Nothing
<%
res <- Response$new()
if (config$todo$doSiteFidelity) {
alog <- c(alog, catPro("Init site fidility", pre=cath2("Site fidelity")))
for (subcon in seq_along(ares$siteFidelity)) {
subconParams <- ares$siteFidelity[[subcon]]$params
for (animal in seq_along(ares$siteFidelity[[subcon]]$animals)) {
alog <- c(alog, catPro(paste0("starting with site fidelity for ", ares$siteFidelity[[subcon]]$animals[[animal]]$name)))
allgood <-tryCatch({
sf <- rhrFidelity(datSub[[animal]], n=subconParams$n)
## Plot
## msd
p1 <- ggplot(data.frame(msd=sf$msd.sim), aes(factor("msd"), msd)) +
geom_jitter(alpha=0.4) + geom_boxplot(alpha=0.3) +
theme_bw() + scale_x_discrete(name="MSD", breaks=NULL) +
scale_y_continuous(name="MSD from Center of Activity (MSD)") + xlab("MSD")
p1 <- p1 + geom_hline(aes(yintercept = yin, colour="red"), data.frame(yin=sf$msd.dat))
## Li
p2 <- ggplot(data.frame(li=sf$li.sim), aes(factor("li"), li)) + geom_jitter(alpha=0.4) +
geom_boxplot(alpha=0.3) + theme_bw() + scale_x_discrete(name="LI", breaks=NULL) +
scale_y_continuous(name="Linearity Index (LI)")
p2 <- p2 + geom_hline(aes(yintercept = yin, colour="red"), data.frame(yin=sf$li.dat))
p <-grid.grabExpr(grid.arrange(p1,p2, ncol=2, main="Site Fidelity"), warp=TRUE)
ares$siteFidelity[[subcon]]$animals[[animal]]$plots <- list()
ares$siteFidelity[[subcon]]$animals[[animal]]$plots[[1]] <- list(filename=paste0("rhr_siteFidelity_id_",
ares$siteFidelity[[subcon]]$animals[[animal]]$name, ".png"),
caption=paste0("Site fidelity plot", ids[animal]))
png(file=file.path(imagepath, ares$siteFidelity[[subcon]]$animals[[animal]]$plots[[1]]$filename))
grid.draw(p)
dev.off()
## Tables
msd.ci <- t.test(sf$msd.sim)$conf.int
li.ci <- t.test(sf$li.sim)$conf.int
sftable <- data.frame(Measure=c("LI", "MSD"),
Observed=c(sf$li.dat, sf$msd.dat),
LCI=c(li.ci[1], msd.ci[1]),
UCI=c(li.ci[2], msd.ci[2]), stringsAsFactors=FALSE)
names(sftable)[3:4] <- c("LCI (95 %)", "UCI (95 %)")
ares$siteFidelity[[subcon]]$animals[[animal]]$tables <- list()
ares$siteFidelity[[subcon]]$animals[[animal]]$tables[[1]] <- list(table=sftable, caption="Sitefidelity results")
## msg
if (sf$li.dat < li.ci[1] & sf$msd.dat < msd.ci[1]) {
msg <- "The mean squared distance from the center of activity and the linearity index of the data are below the 95 % confidence interval of the simulated random trajectories. Therefore, site fidelity can be assumed and calculation of a home range may be appropriate."
} else {
msg <- "Either the mean squared distance from the center of activity (MSD) or the linearity index (LI) of the data are above the 95 % confidence interval of the simulated random trajectories. Therefore, site fidelity can not be assumed and calculation of home ranges may be problematic."
}
ares$siteFidelity[[subcon]]$animals[[animal]]$msgs <- list()
ares$siteFidelity[[subcon]]$animals[[animal]]$msgs[[1]] <- msg
## results
saveRDS(sf, file=file.path(datapath, paste0(paste0("rhr_SiteFidelity_id_", ares$siteFidelity[[subcon]]$animals[[animal]]$name, ".rds"))))
rm(sf, p)
gc(); gc()
}, error=function(e) return(e))
if (inherits(allgood, "error")) {
ares$siteFidelity[[subcon]]$animals[[animal]]$exit <- 1
ares$siteFidelity[[subcon]]$animals[[animal]]$error <- allgood
} else {
ares$siteFidelity[[subcon]]$animals[[animal]]$exit <- 0
}
}
}
showResultHTML(ares$siteFidelity, config$background$siteFidelity)
alog <- c(alog, catPro("generating html output for site fidelity"))
} else {
res$write(rhrAlert("Site fidelity not requested"))
}
res$finish()
%>
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