[Vegan-commits] r2102 - pkg/vegan/tests/Examples
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Feb 21 10:03:18 CET 2012
Author: jarioksa
Date: 2012-02-21 10:03:18 +0100 (Tue, 21 Feb 2012)
New Revision: 2102
Modified:
pkg/vegan/tests/Examples/vegan-Ex.Rout.save
Log:
Squashed commit of the following:
commit 15b43b26bb65248bb07339233646943e8a9d0703
Author: Jari Oksanen <jari.oksanen at oulu.fi>
Date: Tue Feb 21 10:30:45 2012 +0200
update tests for print.summary.simper
Modified: pkg/vegan/tests/Examples/vegan-Ex.Rout.save
===================================================================
--- pkg/vegan/tests/Examples/vegan-Ex.Rout.save 2012-02-21 08:10:02 UTC (rev 2101)
+++ pkg/vegan/tests/Examples/vegan-Ex.Rout.save 2012-02-21 09:03:18 UTC (rev 2102)
@@ -1,8 +1,8 @@
-R version 2.14.1 (2011-12-22)
-Copyright (C) 2011 The R Foundation for Statistical Computing
+R Under development (unstable) (2012-02-21 r58440)
+Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
-Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
+Platform: x86_64-unknown-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
@@ -154,14 +154,14 @@
> plot(ef)
> ordisurf(mod ~ pH, varechem, knots = 1, add = TRUE)
Loading required package: mgcv
-This is mgcv 1.7-12. For overview type 'help("mgcv-package")'.
+This is mgcv 1.7-13. For overview type 'help("mgcv-package")'.
Family: gaussian
Link function: identity
Formula:
y ~ poly(x1, 1) + poly(x2, 1)
-<environment: 0x1021396d8>
+<environment: 0x2cbf5f8>
Total model degrees of freedom 3
GCV score: 0.0427924
@@ -2499,7 +2499,7 @@
Run 17 stress 0.1825664
... New best solution
... procrustes: rmse 0.0421789 max resid 0.1544029
-Run 18 stress 0.1843199
+Run 18 stress 0.1843201
Run 19 stress 0.2570123
Run 20 stress 0.3760596
> (fit <- envfit(ord, varechem, perm = 999))
@@ -2965,7 +2965,7 @@
Run 17 stress 0.1825664
... New best solution
... procrustes: rmse 0.0421789 max resid 0.1544029
-Run 18 stress 0.1843199
+Run 18 stress 0.1843201
Run 19 stress 0.2570123
Run 20 stress 0.3760596
> stressplot(mod)
@@ -4723,17 +4723,17 @@
> vare.mds <- monoMDS(vare.dist)
> with(varechem, ordisurf(vare.mds, Baresoil, bubble = 5))
Loading required package: mgcv
-This is mgcv 1.7-12. For overview type 'help("mgcv-package")'.
+This is mgcv 1.7-13. For overview type 'help("mgcv-package")'.
Family: gaussian
Link function: identity
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x109c72cd8>
+<environment: 0x95688d0>
Estimated degrees of freedom:
-6.4351 total = 7.435071
+6.4351 total = 7.43507
GCV score: 144.1236
>
@@ -4746,7 +4746,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x10969d268>
+<environment: 0x8ced6a8>
Estimated degrees of freedom:
6.1039 total = 7.103853
@@ -4758,13 +4758,13 @@
> ## Get fitted values
> calibrate(fit)
1 2 3 4 5 6 7
-22.0644614 6.0132251 3.6350483 4.1019742 9.0030989 5.9202601 8.6399184
+22.0644615 6.0132250 3.6350484 4.1019743 9.0030990 5.9202602 8.6399182
8 9 10 11 12 13 14
-11.0719303 0.6561781 35.2282118 10.4346331 7.2900018 5.5710617 24.6503110
+11.0719302 0.6561783 35.2282116 10.4346331 7.2900019 5.5710617 24.6503109
15 16 17 18 19 20 21
-18.8754521 29.7286543 5.6158934 9.5869716 3.2876267 2.7111721 10.7832857
+18.8754520 29.7286540 5.6158934 9.5869715 3.2876268 2.7111723 10.7832857
22 23 24
- 3.0020413 9.8128952 7.3656932
+ 3.0020415 9.8128952 7.3656934
>
> ## Plot method
> plot(fit, what = "contour")
@@ -4895,14 +4895,14 @@
> ## Map of PCNMs in the sample plot
> ordisurf(mite.xy, scores(pcnm1, choi=1), bubble = 4, main = "PCNM 1")
Loading required package: mgcv
-This is mgcv 1.7-12. For overview type 'help("mgcv-package")'.
+This is mgcv 1.7-13. For overview type 'help("mgcv-package")'.
