[R-sig-eco] FPT analysis using the adehabitatLT package
Onno Keller
o.a.keller at hotmail.com
Thu Mar 10 10:41:54 CET 2016
Dear all,
For my current research topic I am analyzing the horizontal movement tracks of humpback whales in response to different disturbances.
To quantify movement I am using several methods including FPT analysis included in the adehabitatLT package.
I am currently trying to find an appropriate radius that allows me to identify changes at small scales because exposure times of disturbances are often less than 30 minutes. To do this I first have to compute the FPT for each relocation at different radii so that I may use the varlogfpt command.
This is where I get unexpected output as I will try to explain in the next section.
Track of animal loaded into R:
------------------------------------------------------------------------------------------------
Animal Date Lat Lon
A 9-06-12 19:09 77556433356901 112766724160403
A 9-06-12 19:09 7755668828875 112768309061303
A 9-06-12 19:12 775569607563212 112708437582434
A 9-06-12 19:15 775569981645682 112770230855766
A 9-06-12 19:18 775559880555804 112858061437748
A 9-06-12 19:21 775559185947383 112833893141488
A 9-06-12 19:24 775554937366939 112840817033561
A 9-06-12 19:26 775532430988859 112839886951611
A 9-06-12 19:28 775513906294915 112783397258944
A 9-06-12 19:32 77554751359435 112717334207261
A 9-06-12 19:35 775561175394068 112649544316971
A 9-06-12 19:38 77558608929978 112570044070965
A 9-06-12 19:41 775608917015529 112549548347995
A 9-06-12 19:44 775622243236414 112587320961205
A 9-06-12 19:47 775643415430827 112636334889656
A 9-06-12 19:50 775664602413583 112666013747308
A 9-06-12 19:52 775683912091816 112722633380347
A 9-06-12 19:55 775705799364393 112713649362632
A 9-06-12 19:58 775721428377661 112723338387982
A 9-06-12 20:01 77575009530171 112666632938266
A 9-06-12 20:05 775776792360936 112638096936
A 9-06-12 20:08 775801217657886 112632332685628
A 9-06-12 20:10 775818799827111 11259411452662
A 9-06-12 20:15 775847423035956 112520996378392
A 9-06-12 20:17 775864577577883 112433893034824
A 9-06-12 20:22 775885695438449 112363881650794
A 9-06-12 20:25 775911279252788 112293166451541
A 9-06-12 20:28 775924258408442 11212246841254
A 9-06-12 20:32 775924920643121 111945201583012
A 9-06-12 20:35 775963345621213 112019604780289
A 9-06-12 20:37 775967972252907 111944919795181
A 9-06-12 20:41 775985208225909 111864596165658
A 9-06-12 20:45 775996992684661 111726446440277
A 9-06-12 20:48 776002275259982 111698535583296
A 9-06-12 20:53 775990982300375 111620537532766
A 9-06-12 20:56 775972209616128 111591605702784
A 9-06-12 21:00 775953323942231 111628145732825
A 9-06-12 21:03 775932902276634 111711676377467
A 9-06-12 21:07 775911426108094 11169467095714
A 9-06-12 21:09 775898912069667 111749372126154
A 9-06-12 21:13 775879338573411 111787809215769
A 9-06-12 21:16 775852291221277 11180334979155
A 9-06-12 21:20 775833651450554 111851551686734
A 9-06-12 21:23 775820010715811 11186169708004
A 9-06-12 21:26 775804209184563 111891166802068
A 9-06-12 21:30 775784605949986 111951160316634
A 9-06-12 21:34 775765100409765 111961959815072
A 9-06-12 21:37 775745618414734 111958705827539
A 9-06-12 21:41 775734786323824 11201949011818
A 9-06-12 21:44 775721953626808 112073854839335
A 9-06-12 21:46 775713264927441 112113117234569
A 9-06-12 21:50 775711813890501 112198693401063
A 9-06-12 21:53 775703895869953 112280599907883
A 9-06-12 21:56 775700967415395 112340281060674
A 9-06-12 22:01 775684493677515 112439990007127
A 9-06-12 22:04 775684390490348 112518627207705
A 9-06-12 22:08 775679052187588 112601009903336
A 9-06-12 22:12 775666971518524 112713957884933
A 9-06-12 22:15 775664973145496 112797566711504
A 9-06-12 22:20 775656281813141 112971657868823
A 9-06-12 22:25 775659890959426 113155924150963
A 9-06-12 22:28 775641929488891 113133891373235
A 9-06-12 22:31 775626473358053 11312566488949
----------------------------------------------------------------------------------------------
Script:
Trial <-read.table("mn12_161_Base.txt", sep="\t", dec=",", header=T)
# Store date in POSIXct object
da <- as.character(Trial$Date)
da <- as.POSIXct(strptime(as.character(Trial$Date),"%d-%m-%Y %H:%M:%S"))
#Creat an object of class ltraj, ltraj automatically computes some descriptive parameters including angles etc.
