[Vegan-commits] r2078 - in pkg/vegan: . R inst man tests/Examples
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Feb 9 17:45:22 CET 2012
Author: jarioksa
Date: 2012-02-09 17:45:22 +0100 (Thu, 09 Feb 2012)
New Revision: 2078
Modified:
pkg/vegan/DESCRIPTION
pkg/vegan/NAMESPACE
pkg/vegan/R/simper.R
pkg/vegan/inst/ChangeLog
pkg/vegan/man/simper.Rd
pkg/vegan/tests/Examples/vegan-Ex.Rout.save
Log:
janitorial fixes for r2077: encoding, NAMESPACE, version, tests
Modified: pkg/vegan/DESCRIPTION
===================================================================
--- pkg/vegan/DESCRIPTION 2012-02-09 16:25:02 UTC (rev 2077)
+++ pkg/vegan/DESCRIPTION 2012-02-09 16:45:22 UTC (rev 2078)
@@ -1,7 +1,7 @@
Package: vegan
Title: Community Ecology Package
-Version: 2.1-11
-Date: February 5, 2012
+Version: 2.1-12
+Date: February 9, 2012
Author: Jari Oksanen, F. Guillaume Blanchet, Roeland Kindt, Pierre Legendre,
Peter R. Minchin, R. B. O'Hara, Gavin L. Simpson, Peter Solymos,
M. Henry H. Stevens, Helene Wagner
Modified: pkg/vegan/NAMESPACE
===================================================================
--- pkg/vegan/NAMESPACE 2012-02-09 16:25:02 UTC (rev 2077)
+++ pkg/vegan/NAMESPACE 2012-02-09 16:45:22 UTC (rev 2078)
@@ -22,7 +22,7 @@
orglspider, orgltext, pcnm, permatfull, permatswap, permutest,
poolaccum, postMDS, prc, prestondistr, prestonfit, procrustes,
protest, radfit, radlattice, rankindex, rarefy, rarecurve, raupcrick,
-rda, renyiaccum, renyi, rrarefy, scores, showvarparts, spandepth,
+rda, renyiaccum, renyi, rrarefy, scores, showvarparts, simper, spandepth,
spantree, specaccum, specnumber, specpool2vect, specpool, spenvcor,
stepacross, stressplot, swan, taxa2dist, taxondive, tolerance,
treedist, treedive, treeheight, tsallisaccum, tsallis, varpart,
Modified: pkg/vegan/R/simper.R
===================================================================
--- pkg/vegan/R/simper.R 2012-02-09 16:25:02 UTC (rev 2077)
+++ pkg/vegan/R/simper.R 2012-02-09 16:45:22 UTC (rev 2078)
@@ -25,7 +25,8 @@
#' data(dune.env)
#' with(dune.env, simper(dune, Management))
-simper <- function(comm, group)
+`simper` <-
+ function(comm, group)
{
comp <- t(combn(unique(as.character(group)), 2))
outlist <- NULL
Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog 2012-02-09 16:25:02 UTC (rev 2077)
+++ pkg/vegan/inst/ChangeLog 2012-02-09 16:45:22 UTC (rev 2078)
@@ -2,8 +2,14 @@
VEGAN DEVEL VERSIONS at http://r-forge.r-project.org/
-Version 2.1-11 (opened February 5, 2012)
+Version 2.1-12 (opened February 9, 2012)
+
+ * simper: new function to implement "similarity percentages" of
+ Clarke (Austral Ecology 18, 117-143; 1993) contributed by Eduard
+ Szöcz (Uni Landau, Germany).
+Version 2.1-11 (closed February 9, 2012)
+
* indpower: now can handle input objects without dimnames. This
caused problems with oecosimu, because nullmodel objects have no
dimnames to save memory. Extended example on indpower help page
@@ -42,10 +48,6 @@
* renyi.Rd: fixed a broken link reported by Arne Erpenbach (Uni
Frankfurt, Germany).
- * simper: new function to implement "similarity percentages" of
- Clarke (Austral Ecology 18, 117-143; 1993) contributed by Eduard
- Szöcz (Uni Landau, Germany).