Family: gaussian
Link function: identity
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x109ddf588>
+<environment: 0x7c82a40>
Estimated degrees of freedom:
8.9275 total = 9.927492
@@ -4915,7 +4915,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x1094cc2e8>
+<environment: 0x9fbbb60>
Estimated degrees of freedom:
7.7529 total = 8.75294
@@ -4928,7 +4928,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x10916cb58>
+<environment: 0x7f79688>
Estimated degrees of freedom:
8.8962 total = 9.89616
@@ -5694,8 +5694,8 @@
[2,] 0.1169579 0.9931369
Translation of averages:
- [,1] [,2]
-[1,] 3.893131e-18 -9.725997e-18
+ [,1] [,2]
+[1,] 1.79048e-17 9.246476e-19
Scaling of target:
[1] 0.6736868
@@ -6034,206 +6034,210 @@
53.434466 57.564661 61.543243 65.341300 68.921695 72.432408
> summary(sim)
-$BF_SF
- contr sd ratio av.a av.b cumsum
-Agrsto 6.1373875 0.034193273 179.49108 0.0000000 4.6666667 9.824271
-Alogen 5.2667124 0.036475863 144.38897 0.6666667 4.3333333 18.254830
-Lolper 4.8116494 0.039445076 121.98353 6.0000000 3.0000000 25.956958
-Trirep 4.6297215 0.025525394 181.37708 4.6666667 1.3333333 33.367870
-Poatri 4.6020231 0.033801137 136.14995 3.6666667 4.6666667 40.734444
-Leoaut 4.3697453 0.024922188 175.33554 4.3333333 1.3333333 47.729205
-Brohor 3.3677364 0.025859567 130.23174 2.6666667 0.5000000 53.120026
-Achmil 3.0151964 0.020820614 144.81785 2.3333333 0.1666667 57.946526
-Plalan 2.8585347 0.021548975 132.65293 2.0000000 0.0000000 62.522255
-Elyrep 2.8074412 0.029777588 94.28034 1.3333333 2.0000000 67.016196
-Brarut 2.5500549 0.023901903 106.68837 2.0000000 2.0000000 71.098133
-Poapra 2.5128826 0.023967065 104.84732 4.0000000 2.5000000 75.120568
-Sagpro 2.4325600 0.022148544 109.82934 0.6666667 1.8333333 79.014428
-Belper 1.9858984 0.017087515 116.21926 1.6666667 0.6666667 82.193305
-Elepal 1.8611486 0.042957616 43.32523 0.0000000 1.3333333 85.172493
-Antodo 1.7542572 0.025803830 67.98437 1.3333333 0.0000000 87.980576
-Junbuf 1.6031063 0.023707975 67.61886 0.0000000 1.1666667 90.546709
-Viclat 1.4671255 0.013306461 110.25663 1.0000000 0.0000000 92.895173
-Hyprad 1.0285612 0.015197764 67.67845 0.6666667 0.0000000 94.541617
-Ranfla 0.9305743 0.013595007 68.44971 0.0000000 0.6666667 96.031211
-Junart 0.6979307 0.016109106 43.32523 0.0000000 0.5000000 97.148406
-Calcus 0.6979307 0.016109106 43.32523 0.0000000 0.5000000 98.265601
-Rumace 0.4525878 0.010444461 43.33280 0.0000000 0.3333333 98.990070
-Cirarv 0.3982767 0.009184791 43.36263 0.0000000 0.3333333 99.627602
-Chealb 0.2326436 0.005369702 43.32523 0.0000000 0.1666667 100.000000
-Empnig 0.0000000 0.000000000 NaN 0.0000000 0.0000000 100.000000
-Airpra 0.0000000 0.000000000 NaN 0.0000000 0.0000000 100.000000
-Potpal 0.0000000 0.000000000 NaN 0.0000000 0.0000000 100.000000
-Tripra 0.0000000 0.000000000 NaN 0.0000000 0.0000000 100.000000
-Salrep 0.0000000 0.000000000 NaN 0.0000000 0.0000000 100.000000
-$BF_HF
- contr sd ratio av.a av.b cumsum
-Rumace 3.8666202 0.02605967 148.37562 0.0000000 3.2 8.163219
-Poatri 3.3301297 0.02579295 129.11008 3.6666667 4.8 15.193797
-Plalan 3.1851684 0.01830432 174.01181 2.0000000 3.0 21.918333
-Brohor 2.8651195 0.01799001 159.26170 2.6666667 0.8 27.967181
-Lolper 2.8431092 0.02215330 128.33796 6.0000000 4.0 33.969561
