[R] problems using the thin plate spline method

Mon Dec 5 14:24:58 CET 2011

Thanks Michael

here is my data

structure(list(x1 = c(409.5, 349, 385.5, 273, 543, 746, 198.75,
262.5, 320.5, 259, 399.5, 595.5, 374, 293, 330, 658, 299, 775,
559.75, 251, 402, 395.5, 345.5, 283.5, 452, 816.5, 266.5, 360.25,
386, 160.25, 360, 337, 326, 758, 342.5, 389, 347.5, 819.25, 355.25,
281, 494.5, 514.5, 263, 439, 263, 373.25, 546, 348, 380.5, 606,
460, 352.5, 737, 275, 520.5, 385.25, 354.5, 383.5, 322.5, 309,
502.5, 517, 276, 400.5, 272.5, NA, 253, 311, 389, 157.75, 520,
499.5, 481, 448.5, 335.5, 231.5, 492.5, 477.5, 650, 540.75, 620.5,
400.5, 331.5, 311, 229, 432.5, 422.75, 493.5, 414.25, 487, 369,
425, 233.5, 254.5, 417.5, NA, 583.25, 492.5, 490, 300.25, NA,
270, 307, 319, 374.5, 562.5, 569.5, 389.75, 341.25, 366, 262.75,
776.25, 379.5, 360, 203.75, 517, 539.5, 418.75, 353.5, 269, 475.5,
472, 342, 189, 492.5, 412, 467.5, 209.75, 340.75, 231.5, 185.5,
358.5, 354, 670.5, 686, 364, 138, 272, 183, 365.25, 188, 229.5,
553.5, 582.5, 469, 359.5, 284.25, 582.5, 287, NA, 455.25, 410.5,
477, 239, 313.5, 294.5, 523, 372.5, 231.5, NA, 365, 269.5, 394.5,
281.5, 418.5, 553.5, 245.75, 304, 423.75, 369.5, 330.5, 278,
257, 416.5, 413.25, 465.5, 877.25, 204, 475, 289, 425.75, 405,
494.25, 332, 552.5, 433.75, 821, 841.5, 226.5, 266.75, 552, 157.5,
528.5, 248.5, 245.5, 303, 444.25, 310, 768.25, 265.5, 98.25,
525, 407.75, 163.5, 374.25, 749, 318.5, 367, 250, 408, 341.5,
266.5, 348.5, 398.5, 429.5, 420, 263.5, 581.5, 509.5, 724.75,
476.5, 249.5, 297.5, 245, 139.5, 360.5, 983.5, 465.5, 263.75,
NA, 510, 325, 122.5, 455.5, 531, 318, 373, 487, 401, 451.75,
561, 364.5, 439.5, 733.5, 455, 376.5, 554, 409.5, 1007.5, 462.5,
183, 342.5, 304, 258.25, 380.5, 373, 683, 577, 430, 324.25, 312,
389, 345, 358.5, 551.75, 317.5, 499, 335.5, 450.5, 363.5, 185,
177.5, 477.75, 644.5, 290.25, 457.5, 295.5, 266.5, 348.5, 357.75,
221.5, 739, 445.5, 416, 261.5, 909, 737.5, 194.5, 438.5, 358,
244, 388.5, 512.5, 315.25, 572, 473.75, 627.5, 507.75, 281, 511.5,
309.25, 308.25, 690, 180, 341.5, 273, 571, 694, 345, 497, 219,
311.5, 458.5, 283, 274, 282.5, 187.5, 332, 281.75, 397.75, 336.5,
392.5, 318, 609.5, 203.5, 144.5, 504.75, 647, 374, 149.5, 319,
306, 304.75, 304.5, 247, 329, 442, 308, 316, 219, 556.5, 643.5,
328.5, 301, 467, 452.5, 351.5, 373, 503.5, 287.5, 393.5, 444,
734, 458.5, 1182, 406, 286.5, 283.5, 642.5, 453.5, 206, 258,
412, 551, 784.75, 316.5, 326.5, 202.25, 336.75, 406, 225.5, 266,
916.5, 387, 496.25, 389, 668.5, 192, 396, 282.5, 414.5, 355,
294.5, 396.5, 348.75, 241.75, 347.5, 250, 473.5, 369, 672, 199.5,
318.25, 219.75, 124, 514.25, 600.5, 256, 574.75, 346.25, 397,
195, 494, 567.5, 431.5, 144.5, 440, 525.5, 375.5, 841.5, 386.25,
490.5, 296.5, 812.25, 385, 232.5, 239.25, 316.5, 312.25, 257.75,
NA, 389, 301.5, 242.25, 400.25, 367.25, 321.5, 301, 223, 360,
662.5, 407.5, 736, 379.5, 852, 355, 397, 527.5, 531.25, 473,
559.75, 344, 379.75, 459, 322, 208.5, 424.25, 342.25, 414.5,
308, 574.5, 635, 449.5, 286, 986.25, 563.5, 596, 492, 265, 826.5,