-
Version 2.1-10 (closed February 5, 2012)
* adonis: print info that terms are added sequentially -- this
Modified: pkg/vegan/man/simper.Rd
===================================================================
--- pkg/vegan/man/simper.Rd 2012-02-09 16:25:02 UTC (rev 2077)
+++ pkg/vegan/man/simper.Rd 2012-02-09 16:45:22 UTC (rev 2078)
@@ -1,3 +1,4 @@
+\encoding{UTF-8}
\name{simper}
\alias{simper}
\title{Similarity Percentages}
Modified: pkg/vegan/tests/Examples/vegan-Ex.Rout.save
===================================================================
--- pkg/vegan/tests/Examples/vegan-Ex.Rout.save 2012-02-09 16:25:02 UTC (rev 2077)
+++ pkg/vegan/tests/Examples/vegan-Ex.Rout.save 2012-02-09 16:45:22 UTC (rev 2078)
@@ -1,8 +1,8 @@
-R Under development (unstable) (2012-02-09 r58307)
-Copyright (C) 2012 The R Foundation for Statistical Computing
+R version 2.14.1 (2011-12-22)
+Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
-Platform: x86_64-unknown-linux-gnu (64-bit)
+Platform: x86_64-apple-darwin9.8.0/x86_64 (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 1.7-13. For overview type 'help("mgcv-package")'.
+This is mgcv 1.7-12. For overview type 'help("mgcv-package")'.
Family: gaussian
Link function: identity
Formula:
y ~ poly(x1, 1) + poly(x2, 1)
-<environment: 0x20775d8>
+<environment: 0x102131ae8>
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 0.1843201
+Run 18 stress 0.1843199
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 0.1843201
+Run 18 stress 0.1843199
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 1.7-13. For overview type 'help("mgcv-package")'.
+This is mgcv 1.7-12. For overview type 'help("mgcv-package")'.
Family: gaussian
Link function: identity
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x88f0bb8>
+<environment: 0x10abb98a0>
Estimated degrees of freedom:
-6.4351 total = 7.43507
+6.4351 total = 7.435071
GCV score: 144.1236
>
@@ -4746,7 +4746,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x7cf4060>
+<environment: 0x1097e0438>
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
-22.0644615 6.0132250 3.6350484 4.1019743 9.0030990 5.9202602 8.6399182
+22.0644614 6.0132251 3.6350483 4.1019742 9.0030989 5.9202601 8.6399184
8 9 10 11 12 13 14
-11.0719302 0.6561783 35.2282116 10.4346331 7.2900019 5.5710617 24.6503109
+11.0719303 0.6561781 35.2282118 10.4346331 7.2900018 5.5710617 24.6503110
15 16 17 18 19 20 21
-18.8754520 29.7286540 5.6158934 9.5869715 3.2876268 2.7111723 10.7832857
+18.8754521 29.7286543 5.6158934 9.5869716 3.2876267 2.7111721 10.7832857
22 23 24
- 3.0020415 9.8128952 7.3656934
+ 3.0020413 9.8128952 7.3656932
>
> ## 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 1.7-13. For overview type 'help("mgcv-package")'.
+This is mgcv 1.7-12. For overview type 'help("mgcv-package")'.