-Elyrep 2.7821948 0.02958641 94.03624 1.3333333 2.0 39.843338
-Trirep 2.5837719 0.01655977 156.02708 4.6666667 2.8 45.298204
-Antodo 2.3582034 0.02042340 115.46577 1.3333333 1.8 50.276849
-Achmil 2.3426457 0.01474036 158.92727 2.3333333 1.2 55.222648
-Brarut 2.2732759 0.01801781 126.16829 2.0000000 2.8 60.021994
-Alogen 2.1610138 0.02308107 93.62711 0.6666667 1.6 64.584333
-Tripra 2.1514461 0.02207334 97.46810 0.0000000 1.8 69.126471
-Junart 2.0084049 0.02555374 78.59534 0.0000000 1.6 73.366621
-Leoaut 1.9318258 0.01356486 142.41397 4.3333333 2.8 77.445097
-Belper 1.8289995 0.01486414 123.04777 1.6666667 0.4 81.306485
-Agrsto 1.7605184 0.02284119 77.07646 0.0000000 1.4 85.023296
-Junbuf 1.4999755 0.02066084 72.59994 0.0000000 1.2 88.190049
-Viclat 1.2848484 0.01139618 112.74378 1.0000000 0.0 90.902624
-Sagpro 1.1684667 0.01297192 90.07661 0.6666667 0.8 93.369494
-Elepal 1.0168588 0.02110771 48.17475 0.0000000 0.8 95.516289
-Hyprad 0.8949950 0.01311558 68.23909 0.6666667 0.0 97.405805
-Poapra 0.7203468 0.01009842 71.33262 4.0000000 3.4 98.926603
-Ranfla 0.5084294 0.01055386 48.17475 0.0000000 0.4 100.000000
-Empnig 0.0000000 0.00000000 NaN 0.0000000 0.0 100.000000
-Airpra 0.0000000 0.00000000 NaN 0.0000000 0.0 100.000000
-Cirarv 0.0000000 0.00000000 NaN 0.0000000 0.0 100.000000
-Potpal 0.0000000 0.00000000 NaN 0.0000000 0.0 100.000000
-Calcus 0.0000000 0.00000000 NaN 0.0000000 0.0 100.000000
-Salrep 0.0000000 0.00000000 NaN 0.0000000 0.0 100.000000
-Chealb 0.0000000 0.00000000 NaN 0.0000000 0.0 100.000000
+Contrast: BF_SF
-$BF_NM
- contr sd ratio av.a av.b cumsum
-Lolper 9.0680890 0.02644343 342.92411 6.0000000 0.3333333 12.42718
-Poatri 5.4684115 0.04464645 122.48255 3.6666667 0.0000000 19.92126
-Poapra 5.2511240 0.01812886 289.65557 4.0000000 0.6666667 27.11756
-Trirep 5.1287027 0.02755807 186.10529 4.6666667 1.8333333 34.14609
-Brohor 3.9689114 0.02920386 135.90364 2.6666667 0.0000000 39.58520
-Brarut 3.5722867 0.02868949 124.51550 2.0000000 2.8333333 44.48077
-Elepal 3.3759250 0.03572888 94.48730 0.0000000 2.1666667 49.10724
-Agrsto 3.3446318 0.03473296 96.29563 0.0000000 2.1666667 53.69083
-Achmil 3.3189820 0.02337698 141.97651 2.3333333 0.3333333 58.23926
-Leoaut 3.1356499 0.02025675 154.79531 4.3333333 3.1666667 62.53645
-Antodo 2.8059604 0.03294714 85.16553 1.3333333 1.3333333 66.38182
-Plalan 2.7319482 0.02192961 124.57807 2.0000000 0.8333333 70.12577
-Salrep 2.6770230 0.02927399 91.44715 0.0000000 1.8333333 73.79444
-Belper 2.3528522 0.01909409 123.22410 1.6666667 0.3333333 77.01886
-Hyprad 2.1720695 0.02450331 88.64393 0.6666667 1.1666667 79.99553
-Ranfla 2.0313589 0.02275206 89.28243 0.0000000 1.3333333 82.77937
-Elyrep 1.9993334 0.02926048 68.32880 1.3333333 0.0000000 85.51931
-Calcus 1.7832867 0.02680560 66.52664 0.0000000 1.1666667 87.96318
-Junart 1.7694138 0.02599948 68.05575 0.0000000 1.1666667 90.38804
-Viclat 1.5772799 0.01446762 109.02141 1.0000000 0.1666667 92.54959
-Sagpro 1.5432494 0.01857093 83.10028 0.6666667 0.5000000 94.66451
-Airpra 1.3409953 0.01969485 68.08862 0.0000000 0.8333333 96.50225
-Potpal 1.0739109 0.01571113 68.35352 0.0000000 0.6666667 97.97397
-Alogen 0.9996667 0.01463024 68.32880 0.6666667 0.0000000 99.34394
-Empnig 0.4787240 0.01105165 43.31697 0.0000000 0.3333333 100.00000
