'Error when using DiceKriging function km: 'Error in t.default(T) : argument is not a matrix'
I'm attempting to apply the km function from the DiceKriging package to a multivariate dataset. When I use my entire dataset (dimensions = [938,13]), the algorithm runs without problem. When I use a smaller subset of this dataset (dimensions = [94,13]), I encounter this error:
Error in t.default(T) : argument is not a matrix
I'm not sure what's causing this error to occur when analyzing the data subset. For reference, here's the data and code I'm running:
g<-km(design=sub.ev,response=sub.rv,covtype="matern5_2")
> sub.ev
1 -0.1519272795 1 0 0 27.769 27.45715 8.02 7.330 21.16 17.73979 0.000 4119.280 0.5338750
2 -0.1436123857 1 0 0 27.420 27.45715 8.04 6.895 20.19 17.73979 0.000 4119.280 0.5338750
3 -0.1144934053 1 0 0 27.021 27.45715 8.06 6.690 19.54 17.73979 0.000 4119.280 0.5338750
4 -0.1585420923 1 0 0 26.531 27.45715 8.09 6.160 18.64 17.73979 0.000 4119.280 0.5338750
5 -0.0588867480 1 0 0 26.107 27.45715 8.11 5.790 17.71 17.73979 0.000 4119.280 0.5338750
6 -0.0402306730 1 0 0 25.704 27.45715 8.15 5.840 17.26 17.73979 0.000 4119.280 0.5338750
7 0.0161781773 1 0 0 25.265 27.45715 8.18 5.390 16.77 17.73979 0.000 4119.280 0.5338750
8 0.0660891620 1 0 0 24.967 27.45715 8.21 5.425 16.18 17.73979 0.000 4119.280 0.5338750
9 0.0079745010 1 0 0 24.665 27.45715 8.24 5.250 16.51 17.73979 0.000 4119.280 0.5338750
10 -0.0191421967 1 0 0 24.416 27.45715 8.27 5.090 15.46 17.73979 0.000 4119.280 0.5338750
11 0.0364618430 1 0 0 24.232 27.45715 8.29 4.820 14.47 17.73979 0.000 4119.280 0.5338750
12 0.0160652203 1 0 0 24.077 27.45715 8.31 4.745 15.57 17.73979 0.000 4119.280 0.5338750
13 0.0763233707 1 0 0 23.906 27.45715 8.33 4.680 15.14 17.73979 0.000 4119.280 0.5338750
14 0.0211064293 1 0 0 23.794 27.45715 8.35 4.940 18.25 17.73979 0.000 4119.280 0.5338750
15 0.0166228227 1 0 0 23.642 27.45715 8.36 5.190 14.60 17.73979 0.000 4119.280 0.5338750
16 0.0022511447 1 0 0 23.531 27.45715 8.37 5.425 15.30 17.73979 0.000 4119.280 0.5338750
17 -0.0122220320 1 0 0 23.445 27.45715 8.39 6.110 14.79 17.73979 0.000 4119.280 0.5338750
18 -0.0057961107 1 0 0 23.442 27.45715 8.39 5.940 14.49 17.73979 0.000 4119.280 0.5338750
19 -0.0322631907 1 0 0 23.512 27.45715 8.39 5.380 14.38 17.73979 0.000 4119.280 0.5338750
95 0.0159845000 1 0 0 27.306 27.45715 8.24 7.380 17.14 17.73979 0.000 4119.280 0.5338750
96 -0.0437959553 1 0 0 27.054 27.45715 8.25 7.100 15.35 17.73979 0.000 4119.280 0.5338750
97 -0.0805486920 1 0 0 26.520 26.88009 8.27 6.900 14.87 16.96688 0.000 3725.365 0.5422500
98 -0.0941385073 1 0 0 26.306 26.88009 8.30 6.725 15.19 16.96688 0.000 3725.365 0.5422500
99 -0.1159254400 1 0 0 26.039 26.88009 8.32 6.590 15.42 16.96688 0.000 3725.365 0.5422500
100 -0.0362266430 1 0 0 25.637 26.88009 8.36 6.280 14.34 16.96688 0.000 3725.365 0.5422500
101 0.0326682983 1 0 0 25.299 26.88009 8.38 6.100 14.36 16.96688 0.000 3725.365 0.5422500
102 0.0471005793 1 0 0 24.742 26.88009 8.44 5.955 13.48 16.96688 0.000 3725.365 0.5422500
103 -0.0596346010 1 0 0 24.262 26.88009 8.49 5.530 12.91 16.96688 0.000 3725.365 0.5422500
104 -0.0043536683 1 0 0 23.856 26.88009 8.52 5.315 12.80 16.96688 0.000 3725.365 0.5422500
105 -0.0177714297 1 0 0 23.578 26.88009 8.54 5.240 13.01 16.96688 0.000 3725.365 0.5422500