Trial_ltraj <- as.ltraj(xy = Trial[,c("Lon","Lat")], date = da, id = Trial$Name)
#FPT calculations
i<-fpt(Trial_ltraj, seq(0.,0.14, length=100))
i
The output I get for i is different from what I would expect because I am getting a lot of NA, even for small radii:
-------------------------------------------------------------------------------------------
> i
[[1]]
r1 r2 r3 r4 r5 r6 r7 r8 r9 r10 r11 r12 r13 r14 r15
1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
2 0 NA NA NA NA NA NA NA NA NA NA NA NA NA NA
3 0 344.6375 NA NA NA NA NA NA NA NA NA NA NA NA NA
4 0 258.1202 NA NA NA NA NA NA NA NA NA NA NA NA NA
5 0 674.4649 985.1631 NA NA NA NA NA NA NA NA NA NA NA NA
6 0 748.0733 1134.6472 NA NA NA NA NA NA NA NA NA NA NA NA
7 0 729.2368 1091.5573 NA NA NA NA NA NA NA NA NA NA NA NA
8 0 733.1255 1084.1339 NA NA NA NA NA NA NA NA NA NA NA NA
9 0 294.5591 NA NA NA NA NA NA NA NA NA NA NA NA NA
10 0 307.2180 620.3491 NA NA NA NA NA NA NA NA NA NA NA NA
11 0 299.7344 1253.8778 1834.7958 NA NA NA NA NA NA NA NA NA NA NA
12 0 556.1033 950.1141 1277.7050 2529.3255 NA NA NA NA NA NA NA NA NA NA
13 0 476.6646 850.8415 1189.6811 2655.8799 3104.398 NA NA NA NA NA NA NA NA NA
14 0 620.8436 1053.2058 2150.3288 2796.4636 NA NA NA NA NA NA NA NA NA NA
15 0 421.3395 1520.1129 2421.3037 3389.3135 NA NA NA NA NA NA NA NA NA NA
16 0 393.4383 1364.6252 2486.5748 NA NA NA NA NA NA NA NA NA NA NA
17 0 568.8497 1091.7618 1653.1042 NA NA NA NA NA NA NA NA NA NA NA
18 0 651.1217 1241.0961 1725.5470 NA NA NA NA NA NA NA NA NA NA NA
19 0 601.2497 1217.6464 1660.2531 NA NA NA NA NA NA NA NA NA NA NA
20 0 563.3341 1498.7189 1972.7839 2776.7161 NA NA NA NA NA NA NA NA NA NA
21 0 600.6826 1216.7037 1993.0220 2713.3706 3145.339 NA NA NA NA NA NA NA NA NA
22 0 580.4407 994.0854 1881.3701 2551.0977 3104.858 NA NA NA NA NA NA NA NA NA
23 0 514.5602 930.4308 1452.4218 2576.8718 3108.979 3409.341 NA NA NA NA NA NA NA NA
24 0 295.0017 652.6900 1252.1293 1621.2101 2986.674 3293.020 3534.912 NA NA NA NA NA NA NA
25 0 306.0586 628.1298 944.0977 1380.4156 1691.505 3173.182 3452.472 3704.978 NA NA NA NA NA NA
26 0 370.2110 589.7890 774.2219 1029.8940 1426.411 1813.891 2347.478 3992.852 4309.935 4597.379 NA NA NA NA
27 0 226.6533 480.5771 700.0599 881.4927 1149.310 1750.642 2338.048 2664.809 4220.055 4525.838 4959.074 NA NA NA
28 0 139.6300 279.2600 426.0528 1070.3791 1401.887 1637.533 1857.919 2326.503 2857.790 7751.681 8310.697 9735.137 10009.282 10302.132
29 0 193.2195 746.7581 919.7588 1088.8537 1433.440 1824.170 5500.718 5870.687 6207.190 6479.671 6841.504 7272.666 7785.197 9494.052
30 0 238.9733 693.3732 899.4945 1049.1422 1222.770 1667.134 2124.660 6172.640 6477.207 6839.951 7345.563 7787.369 9452.568 9776.581
31 0 294.4359 741.5590 929.8951 1143.7828 1458.367 1850.267 5410.325 5774.742 6124.558 6411.090 6754.681 7156.565 7717.067 8235.309
32 0 257.6360 489.0948 1083.2537 1383.0705 4385.307 4711.977 5000.641 5299.355 5638.852 6019.302 6310.700 6617.125 6994.920 7554.321
33 0 370.3541 712.7265 2233.2269 2817.7925 3214.330 4123.309 4435.882 4721.449 4977.971 5222.833 5542.386 5911.153 6232.976 6509.439
34 0 428.3577 1611.0865 2042.9567 2545.4944 3070.002 3768.394 4303.758 4591.564 4865.635 5106.471 5388.780 5728.222 6095.917 6375.997
35 0 712.6666 1355.7869 1651.0522 2069.5007 2573.601 3046.903 3785.599 4291.029 4572.840 4839.566 5074.790 5321.443 5646.307 6026.280
36 0 576.9311 923.3175 1532.9022 1934.1300 2329.497 2935.214 3278.819 4201.258 4486.279 4761.453 4992.680 5204.165 5512.152 5869.831
37 0 687.1306 1438.2095 1770.1222 2192.9917 2781.356 3148.951 4111.652 4398.554 4676.951 4920.897 5140.822 5407.222 5744.229 6122.140
