In MrEtmAr/Pratik_atlastools: Tools for High Frequency Tracking Data

Three methods for removing reflections

'Next reasonable speed' method
'Next reasonable distance' method
'Next extreme speed' method

Load libraries

library(data.table)
library(ggplot2)

Next reasonable speed method

This method fails for any reflections of duration $T$, where $T = D/v$, where $D$ is the displacement of the reflected points from the anchor point, and $v$ is the speed cutoff used.

# get displacement distance and speed cutoff combinations
displacement_distance <- c(10 ^ seq(0, 4, 0.1))
speed_cutoffs <- seq(0, 100, 5)

# use formula for algorithm defeat
data <- CJ(displacement_distance, speed_cutoffs)[, 
  time_to_defeat := displacement_distance / speed_cutoffs]

# plot matrix of time to defeat
ggplot(data)+
  geom_tile(aes(speed_cutoffs, displacement_distance,
                fill = time_to_defeat / 60))+
  scale_fill_viridis_c(option = "B",
                       trans = "log10",
                       limits = c(0.3, NA),
                       breaks = c(0.3, 1, 3, 10, 30),
                       labels = as.character(c(0.3, 1, 3, 10, 30)),
                       na.value = "black")+
  scale_y_log10(labels = scales::comma,
                breaks = c(10 ^ seq(0, 5), 500, 5000))+
  scale_x_continuous(breaks = c(3, 10, seq(20, 100, 20)))+
  coord_equal(ratio = 50,
              xlim = c(3, NA),
              ylim = c(100, NA),
              expand = FALSE)+
  theme_test()+
  theme(axis.text.y = element_text(angle = 90, 
                                   hjust = 0.5),
        legend.position = "top")+
  labs(x = expression("speed cutoff" ~ italic("v") ~ "(m/s)"),
       y = expression("displacement distance" ~ italic("D") ~ "(m)"),
       fill = "reflection duration (minutes)")

Next reasonable distance method

# read some simulated data
data <- data.table::fread("vignette_data/simulated_data.csv")

# get speed estimate
data$speed <- atlastools::atl_get_speed(data)

ggplot(data)+
  geom_point(aes(x, y,
                col = speed),
             shape = 16, size = 0.1)+
  geom_path(aes(x, y,
                col = speed),
            size = 0.1)+
  scale_colour_viridis_c(direction = -1,
                         option = "E")+
  theme_void()+
  labs(x = NULL, y = NULL)

And now with refelection removed.

ggplot(atlastools::atl_remove_reflections(data))+
  geom_point(aes(x, y,
                col = speed),
             shape = 16, size = 0.1)+
  geom_path(aes(x, y,
                col = speed),
            size = 0.1)+
  scale_colour_viridis_c(direction = -1,
                         option = "E")+
  theme_void()+
  labs(x = NULL, y = NULL)