[AniMov] First passage time analysis - trouble finding the "optimal" radii
Clément Calenge
clement.calenge at oncfs.gouv.fr
Thu Aug 19 15:08:12 CEST 2010
Dear Julia,
>
> It seems that the most important step of this analysis is to define
> the scale "r". But, how do I choose the "optimal" radii?
The identification of the radius is not a step, but the main aim of FPT.
This is implemented in the function varlogfpt. Once the optimal scale
has been found, the function plot can be used to show the changes in FPT
with time. You should read:
Fauchald, P. and Tveraa, T. 2003. Using first-passage time in the
analysis of area-restricted search and habitat selection. Ecology, 84,
282-288.
For a complete description of this approach.
>
> The example given by R Help (adehabitat manual) is the following:
> data(puechcirc)
> i<- fpt(puechcirc, seq(300,1000, length=30))
> plot(i, scale = 500, warn = FALSE)
> Could someone explain to me the above mentioned steps?
>
> "puechirc" is an object of class "ltraj", but what does "
> seq(300,1000, length=30))" stands for?
try:
> seq(300,1000, length=30)
[1] 300.0000 324.1379 348.2759 372.4138 396.5517 420.6897 444.8276
[8] 468.9655 493.1034 517.2414 541.3793 565.5172 589.6552 613.7931
[15] 637.9310 662.0690 686.2069 710.3448 734.4828 758.6207 782.7586
[22] 806.8966 831.0345 855.1724 879.3103 903.4483 927.5862 951.7241
[29] 975.8621 1000.0000
The help page can be read with:
> ?seq
Which indicates: "Generate regular sequences (...) length.out: desired
length of the sequence."
This command generates a sequence of radii comprised between 300 and
1000 metres.
> and "scale = 500" is the radius?
If you type:
> i
...
attr(,"class")
[1] "fipati"
You can see that the object i is of the class "fipati". Therefore,
"plot(i, scale=500)" calls the function plot.fipati.
The help page
> ?plot.fipati
indicates that scale is indeed the value of the radius to be plotted.
>
> Another example which I don't understand entirely:
> scales<-c(2, seq(5, 45, 5), seq(50, 500, 25)) #what does it mean?
>
Again, have a look at the help page of seq. The vector "scales" contains
2, 5, 10, 15, 20, ..., 45, 50, 75, 100, 125, 150, ..., 500.
> a.cut <- FPT.cut(file=loc1, Long=loc1$Long, Lat=loc1$Lat,
> Date=loc1$DateD, d=2) #cut the trip into intermediate locations of
> 2km, but R doesn't recognise "FPT.cut"
>
> a.fpt <- FPT.calc(a.cut, r=scales) # FPT for the specified scales (it
> can be quite long!)
>
Where did you find these two examples? I do not know anything about the
functions FPT.cut, or FPT.calc
> I have an object of class "ltraj" (tr <- as.ltraj(TB2[,
> c("LON","LAT")], TB2$Date, TB2$Bird) containing the relocations of
> Birds. Further, the maximum foraging trip duration is 35h, total
> distance travelled: 426km, max. distance from the nest: 162km. GPS
> recorded a fix every 5 min (some GPS every 2min and every 4 min
> depending on the tag used). With the fpt I would like to determine the
> ARS of each individual. From my data set, it seems that the birds
> mainly forage at the farthest point of the track and sometimes on the
> way back to the colony.
>
> Now, how do I define the scales where fpt will be calculated? And how
> do I calculate my fpt? Would it be helpful cutting the tracks into
> intermediate locations of 2km for example and then to calculate the
> fpt for a defined scale?
>
> I'm still a R beginner, thus apologies in advance in case I ask some
> "obvious" stuff.
Reading the above cited paper should help you on these aspects.
HTH,
Clément Calenge.
--
Clément CALENGE
Cellule d'appui à l'analyse de données
Office national de la chasse et de la faune sauvage
Saint Benoist - 78610 Auffargis
tel. (33) 01.30.46.54.14
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