-Junbuf 0.0000000 0.00000000 NaN 0.0000000 0.0000000 100.00000
-Rumace 0.0000000 0.00000000 NaN 0.0000000 0.0000000 100.00000
-Cirarv 0.0000000 0.00000000 NaN 0.0000000 0.0000000 100.00000
-Tripra 0.0000000 0.00000000 NaN 0.0000000 0.0000000 100.00000
-Chealb 0.0000000 0.00000000 NaN 0.0000000 0.0000000 100.00000
+ contr sd ratio av.a av.b cumsum
+Agrsto 6.1374 0.034193 179.49 0.0000 4.6667 9.824
+Alogen 5.2667 0.036476 144.39 0.6667 4.3333 18.255
+Lolper 4.8116 0.039445 121.98 6.0000 3.0000 25.957
+Trirep 4.6297 0.025525 181.38 4.6667 1.3333 33.368
+Poatri 4.6020 0.033801 136.15 3.6667 4.6667 40.734
+Leoaut 4.3697 0.024922 175.34 4.3333 1.3333 47.729
+Brohor 3.3677 0.025860 130.23 2.6667 0.5000 53.120
+Achmil 3.0152 0.020821 144.82 2.3333 0.1667 57.947
+Plalan 2.8585 0.021549 132.65 2.0000 0.0000 62.522
+Elyrep 2.8074 0.029778 94.28 1.3333 2.0000 67.016
+Brarut 2.5501 0.023902 106.69 2.0000 2.0000 71.098
+Poapra 2.5129 0.023967 104.85 4.0000 2.5000 75.121
+Sagpro 2.4326 0.022149 109.83 0.6667 1.8333 79.014
+Belper 1.9859 0.017088 116.22 1.6667 0.6667 82.193
+Elepal 1.8611 0.042958 43.33 0.0000 1.3333 85.172
+Antodo 1.7543 0.025804 67.98 1.3333 0.0000 87.981
+Junbuf 1.6031 0.023708 67.62 0.0000 1.1667 90.547
+Viclat 1.4671 0.013306 110.26 1.0000 0.0000 92.895
+Hyprad 1.0286 0.015198 67.68 0.6667 0.0000 94.542
+Ranfla 0.9306 0.013595 68.45 0.0000 0.6667 96.031
+Junart 0.6979 0.016109 43.33 0.0000 0.5000 97.148
+Calcus 0.6979 0.016109 43.33 0.0000 0.5000 98.266
+Rumace 0.4526 0.010444 43.33 0.0000 0.3333 98.990
+Cirarv 0.3983 0.009185 43.36 0.0000 0.3333 99.628
+Chealb 0.2326 0.005370 43.33 0.0000 0.1667 100.000
+Empnig 0.0000 0.000000 NaN 0.0000 0.0000 100.000
+Airpra 0.0000 0.000000 NaN 0.0000 0.0000 100.000
+Potpal 0.0000 0.000000 NaN 0.0000 0.0000 100.000
+Tripra 0.0000 0.000000 NaN 0.0000 0.0000 100.000
+Salrep 0.0000 0.000000 NaN 0.0000 0.0000 100.000
-$SF_HF
- contr sd ratio av.a av.b cumsum
-Agrsto 4.7380081 0.031272715 151.50613 4.6666667 1.4 8.350879
-Alogen 4.6433015 0.032896891 141.14712 4.3333333 1.6 16.534834
-Lolper 4.1985660 0.027006718 155.46377 3.0000000 4.0 23.934930
-Plalan 3.9197607 0.033208288 118.03562 0.0000000 3.0 30.843624
-Rumace 3.8992342 0.027368676 142.47069 0.3333333 3.2 37.716139
-Elyrep 3.1876647 0.029550307 107.87247 2.0000000 2.0 43.334492
-Poatri 2.8466256 0.021521731 132.26750 4.6666667 4.8 48.351753
-Brarut 2.5260809 0.021044097 120.03751 2.0000000 2.8 52.804045
-Elepal 2.4974367 0.038876909 64.23959 1.3333333 0.8 57.205850
-Poapra 2.3932257 0.019179734 124.77888 2.5000000 3.4 61.423981
-Antodo 2.3408728 0.021430212 109.23237 0.0000000 1.8 65.549838
-Sagpro 2.3143518 0.020478964 113.01118 1.8333333 0.8 69.628951
-Tripra 2.3079782 0.023431610 98.49849 0.0000000 1.8 73.696831
-Junart 2.2849877 0.025676555 88.99121 0.5000000 1.6 77.724189
-Trirep 2.2382699 0.019486710 114.86135 1.3333333 2.8 81.669205
-Junbuf 2.1642678 0.022237444 97.32538 1.1666667 1.2 85.483791
-Leoaut 2.0509314 0.016422027 124.88905 1.3333333 2.8 89.098618
-Achmil 1.5183100 0.011393329 133.26307 0.1666667 1.2 91.774684
-Brohor 1.3375437 0.014503626 92.22133 0.5000000 0.8 94.132144
-Ranfla 1.0660700 0.013386946 79.63504 0.6666667 0.4 96.011124
-Belper 0.9990990 0.012570517 79.47955 0.6666667 0.4 97.772065
-Calcus 0.6623417 0.015076322 43.93258 0.5000000 0.0 98.939462