106 0.0169363000 1 0 0 23.313 26.88009 8.56 5.225 12.69 16.96688 0.000 3725.365 0.5422500
107 -0.0170451183 1 0 0 23.023 26.88009 8.59 5.090 12.71 16.96688 0.000 3725.365 0.5422500
108 0.0231896353 1 0 0 22.755 26.88009 8.62 5.280 11.58 16.96688 0.000 3725.365 0.5422500
109 0.0053651757 1 0 0 22.510 26.88009 8.65 5.690 11.28 16.96688 0.000 3725.365 0.5422500
110 0.0281674793 1 0 0 22.342 26.88009 8.68 5.555 11.21 16.96688 0.000 3725.365 0.5422500
111 0.0009483843 1 0 0 22.168 26.88009 8.70 5.770 10.68 16.96688 0.000 3725.365 0.5422500
112 0.0147559413 1 0 0 22.151 26.88009 8.69 5.995 11.57 16.96688 0.000 3725.365 0.5422500
190 -0.0115338953 1 0 0 27.062 25.91990 8.21 8.000 15.35 14.07031 0.000 3949.390 0.5342917
191 -0.0189870410 1 0 0 26.545 25.91990 8.22 7.870 14.21 14.07031 0.000 3949.390 0.5342917
192 -0.0184237180 1 0 0 26.104 25.91990 8.25 7.795 20.04 14.07031 0.000 3949.390 0.5342917
193 -0.0319295797 1 0 0 25.859 25.91990 8.26 7.730 13.14 14.07031 0.000 3949.390 0.5342917
194 -0.0184753123 1 0 0 25.573 25.91990 8.30 7.585 12.93 14.07031 0.000 3949.390 0.5342917
195 -0.0197481060 1 0 0 25.005 25.91990 8.36 7.490 11.29 14.07031 0.000 3949.390 0.5342917
196 -0.0215467360 1 0 0 24.710 25.91990 8.39 7.245 11.10 14.07031 0.000 3949.390 0.5342917
197 0.0265223447 1 0 0 24.455 25.91990 8.42 7.240 11.44 14.07031 0.000 3949.390 0.5342917
198 0.0470763840 1 0 0 24.087 25.91990 8.45 7.225 11.42 14.07031 0.000 3949.390 0.5342917
199 0.0622169450 1 0 0 23.673 25.91990 8.48 7.260 11.20 14.07031 0.000 3949.390 0.5342917
200 -0.0104582193 1 0 0 23.301 25.91990 8.52 7.190 11.57 14.07031 0.000 3949.390 0.5342917
201 0.0121972077 1 0 0 23.005 25.91990 8.55 7.220 10.71 14.07031 0.000 3949.390 0.5342917
202 0.0219721027 1 0 0 22.745 25.91990 8.59 7.245 10.86 14.07031 0.000 3949.390 0.5342917
203 0.0208879210 1 0 0 22.576 25.91990 8.61 7.180 10.62 14.07031 0.000 3949.390 0.5342917
204 0.0192644400 1 0 0 22.417 25.91990 8.63 7.220 10.47 14.07031 0.000 3949.390 0.5342917
205 0.0066226250 1 0 0 22.243 25.91990 8.65 7.170 10.29 14.07031 0.000 3949.390 0.5342917
206 0.0036012053 1 0 0 22.136 25.91990 8.67 7.200 10.86 14.07031 0.000 3949.390 0.5342917
207 -0.0027906963 1 0 0 22.012 25.91990 8.69 7.150 10.57 14.07031 0.000 3949.390 0.5342917
290 0.2266387893 1 0 0 27.763 26.21360 8.21 7.765 23.37 17.97479 0.000 3554.510 0.5938333
291 0.1151646527 1 0 0 27.377 26.21360 8.23 7.720 24.43 17.97479 0.000 3554.510 0.5938333
292 -0.0218444193 1 0 0 27.285 26.21360 8.23 7.655 23.40 17.97479 0.000 3554.510 0.5938333
293 -0.0908422353 1 0 0 26.935 26.21360 8.26 7.590 21.96 17.97479 0.000 3554.510 0.5938333
294 -0.1716709177 1 0 0 26.792 26.21360 8.28 7.540 23.30 17.97479 0.000 3554.510 0.5938333
295 -0.1943201847 1 0 0 26.869 26.21360 8.28 7.420 25.06 17.97479 0.000 3554.510 0.5938333
296 -0.1529985130 1 0 0 26.733 26.21360 8.28 7.310 33.62 17.97479 0.000 3554.510 0.5938333
297 -0.1106344563 1 0 0 26.394 26.21360 8.29 7.160 29.06 17.97479 0.000 3554.510 0.5938333
298 -0.0638089193 1 0 0 25.973 26.21360 8.32 7.010 23.25 17.97479 0.000 3554.510 0.5938333
299 -0.1208449610 1 0 0 25.501 26.21360 8.37 6.970 21.10 17.97479 0.000 3554.510 0.5938333
300 -0.2310616323 1 0 0 25.192 26.21360 8.40 7.010 19.16 17.97479 0.000 3554.510 0.5938333
301 -0.2043969970 1 0 0 24.867 26.21360 8.43 7.030 17.80 17.97479 0.000 3554.510 0.5938333
