[R-sig-eco] R crashes while calculating BRB (Biased Random Bridge)

[Nick van Doormaal]

Hello André,

Thank you very much for your quick reply. Highly appreciated.
I'll check this and come back to you if it worked.

Thanks again!

Nick

> From: andrezehnder at hotmail.com
> To: nickvandoormaal26 at hotmail.com; r-sig-ecology at r-project.org
> Subject: AW: [R-sig-eco] R crashes while calculating BRB (Biased Random Bridge)
> Date: Tue, 16 Jun 2015 10:29:27 +0200
> 
> Hi Nick,
> 
> I had (supposably) the same issue just a few day ago. While the code ran
> without any problems for some of the datasets, R suddenly crashed during the
> computation of other datasets. In my case, the problem was the following:
> 
> When the temporal difference of at least two locations is smaller than the
> chosen tau-value, BRB cannot split the step into its intervals (defined
> through tau) and thus crashes. Therefore I had to ensure that the smallest
> occurring temporal difference is larger than the tau-value. So, even if the
> vast majority of your dataset has sampling intervals that are coarser than
> your tau-value, it may be that only a few ones do not match this
> restriction. Perhaps it solves your issue when you check all of your
> sampling intervals and delete some of them, if necessary.
> 
> You could check the sampling intervals for example with this code:
> 
> for (i in 1:nrow(anim)) {
>   anim$timeDiff[i] <- round(difftime(anim$timestamp[i+1],anim$timestamp[i],
> tz="UTC", units="mins"), digits=0)
> }
> samplingI <- vector()
> samplingI <- anim$timeDiff
> samplingI <- samplingI[2:length(samplingI)] # First value of timeDiff is NA
> 
> plot(table(samplingI), type="h", xlim=c(),col=4, ylab="frequency",
> xlab="sampling interval [min]")
> 
> anim is the name of a data.frame and timestamp a column that contains a
> POSIXct-timestamp (format = "%Y-%m-%d %H:%M:%S" , tz = "UTC").
> 
> Best regards,
> André
> 
> -----Ursprüngliche Nachricht-----
> Von: R-sig-ecology [mailto:r-sig-ecology-bounces at r-project.org] Im Auftrag
> von Nick van Doormaal
> Gesendet: Dienstag, 16. Juni 2015 10:16
> An: r-sig-ecology at r-project.org
> Betreff: [R-sig-eco] R crashes while calculating BRB (Biased Random Bridge)
> 
> Dear list members,
> 
> The past few weeks I've been troubled (and frustrated) about calculating the
> BRB in R, using adehabitatHR. For some reason, unknown to me, the program
> just crashes while calculating the BRB. However, this does not happen for
> all of them. The error occurs for about 10-20% of the data I used so far.
> 
> I've included a part of the dataset and the R-code, I hope it might be of
> use to you in helping me solving this problem. One interesting that I've
> found out so far is that the code works just fine using the first 1000
> relocations. However, I don't think this is a data-size issue, as some other
> datasets are much larger and working without any problem.
> 
> Thank you for your time and effort. If there's anything I need to provide,
> please let me know.
> 
> Kind regards,
> 
> Nick
> 
> 
> ##R CODE FOR BRB 16-6-2015##
> ##LOADING ALL PACKAGES
> library(ade4)
> library(shapefiles)
> library(adehabitatHS)
> library(maptools)
> library(rgdal)
> library(raster)
> 
> ##LOAD DATA
> Dura <- readShapeSpatial("Dura, Jan 25 2013 (WGS 84).shp")
> 
> Dura$DateTime <- substr(Dura$Descriptio, 1, 19) Dura$Date <-
> substr(Dura$Descriptio, 1, 10) Dura$Time <- substr(Dura$Descriptio, 12, 19)
> 
> ##SET COORDINATE SYSTEM
> proj4string(Dura) = CRS("+init=epsg:4326") #4326 IS LAT LONG WGS84
> 
> ##TRANSFORM COORDINATES
> Dura <- spTransform(Dura, CRS("+init=epsg:32736")) #UTM36S
> 
> ##CREATE A LTRAJ-CLASS
> Dura2 <- Dura[!duplicated(Dura$DateTime), ] Dura2$Descriptio <- NULL Dura.da
> <- as.character(Dura2$DateTime) Dura.da <-
> as.POSIXct(strptime(as.character(Dura2$DateTime),"%Y/%m/%d %H:%M:%S"))
> Dura.df <- as.data.frame(Dura2) Dura.xy <- coordinates(Dura2) Dura.ltraj <-
> as.ltraj(xy =Dura.xy, date = Dura.da, id = Dura.df$Date)
> 
> plot(Dura.ltraj[1])
> 
> ##RUN THE MODEL
> Dura.vv = BRB.D(Dura.ltraj[1], Tmax = 60, Lmin = 0) Dura.est = Dura.ltraj[1]
> 
> Dura.id <- BRB(Dura.est, D = Dura.vv, Tmax = 60, tau = 5, Lmin = 0, hmin=25,
> grid = 100, type=("ID"), same4all=TRUE, extent=0.2, maxt = 20,
> filtershort=TRUE) Dura.rd <- BRB(Dura.est, D = Dura.vv, Tmax = 60, tau = 5,
> Lmin = 0, hmin=25, grid = 100, type=("RD"), same4all=TRUE, extent=0.2, maxt
> = 20, filtershort=TRUE) Dura.ud <- BRB(Dura.est, D = Dura.vv, Tmax = 60, tau
> = 5, Lmin = 0, hmin=25, grid = 100, type=("UD"), same4all=TRUE, extent=0.2,
> maxt = 20, filtershort=TRUE)
> 
> ##END
>  		 	   		  
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