-Cirarv 0.3809333 0.008669044 43.94178 0.3333333 0.0 99.610868
-Chealb 0.2207806 0.005025441 43.93258 0.1666667 0.0 100.000000
-Empnig 0.0000000 0.000000000 NaN 0.0000000 0.0 100.000000
-Airpra 0.0000000 0.000000000 NaN 0.0000000 0.0 100.000000
-Viclat 0.0000000 0.000000000 NaN 0.0000000 0.0 100.000000
-Hyprad 0.0000000 0.000000000 NaN 0.0000000 0.0 100.000000
-Potpal 0.0000000 0.000000000 NaN 0.0000000 0.0 100.000000
-Salrep 0.0000000 0.000000000 NaN 0.0000000 0.0 100.000000
+Contrast: BF_HF
-$SF_NM
- contr sd ratio av.a av.b cumsum
-Poatri 7.8284148 0.040947182 191.18324 4.6666667 0.0000000 10.13601
-Alogen 7.1219425 0.046958337 151.66513 4.3333333 0.0000000 19.35731
-Agrsto 5.6508187 0.044176062 127.91585 4.6666667 2.1666667 26.67383
-Lolper 5.4851012 0.059913861 91.54979 3.0000000 0.3333333 33.77578
-Elepal 4.8027074 0.047168454 101.82033 1.3333333 2.1666667 39.99419
-Poapra 4.0724386 0.031790183 128.10365 2.5000000 0.6666667 45.26707
-Brarut 4.0008412 0.034397513 116.31193 2.0000000 2.8333333 50.44725
-Elyrep 3.5598394 0.038515239 92.42678 2.0000000 0.0000000 55.05643
-Leoaut 3.2474710 0.034813104 93.28301 1.3333333 3.1666667 59.26117
-Trirep 3.0429642 0.031634061 96.19265 1.3333333 1.8333333 63.20111
-Sagpro 3.0303946 0.030476566 99.43360 1.8333333 0.5000000 67.12478
-Salrep 2.9275366 0.032014215 91.44490 0.0000000 1.8333333 70.91528
-Antodo 2.4541140 0.036694444 66.87972 0.0000000 1.3333333 74.09279
-Calcus 2.2762575 0.029443338 77.30976 0.5000000 1.1666667 77.04003
-Ranfla 2.2566173 0.022818681 98.89341 0.6666667 1.3333333 79.96183
-Junart 2.2542858 0.028597560 78.82791 0.5000000 1.1666667 82.88062
-Hyprad 2.0108243 0.031290623 64.26284 0.0000000 1.1666667 85.48418
-Junbuf 1.9859538 0.029033704 68.40167 1.1666667 0.0000000 88.05554
-Plalan 1.5420359 0.022769128 67.72486 0.0000000 0.8333333 90.05212
-Airpra 1.4883128 0.021880904 68.01880 0.0000000 0.8333333 91.97915
-Belper 1.2317474 0.015920540 77.36844 0.6666667 0.3333333 93.57398
-Potpal 1.1882720 0.017406896 68.26444 0.0000000 0.6666667 95.11252
-Achmil 0.9293657 0.014931384 62.24244 0.1666667 0.3333333 96.31584
-Brohor 0.7172498 0.016333288 43.91338 0.5000000 0.0000000 97.24451
-Rumace 0.5590144 0.012750682 43.84192 0.3333333 0.0000000 97.96831
-Empnig 0.5225116 0.012000618 43.54039 0.0000000 0.3333333 98.64484
-Cirarv 0.4781666 0.010888859 43.91338 0.3333333 0.0000000 99.26396
-Chealb 0.2893083 0.006601805 43.82261 0.1666667 0.0000000 99.63855
-Viclat 0.2791635 0.006424596 43.45230 0.0000000 0.1666667 100.00000
-Tripra 0.0000000 0.000000000 NaN 0.0000000 0.0000000 100.00000
+ contr sd ratio av.a av.b cumsum
+Rumace 3.8666 0.02606 148.38 0.0000 3.2 8.163
+Poatri 3.3301 0.02579 129.11 3.6667 4.8 15.194
+Plalan 3.1852 0.01830 174.01 2.0000 3.0 21.918
+Brohor 2.8651 0.01799 159.26 2.6667 0.8 27.967
+Lolper 2.8431 0.02215 128.34 6.0000 4.0 33.970
+Elyrep 2.7822 0.02959 94.04 1.3333 2.0 39.843
+Trirep 2.5838 0.01656 156.03 4.6667 2.8 45.298
+Antodo 2.3582 0.02042 115.47 1.3333 1.8 50.277
+Achmil 2.3426 0.01474 158.93 2.3333 1.2 55.223
+Brarut 2.2733 0.01802 126.17 2.0000 2.8 60.022
+Alogen 2.1610 0.02308 93.63 0.6667 1.6 64.584
+Tripra 2.1514 0.02207 97.47 0.0000 1.8 69.126
+Junart 2.0084 0.02555 78.60 0.0000 1.6 73.367
