[R-sig-eco] Topic: creating an object of class ltraj.

[Clement Calenge]

Hi Dylann,


> I am trying to create an object of class ltraj, but not successfully so far.
> Here is a sample of my data (GPS relocations):
>
> idnr name    Date Time Date Time X Y
> L-00094 Bodil 17/02/04 11:05:52 17/02/2004 11:05:52 1566688 7445760
> L-00094 Bodil 17/02/04 14:04:54 17/02/2004 14:04:54 1566392 7444546
> L-00094 Bodil 17/02/04 17:01:04 17/02/2004 17:01:04 1566401 7444543
> L-00094 Bodil 17/02/04 23:00:42 17/02/2004 23:00:42 1566509 7443853
> L-00094 Bodil 18/02/04 02:00:42 18/02/2004 02:00:42 1566813 7443226
>
> and here is my R coding:
>
> #Timestamp: date_time into a POSIXct class:
> timestamp <- as.POSIXct(strptime(as.character(data$Date.Time), "%d/%m/%Y
> %H:%M:%S"), "GMT")
> data_timestamp <- data.frame(data, timestamp=timestamp)
>
> I also tried this way:
>
> date <- as.POSIXct(strptime(paste(data$Date, data$Time), "%d/%m/%Y
> %H:%M:%S"), "GMT")
> data_timestamp <- data.frame(data, timestamp=date)
> (which is not working, dates are displayed Y/M/D and I don't understand
> why!)

It would be great if you could provide us the output of these commands. 
For example, to type:

head(date)

Just a guess: according to your description, it works. Y/M/D is the way 
the dates are displayed (try to type Sys.time() at the command prompt: 
it gives the current date and time in POSIX format)

> and finally:
>
> #Create a ltraj object:
> data_ltraj <- as.ltraj(data, date=timestamp, id=data$name, typeII = TRUE)
>
> and you have to know that I have done that before as well:
>
> #Spatial points data frame:
> coordinates(data) <- c("X", "Y")
> proj4string(data) <- CRS("+init=epsg:3021")

You don't have to. Objects of class ltraj are not Spatial* objects. Look 
at the help page of as.ltraj:

      as.ltraj(xy, date, id, burst = id, typeII = TRUE,
               slsp = c("remove", "missing"),
               infolocs = data.frame(pkey = paste(id, date, sep=".")))

with xy: a data.frame containing the x and y coordinates of the
           relocations
if you type coordinates(data) <- c("X","Y"), xy is no longer a 
dataframe, but a SpatialPointsDataFrame (check it with class(data)).
So avoid this command before defining your ltraj object. Then, the 
following commands should work:

date <- as.POSIXct(strptime(paste(data$Date, data$Time), "%d/%m/%Y
%H:%M:%S"), "GMT")
data_timestamp <- data.frame(data, timestamp=date)
traj <- as.ltraj(data_timestamp[,c("X","Y")],  date=date, id=data_timestamp$name, typeII=TRUE)


HTH,

Clément Calenge


> >From that I either have this warning message:
>
> Erreur dans data.frame(..., check.names = FALSE) :
>    arguments imply differing number of rows: 1, 12328, 0
>
>
> or the following
>
>
>
> Messages d'avis :1: In Ops.factor(x1$x, x2$x) : - not meaningful for
> factors2: In Ops.factor(x1$y, x2$y) : - not meaningful for factors3:
> In Ops.factor(x$x, x$x[1]) : - not meaningful for factors4: In
> Ops.factor(x$y, x$y[1]) : - not meaningful for factors5: In
> Ops.factor(x1$x, x2$x) : - not meaningful for factors6: In
> Ops.factor(x1$y, x2$y) : - not meaningful for factors7: In
> Ops.factor(df[-nrow(df), "x"], df[-1, "x"]) :
>    - not meaningful for factors8: In Ops.factor(df[-nrow(df), "y"],
> df[-1, "y"]) :
>    - not meaningful for factors
>
>
> but only when I enter: data_ltraj <- as.ltraj(data_timestamp,
> date=timestamp, id=data$name, typeII = TRUE)
>
> Am I missing something?
> Thanx for helping, I appreciate.
>
> --
> Dylann Kersusan
> Master Biodiversity and Conservation
> Zoology dept. Stockholm University
>
> 	[[alternative HTML version deleted]]
>
> _______________________________________________
> R-sig-ecology mailing list
> R-sig-ecology at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
> .
>


-- 
Clément CALENGE
Cellule d'appui à l'analyse de données
Direction des Etudes et de la Recherche
Office national de la chasse et de la faune sauvage
Saint Benoist - 78610 Auffargis
tel. (33) 01.30.46.54.14