[R-sig-eco] FPT and Adehabitat
Samantha Patrick
samantha.patrick at plymouth.ac.uk
Wed Apr 21 15:18:47 CEST 2010
Thank you so much - you have been a huge help. I have followed you recommendation and now I have my trajectories sampled at an equal time period and the missing values entered as NAs. To continue with my analysis I have been trying to find a way to output the object of class ltraj (in this case yaya3) so I can see where R has placed the NAs and the corresponding co-ordinates of points with FP values (to allow spatial analysis). However I can only find a function to plot the positions of NAs - the final hurdle!
Many Thanks again
Sam
Dr Samantha Patrick
EU INTERREG Post Doc
Marine Biology & Ecology Research Centre
University of Plymouth
Plymouth
PL4 8AA
T: 01752 584699
M: 07740472719
-----Original Message-----
From: Clément Calenge [mailto:clement.calenge at oncfs.gouv.fr]
Sent: 21 April 2010 12:12
To: Samantha Patrick
Cc: r-sig-ecology at r-project.org
Subject: Re: [R-sig-eco] FPT and Adehabitat
Samantha Patrick wrote:
> The data set is pasted at the bottom of the email and this is the code I am using (excluding data read):
>
> ddate <-as.POSIXct(datetime)
> burst<-as.factor(FPT[,6])
> id<-as.factor(FPT[,6])
> xy<-data.frame (FPT[,7], FPT[,8])
> yaya<-as.ltraj(xy,ddate,id, burst, typeII = TRUE, slsp = c("remove", "missing"))
> summary.ltraj(yaya)
> ayayGPS <- redisltraj(yaya, 500)
>
> fptshort=fpt(ayayGPS, seq(5000,30000, length=6))
>
> I am wondering if the outputs are for the redistributed locations? If this is the case, is there any way to get FPT for raw locations (I want to compare the results with other measures of sinuosity etc.)? The timing of bursts is not constant though...
>
Actually, when you use redisltraj, you redicretize your trajectory so
that the step length is constant (you fix it to 500 metres). Your
original dataset has 139 relocations, but when you rediscretize the
trajectory, you increase the number of relocations. Indeed, have a look
at the contents of ayayGPS:
> ayayGPS
*********** List of class ltraj ***********
Type of the traject: Type II (time recorded)
Irregular traject. Variable time lag between two locs
Characteristics of the bursts:
id burst nb.reloc NAs date.begin date.end
1 6.2 6.2.R500 295 0 2006-06-21 15:09:48 2006-06-21 21:16:01
There are 295 relocations in your new trajectory. This explains why the
fpt returns a data frame with 295 data points. Now the question is: why
do you rediscretize the trajectory? You note that "The timing of bursts
is not constant". This is expected: the function redisltraj does not
transform an irregular trajectory into a regular one (the help page of
this function indicates that it is used for "Rediscretization of a
Trajectory With Regular Step Length").
Looking at the time lag between successive relocations:
plotltr(yaya,"dt/60")
it appears that a relocation was collected approximately every 2 min...
and that there are missing values. Two points are important here:
* there should be missing values in the trajectory at several places.
Therefore the function setNA may be useful here to fill in these NAs
(have a look at the help page of the function setNA):
yaya2 <- setNA(yaya, as.POSIXct("2010-01-01"), 2, units="min")
have a look at yaya2:
> yaya2
*********** List of class ltraj ***********
Type of the traject: Type II (time recorded)
Irregular traject. Variable time lag between two locs
Characteristics of the bursts:
id burst nb.reloc NAs date.begin date.end
1 6.2 6.2 195 56 2006-06-21 15:09:48 2006-06-21 21:37:55
The number of relocations have increased (there are now 195 relocations,
because 56 are missing)
* the timings are only approximate. We can "round" the timing to make
the trajectory exactly regular (see the help page of sett0):
yaya3 <- sett0(yaya2, as.POSIXct("2010-01-01"), 2, units="min")
yaya3 is now exactly regular:
> yaya3
*********** List of class ltraj ***********
Type of the traject: Type II (time recorded)
Regular traject. Time lag between two locs: 120 seconds
Characteristics of the bursts:
id burst nb.reloc NAs date.begin date.end
1 6.2 6.2 195 56 2006-06-21 15:10:00 2006-06-21 21:38:00
the time lag between relocations is now constant. This dataset yaya3
contains only the original relocations (with rounded timings) + missing
values.
**But note that the step length is no longer constant** (but why do you
need constant step length in FPT analysis?). Finally use the function fpt:
fptshort <- fpt(yaya3, seq(5000,30000, length=6))
Hope this helps
Clément Calenge.
