[Vegan-commits] r1582 - pkg/vegan/tests/Examples
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sat Apr 9 10:09:31 CEST 2011
Author: jarioksa
Date: 2011-04-09 10:09:31 +0200 (Sat, 09 Apr 2011)
New Revision: 1582
Modified:
pkg/vegan/tests/Examples/vegan-Ex.Rout.save
Log:
update
Modified: pkg/vegan/tests/Examples/vegan-Ex.Rout.save
===================================================================
--- pkg/vegan/tests/Examples/vegan-Ex.Rout.save 2011-04-09 08:08:07 UTC (rev 1581)
+++ pkg/vegan/tests/Examples/vegan-Ex.Rout.save 2011-04-09 08:09:31 UTC (rev 1582)
@@ -631,16 +631,10 @@
>
> Y <- data.frame(Agropyron, Schizachyrium)
> mod <- metaMDS(Y)
-Run 0 stress 0.1560545
-Run 1 stress 0.08556612
-... New best solution
-... procrustes: rmse 0.2476582 max resid 0.4167042
-Run 2 stress 0.1560554
-Run 3 stress 0.2162345
-Run 4 stress 0.2062595
-Run 5 stress 0.08556601
-... New best solution
-... procrustes: rmse 0.0001113815 max resid 0.0001929155
+Run 0 stress 0.08556588
+Run 1 stress 0.1560545
+Run 2 stress 0.08556612
+... procrustes: rmse 0.0001630123 max resid 0.0003642025
*** Solution reached
> plot(mod)
@@ -2417,54 +2411,46 @@
> ord <- metaMDS(varespec)
Square root transformation
Wisconsin double standardization
-Run 0 stress 0.2455937
-Run 1 stress 0.2169416
+Run 0 stress 0.1843204
+Run 1 stress 0.2455937
+Run 2 stress 0.2169416
+Run 3 stress 0.2313238
+Run 4 stress 0.1974421
+Run 5 stress 0.1858424
+Run 6 stress 0.1948436
+Run 7 stress 0.2265718
+Run 8 stress 0.2225085
+Run 9 stress 0.2023228
+Run 10 stress 0.2673177
+Run 11 stress 0.1976154
+Run 12 stress 0.1852405
+Run 13 stress 0.2341085
+Run 14 stress 0.1955872
+Run 15 stress 0.2137414
+Run 16 stress 0.2109643
+Run 17 stress 0.1825664
... New best solution
-... procrustes: rmse 0.1701481 max resid 0.3710944
-Run 2 stress 0.2313238
-Run 3 stress 0.1974421
-... New best solution
-... procrustes: rmse 0.1031564 max resid 0.2251109
-Run 4 stress 0.1858424
-... New best solution
-... procrustes: rmse 0.1299653 max resid 0.5189456
-Run 5 stress 0.1948436
-Run 6 stress 0.2265718
-Run 7 stress 0.2225085
-Run 8 stress 0.2023228
-Run 9 stress 0.2673177
-Run 10 stress 0.1976154
-Run 11 stress 0.1852405
-... New best solution
-... procrustes: rmse 0.06229216 max resid 0.150469
-Run 12 stress 0.2341085
-Run 13 stress 0.1955872
-Run 14 stress 0.2137414
-Run 15 stress 0.2109643
-Run 16 stress 0.1825664
-... New best solution
-... procrustes: rmse 0.03764707 max resid 0.1441352
-Run 17 stress 0.1843199
-Run 18 stress 0.2570123
-Run 19 stress 0.3760596
-Run 20 stress 0.202883
+... procrustes: rmse 0.0421789 max resid 0.1544029
+Run 18 stress 0.1843199
+Run 19 stress 0.2570123
+Run 20 stress 0.3760596
> (fit <- envfit(ord, varechem, perm = 999))
***VECTORS
NMDS1 NMDS2 r2 Pr(>r)
N 0.056188 0.998420 0.2542 0.046 *
-P -0.618628 -0.785684 0.1936 0.102
-K -0.765142 -0.643862 0.1809 0.142
+P -0.618628 -0.785684 0.1936 0.103
+K -0.765142 -0.643862 0.1809 0.143
Ca -0.683985 -0.729496 0.4120 0.008 **
Mg -0.631457 -0.775411 0.4273 0.004 **
-S -0.190091 -0.981767 0.1754 0.139
+S -0.190091 -0.981767 0.1754 0.140
Al 0.872443 -0.488715 0.5270 0.001 ***
Fe 0.937013 -0.349294 0.4452 0.002 **
Mn -0.799058 0.601253 0.5228 0.001 ***
-Zn -0.616932 -0.787017 0.1878 0.124
+Zn -0.616932 -0.787017 0.1878 0.125
Mo 0.903112 -0.429406 0.0609 0.539
-Baresoil -0.926090 0.377302 0.2509 0.039 *
+Baresoil -0.926090 0.377302 0.2509 0.038 *
Humdepth -0.933540 0.358473 0.5198 0.002 **
pH 0.648970 -0.760814 0.2306 0.060 .
