), PlotData = FALSE) # Please see the vignettes for detailed example usage. # vignette("PupilPre_Basic_Preprocessing", package="PupilPre")
rm_sparse_events removes events with less data than the
specified amount.
rm_sparse_events(data = data, BaselineWindow = NULL, CriticalWindow = NULL, BaselineRequired = NULL, CriticalRequired = NULL)rm_sparse_events(data = data, BaselineWindow = NULL, CriticalWindow = NULL, BaselineRequired = NULL, CriticalRequired = NULL)
data |
A data table object output after having run
|
BaselineWindow |
A numeric vector of length 1 or 2 specifying the time points of the baseline window to be examined. Providing two values indicates the start time and the end time of the baseline, respectively. Providing a single value (i.e., time point) assumes that every preceding time point is part of the baseline (N.B. trials may vary in the size of the baseline window and will result in an error). |
CriticalWindow |
A numeric vector of length 1 or 2 specifying the time points of the critical (i.e., post-stimulus) window to be examined. Providing two values indicates the start time and the end time of the window, respectively. Providing a single value (i.e., time point) assumes that every subsequent time point is part of the window. |
BaselineRequired |
A number indicating the percentage of data required in the baseline to be included (i.e., drop events with less than this amount of data). |
CriticalRequired |
A number indicating the percentage of data required in the critical window to be included (i.e., drop events with less than this amount of data). |
An object of type data table as described in tibble.
# Load example data data("Pupilex3") dat <- rm_sparse_events(data = Pupilex3, BaselineWindow = c(-500, 0), CriticalWindow = c(200, 2000), BaselineRequired = 50, CriticalRequired = 50) # Please see the vignettes for detailed example usage. # vignette("PupilPre_Basic_Preprocessing", package="PupilPre")# Load example data data("Pupilex3") dat <- rm_sparse_events(data = Pupilex3, BaselineWindow = c(-500, 0), CriticalWindow = c(200, 2000), BaselineRequired = 50, CriticalRequired = 50) # Please see the vignettes for detailed example usage. # vignette("PupilPre_Basic_Preprocessing", package="PupilPre")
trim_filtered removes events skipped by the filter as well as a
specified number of milliseconds from the beginning and the end of each
filtered event (as to remove artifacts created by the filter).
trim_filtered(data = data, RmSkipped = NULL, RmEdges = NULL)trim_filtered(data = data, RmSkipped = NULL, RmEdges = NULL)
data |
A data frame object created from |
RmSkipped |
A logical value indicating whether or not to remove events that were skipped during the filtering process (due to NAs). |
RmEdges |
A numeric vector of length 2 indicating the number of milliseconds to remove from the beginning and end of each event. |
An object of type data table as described in tibble.
# Load example data data("Pupilex6") dat <- trim_filtered(data = Pupilex6, RmSkipped = TRUE, RmEdges = c(75, 75)) # Please see the vignettes for detailed example usage. vignette("PupilPre_Interpolation_and_Filtering", package="PupilPre")# Load example data data("Pupilex6") dat <- trim_filtered(data = Pupilex6, RmSkipped = TRUE, RmEdges = c(75, 75)) # Please see the vignettes for detailed example usage. vignette("PupilPre_Interpolation_and_Filtering", package="PupilPre")
user_cleanup_app plots current pupil data and allows the user to
select data points which should be removed (changed to NA). The app saves
a record of the to-be-executed changes in an RDS file.
user_cleanup_app(data = data, LogFile = NULL)user_cleanup_app(data = data, LogFile = NULL)
data |
A data table object. |
LogFile |
A character string indicating the name (and location) of the log file to be read/written. |
if (interactive()) { # Load example data data("Pupilex4") # Writing log file to temporary folder for the example user_cleanup_app(Pupilex4, LogFile = paste0(tempdir(),"/UserCleanupLog.rds")) } # Please see the vignettes for detailed example usage. # vignette("PupilPre_Cleanup", package="PupilPre")if (interactive()) { # Load example data data("Pupilex4") # Writing log file to temporary folder for the example user_cleanup_app(Pupilex4, LogFile = paste0(tempdir(),"/UserCleanupLog.rds")) } # Please see the vignettes for detailed example usage. # vignette("PupilPre_Cleanup", package="PupilPre")
verify_cleanup_app plots the data points changed during the
previously completed auto cleanup and allows the user to verify the cleanup
for specific events. The app saves the selection to the RDS file, which can
then be used to apply the changes to the data set.
verify_cleanup_app(data = data, LogFile = NULL)verify_cleanup_app(data = data, LogFile = NULL)
data |
A data table object. |
LogFile |
A character string indicating the name (and location) of the log file. |
if (interactive()) { # Load example data data("Pupilex3") # Ensure the log file exists by running cleanup # Writing log file to temporary folder for the example dat <- clean_blink(Pupilex3, BlinkPadding = c(100, 100), Delta = 5, MaxValueRun = 5, NAsAroundRun = c(2,2), LogFile = paste0(tempdir(),"/BlinkCleanupLog.rds")) # Read log file from temporary folder verify_cleanup_app(dat, LogFile = paste0(tempdir(),"/BlinkCleanupLog.rds")) } # Please see the vignettes for detailed example usage. # vignette("PupilPre_Cleanup", package="PupilPre")if (interactive()) { # Load example data data("Pupilex3") # Ensure the log file exists by running cleanup # Writing log file to temporary folder for the example dat <- clean_blink(Pupilex3, BlinkPadding = c(100, 100), Delta = 5, MaxValueRun = 5, NAsAroundRun = c(2,2), LogFile = paste0(tempdir(),"/BlinkCleanupLog.rds")) # Read log file from temporary folder verify_cleanup_app(dat, LogFile = paste0(tempdir(),"/BlinkCleanupLog.rds")) } # Please see the vignettes for detailed example usage. # vignette("PupilPre_Cleanup", package="PupilPre")