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393.25, 331, 391, 274, 707.75, 467.5, 160.5, 569.5, 340.5, 259,
321.75, 286.25, 416.5, 459.25, 276.5, 280.25, 258.5, 309.5, 424.5,
365, 809, 238.75, 524, 563.5, 419, 354.5, 303, 167.5, 236.25,
268, 330.5, 251.5, 249, 443.5, 411.5, 323.5, 485.25, 356.5, 221.5,
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386, 286, 448, 379.75, 293.5, 410, 335.5, 444.5, 464.75, 364.25,
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268, 507.5, 441.5, 188.5, 186.5, 679, 249, 200, 419.5, 294.25,
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336, 217, 245.5, 608.75, 375, 555.5, 621, 488.5, 271.5, 331.5,
286, 555, 345, 529.5, 370, 584.25, 208.5, 473.5, 244, 296.25,
598, 456.25, 371, 505.5, 269.5, 284, 420.75, 358.25, 476.75,
363, 485.75, 570, 567.25, 355.5, 444, 629, 367.5, 174.5, 217,
239, 378.5, 179.5, 188, 355, 304.5, 354.5, 207.5, 615, 163.5,
374, 316.5, 79, 409, 218.25, 452, 398, 277.5, 289.25, 491, 515
), x2 = c(673, 335, 1737, 457, 2325, 1255, 388, 104, 786, 516,
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456, 400, 388, 941, 307, 683, 528, 368, 455, 488, 702, 1040,
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340, 572, 441, 833, 775, 129, 350, 1445, 328, 585, 412, 446,
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676, 253, 923, 791, 415, 349, 825, 486, 508, 191, 282, 267, 372,
639, 687, 1427, 847, 368, 616, 1723, 310, 449, 301, 378, 573,
273, 405, 653, 606, 943, 926, 399, 282, 1112, 484, 408, 434,
595, 223, 517, 323, 353, 628, 334, 502, 861, 361, 464, 285, 693,
129, 817, 516, 291, 211, 232, 269, 378, 2560.5, 662, 580, 531,
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343, 437, 972, 1403, 471, 368, 459, 617, 444, 312, 963, 315,
549, 1022, 423, 384, 195, 265, 827, 827, 309, 546, 385, 380,
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254, 243, 332, 871, 562, 1761, 689, 623, 286, 233, 668, 1078,
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335, 339, 289, 431, 549, 334, 482, 363, 663, 192, 60, 468, 582,
365, 479, 983, 668, 605, 231, 457, 469, 664, 490, 274, 580, 476,
385, 302, 607, 1723, 441, 463, 229, 138, 279, 245, 1081, 1080,
1745, 1157, 338, 571, 211, 2256, 778, 224, 158, 393, 661.5, 4828,
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567, 726, 742, 515, 245, 501, 359, 220, 555, 424, 592, 1470,
441, 177, 1302, 245, 429, 597, 809, 835, 1548, 568, 310, 218,
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830, 565, 883, 1569, 1071, 261, 564, 645, 365, 587, 585, 395,
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171, 834, 466, 861, 1624, 648, 394, 1008, 626, 442, 530, 716,
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330, 366, 169, 882, 3209, 225, 1158, 701, 316, 646, 682, 414,
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527, 511, 538, 339, 803, 232, 773, 1739, 567, 248, 1375, 1340,
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1212, 624, 469, 294, 1194, 620, 234, 446, 177, 893, 489, 426,
699, 539, 486, 887, 321, 235, 501, 586, 509, 687, 520, 820, 758,