> Many thanks for your help
>
> Best Wishes
>
> Sam
>
>
> dddate tttime Lat Lon ID Burst xx yy
> 2006-06-21 15:09:48 -5.48138 51.73081 6.2 6.2 742965.87000 5736959.30000
> 2006-06-21 15:12:01 -5.48146 51.73082 6.2 6.2 742960.28000 5736960.50000
> 2006-06-21 15:14:58 -5.48583 51.72864 6.2 6.2 742670.66000 5736703.30000
> 2006-06-21 15:17:24 -5.48699 51.72929 6.2 6.2 742586.76000 5736771.50000
> 2006-06-21 15:20:30 -5.49569 51.73421 6.2 6.2 741960.22000 5737289.50000
> 2006-06-21 15:22:43 -5.51323 51.73561 6.2 6.2 740742.05000 5737387.10000
> 2006-06-21 15:24:56 -5.52846 51.74312 6.2 6.2 739650.90000 5738172.20000
> 2006-06-21 15:27:18 -5.54604 51.74984 6.2 6.2 738402.38000 5738861.10000
> 2006-06-21 15:29:36 -5.56479 51.75534 6.2 6.2 737079.38000 5739411.70000
> 2006-06-21 15:31:55 -5.58231 51.76059 6.2 6.2 735843.10000 5739938.30000
> 2006-06-21 15:34:31 -5.60271 51.76500 6.2 6.2 734413.21000 5740363.20000
> 2006-06-21 15:37:07 -5.62265 51.76815 6.2 6.2 733021.53000 5740648.70000
> 2006-06-21 15:39:26 -5.64052 51.77049 6.2 6.2 731776.44000 5740852.10000
> 2006-06-21 15:42:20 -5.66318 51.77429 6.2 6.2 730194.48000 5741203.40000
> 2006-06-21 15:44:42 -5.68139 51.78069 6.2 6.2 728906.38000 5741857.50000
> 2006-06-21 15:46:55 -5.69897 51.78288 6.2 6.2 727682.52000 5742045.20000
> 2006-06-21 15:49:13 -5.71702 51.78535 6.2 6.2 726426.04000 5742264.20000
> 2006-06-21 15:52:13 -5.74030 51.79218 6.2 6.2 724786.32000 5742950.60000
> 2006-06-21 15:54:37 -5.75805 51.79961 6.2 6.2 723526.28000 5743722.30000
> 2006-06-21 15:57:25 -5.78056 51.80464 6.2 6.2 721949.58000 5744212.70000
> 2006-06-21 15:59:37 -5.78381 51.80597 6.2 6.2 721719.39000 5744350.60000
> 2006-06-21 16:01:48 -5.78273 51.80650 6.2 6.2 721790.85000 5744413.50000
> 2006-06-21 16:04:06 -5.78262 51.80813 6.2 6.2 721790.77000 5744595.10000
> 2006-06-21 16:06:19 -5.78165 51.80903 6.2 6.2 721852.86000 5744698.10000
> 2006-06-21 16:08:31 -5.78108 51.81042 6.2 6.2 721885.22000 5744853.70000
> 2006-06-21 16:11:07 -5.78012 51.81167 6.2 6.2 721945.56000 5744996.10000
> 2006-06-21 16:13:31 -5.78455 51.81492 6.2 6.2 721624.44000 5745343.80000
> 2006-06-21 16:15:42 -5.80296 51.82131 6.2 6.2 720324.79000 5745997.80000
> 2006-06-21 16:18:00 -5.82177 51.82815 6.2 6.2 718995.58000 5746702.40000
> 2006-06-21 16:20:25 -5.84190 51.83592 6.2 6.2 717570.85000 5747505.00000
> 2006-06-21 16:22:42 -5.86282 51.83992 6.2 6.2 716111.21000 5747888.20000
> 2006-06-21 16:25:02 -5.88449 51.84056 6.2 6.2 714615.50000 5747895.30000
> 2006-06-21 16:27:25 -5.90739 51.84269 6.2 6.2 713028.46000 5748064.10000
> 2006-06-21 16:29:37 -5.92828 51.84313 6.2 6.2 711587.50000 5748052.60000
> 2006-06-21 16:32:01 -5.95060 51.84389 6.2 6.2 710047.08000 5748072.50000
> 2006-06-21 16:56:55 -6.17119 51.87331 6.2 6.2 694728.69000 5750729.80000
> 2006-06-21 16:59:07 -6.18950 51.87581 6.2 6.2 693457.32000 5750959.20000
> 2006-06-21 17:01:18 -6.20822 51.87589 6.2 6.2 692168.53000 5750918.60000
> 2006-06-21 17:03:31 -6.22717 51.87621 6.2 6.2 690863.23000 5750904.90000