Family: gaussian
Link function: identity
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x706cbd8>
+<environment: 0x10acb8a28>
Estimated degrees of freedom:
8.9275 total = 9.927492
@@ -4915,7 +4915,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x576bdd0>
+<environment: 0x109f4be98>
Estimated degrees of freedom:
7.7529 total = 8.75294
@@ -4928,7 +4928,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x9068100>
+<environment: 0x10a85bdf8>
Estimated degrees of freedom:
8.8962 total = 9.89616
@@ -5694,8 +5694,8 @@
[2,] 0.1169579 0.9931369
Translation of averages:
- [,1] [,2]
-[1,] 1.79048e-17 9.246476e-19
+ [,1] [,2]
+[1,] 3.893131e-18 -9.725997e-18
Scaling of target:
[1] 0.6736868
@@ -5980,6 +5980,223 @@
>
>
> cleanEx()
+> nameEx("simper")
+> ### * simper
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: simper
+> ### Title: Similarity Percentages
+> ### Aliases: simper
+> ### Keywords: multivariate
+>
+> ### ** Examples
+>
+> data(dune)
+> data(dune.env)
+> with(dune.env, simper(dune, Management))
+$BF_SF
+ contr sd contr/sd av_BF av_SF cum
+Agrsto 6.1373875 0.034193273 0.005571308 0.0000000 4.6666667 9.824271
+Alogen 5.2667124 0.036475863 0.006925737 0.6666667 4.3333333 18.254830
+Lolper 4.8116494 0.039445076 0.008197828 6.0000000 3.0000000 25.956958
+Trirep 4.6297215 0.025525394 0.005513376 4.6666667 1.3333333 33.367870
+Poatri 4.6020231 0.033801137 0.007344843 3.6666667 4.6666667 40.734444
+Leoaut 4.3697453 0.024922188 0.005703350 4.3333333 1.3333333 47.729205
+Brohor 3.3677364 0.025859567 0.007678620 2.6666667 0.5000000 53.120026
+Achmil 3.0151964 0.020820614 0.006905226 2.3333333 0.1666667 57.946526
+Plalan 2.8585347 0.021548975 0.007538469 2.0000000 0.0000000 62.522255
+Elyrep 2.8074412 0.029777588 0.010606665 1.3333333 2.0000000 67.016196
+Brarut 2.5500549 0.023901903 0.009373093 2.0000000 2.0000000 71.098133
+Poapra 2.5128826 0.023967065 0.009537678 4.0000000 2.5000000 75.120568
+Sagpro 2.4325600 0.022148544 0.009105035 0.6666667 1.8333333 79.014428
+Belper 1.9858984 0.017087515 0.008604426 1.6666667 0.6666667 82.193305
+Elepal 1.8611486 0.042957616 0.023081239 0.0000000 1.3333333 85.172493
+Antodo 1.7542572 0.025803830 0.014709263 1.3333333 0.0000000 87.980576
+Junbuf 1.6031063 0.023707975 0.014788773 0.0000000 1.1666667 90.546709
+Viclat 1.4671255 0.013306461 0.009069750 1.0000000 0.0000000 92.895173
+Hyprad 1.0285612 0.015197764 0.014775751 0.6666667 0.0000000 94.541617
+Ranfla 0.9305743 0.013595007 0.014609265 0.0000000 0.6666667 96.031211
+Junart 0.6979307 0.016109106 0.023081239 0.0000000 0.5000000 97.148406
+Calcus 0.6979307 0.016109106 0.023081239 0.0000000 0.5000000 98.265601
+Rumace 0.4525878 0.010444461 0.023077206 0.0000000 0.3333333 98.990070
+Cirarv 0.3982767 0.009184791 0.023061332 0.0000000 0.3333333 99.627602
+Chealb 0.2326436 0.005369702 0.023081239 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 contr/sd av_BF av_HF cum
+Rumace 3.8666202 0.02605967 0.006739652 0.0000000 3.2 8.163219
+Poatri 3.3301297 0.02579295 0.007745329 3.6666667 4.8 15.193797
+Plalan 3.1851684 0.01830432 0.005746736 2.0000000 3.0 21.918333
+Brohor 2.8651195 0.01799001 0.006278973 2.6666667 0.8 27.967181
+Lolper 2.8431092 0.02215330 0.007791927 6.0000000 4.0 33.969561
