Filter locations using a data driven filter
Function to remove locations by a data driven filter as described in Shimada et al. (2012).
ddfilter(sdata, vmax = 8.9, vmaxlp = 1.8, qi = 4, ia = 90, method = 1)
sdata |
A data frame containing columns with the following headers: "id", "DateTime", "lat", "lon", "qi".
See the data |
vmax |
A numeric value specifying a threshold of speed from a previous and/or to a subsequent fix.
Default is 8.9km/h.
If this value is unknown, it can be estimated from sdata using the function |
vmaxlp |
A numeric value specifying a threshold of speed, which is used to evaluate the locations of loop trips.
Default is 1.8 km/h.
If this value is unknown, it can be estimated from sdata using the function |
qi |
An integer specifying a threshold of quality index, which is used to evaluate the locations of loop trips. Default is 4. |
ia |
An integer specifying a threshold of inner angle, which is used to evaluate the locations of loop trips. Default is 90 degrees. |
method |
An integer specifying how locations should be filtered with vmax. A location is removed if the speed from a previous and(1)/or(2) to a subsequent location exceeds vmax. Default is 1 (both way). |
Locations are removed if the speed from a previous and/or to a subsequent location exceeds vmax,
or if all of the following criteria apply: the associated quality index is less than or equal to qi,
the inner angle is less than or equal to ia and the speed either from a previous
or to a subsequent location exceeds vmaxlp.
If vmax and vmaxlp are unknown, they can be estimated using the functions vmax and vmaxlp respectively.
The input data is returned without locations identified by this filter. The following columns are added: "pTime", "sTime", "pDist", "sDist", "pSpeed", "sSpeed", "inAng". "pTime" and "sTime" are hours from a previous and to a subsequent fix respectively. "pDist" and "sDist" are straight distances in kilometres from a previous and to a subsequent fix respectively. "pSpeed" and "sSpeed" are linear speed from a previous and to a subsequent fix respectively. "inAng" is the degree between the bearings of lines joining successive location points.
Takahiro Shimada
Shimada T, Jones R, Limpus C, Hamann M (2012) Improving data retention and home range estimates by data-driven screening. Marine Ecology Progress Series 457:171-180 doi: 10.3354/meps09747
#### Load data sets
## Fastloc GPS data obtained from a green turtle
data(turtle)
## A Map for the example site
data(Australia)
data(SandyStrait)
#### Filter temporal and/or spatial duplicates
turtle.dup <- dupfilter(turtle, step.time=5/60, step.dist=0.001)
#### ddfilter
## Using the built-in function to estimate the threshold speeds
V <- vmax(turtle.dup)
VLP <- vmaxlp(turtle.dup)
turtle.dd <- ddfilter(turtle.dup, vmax=V, vmaxlp=VLP)
## Or using user specified threshold speeds
turtle.dd <- ddfilter(turtle.dup, vmax=9.9, qi=4, ia=90, vmaxlp=2.0)
#### Plot data removed or retained by ddfilter
## Entire area
p1<-map_track(turtle.dup, bgmap=Australia, point.size = 2, line.size = 0.5, axes.lab.size = 0,
sb.distance=200, multiplot = FALSE, point.bg = "red",
title.size=15, title="Entire area")[[1]] +
geom_point(aes(x=lon, y=lat), data=turtle.dd, size=2, fill="yellow", shape=21)+
geom_point(aes(x=x, y=y), data=data.frame(x=c(154, 154), y=c(-22, -22.5)),
size=3, fill=c("yellow", "red"), shape=21) +
annotate("text", x=c(154.3, 154.3), y=c(-22, -22.5), label=c("Retained", "Removed"),
colour="black", size=4, hjust = 0)
## Zoomed in
p2<-map_track(turtle.dup, bgmap=SandyStrait, xlim=c(152.7, 153.2), ylim=(c(-25.75, -25.24)),
axes.lab.size = 0, sb.distance=10, point.size = 2, point.bg = "red", line.size = 0.5,
multiplot = FALSE, title.size=15, title="Zoomed in")[[1]] +
geom_path(aes(x=lon, y=lat), data=turtle.dd, size=0.5, colour="black", linetype=1) +
geom_point(aes(x=lon, y=lat), data=turtle.dd, size=2, colour="black", shape=21, fill="yellow")
gridExtra::marrangeGrob(list(p1, p2), nrow=1, ncol=2)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.