> 2006-06-21 17:05:57 -6.24819 51.87824 6.2 6.2 689408.33000 5751075.00000
> 2006-06-21 17:08:06 -6.26652 51.88070 6.2 6.2 688136.15000 5751301.30000
> 2006-06-21 17:10:24 -6.28705 51.88118 6.2 6.2 686721.86000 5751302.10000
> 2006-06-21 17:30:53 -6.45187 51.88101 6.2 6.2 675380.21000 5750873.30000
> 2006-06-21 17:33:01 -6.45097 51.88106 6.2 6.2 675441.74000 5750880.30000
> 2006-06-21 17:35:12 -6.45016 51.88134 6.2 6.2 675496.73000 5750913.60000
> 2006-06-21 17:37:36 -6.44931 51.88168 6.2 6.2 675554.00000 5750953.90000
> 2006-06-21 17:40:01 -6.45036 51.88182 6.2 6.2 675481.09000 5750966.70000
> 2006-06-21 17:42:25 -6.46744 51.87689 6.2 6.2 674324.60000 5750376.90000
> 2006-06-21 17:47:04 -6.47118 51.86575 6.2 6.2 674110.57000 5749129.60000
> 2006-06-21 17:49:42 -6.47089 51.85771 6.2 6.2 674161.22000 5748236.80000
> 2006-06-21 17:52:00 -6.47270 51.86890 6.2 6.2 673993.44000 5749475.90000
> 2006-06-21 17:54:15 -6.48392 51.87681 6.2 6.2 673191.15000 5750328.90000
> 2006-06-21 17:57:24 -6.48532 51.88458 6.2 6.2 673064.58000 5751190.20000
> 2006-06-21 17:59:38 -6.48502 51.88476 6.2 6.2 673084.53000 5751210.90000
> 2006-06-21 18:01:48 -6.48431 51.88493 6.2 6.2 673132.65000 5751230.60000
> 2006-06-21 18:04:00 -6.48373 51.88517 6.2 6.2 673172.08000 5751259.30000
> 2006-06-21 18:06:37 -6.48307 51.88531 6.2 6.2 673216.72000 5751276.60000
> 2006-06-21 18:08:48 -6.48249 51.88548 6.2 6.2 673255.87000 5751296.70000
> 2006-06-21 18:11:37 -6.48168 51.88556 6.2 6.2 673311.19000 5751307.30000
> 2006-06-21 18:13:48 -6.48085 51.88569 6.2 6.2 673368.13000 5751324.30000
> 2006-06-21 18:16:36 -6.48000 51.88609 6.2 6.2 673425.07000 5751370.80000
> 2006-06-21 18:18:48 -6.47963 51.88632 6.2 6.2 673449.43000 5751396.90000
> 2006-06-21 18:21:37 -6.47898 51.88742 6.2 6.2 673489.80000 5751521.00000
> 2006-06-21 18:24:42 -6.47843 51.88777 6.2 6.2 673526.54000 5751560.80000
> 2006-06-21 18:27:44 -6.47785 51.88806 6.2 6.2 673565.54000 5751595.00000
> 2006-06-21 18:31:54 -6.47595 51.88390 6.2 6.2 673711.97000 5751136.90000
> 2006-06-21 18:34:13 -6.47883 51.88695 6.2 6.2 673501.81000 5751469.10000
> 2006-06-21 18:36:43 -6.48925 51.89100 6.2 6.2 672769.77000 5751894.20000
> 2006-06-21 18:39:07 -6.48853 51.89066 6.2 6.2 672820.50000 5751858.10000
> 2006-06-21 18:41:24 -6.48806 51.89093 6.2 6.2 672851.47000 5751888.90000
> 2006-06-21 18:43:43 -6.48760 51.89111 6.2 6.2 672882.66000 5751910.00000
> 2006-06-21 18:46:14 -6.50280 51.89640 6.2 6.2 671816.44000 5752462.80000
> 2006-06-21 18:48:24 -6.51535 51.90130 6.2 6.2 670934.59000 5752978.30000
> 2006-06-21 18:50:43 -6.53180 51.90659 6.2 6.2 669783.44000 5753528.10000
> 2006-06-21 18:52:54 -6.54770 51.91159 6.2 6.2 668670.70000 5754046.20000
> 2006-06-21 18:55:07 -6.56365 51.91854 6.2 6.2 667548.36000 5754782.80000
> 2006-06-21 18:57:43 -6.58125 51.92617 6.2 6.2 666310.08000 5755590.80000
> 2006-06-21 19:00:19 -6.59594 51.92229 6.2 6.2 665313.97000 5755125.60000
> 2006-06-21 19:03:32 -6.61737 51.92219 6.2 6.2 663841.38000 5755066.00000
> 2006-06-21 19:06:07 -6.63860 51.92683 6.2 6.2 662364.38000 5755534.10000
