The trip package

Introduction

Basic use of the trip package.

Data input and validation

Tracking data is in essence a grouped series of one-dimensional data[^1] records.

It is grouped because we may track more than one object, each with its on independent time sequence.

It is one-dimensional because the topology of the data is a linear stream of values. It makes sense that time is constantly increasing, and it is the primary dimension of the process. (Location is often something that we must estimate, but time is usually directly measured and robust).

Commonly we have records in a data frame, and the primary workflow is to provide the trip() function with information about the spatial locations, the temporal data, and the grouping.

The data may contain any other columns, and in general they can be called anything and be in any order, but the simplest way to create a trip is to put the first four columns as X, Y, date-time, grouping.

library(trip)
d <- data.frame(x=1:10,y=rnorm(10), tms=Sys.time() + 1:10, id=gl(2, 5))
tr <- trip(d)
summary(tr)

(There may be only one group, but we have to be explicit, with a column that identifies at least one group).

When a print or summary is made the data are presented in terms of their grouping, with some handy summary values. When converting to sf or sp form as lines these summary values are recorded with each "multi"-line.

Simple plotting

To plot a trip we use base graphics in the usual ways.

plot(tr)
lines(tr)

The trip object acts as a sp data frame of points, but with the underlying grouping as lines when that is relevant.

plot(tr,pch = ".", col = rainbow(nrow(tr)))
lines(tr, col = c("dodgerblue", "firebrick"))

Gridding for time spent

There is a key functionality to determine the time spent in area on a grid, by leveraging the rasterize() generic function in the raster package. Any raster object may be used, so the specification of pixel area, extent and map projection is up to the user. (The trip line segments must all fall within the raster).

tg <- rasterize(tr)
plot(tg, col = c("transparent", heat.colors(25)))

As with raster::rasterize() the field used may be chosen, by default the time difference between each point in a trip is used, and the final grid contains the sum of these durations.

There is an older version of this in the tripGrid.interp function that uses approximate methods by allowing interpolation to an 'equal time' step.

Reading from Argos files

Service Argos has provide various message formats, and the readArgos() function understands some variants of the 'PRV' form. Multiple files can be provided, and all messages will be normalized and turned into a trip object with no need for the user to group or clean them in any way.

argosfile <- 
 system.file("extdata/argos/98feb.dat", package = "trip", mustWork = TRUE)
argos <- readArgos(argosfile) 

summary(argos)

Note that the form of the coordinates is native to the PRV file, and in this case contains longitude values that are greater than 180. Some forms of these files provide wrapped forms, but in general the data are read as-is.

(We need "world2" because we are at 40W, but +360).

plot(argos, pch = ".")
lines(argos)
maps::map("world2", add = TRUE)
axis(1)
sp::degAxis(2)

Destructive filtering

There are some classic data filters based on speed and angle, and we may chain these together for some cheap improvements to track data, or use them separately.

argos$spd <- speedfilter(argos, max.speed = 4)  ## km/h
mean(argos$spd)  ## more than 5% are too fast

plot(argos)
lines(argos[argos$spd & argos$class > "A", ])


argos$sda <- sda(argos, smax = 12)  ## defaults based on argosfilter, Freitas et al. (2008) 
mean(argos$sda)
plot(argos)
lines(argos[argos$sda, ])

Map projections

Data may be stored in longitude latitude or using a map projection, an in-built data set uses the Azimuthal Equidistant family near the anti-meridian in the Bering Strait.

raster::projection(walrus818)
data("walrus818")

plot(walrus818, pch = ".")
lines(walrus818)

axis(1)
axis(2)
data("world_north", package= "trip")
p <- par(mar = rep(0.5, 4))
plot(raster::extent(walrus818) + 600000)
plot(walrus818, pch = ".", add = TRUE)
plot(world_north, add = TRUE, col = "grey")
lines(walrus818)
par(p)

Data conversions

There are various conversions from other tracking data types, the trip() function aims to be a helpful function like raster::raster(), simply understanding many formats.

It's possible to export trips to Google Earth, for interacting with the time slider in continuous time. Use write_track_kml() to produce a 'KML/KMZ' file.

When converting to spatial forms we may choose multi-lines, points, or segments.

Conversion to points, in sp or spatstat.

## as points
as(walrus818, "SpatialPointsDataFrame")
as(walrus818, "ppp")

Conversion to lines, in sp, sf, or adehabitatLT.

## as lines
as(walrus818, "SpatialLinesDataFrame")
class(as(walrus818, "sf"))
class(as(walrus818, "sf")$geom)
as(walrus818, "ltraj")

Conversions to segments, in sp, spatstat.

## as segments
explode(walrus818)
as(walrus818, "psp")

Why not sf?

The trip package cops a bit of dismissive criticism because it's based on sp which is somehow seen as hopelessly legacy. Trip uses sp in powerful ways, but the greatest power is

There's some excitement about the new sf package, and some moves to write yet another trajectory formalism based on sf. I would never use it, sf is a non starter for track data. If these things change I would reconsider, but I don't see that happening as sf is extremely brittle now, also these suggestions were made early and ignored.

Trip has a lot of problems, but these basic things are just no-go. It's been said trip is only point-based, but the time-spent gridding, the speed filtering, and the conversion to line segments is all clearly line-based. I'm still looking for sensible collaboration for a better system in R, but to me it's as simple as a grouped data frame with dplyr/ggplot2 semantics. Anything more requires a multi-table system and shoe-horning into the sf straitjacket is not going to work.

See vignette 'trip-rationale' for a longer version.

[^1]: One-dimensional, are you crazy? Yes, the measurement process is one-dimensional and that is how we can arrange the primary data we collect. We collect location (x, y, z), time, and many other variables such as temperature, air pressure, happiness and colour, these are the geometry of our measurements, but the collection itself is very much a one-dimensional topology.



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trip documentation built on March 16, 2021, 9:08 a.m.