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Update to spatstat 2.0. #27

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2 changes: 1 addition & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@ Depends: R (>= 3.0.0)
Imports: stats, utils, graphics, methods, lattice, sp (>= 1.1-0),
spacetime (>= 1.0-0), zoo
Suggests: rgdal, rgeos, OpenStreetMap, RCurl, rjson, adehabitatLT, xts,
knitr, rgl, forecast, MASS, spatstat, taxidata
knitr, rgl, forecast, MASS, spatstat.geom, spatstat.core, spatstat (>= 2.0-0), taxidata
Description: Classes and methods for trajectory data, with support for nesting individual Track objects in track sets (Tracks) and track sets for different entities in collections of Tracks. Methods include selection, generalization, aggregation, intersection, simulation, and plotting.
License: GPL (>= 2)
URL: http://github.com/edzer/trajectories
Expand Down
84 changes: 42 additions & 42 deletions R/Trackstat.R
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Expand Up @@ -88,6 +88,18 @@ tsqTracks <- function(X, timestamp){



check_spatstat <- function(pkg){
if(!requireNamespace(pkg, quietly = TRUE)){
stop("package ", pkg, " required, please install it (or the full spatstat package) first")
} else{
spst_ver <- try(packageVersion("spatstat"), silent = TRUE)
if(!inherits(spst_ver, "try-error") && spst_ver < 2.0-0){
stop("You have an old version of spatstat installed which is incompatible with ", pkg,
". Please update spatstat (or uninstall it).")
}
}
}

# function avedistTrack accepts X as a list of tracks and reports the average distance between
# tracks over time, output is an object of class "distrack"
avedistTrack <- function(X,timestamp){
Expand All @@ -97,17 +109,16 @@ avedistTrack <- function(X,timestamp){
if (class(X)=="TracksCollection") X <- as.list.TracksCollection(X)

stopifnot(length(X)>1 & is.list(X))
if (!requireNamespace("spatstat", quietly = TRUE))
stop("spatstat required: install first?")

check_spatstat("spatstat.geom")

if (missing(timestamp)) stop("set timestamp")
# calculate a sequance of time to interpolate tracks within this sequance
timeseq <- tsqTracks(X,timestamp = timestamp)

Y <- as.Track.ppp(X,timestamp)

avedist <- lapply(X=1:length(Y), function(i){
pd <- spatstat::pairdist(Y[[i]])
pd <- spatstat.geom::pairdist(Y[[i]])
mean(pd[pd>0])
})

Expand All @@ -133,7 +144,6 @@ unique.Track <- function(x,...){
return(as.Track(x[,1],x[,2],x[,3]))
}


as.Track.ppp <- function(X,timestamp){

stopifnot(class(X)=="list" | class(X)=="Tracks" | class(X)=="TracksCollection")
Expand All @@ -142,9 +152,7 @@ as.Track.ppp <- function(X,timestamp){
if (class(X)=="TracksCollection") X <- as.list.TracksCollection(X)
stopifnot(length(X)>1 & is.list(X))

if (!requireNamespace("spatstat", quietly = TRUE))
stop("spatstat required: install first?")

check_spatstat("spatstat.geom")

if (missing(timestamp)) stop("set timestamp")
# calculate a sequance of time to interpolate tracks within this sequance
Expand All @@ -158,11 +166,11 @@ as.Track.ppp <- function(X,timestamp){
allZ <- split(Z,Z[,3])
dx <- (max(Z$xcoor)-min(Z$xcoor))/1000
dy <- (max(Z$ycoor)-min(Z$ycoor))/1000
w <- spatstat::owin(c(min(Z$xcoor)-dx,max(Z$xcoor)+dx),c(min(Z$ycoor)-dy,max(Z$ycoor)+dy))
w <- spatstat.geom::owin(c(min(Z$xcoor)-dx,max(Z$xcoor)+dx),c(min(Z$ycoor)-dy,max(Z$ycoor)+dy))