+Elyrep 2.7821948 0.02958641 0.010634198 1.3333333 2.0 39.843338
+Trirep 2.5837719 0.01655977 0.006409144 4.6666667 2.8 45.298204
+Antodo 2.3582034 0.02042340 0.008660576 1.3333333 1.8 50.276849
+Achmil 2.3426457 0.01474036 0.006292186 2.3333333 1.2 55.222648
+Brarut 2.2732759 0.01801781 0.007925922 2.0000000 2.8 60.021994
+Alogen 2.1610138 0.02308107 0.010680667 0.6666667 1.6 64.584333
+Tripra 2.1514461 0.02207334 0.010259767 0.0000000 1.8 69.126471
+Junart 2.0084049 0.02555374 0.012723400 0.0000000 1.6 73.366621
+Leoaut 1.9318258 0.01356486 0.007021783 4.3333333 2.8 77.445097
+Belper 1.8289995 0.01486414 0.008126925 1.6666667 0.4 81.306485
+Agrsto 1.7605184 0.02284119 0.012974130 0.0000000 1.4 85.023296
+Junbuf 1.4999755 0.02066084 0.013774115 0.0000000 1.2 88.190049
+Viclat 1.2848484 0.01139618 0.008869669 1.0000000 0.0 90.902624
+Sagpro 1.1684667 0.01297192 0.011101662 0.6666667 0.8 93.369494
+Elepal 1.0168588 0.02110771 0.020757761 0.0000000 0.8 95.516289
+Hyprad 0.8949950 0.01311558 0.014654358 0.6666667 0.0 97.405805
+Poapra 0.7203468 0.01009842 0.014018831 4.0000000 3.4 98.926603
+Ranfla 0.5084294 0.01055386 0.020757761 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
+
+$BF_NM
+ contr sd contr/sd av_BF av_NM cum
+Lolper 9.0680890 0.02644343 0.002916097 6.0000000 0.3333333 12.42718
+Poatri 5.4684115 0.04464645 0.008164428 3.6666667 0.0000000 19.92126
+Poapra 5.2511240 0.01812886 0.003452376 4.0000000 0.6666667 27.11756
+Trirep 5.1287027 0.02755807 0.005373302 4.6666667 1.8333333 34.14609
+Brohor 3.9689114 0.02920386 0.007358154 2.6666667 0.0000000 39.58520
+Brarut 3.5722867 0.02868949 0.008031129 2.0000000 2.8333333 44.48077
+Elepal 3.3759250 0.03572888 0.010583433 0.0000000 2.1666667 49.10724
+Agrsto 3.3446318 0.03473296 0.010384687 0.0000000 2.1666667 53.69083
+Achmil 3.3189820 0.02337698 0.007043419 2.3333333 0.3333333 58.23926
+Leoaut 3.1356499 0.02025675 0.006460144 4.3333333 3.1666667 62.53645
+Antodo 2.8059604 0.03294714 0.011741840 1.3333333 1.3333333 66.38182
+Plalan 2.7319482 0.02192961 0.008027095 2.0000000 0.8333333 70.12577
+Salrep 2.6770230 0.02927399 0.010935277 0.0000000 1.8333333 73.79444
+Belper 2.3528522 0.01909409 0.008115295 1.6666667 0.3333333 77.01886
+Hyprad 2.1720695 0.02450331 0.011281089 0.6666667 1.1666667 79.99553
+Ranfla 2.0313589 0.02275206 0.011200412 0.0000000 1.3333333 82.77937
+Elyrep 1.9993334 0.02926048 0.014635117 1.3333333 0.0000000 85.51931
+Calcus 1.7832867 0.02680560 0.015031571 0.0000000 1.1666667 87.96318
+Junart 1.7694138 0.02599948 0.014693836 0.0000000 1.1666667 90.38804
+Viclat 1.5772799 0.01446762 0.009172510 1.0000000 0.1666667 92.54959
+Sagpro 1.5432494 0.01857093 0.012033654 0.6666667 0.5000000 94.66451
+Airpra 1.3409953 0.01969485 0.014686741 0.0000000 0.8333333 96.50225
+Potpal 1.0739109 0.01571113 0.014629824 0.0000000 0.6666667 97.97397
+Alogen 0.9996667 0.01463024 0.014635117 0.6666667 0.0000000 99.34394
+Empnig 0.4787240 0.01105165 0.023085641 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
+
+$SF_HF
+ contr sd contr/sd av_SF av_HF cum
+Agrsto 4.7380081 0.031272715 0.006600393 4.6666667 1.4 8.350879
+Alogen 4.6433015 0.032896891 0.007084806 4.3333333 1.6 16.534834
+Lolper 4.1985660 0.027006718 0.006432367 3.0000000 4.0 23.934930