> 2006-06-21 19:08:50 -6.65449 51.93002 6.2 6.2 661260.75000 5755853.80000
> 2006-06-21 19:11:00 -6.66988 51.92770 6.2 6.2 660211.40000 5755561.50000
> 2006-06-21 19:19:55 -6.73595 51.92041 6.2 6.2 655694.34000 5754607.40000
> 2006-06-21 19:22:07 -6.75289 51.92037 6.2 6.2 654529.67000 5754567.40000
> 2006-06-21 19:24:18 -6.76489 51.91180 6.2 6.2 653733.38000 5753589.00000
> 2006-06-21 19:26:49 -6.77896 51.91149 6.2 6.2 652767.36000 5753525.10000
> 2006-06-21 19:29:00 -6.79281 51.91160 6.2 6.2 651814.25000 5753508.20000
> 2006-06-21 19:31:49 -6.80859 51.90841 6.2 6.2 650739.36000 5753120.10000
> 2006-06-21 19:34:13 -6.81951 51.90515 6.2 6.2 649999.50000 5752735.00000
> 2006-06-21 19:37:31 -6.83476 51.90308 6.2 6.2 648957.17000 5752473.50000
> 2006-06-21 19:39:55 -6.84750 51.90275 6.2 6.2 648081.77000 5752411.50000
> 2006-06-21 19:42:22 -6.86246 51.90572 6.2 6.2 647043.59000 5752711.30000
> 2006-06-21 19:44:32 -6.87491 51.90647 6.2 6.2 646184.81000 5752769.00000
> 2006-06-21 19:47:01 -6.88648 51.89641 6.2 6.2 645421.25000 5751627.70000
> 2006-06-21 19:51:26 -6.89770 51.89913 6.2 6.2 644640.49000 5751907.60000
> 2006-06-21 19:53:36 -6.90755 51.90497 6.2 6.2 643943.96000 5752537.70000
> 2006-06-21 19:55:50 -6.92119 51.90624 6.2 6.2 643001.95000 5752651.50000
> 2006-06-21 19:58:00 -6.93272 51.90531 6.2 6.2 642212.04000 5752525.70000
> 2006-06-21 20:00:14 -6.94620 51.91235 6.2 6.2 641262.59000 5753283.00000
> 2006-06-21 20:02:31 -6.95391 51.92287 6.2 6.2 640699.10000 5754437.90000
> 2006-06-21 20:04:55 -6.96821 51.92892 6.2 6.2 639697.30000 5755083.10000
> 2006-06-21 20:07:07 -6.98130 51.93282 6.2 6.2 638785.69000 5755491.50000
> 2006-06-21 20:09:19 -6.99558 51.93392 6.2 6.2 637800.23000 5755586.10000
> 2006-06-21 20:11:30 -7.00972 51.93806 6.2 6.2 636815.72000 5756020.60000
> 2006-06-21 20:13:43 -7.02412 51.94170 6.2 6.2 635814.93000 5756398.40000
> 2006-06-21 20:15:56 -7.03805 51.94504 6.2 6.2 634847.64000 5756743.40000
> 2006-06-21 20:18:19 -7.05357 51.94017 6.2 6.2 633795.50000 5756173.70000
> 2006-06-21 20:20:49 -7.07035 51.93468 6.2 6.2 632658.47000 5755532.50000
> 2006-06-21 20:23:19 -7.08226 51.93128 6.2 6.2 631849.87000 5755132.10000
> 2006-06-21 20:25:31 -7.09397 51.93145 6.2 6.2 631044.01000 5755129.70000
> 2006-06-21 20:27:49 -7.10594 51.93418 6.2 6.2 630213.31000 5755412.60000
> 2006-06-21 20:30:07 -7.11838 51.93647 6.2 6.2 629351.69000 5755644.60000
> 2006-06-21 20:32:20 -7.13231 51.93359 6.2 6.2 628402.16000 5755299.60000
> 2006-06-21 20:34:43 -7.14559 51.92439 6.2 6.2 627515.21000 5754252.80000
> 2006-06-21 20:37:01 -7.15992 51.91804 6.2 6.2 626547.66000 5753521.60000
> 2006-06-21 20:39:20 -7.17634 51.91853 6.2 6.2 625417.35000 5753548.20000
> 2006-06-21 20:41:30 -7.19056 51.91872 6.2 6.2 624438.97000 5753544.40000
> 2006-06-21 20:43:49 -7.20412 51.91658 6.2 6.2 623512.48000 5753283.70000
> 2006-06-21 20:46:07 -7.21879 51.91735 6.2 6.2 622501.41000 5753344.50000
> 2006-06-21 20:48:19 -7.23236 51.91628 6.2 6.2 621571.44000 5753203.20000