Tppp <- lapply(X=1:length(allZ), function(i){
p <- spatstat::as.ppp(allZ[[i]][,-c(3,4)],W=w)
p <- spatstat::`marks<-`(p, value = allZ[[i]][,4])
p <- spatstat.geom::as.ppp(allZ[[i]][,-c(3,4)],W=w)
p <- spatstat.geom::`marks<-`(p, value = allZ[[i]][,4])
return(p)
})
class(Tppp) <- c("list","ppplist")
Expand All @@ -182,14 +190,13 @@ density.list <- function(x, timestamp, ...) {
if (class(x)=="TracksCollection") x <- as.list.TracksCollection(x)

stopifnot(length(x)>1 & is.list(x))
if (!requireNamespace("spatstat", quietly = TRUE))
stop("spatstat required: install first?")
check_spatstat("spatstat.core")

if (missing(timestamp)) stop("set timestamp")

p <- as.Track.ppp(x, timestamp)
p <- p[!sapply(p, is.null)]
imlist <- lapply(p, spatstat::density.ppp, ...)
imlist <- lapply(p, spatstat.core::density.ppp, ...)
out <- Reduce("+", imlist) / length(imlist)
attr(out, "Tracksim") <- imlist
attr(out, "ppps") <- p
Expand All @@ -202,8 +209,7 @@ as.Track.arrow <- function(X,timestamp,epsilon=epsilon){
if(class(X)=="Tracks") X <- as.list.Tracks(X)
if (class(X)=="TracksCollection") X <- as.list.TracksCollection(X)
stopifnot(length(X)>1 & is.list(X))
if (!requireNamespace("spatstat", quietly = TRUE))
stop("spatstat required: install first?")
check_spatstat("spatstat.geom")

if (missing(timestamp)) stop("set timestamp")
if(missing(epsilon)) epsilon <- 0
Expand All @@ -217,17 +223,17 @@ as.Track.arrow <- function(X,timestamp,epsilon=epsilon){
for (i in 1:length(Z)) {
if(i==length(Z)) break()
j <- i+1
m1 <- match(spatstat::marks(Z[[i]]),spatstat::marks(Z[[j]]))
m2 <- match(spatstat::marks(Z[[j]]),spatstat::marks(Z[[i]]))
m1 <- match(spatstat.geom::marks(Z[[i]]),spatstat.geom::marks(Z[[j]]))
m2 <- match(spatstat.geom::marks(Z[[j]]),spatstat.geom::marks(Z[[i]]))
m1 <- m1[!is.na(m1)]
m2 <- m2[!is.na(m2)]
x <- Z[[j]][m1]
y <- Z[[i]][m2]
l <- spatstat::psp(y$x,y$y,x$x,x$y,window = wind)
l <- spatstat.geom::psp(y$x,y$y,x$x,x$y,window = wind)
arrows[[i]] <- l
center <- spatstat::midpoints.psp(l)
mark <- spatstat::lengths.psp(l)
center <- spatstat::`marks<-`(center, value = mark)
center <- spatstat.geom::midpoints.psp(l)
mark <- spatstat.geom::lengths_psp(l)
center <- spatstat.geom::`marks<-`(center, value = mark)
if (missing(epsilon)) epsilon <- 0
Y[[i]] <- center[mark>epsilon]
}
Expand All @@ -253,7 +259,8 @@ Track.idw <- function(X,timestamp,epsilon=epsilon,...){
if(missing(epsilon)) epsilon <- 0

Y <- as.Track.arrow(X,timestamp,epsilon=epsilon)
Z <- lapply(Y, spatstat::idw, ...)
check_spatstat("spatstat.core")
Z <- lapply(Y, spatstat.core::idw, ...)
meanIDW <- Reduce("+",Z)/length(Z)
return(meanIDW)
}
Expand All @@ -264,16 +271,15 @@ avemove <- function(X,timestamp,epsilon=epsilon){
if(class(X)=="Tracks") X <- as.list.Tracks(X)
if (class(X)=="TracksCollection") X <- as.list.TracksCollection(X)
stopifnot(length(X)>1 & is.list(X))
if (!requireNamespace("spatstat", quietly = TRUE))
stop("spatstat required: install first?")
check_spatstat("spatstat.geom")

if (missing(timestamp)) stop("set timestamp")
timeseq <- tsqTracks(X,timestamp = timestamp)
if (missing(epsilon)) epsilon <- 0
Y <- as.Track.arrow(X,timestamp,epsilon=epsilon)
Z <- attr(Y,"psp")
preout <- lapply(X=1:length(Z), function(i){
mean(spatstat::lengths.psp(Z[[i]]))
mean(spatstat.geom::lengths_psp(Z[[i]]))
})
out <- unlist(preout)
class(out) <- c("numeric", "arwlen")
Expand All @@ -286,8 +292,7 @@ print.arwlen <- function(x, ...){
}