+Leoaut 1.9318 0.01356 142.41 4.3333 2.8 77.445
+Belper 1.8290 0.01486 123.05 1.6667 0.4 81.306
+Agrsto 1.7605 0.02284 77.08 0.0000 1.4 85.023
+Junbuf 1.5000 0.02066 72.60 0.0000 1.2 88.190
+Viclat 1.2848 0.01140 112.74 1.0000 0.0 90.903
+Sagpro 1.1685 0.01297 90.08 0.6667 0.8 93.369
+Elepal 1.0169 0.02111 48.17 0.0000 0.8 95.516
+Hyprad 0.8950 0.01312 68.24 0.6667 0.0 97.406
+Poapra 0.7203 0.01010 71.33 4.0000 3.4 98.927
+Ranfla 0.5084 0.01055 48.17 0.0000 0.4 100.000
+Empnig 0.0000 0.00000 NaN 0.0000 0.0 100.000
+Airpra 0.0000 0.00000 NaN 0.0000 0.0 100.000
+Cirarv 0.0000 0.00000 NaN 0.0000 0.0 100.000
+Potpal 0.0000 0.00000 NaN 0.0000 0.0 100.000
+Calcus 0.0000 0.00000 NaN 0.0000 0.0 100.000
+Salrep 0.0000 0.00000 NaN 0.0000 0.0 100.000
+Chealb 0.0000 0.00000 NaN 0.0000 0.0 100.000
-$HF_NM
- contr sd ratio av.a av.b cumsum
-Poatri 7.1552962 0.013680801 523.01735 4.8 0.0000000 9.913221
-Lolper 5.4533212 0.029624608 184.08079 4.0 0.3333333 17.468460
-Rumace 4.6546497 0.030806132 151.09491 3.2 0.0000000 23.917190
-Poapra 4.1749543 0.018851704 221.46297 3.4 0.6666667 29.701331
-Plalan 4.1632907 0.029559966 140.84220 3.0 0.8333333 35.469313
-Brarut 3.5340259 0.020103791 175.78903 2.8 2.8333333 40.365488
-Elepal 3.2043023 0.032314877 99.15873 0.8 2.1666667 44.804851
-Agrsto 3.1915495 0.028887302 110.48278 1.4 2.1666667 49.226546
-Trirep 3.0372486 0.022871293 132.79742 2.8 1.8333333 53.434466
-Elyrep 2.9811469 0.038675842 77.08033 2.0 0.0000000 57.564661
-Antodo 2.8717143 0.024799203 115.79865 1.8 1.3333333 61.543243
-Junart 2.7414119 0.028536540 96.06672 1.6 1.1666667 65.341300
-Tripra 2.5843049 0.025971573 99.50514 1.8 0.0000000 68.921695
-Salrep 2.5340091 0.027291287 92.85048 0.0 1.8333333 72.432408
-Alogen 2.4459371 0.032399067 75.49406 1.6 0.0000000 75.821103
-Leoaut 2.0703325 0.014124614 146.57622 2.8 3.1666667 78.689420
-Ranfla 1.9284693 0.019938840 96.71923 0.4 1.3333333 81.361196
-Junbuf 1.8180949 0.024648229 73.76168 1.2 0.0000000 83.880054
-Hyprad 1.7141357 0.026547931 64.56758 0.0 1.1666667 86.254883
-Calcus 1.6832709 0.024900688 67.59937 0.0 1.1666667 88.586951
-Achmil 1.6555393 0.014899781 111.11165 1.2 0.3333333 90.880598
-Sagpro 1.5282469 0.016534777 92.42622 0.8 0.5000000 92.997890
-Airpra 1.2605398 0.018242589 69.09873 0.0 0.8333333 94.744290
-Brohor 1.2093682 0.015168791 79.72739 0.8 0.0000000 96.419795
-Potpal 1.0105496 0.014556161 69.42419 0.0 0.6666667 97.819849
-Belper 0.8801475 0.013732352 64.09299 0.4 0.3333333 99.039239
-Empnig 0.4535959 0.010325282 43.93061 0.0 0.3333333 99.667668
-Viclat 0.2398752 0.005460872 43.92616 0.0 0.1666667 100.000000
-Cirarv 0.0000000 0.000000000 NaN 0.0 0.0000000 100.000000
-Chealb 0.0000000 0.000000000 NaN 0.0 0.0000000 100.000000
+Contrast: BF_NM
-attr(,"class")
-[1] "summary.simper"
+ contr sd ratio av.a av.b cumsum
+Lolper 9.0681 0.02644 342.92 6.0000 0.3333 12.43
+Poatri 5.4684 0.04465 122.48 3.6667 0.0000 19.92
+Poapra 5.2511 0.01813 289.66 4.0000 0.6667 27.12
+Trirep 5.1287 0.02756 186.11 4.6667 1.8333 34.15
+Brohor 3.9689 0.02920 135.90 2.6667 0.0000 39.59
+Brarut 3.5723 0.02869 124.52 2.0000 2.8333 44.48
+Elepal 3.3759 0.03573 94.49 0.0000 2.1667 49.11
+Agrsto 3.3446 0.03473 96.30 0.0000 2.1667 53.69
+Achmil 3.3190 0.02338 141.98 2.3333 0.3333 58.24
+Leoaut 3.1356 0.02026 154.80 4.3333 3.1667 62.54