441, 876, 661, 638, 512, 518, 695, 397, 179, 450, 98, 94, 100,
216, 86, 149, 338, 324, 460, 124, 375, 255, 356, 263, 64, 374,
477, 664, 370, 416, 416, 741, 1136), y = c(1082.5, 684, 2122.5,
730, 2868, 2001, 586.75, 366.5, 1106.5, 775, 941.5, 1511.5, 1631,
522, 820, 1674, 565, 1914, 1582.75, 404, 655, 714.5, 801.5, 683.5,
840, 1757.5, 573.5, 1043.25, 914, 528.25, 815, 825, 1028, 1798,
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988, 713, 1585.25, 1092, 833, 758.5, 1204, 1298, 871.5, 1361,
460, 1152.5, 1081.75, 878.5, 1001.5, 703.5, 689, 1126.5, 1129,
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635, 1573.5, 856, 830, 370, 5834.5, 845, 1942.5, 689.75, 547.75,
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1386.25, 1372, 349, 778.5, 1216, 1295, 1308, 784, 841, 516, 695.5,
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681, 1272.5, 395.5, 204.5, 972.75, 1229, 739, 658.5, 1302, 974,
909.75, 535.5, 704, 798, 1106, 798, 590, 799, 1032.5, 1028.5,
630.5, 908, 2190, 893.5, 814.5, 602, 641.5, 566.5, 638.5, 1525,
1814, 2203.5, 2339, 744, 857.5, 494.5, 2898.5, 1231.5, 430, 416,
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537, 1765.5, 703, 1281.25, 853, 1177.5, 530, 963, 1008.5, 1156.5,
870, 539.5, 897.5, 707.75, 461.75, 902.5, 674, 1065.5, 1839,
1113, 376.5, 1620.25, 464.75, 553, 1111.25, 1409.5, 1091, 2122.75,
914.25, 707, 413, 1398, 1843.5, 969.5, 459.5, 966, 1129.5, 881.5,
2677.5, 751.25, 1379.5, 804.5, 1258.25, 1384, 624.5, 428.25,
693.5, 647.25, 471.75, NA, 919, 498.5, 872.25, 1214.25, 1672.25,
1253.5, 1054, 584, 1499, 1301.5, 1315.5, 2271, 862.5, 1638, 831,
864, 1230.5, 1361.25, 1038, 1442.75, 1913, 1450.75, 720, 886,
853.5, 789.25, 929.25, 999.5, 703, 1247.5, 1575, 1451.5, 511,
2297.25, 1034.5, 1225, 925, 478, 2161.5, 1219, 952.5, 1559.5,
906, 1130, 772.5, 1123.75, 1631, 829.25, 1210.25, 751, 934.25,
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1339, 1017, 716, 1237.75, 1183.5, 371.5, 1530, 851.5, 594, 773.75,
947.25, 719.5, 870.25, 612.5, 961.25, 708.5, 655.5, 841.5, 823,
2122, 1033.75, 1053, 766.5, 1118, 854.5, 585, 506.5, 715.25,
629, 660.5, 617.5, 418, 1325.5, 3620.5, 548.5, 1643.25, 1057.5,
537.5, 1161.5, 1144, 736.5, 1471.5, 1207.25, 1134.75, 1037.5,
NA, 482.5, 1520.5, 1294, 1164, 1057, 898.75, 606.5, 937, 846.5,
982.5, 803.75, 1167.25, 592, 1362, 2285.5, 1037, 552.5, NA, 1841.5,
915.5, 2185, 808, 765, 664, 1073.5, 1109.5, 743.5, 384.5, 2158,
478, 427, 919.5, 854.25, 1523, 807.75, 717.75, 809.5, 890.75,
603.5, 589.5, 1117.5, 848.75, 762, 578, 1457.5, 1232.75, 844,
849.5, 1815, 1108.5, 505.5, 777.5, 463, 1448, 834, 955.5, 1069,
1123.25, 694.5, 1360.5, 565, 531.25, 1099, 1042.25, 880, 1192.5,
789.5, 1104, 1178.75, 799.25, 1352.75, 1024, 1123.75, 1082, 1085.25,
1050.5, 841, 808, 817.5, 272.5, 311, 339, 594.5, 265.5, 337,
693, 628.5, 814.5, 331.5, 990, 418.5, 730, 579.5, 143, 783, 695.25,
1116, 768, 693.5, 705.25, 1232, 1651)), .Names = c("x1", "x2",
"y"), class = "data.frame", row.names = c(NA, -629L))