+Plalan 3.9197607 0.033208288 0.008472019 0.0000000 3.0 30.843624
+Rumace 3.8992342 0.027368676 0.007018988 0.3333333 3.2 37.716139
+Elyrep 3.1876647 0.029550307 0.009270206 2.0000000 2.0 43.334492
+Poatri 2.8466256 0.021521731 0.007560436 4.6666667 4.8 48.351753
+Brarut 2.5260809 0.021044097 0.008330729 2.0000000 2.8 52.804045
+Elepal 2.4974367 0.038876909 0.015566724 1.3333333 0.8 57.205850
+Poapra 2.3932257 0.019179734 0.008014177 2.5000000 3.4 61.423981
+Antodo 2.3408728 0.021430212 0.009154796 0.0000000 1.8 65.549838
+Sagpro 2.3143518 0.020478964 0.008848682 1.8333333 0.8 69.628951
+Tripra 2.3079782 0.023431610 0.010152440 0.0000000 1.8 73.696831
+Junart 2.2849877 0.025676555 0.011237065 0.5000000 1.6 77.724189
+Trirep 2.2382699 0.019486710 0.008706148 1.3333333 2.8 81.669205
+Junbuf 2.1642678 0.022237444 0.010274812 1.1666667 1.2 85.483791
+Leoaut 2.0509314 0.016422027 0.008007107 1.3333333 2.8 89.098618
+Achmil 1.5183100 0.011393329 0.007503955 0.1666667 1.2 91.774684
+Brohor 1.3375437 0.014503626 0.010843479 0.5000000 0.8 94.132144
+Ranfla 1.0660700 0.013386946 0.012557287 0.6666667 0.4 96.011124
+Belper 0.9990990 0.012570517 0.012581853 0.6666667 0.4 97.772065
+Calcus 0.6623417 0.015076322 0.022762152 0.5000000 0.0 98.939462
+Cirarv 0.3809333 0.008669044 0.022757383 0.3333333 0.0 99.610868
+Chealb 0.2207806 0.005025441 0.022762152 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
+
+$SF_NM
+ contr sd contr/sd av_SF av_NM cum
+Poatri 7.8284148 0.040947182 0.005230584 4.6666667 0.0000000 10.13601
+Alogen 7.1219425 0.046958337 0.006593473 4.3333333 0.0000000 19.35731
+Agrsto 5.6508187 0.044176062 0.007817639 4.6666667 2.1666667 26.67383
+Lolper 5.4851012 0.059913861 0.010923018 3.0000000 0.3333333 33.77578
+Elepal 4.8027074 0.047168454 0.009821222 1.3333333 2.1666667 39.99419
+Poapra 4.0724386 0.031790183 0.007806179 2.5000000 0.6666667 45.26707
+Brarut 4.0008412 0.034397513 0.008597570 2.0000000 2.8333333 50.44725
+Elyrep 3.5598394 0.038515239 0.010819375 2.0000000 0.0000000 55.05643
+Leoaut 3.2474710 0.034813104 0.010720066 1.3333333 3.1666667 59.26117
+Trirep 3.0429642 0.031634061 0.010395804 1.3333333 1.8333333 63.20111
+Sagpro 3.0303946 0.030476566 0.010056963 1.8333333 0.5000000 67.12478
+Salrep 2.9275366 0.032014215 0.010935547 0.0000000 1.8333333 70.91528
+Antodo 2.4541140 0.036694444 0.014952216 0.0000000 1.3333333 74.09279
+Calcus 2.2762575 0.029443338 0.012934977 0.5000000 1.1666667 77.04003
+Ranfla 2.2566173 0.022818681 0.010111897 0.6666667 1.3333333 79.96183
+Junart 2.2542858 0.028597560 0.012685863 0.5000000 1.1666667 82.88062
+Hyprad 2.0108243 0.031290623 0.015561092 0.0000000 1.1666667 85.48418
+Junbuf 1.9859538 0.029033704 0.014619526 1.1666667 0.0000000 88.05554
+Plalan 1.5420359 0.022769128 0.014765628 0.0000000 0.8333333 90.05212
+Airpra 1.4883128 0.021880904 0.014701818 0.0000000 0.8333333 91.97915
+Belper 1.2317474 0.015920540 0.012925167 0.6666667 0.3333333 93.57398
+Potpal 1.1882720 0.017406896 0.014648916 0.0000000 0.6666667 95.11252
+Achmil 0.9293657 0.014931384 0.016066209 0.1666667 0.3333333 96.31584
+Brohor 0.7172498 0.016333288 0.022772104 0.5000000 0.0000000 97.24451
+Rumace 0.5590144 0.012750682 0.022809219 0.3333333 0.0000000 97.96831
+Empnig 0.5225116 0.012000618 0.022967182 0.0000000 0.3333333 98.64484