+Antodo 2.8060 0.03295 85.17 1.3333 1.3333 66.38
+Plalan 2.7319 0.02193 124.58 2.0000 0.8333 70.13
+Salrep 2.6770 0.02927 91.45 0.0000 1.8333 73.79
+Belper 2.3529 0.01909 123.22 1.6667 0.3333 77.02
+Hyprad 2.1721 0.02450 88.64 0.6667 1.1667 80.00
+Ranfla 2.0314 0.02275 89.28 0.0000 1.3333 82.78
+Elyrep 1.9993 0.02926 68.33 1.3333 0.0000 85.52
+Calcus 1.7833 0.02681 66.53 0.0000 1.1667 87.96
+Junart 1.7694 0.02600 68.06 0.0000 1.1667 90.39
+Viclat 1.5773 0.01447 109.02 1.0000 0.1667 92.55
+Sagpro 1.5432 0.01857 83.10 0.6667 0.5000 94.66
+Airpra 1.3410 0.01969 68.09 0.0000 0.8333 96.50
+Potpal 1.0739 0.01571 68.35 0.0000 0.6667 97.97
+Alogen 0.9997 0.01463 68.33 0.6667 0.0000 99.34
+Empnig 0.4787 0.01105 43.32 0.0000 0.3333 100.00
+Junbuf 0.0000 0.00000 NaN 0.0000 0.0000 100.00
+Rumace 0.0000 0.00000 NaN 0.0000 0.0000 100.00
+Cirarv 0.0000 0.00000 NaN 0.0000 0.0000 100.00
+Tripra 0.0000 0.00000 NaN 0.0000 0.0000 100.00
+Chealb 0.0000 0.00000 NaN 0.0000 0.0000 100.00
+
+Contrast: SF_HF
+
+ contr sd ratio av.a av.b cumsum
+Agrsto 4.7380 0.031273 151.51 4.6667 1.4 8.351
+Alogen 4.6433 0.032897 141.15 4.3333 1.6 16.535
+Lolper 4.1986 0.027007 155.46 3.0000 4.0 23.935
+Plalan 3.9198 0.033208 118.04 0.0000 3.0 30.844
+Rumace 3.8992 0.027369 142.47 0.3333 3.2 37.716
+Elyrep 3.1877 0.029550 107.87 2.0000 2.0 43.334
+Poatri 2.8466 0.021522 132.27 4.6667 4.8 48.352
+Brarut 2.5261 0.021044 120.04 2.0000 2.8 52.804
+Elepal 2.4974 0.038877 64.24 1.3333 0.8 57.206
+Poapra 2.3932 0.019180 124.78 2.5000 3.4 61.424
+Antodo 2.3409 0.021430 109.23 0.0000 1.8 65.550
+Sagpro 2.3144 0.020479 113.01 1.8333 0.8 69.629
+Tripra 2.3080 0.023432 98.50 0.0000 1.8 73.697
+Junart 2.2850 0.025677 88.99 0.5000 1.6 77.724
+Trirep 2.2383 0.019487 114.86 1.3333 2.8 81.669
+Junbuf 2.1643 0.022237 97.33 1.1667 1.2 85.484
+Leoaut 2.0509 0.016422 124.89 1.3333 2.8 89.099
+Achmil 1.5183 0.011393 133.26 0.1667 1.2 91.775
+Brohor 1.3375 0.014504 92.22 0.5000 0.8 94.132
+Ranfla 1.0661 0.013387 79.64 0.6667 0.4 96.011
+Belper 0.9991 0.012571 79.48 0.6667 0.4 97.772
+Calcus 0.6623 0.015076 43.93 0.5000 0.0 98.939
+Cirarv 0.3809 0.008669 43.94 0.3333 0.0 99.611
+Chealb 0.2208 0.005025 43.93 0.1667 0.0 100.000
+Empnig 0.0000 0.000000 NaN 0.0000 0.0 100.000
+Airpra 0.0000 0.000000 NaN 0.0000 0.0 100.000
+Viclat 0.0000 0.000000 NaN 0.0000 0.0 100.000
+Hyprad 0.0000 0.000000 NaN 0.0000 0.0 100.000
+Potpal 0.0000 0.000000 NaN 0.0000 0.0 100.000
+Salrep 0.0000 0.000000 NaN 0.0000 0.0 100.000
+
+Contrast: SF_NM
+
+ contr sd ratio av.a av.b cumsum
+Poatri 7.8284 0.040947 191.18 4.6667 0.0000 10.14
+Alogen 7.1219 0.046958 151.67 4.3333 0.0000 19.36
+Agrsto 5.6508 0.044176 127.92 4.6667 2.1667 26.67
+Lolper 5.4851 0.059914 91.55 3.0000 0.3333 33.78
+Elepal 4.8027 0.047168 101.82 1.3333 2.1667 39.99
+Poapra 4.0724 0.031790 128.10 2.5000 0.6667 45.27
+Brarut 4.0008 0.034398 116.31 2.0000 2.8333 50.45
+Elyrep 3.5598 0.038515 92.43 2.0000 0.0000 55.06
+Leoaut 3.2475 0.034813 93.28 1.3333 3.1667 59.26
+Trirep 3.0430 0.031634 96.19 1.3333 1.8333 63.20
+Sagpro 3.0304 0.030477 99.43 1.8333 0.5000 67.12
+Salrep 2.9275 0.032014 91.44 0.0000 1.8333 70.92
+Antodo 2.4541 0.036694 66.88 0.0000 1.3333 74.09
+Calcus 2.2763 0.029443 77.31 0.5000 1.1667 77.04