mintewab
________________________________________
Från: R. Michael Weylandt <michael.weylandt at gmail.com> [michael.weylandt at gmail.com]
Skickat: den 5 december 2011 14:04
Till: Mintewab Bezabih
Kopia: Jeff Newmiller; Sarah Goslee; r-help at r-project.org
Ämne: Re: [R] problems using the thin plate spline method

Your data was scrubbed by the server. Use dput() to create a plain text representation of dat you can put in the body of the email.

Michael

On Dec 5, 2011, at 6:54 AM, Mintewab Bezabih <Mintewab.Bezabih at economics.gu.se> wrote:

> Dear Jeff and R users,
>
> Thanks Jeff.
>
> Your first plot suggestion worked. And when I stick dat$x1, dat$x2,dat$y, tpsfit seems to work as well. But it gives me a new error message
>
> tpsfit <- Tps(cbind(dat$x1, dat$x2), dat$y, scale.type="unscaled")
>
> Warning message:
> In gcv.Krig(out, nstep.cv = nstep.cv, verbose = verbose, cost = out$cost,  :
>  Value of pure error estimate  is outside possible range
>
> Then I get error messages for the subsequent lines as well.
>
> I have now attached the data. And here is the full code I am trying to run.
>
>
> dat <- read.table("E:/thin plate/thin plate.csv", header=T, sep=",")
> names(dat) <- c("x1", "x2", "y")
> library(fields)
> plot (dat)
>
> #load the fields package (containing Tps) and fit a thin plate spline
> tpsfit <- Tps(cbind(dat$x1, dat$x2), dat$y, scale.type="unscaled")
>
> #predict the thin plate spline on the fine grid and plot the fitting
> ngrid <- length(xf); grid <- cbind(rep(xf, ngrid), rep(xf, rep(ngrid, ngrid)))
> out.p1 <- predict(tpsfit, grid)
>
>
> persp(xf, xf, matrix(out.p1, ngrid, ngrid, byrow=F), theta=130, phi=20,
>      expand=0.45, xlab="x1", ylab="x2", zlab="y", xlim=c(0,1), ylim=c(0,1),
>      zlim=range(zf), ticktype="detailed", scale=F, main="gcv fitting")
>
> Many thanks once again.
>
> regards
> mintewab
>
>
>
> Från: Jeff Newmiller [jdnewmil at dcn.davis.ca.us]
> Skickat: den 5 december 2011 12:39
> Till: Mintewab Bezabih; Sarah Goslee
> Kopia: r-help at r-project.org
> Ämne: Re: [R] problems using the thin plate spline method
>
> Try
>
> plot( dat$x1, dat$y )
>
> or
>
> plot( x1, y, data=dat )
>
> Note that your example is still not reproducible because you have not supplied the data or a shortened version of your data for us to work with. Also, your problem is not with thin plates but with plot, and reading the help for that function by typing
>
> ?plot
>
> at the R command line would have provided you with more examples and usage info on how to get around this problem.
> ---------------------------------------------------------------------------
> Jeff Newmiller                        The     .....       .....  Go Live...
> DCN:<jdnewmil at dcn.davis.ca.us>        Basics: ##.#.       ##.#.  Live Go...
>                                      Live:   OO#.. Dead: OO#..  Playing
> Research Engineer (Solar/Batteries            O.O#.       #.O#.  with
> /Software/Embedded Controllers)               .OO#.       .OO#.  rocks...1k
> ---------------------------------------------------------------------------
> Sent from my phone. Please excuse my brevity.
>
> Mintewab Bezabih <Mintewab.Bezabih at economics.gu.se> wrote:
>
>> Dear Sarah and R users,
>>
>> Sorry again for not being explicit enough. Here is my full problem
>>
>>
>> dat <- read.table("E:/thin plate/thin plate.csv", header=T, sep=",")
>> dat
>> names(dat) <- c("x1", "x2", "y")
>> library(fields)
>> plot (dat)
>>
>> #load the fields package (containing Tps) and fit a thin plate spline
>> tpsfit <- Tps(cbind(x1, x2), y, scale.type="unscaled")
>>
>> What I meant when I said the graph works is when I do plot(dat) it does
