clintools (version 0.9.10.1)

dilations: 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))

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).

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.

Examples

 if (FALSE) {
   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

 }