---
@@ -2839,64 +2825,52 @@
> ### Name: goodness.metaMDS
> ### Title: Goodness of Fit and Shepard Plot for Nonmetric Multidimensional
> ### Scaling
-> ### Aliases: goodness.metaMDS stressplot
+> ### Aliases: goodness.metaMDS goodness.monoMDS stressplot
+> ### stressplot.default stressplot.monoMDS
> ### Keywords: multivariate
>
> ### ** Examples
>
> data(varespec)
-> mod <- metaMDS(varespec, engine = "isoMDS")
+> mod <- metaMDS(varespec)
Square root transformation
Wisconsin double standardization
-Loading required package: MASS
-Run 0 stress 18.44915
-Run 1 stress 18.458
-... procrustes: rmse 0.05246287 max resid 0.1748373
-Run 2 stress 24.19514
-Run 3 stress 19.69805
-Run 4 stress 19.74406
-Run 5 stress 18.43204
+Run 0 stress 0.1843204
+Run 1 stress 0.2455937
+Run 2 stress 0.2169416
+Run 3 stress 0.2313238
+Run 4 stress 0.1974421
+Run 5 stress 0.1858424
+Run 6 stress 0.1948436
+Run 7 stress 0.2265718
+Run 8 stress 0.2225085
+Run 9 stress 0.2023228
+Run 10 stress 0.2673177
+Run 11 stress 0.1976154
+Run 12 stress 0.1852405
+Run 13 stress 0.2341085
+Run 14 stress 0.1955872
+Run 15 stress 0.2137414
+Run 16 stress 0.2109643
+Run 17 stress 0.1825664
... New best solution
-... procrustes: rmse 0.00448445 max resid 0.01722444
-Run 6 stress 19.48415
-Run 7 stress 19.48414
-Run 8 stress 20.57245
-Run 9 stress 21.00656
-Run 10 stress 20.06893
-Run 11 stress 18.52397
-Run 12 stress 21.37384
-Run 13 stress 19.5049
-Run 14 stress 21.6715
-Run 15 stress 22.65719
-Run 16 stress 21.0961
-Run 17 stress 18.25659
-... New best solution
-... procrustes: rmse 0.04191616 max resid 0.1532558
-Run 18 stress 19.48413
-Run 19 stress 21.77541
-Run 20 stress 22.24925
+... procrustes: rmse 0.0421789 max resid 0.1544029
+Run 18 stress 0.1843199
+Run 19 stress 0.2570123
+Run 20 stress 0.3760596
> stressplot(mod)
-Square root transformation
-Wisconsin double standardization
> gof <- goodness(mod)
-Square root transformation
-Wisconsin double standardization
> gof
- 18 15 24 27 23 19 22 16
-2.984496 3.514129 4.188692 4.598210 4.002773 3.441293 3.294609 3.051738
- 28 13 14 20 25 7 5 6
-3.060659 2.993482 3.526967 2.621578 3.829350 2.982187 3.370348 2.226679
- 3 4 2 9 12 10 11 21
-3.561311 3.506032 6.577579 3.268019 3.502878 2.957059 5.167546 4.601390
+ [1] 0.02985151 0.03513602 0.04181211 0.04601046 0.04005199 0.03443943
+ [7] 0.03290447 0.03048909 0.03058684 0.02992410 0.03531117 0.02620375
+[13] 0.03833499 0.02979202 0.03376558 0.02225449 0.03559163 0.03504082
+[19] 0.06578666 0.03269039 0.03507122 0.02956140 0.05162094 0.04604686
> plot(mod, display = "sites", type = "n")
-> points(mod, display = "sites", cex = gof/2)
+> points(mod, display = "sites", cex = 2*gof/mean(gof))
>
>
>
> cleanEx()
-
-detaching ‘package:MASS’
-
> nameEx("humpfit")
> ### * humpfit
>
@@ -3416,10 +3390,13 @@
> library(MASS) ## isoMDS
> # NMDS
> sol <- metaMDS(dune)
-Run 0 stress 0.1808932
