In hejtmy/navr: Collection of functions that find typical use in human navigation cognitive paradigms

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  warning = F,
  message = F,
  out.width = '60%'
)

library(navr)
library(ggplot2)
obj <- navr_object_preprocessed

Speed clearning

Firstly we clear the speeds of any unreal ones

obj <- remove_unreal_speeds(obj, type = "std", cutoff = 3, total_recalculate = TRUE)
plot_speed(obj) + xlim(100,150)

And then we smooth it

obj <- smooth_speed(obj, type = "median", points = 11)
plot_speed(obj) + xlim(100, 150) 

Onset search

There are several options to onset searching. Let's start with the simple every time it is above certain threshold and for at least 1 s

onsets <- search_onsets(obj, speed_threshold = 5, min_duration = 2)
plot_speed(obj) +
  geom_navr_timeseries_events(onsets$time_since_start, durations = onsets$duration, color=NA, size=1.5) +
  xlim(200,500)

Seems to be working well. Now we can modify the onset search to only capture onsets which are preceded by stillness

onsets <- search_onsets(obj, speed_threshold = 5, min_duration = 2, still_duration = 3)
plot_speed(obj) +
  geom_navr_timeseries_events(onsets$time_since_start, durations = onsets$duration, color=NA, size=1.5) +
  xlim(200,500)

And next we can also designate slightly different speeds for still and moving speeds

onsets <- search_onsets(obj, speed_threshold = 5, min_duration = 1, still_duration = 2, still_speed_threshold = 2)
plot_speed(obj) + 
  geom_navr_timeseries_events(onsets$time_since_start, color="green", size=1.5) + 
  xlim(200,500)

Allowing slight pauses

Let's take a look at the slightly jumpy section between 170 and 250. At time 225, there is a sudden dip which is not considered part of the onset event.

onsets <- search_onsets(obj, speed_threshold = 5, min_duration = 1, still_duration = 1, still_speed_threshold = 2)
plot_speed(obj) + 
  geom_navr_timeseries_events(onsets$time_since_start, onsets$duration, color="green", size=1.5) + 
  xlim(150,250) + geom_vline(xintercept=225, size = 1, color = "red")

If we want to include it, we can use the pause_duration parameter and set it to 1 s. Other option might be to better smooth the speeds with smooth_speed.

onsets <- search_onsets(obj, speed_threshold = 5, min_duration = 1, still_duration = 1, 
                        still_speed_threshold = 2, pause_duration = 1)
plot_speed(obj) + 
  geom_navr_timeseries_events(onsets$time_since_start, onsets$duration, color="green", size=1.5) + 
  xlim(150,250) + geom_vline(xintercept=225, size = 1, color = "red")

hejtmy/navr documentation built on March 3, 2023, 5:24 p.m.