[R-sig-Geo] Calculating distance to nest with spDistsN1
Roger Bivand
Roger.Bivand at nhh.no
Tue Sep 30 08:38:22 CEST 2014
On Tue, 30 Sep 2014, Frede Aakmann Tøgersen wrote:
> Hi
>
> Using spDists will also give Anna-Maria the distance between a bird's
> nest and the endpoints of another birds trips.
>
> Here is a way to achieve what I think Anna-Maria wants. Working with a
> SpatialPointsDataFrame objects complicates things so I will show how to
> it with an ordinary data.frame. Also I think that Anna-Maria has coded
> the trip_no, bird_id, and trip_id variables in a wrong way (see how I
> think the data should look below).
Right, the representation in SpatialPointsDataFrame objects is not ideal
for this kind of data.
I suggest looking at the new trajectories package on CRAN, which has a
vignette explaining the new classes defined there, and which seem to
match the birds well.
It is very possible that the authors of the package could provide a method
for this kind of distance calculation (between trajectories and points).
In addition, given the restricted extent of the data, it would almost
certainly be of advantage to project to the plane, then using measures in
m.
Roger
>
> My assumptions:
>
> 1. The coordinates(dat) is the coordinates of end of trips
> 2. col_lat and col_long is the coordinates of nests
> 3. My example has two birds with id 1 and 2
> 4. Bird 1 has 4 trips with id 1,2,3,4 and bird 2 has 3 trips with id 1,2,3
>
> ## Here is a somewhat altered version of Anna-Maria's data:
> dat <- read.table(text =
> "lon lat Date Time Speed Direction col_lat col_long dist_col trip_no bird_id trip_id DT date_time
> 7.87248 54.1866 '04.07.2014' '09:25:00' 0.02 314.57 54.1866 7.8724 0.0 1 1 1.1 '04.07.2014 09:25:00' '2014-07-04 09:25:00'
> 7.87148 54.1869 '04.07.2014' '09:30:00' 19.11 1.31 54.1866 7.8724 0.1 2 1 2.1 '04.07.2014 09:30:00' '2014-07-04 09:30:00'
> 7.87166 54.1850 '04.07.2014' '09:35:00' 14.98 224.79 54.1866 7.8724 0.2 3 1 3.1 '04.07.2014 09:35:00' '2014-07-04 09:35:00'
> 7.87168 54.1851 '04.07.2014' '09:35:00' 14.98 224.79 54.1866 7.8724 0.2 4 1 4.1 '04.07.2014 09:35:00' '2014-07-04 09:35:00'
> 7.88635 54.1569 '04.07.2014' '09:40:00' 11.44 136.97 54.2 7.9 3.4 1 2 1.2 '04.07.2014 09:40:00' '2014-07-04 09:40:00'
> 7.92096 54.1363 '04.07.2014' '09:45:00' 0.28 262.14 54.2 7.9 6.4 2 2 2.2 '04.07.2014 09:45:00' '2014-07-04 09:45:00'
> 7.91931 54.1360 '04.07.2014' '09:50:00' 0.42 218.89 54.2 7.9 6.4 3 2 3.2 '04.07.2014 09:50:00' '2014-07-04 09:50:00'",
> h = TRUE, sep = " ")
>
> ## Now for each bird nest find the distances in km to end point of each birds trips:
> trip_distances <- sapply(unique(dat$bird_id), function(id)
> spDistsN1(as.matrix(subset(dat, bird_id == id , select = c("lon", "lat"))),
> as.matrix(subset(dat, bird_id == id, select = c("col_long", "col_lat"))[1,]), longlat=T))
>
> ## have a look at the result
> print(trip_distances)
>
> ## unlist the trip_distances and add that as a column to dat. The order of the unlist should match the row order of dat.
> dat$trip_distances <- unlist(trip_distances)
>
> ## print dat
> print(dat)
>
> Hope that is what Anna-Maria really wants.
>
> Yours sincerely / Med venlig hilsen
>
>
> Frede Aakmann Tøgersen
> Specialist, M.Sc., Ph.D.