302 -0.2003585363 1 0 0 24.634 26.21360 8.45 7.080 17.01 17.97479 0.000 3554.510 0.5938333
303 -0.2535806687 1 0 0 24.468 26.21360 8.47 7.130 16.41 17.97479 0.000 3554.510 0.5938333
304 -0.2464920640 1 0 0 24.234 26.21360 8.50 7.055 15.50 17.97479 0.000 3554.510 0.5938333
389 0.2461277410 1 0 0 27.981 26.78711 8.29 6.760 20.65 22.02125 0.000 3589.260 0.7715417
390 0.1660650063 1 0 0 27.915 26.78711 8.29 6.575 22.44 22.02125 0.000 3589.260 0.7715417
391 -0.0609562143 1 0 0 27.757 26.78711 8.30 6.580 22.92 22.02125 0.000 3589.260 0.7715417
392 -0.2020911323 1 0 0 27.527 26.78711 8.32 6.590 22.91 22.02125 0.000 3589.260 0.7715417
393 -0.2980735343 1 0 0 27.563 26.78711 8.31 6.510 24.30 22.02125 0.000 3589.260 0.7715417
394 -0.2370078227 1 0 0 27.400 26.78711 8.32 6.525 22.67 22.02125 0.000 3589.260 0.7715417
395 -0.3440380117 1 0 0 27.274 26.78711 8.32 6.530 22.45 22.02125 0.000 3589.260 0.7715417
396 -0.0057092573 1 0 0 27.132 26.78711 8.30 6.490 22.08 22.02125 0.000 3589.260 0.7715417
397 -0.0241878650 1 0 0 27.018 26.78711 8.30 6.450 24.00 22.02125 0.000 3589.260 0.7715417
398 -0.2080665820 1 0 0 26.834 26.78711 8.32 6.405 25.81 22.02125 0.000 3589.260 0.7715417
399 -0.1716383953 1 0 0 26.637 26.78711 8.33 6.340 25.19 22.02125 0.000 3589.260 0.7715417
400 -0.2570107420 1 0 0 26.476 26.78711 8.34 6.300 22.05 22.02125 0.000 3589.260 0.7715417
495 -0.1302196527 1 0 0 25.967 26.53893 8.40 6.300 11.90 15.57448 2.286 2313.087 0.6087083
496 -0.0391473870 1 0 0 25.708 26.53893 8.41 6.260 10.77 15.57448 2.286 2313.087 0.6087083
587 -0.0382961500 1 0 0 28.647 26.98353 8.28 8.110 17.52 12.12667 0.000 3980.156 0.4227083
588 -0.0035965477 1 0 0 28.652 26.98353 8.26 7.920 21.14 12.12667 0.000 3980.156 0.4227083
589 -0.0050414577 1 0 0 28.307 26.98353 8.27 7.830 18.39 12.12667 0.000 3980.156 0.4227083
590 0.0354186967 1 0 0 27.896 26.98353 8.27 6.825 17.35 12.12667 0.000 3980.156 0.4227083
591 -0.0676664363 1 0 0 27.581 26.98353 8.27 6.110 16.06 12.12667 0.000 3980.156 0.4227083
592 -0.1723716683 1 0 0 27.223 26.98353 8.29 6.245 15.14 12.12667 0.000 3980.156 0.4227083
688 0.1598606430 1 0 0 28.738 27.54833 8.35 5.965 24.99 15.51010 0.000 2554.804 0.4730417
912 -0.1977195740 1 0 0 26.653 27.24447 9.09 7.635 11.38 12.71729 0.000 4002.945 0.5135417
913 -0.1306465143 1 0 0 27.399 27.24447 9.07 7.420 12.84 12.71729 0.000 4002.945 0.5135417
914 -0.1175953210 1 0 0 28.024 27.24447 9.01 7.270 13.91 12.71729 0.000 4002.945 0.5135417
> sub.rv
[1] 3.24 2.65 2.18 1.75 1.52 1.32 1.25 1.18 1.16 1.10 1.05 1.01 0.95 0.88 0.83 0.76 0.72 0.61 0.58 3.64 3.46 2.97 2.64 2.27 2.07 1.72 1.33 1.03 0.89 0.82 0.69 0.64 0.60
[34] 0.55 0.44 0.33 0.26 4.65 4.10 3.55 3.30 2.70 2.12 1.74 1.53 1.27 1.02 0.88 0.76 0.66 0.58 0.54 0.47 0.40 0.28 5.87 5.24 5.09 4.22 3.90 3.94 3.41 2.75 2.18 1.86 1.67
[67] 1.52 1.42 1.34 1.35 5.88 5.56 4.88 3.98 3.76 3.31 3.11 2.78 2.41 1.97 1.65 1.39 1.63 1.44 4.08 4.83 3.84 3.23 2.83 2.36 4.33 1.86 3.17 4.48
Solution 1:[1]
I've run into the same issue. It is resolved when you remove the variables in your design matrix that have 0 variance (as these are simply constants). In your case, you need to remove columns (3:5).
Sources
This article follows the attribution requirements of Stack Overflow and is licensed under CC BY-SA 3.0.
Source: Stack Overflow
| Solution | Source |
|---|---|
| Solution 1 | watkilj |