plot.arwlen <- function(x,...){
if (!requireNamespace("spatstat", quietly = TRUE))
stop("spatstat required: install first?")
check_spatstat("spatstat.core") ## ER: I don't see what spatstat is used for here
x = unclass(x)
tsq <- attr(x,"time")
plot(tsq,x,xlab="time",ylab="average movement",...)
Expand All @@ -300,8 +305,7 @@ chimaps <- function(X,timestamp,rank,...){
if (class(X)=="TracksCollection") X <- as.list.TracksCollection(X)
stopifnot(length(X)>1 & is.list(X))

if (!requireNamespace("spatstat", quietly = TRUE))
stop("spatstat required: install first?")
check_spatstat("spatstat.geom") ## Looks like `Math.im` is used below for `*` etc.

if(missing(rank)) rank <- 1
if (!is.numeric(rank)) stop("rank must be numeric")
Expand Down Expand Up @@ -333,8 +337,7 @@ Kinhom.Track <- function(X,timestamp,
if(class(X)=="Tracks") X <- as.list.Tracks(X)
if (class(X)=="TracksCollection") X <- as.list.TracksCollection(X)

if (!requireNamespace("spatstat", quietly = TRUE))
stop("spatstat required: install first?")
check_spatstat("spatstat.core")
stopifnot(length(X)>1 & is.list(X))

if (missing(timestamp)) stop("set timestamp")
Expand All @@ -349,7 +352,7 @@ Kinhom.Track <- function(X,timestamp,
rr <- seq(0,ripley,length.out = 513)

K <- lapply(X=1:length(Y), function(i){
kk <- spatstat::Kinhom(Y[[i]],correction=cor,r=rr,...)
kk <- spatstat.core::Kinhom(Y[[i]],correction=cor,r=rr,...)
return(as.data.frame(kk))
})
Kmat <- matrix(nrow = length(K[[1]]$theo),ncol = length(K))
Expand All @@ -368,7 +371,7 @@ Kinhom.Track <- function(X,timestamp,
rr <- seq(0,ripley,length.out = 513)

K <- lapply(X=1:length(Y), function(i){
kk <- spatstat::Kinhom(Y[[i]],lambda = Z[[i]],correction=cor,r=rr,...)
kk <- spatstat.core::Kinhom(Y[[i]],lambda = Z[[i]],correction=cor,r=rr,...)
return(as.data.frame(kk))
})
Kmat <- matrix(nrow = length(K[[1]]$theo),ncol = length(K))
Expand Down Expand Up @@ -397,8 +400,7 @@ print.KTrack <- function(x, ...){
}

plot.KTrack <- function(x,type="l",col= "grey70",cex=1,line=2.2,...){
if (!requireNamespace("spatstat", quietly = TRUE))
stop("spatstat required: install first?")
check_spatstat("spatstat.core") ## ER: I don't see what spatstat is used for here
ylim <- c(min(c(x$lowk,x$theo)),max(c(x$upk,x$theo)))
plot(x$r,x$lowk,ylim=ylim,type=type,ylab="",xlab="r",...)
title(ylab=expression(K[inhom](r)),line = line,...)
Expand All @@ -421,8 +423,7 @@ pcfinhom.Track <- function(X,timestamp,
if(class(X)=="Tracks") X <- as.list.Tracks(X)
if (class(X)=="TracksCollection") X <- as.list.TracksCollection(X)

if (!requireNamespace("spatstat", quietly = TRUE))
stop("spatstat required: install first?")
check_spatstat("spatstat.core")
stopifnot(length(X)>1 & is.list(X))

if (missing(timestamp)) stop("set timestamp")
Expand All @@ -439,7 +440,7 @@ pcfinhom.Track <- function(X,timestamp,
rr <- seq(0,ripley,length.out = 513)