38 0 539.8671 1080.0077 2371.7589 2957.0739 3370.371 4230.967 4519.292 4790.948 5024.581 5235.346 5555.643 5924.042 6253.966 6512.305
39 0 502.5727 1098.8807 2263.7699 2876.7800 3275.157 4196.464 4480.357 4757.002 4986.748 5196.228 5485.442 5839.941 6197.878 6456.624
40 0 708.3758 1113.2496 2816.6642 3201.9093 4171.379 4459.573 4741.820 4973.468 5185.521 5468.282 5820.922 6185.233 6445.831 6777.702
41 0 557.8089 1376.5757 1717.5131 3789.6367 4374.924 4661.983 4906.295 5126.328 5366.099 5700.954 6093.895 6373.318 6662.277 7052.016
42 0 630.2661 1193.3800 1873.1848 2570.3404 4480.458 4760.433 4989.828 5196.567 5467.604 5825.079 6199.229 6455.391 6788.114 7185.957
43 0 693.2642 1258.6225 1972.1365 2542.3680 2998.083 4954.106 5165.311 5409.632 5760.718 6158.485 6419.620 6730.438 7126.538 7698.261
44 0 659.0779 1424.3069 1985.2594 2562.8746 2956.804 5000.693 5205.326 5468.793 5833.932 6215.386 6468.055 6805.847 7199.270 7768.425
45 0 622.3183 1508.8291 2004.5159 2617.4568 2906.259 5105.491 5310.809 5640.120 6037.259 6350.617 6617.429 7010.112 7567.029 7935.106
46 0 748.1320 1420.2905 1918.0444 2387.3146 2944.222 3200.280 5638.642 6042.090 6359.177 6630.009 7026.052 7589.457 7953.123 9750.808
47 0 776.8924 1295.0113 1850.4047 2345.2464 2684.623 3198.436 3560.258 6111.756 6406.718 6704.037 7106.426 7688.063 8020.653 9826.634
48 0 747.8301 1239.3244 1821.7368 2307.3685 2662.949 3181.705 3520.586 6077.367 6392.165 6678.445 7082.122 7663.593 8009.702 9829.559
49 0 393.4405 1177.9598 1609.1929 2131.2111 2603.489 2973.969 3531.979 3860.269 6685.946 7094.584 7684.306 8027.297 9845.986 10121.594
50 0 390.1414 743.8896 1481.0651 1903.5644 2440.425 2956.124 3306.767 3835.756 4209.547 7645.069 8005.137 9831.567 10109.160 NA
51 0 362.0675 703.6954 1426.9361 1783.0602 2396.771 2841.141 3291.330 3881.757 4126.403 7898.816 9736.808 10025.405 10748.965 NA
52 0 291.4742 618.8264 982.8837 1358.4474 2116.623 2548.785 3111.380 3553.447 3855.896 4383.907 4684.176 NA NA NA
53 0 279.8816 605.5687 937.5612 1281.5761 1655.178 2415.930 2717.749 3279.507 3763.386 4094.186 4587.000 4800.000 NA NA
54 0 322.8420 626.1536 911.6326 1250.8055 1594.668 1888.862 2639.129 2984.677 3518.672 3957.830 4287.510 4781.669 4999.944 NA
55 0 315.5918 650.3962 953.5294 1185.6491 1450.562 1775.865 2079.556 2370.648 3086.402 3435.790 3939.198 4388.004 NA NA
56 0 317.4154 613.4286 889.4016 1165.8956 1439.092 1678.931 1931.073 2232.853 2525.786 3248.952 NA NA NA NA
57 0 276.7260 531.1405 826.6545 1120.4563 1375.921 1610.042 1841.894 2093.399 2379.462 NA NA NA NA NA
58 0 244.4130 462.7608 737.0829 984.1782 1228.584 1502.651 1757.180 NA NA NA NA NA NA NA
59 0 241.9073 454.8290 645.5639 889.2351 1155.662 1388.209 NA NA NA NA NA NA NA NA
60 0 188.9915 377.9831 567.6136 NA NA NA NA NA NA NA NA NA NA NA
61 0 NA NA NA NA NA NA NA NA NA NA NA NA NA NA
62 0 NA NA NA NA NA NA NA NA NA NA NA NA NA NA
63 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
-----------------------------------------------------------------------------------------
What I do not understand is why the output is triangle shaped like this.
Why for example am I not given an FPT value for relocation #9 for r3 while I do get a value for r3 at relocation #10. The track is definitely crossing the circle with the specific radius.
It seems that I am not given an FPT value when the relocation that comes after the one from which the FPT is calculated falls within the radius it is calculating the FPT for.
Hopefully my question is clear, please let me know if anything is unclear.
Thanks in advance,
Onno Keller
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