dilations {clintools} | R Documentation |
Assess dilations from PLR3000
-output.
Description
dilations()
is a function which converts longformat recording of pupillary size and uses markers to generate a dataframe, plot, and markdown output to inspect the results.
Usage
dilations(pupils, markers,
remove_markers = NULL, add_markers = NULL,
not_assess = NULL, artefacts_static = c(0.55,9.95),
artefacts_dynamic = c(`1` = 1.5, `0.66` = 1, `0.33` = 0.5),
time_assess = c(`1` = 10, `3` = 5),
sig.level = 0.05, min_change = NULL,
resting_delay = c(`3` = 0))
Arguments
pupils |
recording of pupillary function. long format dataframe with at least three columns: record_id, time, and size. |
markers |
time of markers. long format dataframe with at least two columns: record_id and time. |
remove_markers |
markers which should be removed. long format dataframe with at least two columns: record_id and time. The time column need one decimal. |
add_markers |
markers which should be added. long format dataframe with at least two columns: record_id and time. The time column need one decimal. |
not_assess |
a list of record ids which should no be assessed. |
artefacts_static |
a list of the limits of the artefacts. The first number in the list is the minimum size to be assessed and the second is the maximum size to be assessed |
artefacts_dynamic |
a named list where max change in millimeter within the duration (name in list) is removed. Will use the first 1 second of the recording to create a baseline, thus suspectible to artefacts in the start of the recording. |
time_assess |
This named list define the number of seconds which should be used in the assessment of dilatios. The name is the number of periods-of-interest and the value is the seconds. |
sig.level |
This is the significance level to be used when comparing the size of the period-of-interest. The significance level corresponds to the Wilcox.test used. |
min_change |
This is the minimum size of mm which needs to change before a dilation can be identified. Default is no minimum requirement. |
resting_delay |
This can be used if the subsequent resting period to compare should be delayed, i.e. if we should wait 5 second for those investigations with three periods of interest create a named list with periods of interest as names and seconds to delay as input. |
Value
Returns a nested list one dataframe of the results ($dilations), plot ($plot$id[record id]), and a markdown output ($plot$markdown$id[record_id]). The dilations dataframe include the following columns: Record ID (record_id); Patient ID (pt_id); Date (date); pupil side (side); start of the period (min); end of the period (max); length of period (rec_length); number of measurements (n); median size (median); P value when comparing with the previous period (p_before); P value when comparing with the following period (p_after); and if dilation is identified (dilation, 1 is successful dilation and 0 is no dilation).
Examples
## Not run:
recordings <- PLR3000("C:/PLR3000/R_20200105_205901.xls")
dilations <- dilations(recordings$pupils,recordings$markers)
# The dataframe of the results
dilations$dilations
# The plot of one of the recordings
dilations$plot$id833
# The markdown output of one of the recordings
dilations$markdown$id833
## End(Not run)