> Plant Performance & Modeling
>
> Technology & Service Solutions
> T +45 9730 5135
> M +45 2547 6050
> frtog at vestas.com
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>
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>
>> -----Original Message-----
>> From: r-sig-geo-bounces at r-project.org [mailto:r-sig-geo-bounces at r-
>> project.org] On Behalf Of St John Brown
>> Sent: 30. september 2014 03:04
>> To: Anna-Marie Corman; R-sig-Geo at r-project.org
>> Subject: Re: [R-sig-Geo] Calculating distance to nest with spDistsN1
>>
>> Anna-Marie,
>>
>> If you look at the documentation for spDistsN1 (i.e. run "?spDistsN1"), you
>> will see that the second argument is suppose to be a single 2D point, and not
>> many 2D points. As per the documentation descripttion, "the function
>> returns a vector of distances between a matrix of 2D points ... and a single 2D
>> point."
>>
>> I am not 100% sure I understand what you are trying to do, but I think what
>> you are looking for is the spDists function. Compare the results of my output
>> from using spDistsN1 versus spDists.
>>
>> I hope this helps.
>>
>> St. John
>>
>> make_locations = function(n){
>> lon = runif(n=n,min=7,max=8)
>> lat = runif(n=n,min=50,max=60)
>> locations = matrix(append(lon, lat), nrow=n, ncol=2)
>> colnames(locations) = c("lon", "lat")
>> rownames(locations) = 1:n
>> return(locations)
>> }
>>
>> set.seed(1)
>> flight_locations = make_locations(n=3)
>> nest_locations = make_locations(n=3)
>>
>> flight_locations
>> nest_locations
>>
>> spDistsN1(flight_locations, nest_locations[1,], longlat=T)
>> spDists(flight_locations, nest_locations, longlat=T)
>>
>>
>> On Monday, September 29, 2014 5:47 AM, Anna-Marie Corman
>> <annajess at gmx.de> wrote:
>>
>>
>>
>> Dear list,
>>
>> I have a question regarding the spDistsN1 function. I want to calculate
>> the distance of each flight position to the relevant nest position. My
>> dataset consists of several birds with a differing number of trips.
>> There is a unique trip_id with the first number regarding to the bird
>> and the second number regarding to the trip.
>>
>> coordinates Date Time Speed Direction col_lat col_long dist_col
>> 1 (7.87248, 54.1866) 04.07.2014 09:25:00 0.02 314.57 54.1866 7.8724 0.0
>> 2 (7.87148, 54.1869) 04.07.2014 09:30:00 19.11 1.31 54.1866 7.8724 0.1
>> 3 (7.87166, 54.185) 04.07.2014 09:35:00 14.98 224.79 54.1866 7.8724 0.2
>> 4 (7.88635, 54.1569) 04.07.2014 09:40:00 11.44 136.97 54.1866 7.8724 3.4
>> 5 (7.92096, 54.1363) 04.07.2014 09:45:00 0.28 262.14 54.1866 7.8724 6.4
>> 6 (7.91931, 54.136) 04.07.2014 09:50:00 0.42 218.89 54.1866 7.8724 6.4
>> trip_no bird_id trip_id DT date_time
>> 1 1 1 1.1 04.07.2014 09:25:00 2014-07-04 09:25:00
>> 2 1 1 1.1 04.07.2014 09:30:00 2014-07-04 09:30:00
>> 3 1 1 1.1 04.07.2014 09:35:00 2014-07-04 09:35:00
>> 4 1 1 1.1 04.07.2014 09:40:00 2014-07-04 09:40:00
>> 5 1 1 1.1 04.07.2014 09:45:00 2014-07-04 09:45:00
>> 6 1 1 1.1 04.07.2014 09:50:00 2014-07-04 09:50:00
>>
>>
>>
>> Formerly, when I only had one bird and so only one nest position (here
>> col_lat & col_long), I did the following:
>>
>> spDistsN1(coordinates(dat at coords), matrix(c(8.3495235,54.7042698), nrow
>> = 1), longlat = T)
>>
>> and this worked fine.
>>
>> But now I want to calculate the distance from nest for each bird
>> simultaneously. Must be simple, but I do not get it. I thought I could
>> simply use
>>
>> spDistsN1(coordinates(dat at coords), matrix(c(dat$col_long,dat$col_lat),
>> nrow = 1), longlat = T)
>>
>> instead, but it does not work.
>>
>> Do you have any idea how to solve the "problem"?
>>
>> Thanks a lot in advance.
>>
>> Best,
>> Anna
>>
>> [[alternative HTML version deleted]]
>>
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--
Roger Bivand
Department of Economics, Norwegian School of Economics,
Helleveien 30, N-5045 Bergen, Norway.
voice: +47 55 95 93 55; fax +47 55 95 91 00
e-mail: Roger.Bivand at nhh.no
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