+Ranfla 2.2566 0.022819 98.89 0.6667 1.3333 79.96
+Junart 2.2543 0.028598 78.83 0.5000 1.1667 82.88
+Hyprad 2.0108 0.031291 64.26 0.0000 1.1667 85.48
+Junbuf 1.9860 0.029034 68.40 1.1667 0.0000 88.06
+Plalan 1.5420 0.022769 67.72 0.0000 0.8333 90.05
+Airpra 1.4883 0.021881 68.02 0.0000 0.8333 91.98
+Belper 1.2317 0.015921 77.37 0.6667 0.3333 93.57
+Potpal 1.1883 0.017407 68.26 0.0000 0.6667 95.11
+Achmil 0.9294 0.014931 62.24 0.1667 0.3333 96.32
+Brohor 0.7172 0.016333 43.91 0.5000 0.0000 97.24
+Rumace 0.5590 0.012751 43.84 0.3333 0.0000 97.97
+Empnig 0.5225 0.012001 43.54 0.0000 0.3333 98.64
+Cirarv 0.4782 0.010889 43.91 0.3333 0.0000 99.26
+Chealb 0.2893 0.006602 43.82 0.1667 0.0000 99.64
+Viclat 0.2792 0.006425 43.45 0.0000 0.1667 100.00
+Tripra 0.0000 0.000000 NaN 0.0000 0.0000 100.00
+
+Contrast: HF_NM
+
+ contr sd ratio av.a av.b cumsum
+Poatri 7.1553 0.013681 523.02 4.8 0.0000 9.913
+Lolper 5.4533 0.029625 184.08 4.0 0.3333 17.468
+Rumace 4.6546 0.030806 151.09 3.2 0.0000 23.917
+Poapra 4.1750 0.018852 221.46 3.4 0.6667 29.701
+Plalan 4.1633 0.029560 140.84 3.0 0.8333 35.469
+Brarut 3.5340 0.020104 175.79 2.8 2.8333 40.365
+Elepal 3.2043 0.032315 99.16 0.8 2.1667 44.805
+Agrsto 3.1915 0.028887 110.48 1.4 2.1667 49.227
+Trirep 3.0372 0.022871 132.80 2.8 1.8333 53.434
+Elyrep 2.9811 0.038676 77.08 2.0 0.0000 57.565
+Antodo 2.8717 0.024799 115.80 1.8 1.3333 61.543
+Junart 2.7414 0.028537 96.07 1.6 1.1667 65.341
+Tripra 2.5843 0.025972 99.51 1.8 0.0000 68.922
+Salrep 2.5340 0.027291 92.85 0.0 1.8333 72.432
+Alogen 2.4459 0.032399 75.49 1.6 0.0000 75.821
+Leoaut 2.0703 0.014125 146.58 2.8 3.1667 78.689
+Ranfla 1.9285 0.019939 96.72 0.4 1.3333 81.361
+Junbuf 1.8181 0.024648 73.76 1.2 0.0000 83.880
+Hyprad 1.7141 0.026548 64.57 0.0 1.1667 86.255
+Calcus 1.6833 0.024901 67.60 0.0 1.1667 88.587
+Achmil 1.6555 0.014900 111.11 1.2 0.3333 90.881
+Sagpro 1.5282 0.016535 92.43 0.8 0.5000 92.998
+Airpra 1.2605 0.018243 69.10 0.0 0.8333 94.744
+Brohor 1.2094 0.015169 79.73 0.8 0.0000 96.420
+Potpal 1.0105 0.014556 69.42 0.0 0.6667 97.820
+Belper 0.8801 0.013732 64.09 0.4 0.3333 99.039
+Empnig 0.4536 0.010325 43.93 0.0 0.3333 99.668
+Viclat 0.2399 0.005461 43.93 0.0 0.1667 100.000
+Cirarv 0.0000 0.000000 NaN 0.0 0.0000 100.000
+Chealb 0.0000 0.000000 NaN 0.0 0.0000 100.000
>
>
>
@@ -7286,7 +7290,7 @@
Run 17 stress 0.1825664
... New best solution
... procrustes: rmse 0.0421789 max resid 0.1544029
-Run 18 stress 0.1843199
+Run 18 stress 0.1843201
Run 19 stress 0.2570123
Run 20 stress 0.3760596
> plot(ord, type = "t")
@@ -7456,14 +7460,14 @@
> ## add fitted surface of diversity to the model
> ordisurf(mod, diversity(dune), add = TRUE)
Loading required package: mgcv
-This is mgcv 1.7-12. For overview type 'help("mgcv-package")'.
+This is mgcv 1.7-13. For overview type 'help("mgcv-package")'.
Family: gaussian
Link function: identity
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x109f0bf90>
+<environment: 0x9a3e668>
Estimated degrees of freedom:
2 total = 3
@@ -7943,7 +7947,7 @@
> ### * <FOOTER>
> ###
> cat("Time elapsed: ", proc.time() - get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed: 81.254 1.591 83.713 0 0
+Time elapsed: 25.013 0.088 25.186 0 0
> grDevices::dev.off()
null device
1
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