problems with variogram calculation

[Gianluca Roncalli]

Hi,

Could I have some helps with this problem?

I'll attach my r script and my database. 

When calculating the variogram, I 'm having this error 

"Error in rep(CTMM$error^2/length(axes), n) : invalid 'times' argument"

I've timestamp in the correct way, so I'm not sure about what I'm doing in the wrong way. 

Thank you in advance for the help

--

Gianluca Roncalli

ISPRA (Istituto Superiore per la Protezione e la Ricerca Ambientale)

Area per l'Avifauna Migratrice (BIO-AVM)

Via Cà Fornacetta 9,  

40064 Ozzano dell'Emilia, BO 

Italy

 

[Christen Fleming]

Hi Gianluca,

By supplying drop=FALSE to as.telemetry(), you ensure that the output is a list of telemetry objects, even if there is only one. Then you are feeding the list object into variogram() and not the variogram object. The following works:

variogramma<-variogram(bacucco181614_t[[1]])

Best,

Chris

[Skye Fenton]

Hello Chris and apologies, I cannot seem to start a new thread.

I'm new to the package and am trying to get home range area estimates and contours to plot for some animals.

I'm getting the same error as Gianluca but in response to a different command. I'm attempting to export my akde UD object using SpatialPolygonsDataFrame.telemetry() to get the 50% and 95% contours for plotting. But my command returns the error...

cass_sp_akde <- SpatialPolygonsDataFrame.telemetry(object = AKDE, level.UD = 0.95)

>Error in rep(CTMM$error^2/length(axes), n) : invalid 'times' argument

I successfully plotted AKDE with plot() so I'm not sure where the problem is. I am very willing to send you the data and script for assistance but wonder if I could send it directly rather than make it public.

Thanks so much in advance,

Skye

[Christen Fleming]

Hi Skye,

I'm not sure why you were not able to post, but I will say that I had to switch back to the "classic" Google group view because the revamped version is quite buggy and many features do not work or are missing.

SpatialPolygonsDataFrame.telemetry() is for telemetry objects. The command that you are looking for is probably SpatialPolygonsDataFrame.UD(). Ideally, you would just run SpatialPolygonsDataFrame() and it would just work, but the way these functions are coded in the sp package does not allow them to be cast as generic functions, unfortunately.

Best,

Chris

[Skye Fenton]

Hi Chris,

Thank you! I see my error. I'm now using SpatialPolygonsDataFrame.telemetry() to try and export the 50% and 95% estimate ellipses so I can plot them in ggplot. I'm using them on my telemetry object now, but when i try to plot the resulting SpatialPolygonsDataFrame, I get an error. When turning this spdf into a normal data frame, I see there are only two columns, one called 'identity' that says unknown for every row, and one with timestamps. Any suggestions about what I'm doing wrong there? I've attached a picture of the resulting data frame.  Thank you again!!

cnona_move <- move(x=cnona$x, y=cnona$y, 

                  time=as.POSIXct(cnona$date, format="%Y-%m-%d %H:%M:%S", tz="UTC"), 

                  proj=CRS("+init=epsg:3035"), 

                  data=cnona, animal=cnona$animal_id)

b <- as.telemetry(cnona_move)

cass_sp_akde <- SpatialPolygonsDataFrame.telemetry(object = b, level.UD = 0.95)

plot(cass_sp_akde)

>Error in as.double(y) : 

  cannot coerce type 'S4' to vector of type 'double'

[Skye Fenton]

Additionally, is there a way to calculate the home range areas for UDs other than 95%? (e.g. 50% core area, 90%).... Apologies for the add on question, thank you so much for running this forum!

[Christen Fleming]

Hi Skye,

Did that data have error circle/ellipse information in it, which you can see when plotting the telemetry object?

Best,

Chris

[Christen Fleming]

Yes, check out the level.UD argument in any function that calculates with home-range areas.

Best,

Chris

[Skye Fenton]

There are no ellipses when I plot b by itself, but when I plot it with the UD object I made, plot(b, UD = AKDE), there are ellipses. When I try SpatialPolygonsDataFrame.UD(AKDE) with my UD object and try to plot the resulting spdf, I get the same error as before about the  's4' object. The spdf creates a data frame that is similarly unusual...

Thank you!!

[Christen Fleming]

Hi Skye,

I don't see any error information being plotted in in your telemetry data, so I don't think there was anything there to be exported via SpatialPolygonsDataFrame.telemetry(). I will code that function to return an error when you try to do that. See vignette("error") for an example of what location errors look like. If you just want to export location data (with out error circle/ellipses) then you would want to use the spatial points functions instead of spatial polygons functions.

As for "unknown", that shouldn't be happening if you have the animal_id column in your data.frame, as your code suggests. Is this correct?

Best,

Chris

[Skye Fenton]

Hi Chris,

Thanks again for your response. I think I am confused; I want to export the 95% contour for the density function that I see when I plot my UD object as a spatial polygon or dataframe of points in order to plot them. Is that possible?

[Skye Fenton]

And yes, the animal id column has a numeric value of 1.

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[Skye Fenton]

* in order to plot the contours in ggplot rather that the plot function

[Christen Fleming]

Hi Skye

You should be able to export the AKDE contours by applying SpatialPolygonsDataFrame.UD() to the AKDE object. Have you tried running sp::plot() instead of just plot() to avoid namepsace collision. Often times R becomes confused with multiple packages loaded that all have dispatch methods of the same name, even if their object classes are different.

As for the naming issue, if you can send me a copy of the data, then I can take a look at that. I can look at the other issues too, if they still aren't resolved.

Best,

Chris