g <- lapply(X=1:length(Y), function(i){
gg <- spatstat::pcfinhom(Y[[i]],correction=cor,r=rr,...)
gg <- spatstat.core::pcfinhom(Y[[i]],correction=cor,r=rr,...)
return(as.data.frame(gg))
})
gmat <- matrix(nrow = length(g[[1]]$theo),ncol = length(g))
Expand All @@ -456,7 +457,7 @@ pcfinhom.Track <- function(X,timestamp,
Y <- attr(ZZ,"ppps")

g <- lapply(X=1:length(Y), function(i){
gg <- spatstat::pcfinhom(Y[[i]],lambda = Z[[i]],correction=cor,...)
gg <- spatstat.core::pcfinhom(Y[[i]],lambda = Z[[i]],correction=cor,...)
return(as.data.frame(gg))
})
gmat <- matrix(nrow = length(g[[1]]$theo),ncol = length(g))
Expand Down Expand Up @@ -487,8 +488,7 @@ print.gTrack <- function(x, ...){
}

plot.gTrack <- function(x,type="l",col= "grey70",cex=1,line=2.2,...){
if (!requireNamespace("spatstat", quietly = TRUE))
stop("spatstat required: install first?")
check_spatstat("spatstat.core") ## ER: I don't see what spatstat is used for here
ylim <- c(min(x$lowg),max(x$upg))
plot(x$r,x$lowg,ylim=ylim,xlab="r",ylab="",type=type,...)
title(ylab=expression(g[inhom](r)),line = line,...)
Expand Down
2 changes: 1 addition & 1 deletion man/Kinhom.Track.Rd
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Expand Up @@ -35,7 +35,7 @@ Mohammad Mehdi Moradi <moradi@uji.es>
%% ~Make other sections like Warning with \section{Warning }{....} ~

\seealso{
\link{rTrack}, \link{as.Track.ppp}, \link[spatstat]{Kinhom}}
\link{rTrack}, \link{as.Track.ppp}, \link[spatstat.core]{Kinhom}}
\examples{
library(spatstat)
X <- list()
Expand Down
2 changes: 1 addition & 1 deletion man/Track.idw.Rd
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Expand Up @@ -34,7 +34,7 @@ Mohammad Mehdi Moradi <moradi@uji.es>
%% ~Make other sections like Warning with \section{Warning }{....} ~

\seealso{
\link{as.Track.arrow}, \link[spatstat]{idw}}
\link{as.Track.arrow}, \link[spatstat.core]{idw}}
\examples{
X <- list()
for(i in 1:10){
Expand Down
2 changes: 1 addition & 1 deletion man/as.Track.ppp.Rd
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Expand Up @@ -27,7 +27,7 @@ Mohammad Mehdi Moradi <moradi@uji.es>}
%% ~Make other sections like Warning with \section{Warning }{....} ~

\seealso{
\link{avedistTrack}, \link[spatstat]{as.ppp}
\link{avedistTrack}, \link[spatstat.geom]{as.ppp}
}
\examples{
X <- list()
Expand Down
2 changes: 1 addition & 1 deletion man/chimaps.Rd
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Expand Up @@ -31,7 +31,7 @@ Mohammad Mehdi Moradi <moradi@uji.es>
%% ~Make other sections like Warning with \section{Warning }{....} ~

\seealso{
\link{density.list}, \link[spatstat]{density.ppp}
\link{density.list}, \link[spatstat.core]{density.ppp}
}
\examples{
X <- list()
Expand Down
2 changes: 1 addition & 1 deletion man/density.list.Rd
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Expand Up @@ -31,7 +31,7 @@ Mohammad Mehdi Moradi <moradi@uji.es>
%% ~Make other sections like Warning with \section{Warning }{....} ~

\seealso{
\link{rTrack}, \link[spatstat]{density.ppp}
\link{rTrack}, \link[spatstat.core]{density.ppp}
}
\examples{
X <- list()
Expand Down
2 changes: 1 addition & 1 deletion man/pcfinhom.Track.Rd
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Expand Up @@ -35,7 +35,7 @@ Mohammad Mehdi Moradi <moradi@uji.es>
%% ~Make other sections like Warning with \section{Warning }{....} ~

\seealso{
\link{rTrack}, \link{as.Track.ppp}, \link[spatstat]{pcfinhom}}
\link{rTrack}, \link{as.Track.ppp}, \link[spatstat.core]{pcfinhom}}
\examples{
X <- list()
for(i in 1:100){
Expand Down