>> plot of all my three variables. If I do plot(x1,y), though, I get the
>> 'object x1 not found' error message.
>>
>> Same when I do the next line tpsfit <- Tps(cbind(x1, x2), y,
>> scale.type="unscaled"). I get the same error message.
>>
>> I tried your suggestion of checking str(x1) and I get the same error
>> message (object x1 not found).
>> I also typed ls() and I get "dat" after that command.
>>
>> I followed the r tutorial guide to read my data and I am following the
>> r tutorial to guide me to apply the thin plate spline method.
>>
>> Regards,
>>
>> Mintewab
>> ________________________________________
>> Från: Sarah Goslee [sarah.goslee at gmail.com]
>> Skickat: den 4 december 2011 15:21
>> Till: Mintewab Bezabih
>> Kopia: r-help at r-project.org
>> Ämne: Re: [R] problems using the thin plate spline method
>>
>> Hello,
>>
>> On Sun, Dec 4, 2011 at 8:08 AM, Mintewab Bezabih
>> <Mintewab.Bezabih at economics.gu.se> wrote:
>>> Dear R users and Jeff,
>>>
>>> Sorry for not being quite explicit in my earlier message.
>>
>> And you are still not explicit. We have no idea what you've done.
>>
>>> My main problem is while my data seem to be read into R well (I
>> manage to graph them and all), I cannot get the following line to work.
>>>
>>> tpsfit <- Tps(cbind(x1, x2), y, scale.type="unscaled")
>>>
>>> and I get the following error message
>>>
>>> Error in as.matrix(x) :
>>> error in evaluating the argument 'x' in selecting a method for
>> function 'as.matrix': Error: object 'x1' not found
>>
>> I'd have to guess that there's no object x1. What does ls() tell you?
>> str(x1)?
>>
>> What do your data look like? You were already given instructions on how
>> to
>> include sample data to construct a reproducible example. You said that
>> graphing your data worked; how did you do so?
>>
>> The posting guide and the advice you were already given were both
>> offered for a reason. The querent needs to do the work of formulating
>> an understandable and answerable question.
>>
>> Sarah
>>
>>> thanks for help
>>> minti
>>> ________________________________________
>>> Från: Jeff Newmiller [jdnewmil at dcn.davis.ca.us]
>>> Skickat: den 3 december 2011 17:45
>>> Till: Mintewab Bezabih; r-help at r-project.org
>>> Ämne: Re: [R] problems using the thin plate spline method
>>>
>>> I can tell that you are puzzled and confused. Unfortunately, I am not
>> psychic, so I cannot tell what you did, and therefore cannot tell where
>> you went astray.
>>>
>>> The solution is for you to read the posting guide mentioned at the
>> bottom of every R-help message. Spend a little time to create a small
>> bit of data like yours if your actual data is large (subset and dput
>> are useful for this). Remember to include the output of sessionInfo,
>> and so on. Many times you are likely to find the answer yourself by
>> going through these steps, but they are essential for communication.
>>>
>>> Good luck.
>>> Sent from my phone. Please excuse my brevity.
>>>
>>> Mintewab Bezabih <Mintewab.Bezabih at economics.gu.se> wrote:
>>>
>>>> Dear R users,
>>>>
>>>> I am a beginner in R trying to apply the thin plate spline method to
>> my
>>>> climate data. I used the example in R to do so, and the lines seem to
>>>> run fine ( I am not getting errors) but I am not getting any output
>> in
>>>> the form of graph or anything. I got a warning message saying that
>>>> 'surface extends beyond box'.
>>>>
>>>> Any help is much appreciated.
>>>> thanks
>>>> minti
>>
>>
>> --
>> Sarah Goslee
>> http://www.functionaldiversity.org
>>
>> ______________________________________________
>> R-help at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.