> 2006-06-21 20:50:37 -7.24680 51.91654 6.2 6.2 620577.46000 5753208.20000
> 2006-06-21 20:52:48 -7.26108 51.91442 6.2 6.2 619601.28000 5752948.50000
> 2006-06-21 20:55:01 -7.27334 51.91375 6.2 6.2 618759.89000 5752853.70000
> 2006-06-21 20:57:14 -7.28510 51.91937 6.2 6.2 617936.13000 5753459.80000
> 2006-06-21 20:59:25 -7.29653 51.92360 6.2 6.2 617138.78000 5753911.50000
> 2006-06-21 21:01:36 -7.30587 51.92531 6.2 6.2 616492.58000 5754087.30000
> 2006-06-21 21:03:56 -7.32102 51.92161 6.2 6.2 615459.95000 5753651.10000
> 2006-06-21 21:06:06 -7.33423 51.92266 6.2 6.2 614549.49000 5753746.70000
> 2006-06-21 21:08:18 -7.34527 51.92961 6.2 6.2 613772.55000 5754502.50000
> 2006-06-21 21:10:37 -7.36041 51.93295 6.2 6.2 612723.16000 5754850.90000
> 2006-06-21 21:16:36 -7.40056 51.94133 6.2 6.2 609942.27000 5755721.40000
> 2006-06-21 21:18:49 -7.40028 51.94125 6.2 6.2 609962.29000 5755712.40000
> 2006-06-21 21:21:01 -7.40044 51.94117 6.2 6.2 609951.37000 5755703.60000
> 2006-06-21 21:23:25 -7.40046 51.94107 6.2 6.2 609949.79000 5755692.10000
> 2006-06-21 21:25:37 -7.40008 51.94118 6.2 6.2 609976.09000 5755705.00000
> 2006-06-21 21:27:55 -7.40016 51.94100 6.2 6.2 609971.02000 5755685.30000
> 2006-06-21 21:31:25 -7.40075 51.94086 6.2 6.2 609930.70000 5755669.00000
> 2006-06-21 21:34:33 -7.40036 51.94086 6.2 6.2 609957.63000 5755668.90000
> 2006-06-21 21:37:55 -7.40036 51.94075 6.2 6.2 609957.56000 5755656.40000
>
> Dr Samantha Patrick
> EU INTERREG Post Doc
> Marine Biology & Ecology Research Centre
> University of Plymouth
> Plymouth
> PL4 8AA
>
> T: 01752 584699
> M: 07740472719
>
> -----Original Message-----
> From: Clément Calenge [mailto:clement.calenge at oncfs.gouv.fr]
> Sent: 21 April 2010 11:18
> To: Samantha Patrick
> Cc: r-sig-ecology at r-project.org
> Subject: Re: [R-sig-eco] FPT and Adehabitat
>
> Hard to say without any reproducible example... could you post an
> example (minimum dataset + R code)?
> Best regards,
>
> Clément Calenge
>
> Samantha Patrick wrote:
>
>> I am calculating First Passage Time for GPS movements. The code all runs fine and R recognises that an individual, for example, has 139 relocations. However when I then view the FPT output there are 295 data points. I have checked back and the data file, the imported data and the number of time points all equal 139. In the help it says that the FPT output is a data frame per individual with a row for each relocation so I cannot understand why it is outputting so many rows. This happens for many individuals but there doesn't not seem to be any pattern in the number of output rows and occurs if I run individuals separately. Has anyone ever come across this or have any ideas?
>>
>> Many Thanks
>>
>> Sam
>>
>>
>> Dr Samantha Patrick
>> EU INTERREG Post Doc
>> Marine Biology & Ecology Research Centre
>> University of Plymouth
>> Plymouth
>> PL4 8AA
>>
>> T: 01752 584699
>> M: 07740472719
>>
>>
>> [[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
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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