+Cirarv 0.4781666 0.010888859 0.022772104 0.3333333 0.0000000 99.26396
+Chealb 0.2893083 0.006601805 0.022819268 0.1666667 0.0000000 99.63855
+Viclat 0.2791635 0.006424596 0.023013743 0.0000000 0.1666667 100.00000
+Tripra 0.0000000 0.000000000 NaN 0.0000000 0.0000000 100.00000
+
+$HF_NM
+ contr sd contr/sd av_HF av_NM cum
+Poatri 7.1552962 0.013680801 0.001911982 4.8 0.0000000 9.913221
+Lolper 5.4533212 0.029624608 0.005432397 4.0 0.3333333 17.468460
+Rumace 4.6546497 0.030806132 0.006618357 3.2 0.0000000 23.917190
+Poapra 4.1749543 0.018851704 0.004515427 3.4 0.6666667 29.701331
+Plalan 4.1632907 0.029559966 0.007100145 3.0 0.8333333 35.469313
+Brarut 3.5340259 0.020103791 0.005688637 2.8 2.8333333 40.365488
+Elepal 3.2043023 0.032314877 0.010084840 0.8 2.1666667 44.804851
+Agrsto 3.1915495 0.028887302 0.009051184 1.4 2.1666667 49.226546
+Trirep 3.0372486 0.022871293 0.007530267 2.8 1.8333333 53.434466
+Elyrep 2.9811469 0.038675842 0.012973478 2.0 0.0000000 57.564661
+Antodo 2.8717143 0.024799203 0.008635679 1.8 1.3333333 61.543243
+Junart 2.7414119 0.028536540 0.010409432 1.6 1.1666667 65.341300
+Tripra 2.5843049 0.025971573 0.010049732 1.8 0.0000000 68.921695
+Salrep 2.5340091 0.027291287 0.010770004 0.0 1.8333333 72.432408
+Alogen 2.4459371 0.032399067 0.013246075 1.6 0.0000000 75.821103
+Leoaut 2.0703325 0.014124614 0.006822389 2.8 3.1666667 78.689420
+Ranfla 1.9284693 0.019938840 0.010339205 0.4 1.3333333 81.361196
+Junbuf 1.8180949 0.024648229 0.013557174 1.2 0.0000000 83.880054
+Hyprad 1.7141357 0.026547931 0.015487648 0.0 1.1666667 86.254883
+Calcus 1.6832709 0.024900688 0.014793037 0.0 1.1666667 88.586951
+Achmil 1.6555393 0.014899781 0.008999956 1.2 0.3333333 90.880598
+Sagpro 1.5282469 0.016534777 0.010819441 0.8 0.5000000 92.997890
+Airpra 1.2605398 0.018242589 0.014472046 0.0 0.8333333 94.744290
+Brohor 1.2093682 0.015168791 0.012542740 0.8 0.0000000 96.419795
+Potpal 1.0105496 0.014556161 0.014404201 0.0 0.6666667 97.819849
+Belper 0.8801475 0.013732352 0.015602330 0.4 0.3333333 99.039239
+Empnig 0.4535959 0.010325282 0.022763173 0.0 0.3333333 99.667668
+Viclat 0.2398752 0.005460872 0.022765475 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
+
+>
+>
+>
+> cleanEx()
> nameEx("simulate.rda")
> ### * simulate.rda
>
@@ -7028,7 +7245,7 @@
Run 17 stress 0.1825664
... New best solution
... procrustes: rmse 0.0421789 max resid 0.1544029
-Run 18 stress 0.1843201
+Run 18 stress 0.1843199
Run 19 stress 0.2570123
Run 20 stress 0.3760596
> plot(ord, type = "t")
@@ -7198,14 +7415,14 @@
> ## add fitted surface of diversity to the model
> ordisurf(mod, diversity(dune), add = TRUE)
Loading required package: mgcv
-This is mgcv 1.7-13. For overview type 'help("mgcv-package")'.
+This is mgcv 1.7-12. For overview type 'help("mgcv-package")'.
Family: gaussian
Link function: identity
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x8db4a60>
+<environment: 0x10b0e19f0>
Estimated degrees of freedom:
2 total = 3
@@ -7685,7 +7902,7 @@
> ### * <FOOTER>
> ###
> cat("Time elapsed: ", proc.time() - get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed: 24.973 0.116 25.177 0 0
+Time elapsed: 84.542 1.578 86.391 0 0
> grDevices::dev.off()
null device
1
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