-Run 1 stress 0.1808918
-... New best solution
-... procrustes: rmse 0.001095961 max resid 0.003218655
+Run 0 stress 0.1192691
+Run 1 stress 0.1808932
+Run 2 stress 0.1808918
+Run 3 stress 0.1808912
+Run 4 stress 0.2035431
+Run 5 stress 0.1192719
+... procrustes: rmse 0.001450932 max resid 0.004117039
*** Solution reached
> sol
@@ -3427,14 +3404,14 @@
Call:
metaMDS(comm = dune)
-Nonmetric Multidimensional Scaling using monoMDS
+global Multidimensional Scaling using monoMDS
Data: dune
Distance: bray
Dimensions: 2
-Stress: 0.1808918
-Two convergent solutions found after 1 tries
+Stress: 0.1192691
+Two convergent solutions found after 5 tries
Scaling: centring, PC rotation, halfchange scaling
Species: expanded scores based on ‘dune’
@@ -3442,11 +3419,12 @@
>
> ## Start from previous best solution
> sol2 <- metaMDS(dune, previous.best = sol)
-Starting from a previous solution
-Run 0 stress 0.1808918
-Run 1 stress 0.1808912
+Starting from 2-dimensional configuration
+Run 0 stress 0.1192691
+Run 1 stress 0.1939205
+Run 2 stress 0.1192685
... New best solution
-... procrustes: rmse 0.0005388664 max resid 0.001425574
+... procrustes: rmse 0.000737655 max resid 0.001867068
*** Solution reached
>
@@ -3630,9 +3608,10 @@
> layout(matrix(1:2,nr=1))
>
> plot(dune.ord <- metaMDS(dune), type="text", display="sites" )
-Run 0 stress 0.1192689
-Run 1 stress 0.1192718
-... procrustes: rmse 0.001708735 max resid 0.005233673
+Run 0 stress 0.1192691
+Run 1 stress 0.1192689
+... New best solution
+... procrustes: rmse 0.0006819572 max resid 0.001730883
*** Solution reached
> ordihull(dune.ord, dune.env$Management)
@@ -4684,7 +4663,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x103d3b988>
+<environment: 0x1036f60a0>
Estimated degrees of freedom:
6.2955 total = 7.295494
@@ -4700,7 +4679,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x10593c430>
+<environment: 0x1060bec30>
Estimated degrees of freedom:
4.9207 total = 5.920718
@@ -4856,7 +4835,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x105cd3148>
+<environment: 0x106c72e68>
Estimated degrees of freedom:
8.9275 total = 9.927492
@@ -4869,7 +4848,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x106f35800>
+<environment: 0x10707ca38>
Estimated degrees of freedom:
7.7529 total = 8.75294
@@ -4882,7 +4861,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x106fb1678>
+<environment: 0x10704a200>
Estimated degrees of freedom:
8.8962 total = 9.89616
@@ -7383,37 +7362,29 @@
> ord <- metaMDS(varespec)
Square root transformation
Wisconsin double standardization
-Run 0 stress 0.2455937
-Run 1 stress 0.2169416
+Run 0 stress 0.1843204
+Run 1 stress 0.2455937
+Run 2 stress 0.2169416
+Run 3 stress 0.2313238
+Run 4 stress 0.1974421
+Run 5 stress 0.1858424
+Run 6 stress 0.1948436
+Run 7 stress 0.2265718
+Run 8 stress 0.2225085
+Run 9 stress 0.2023228
+Run 10 stress 0.2673177
+Run 11 stress 0.1976154
+Run 12 stress 0.1852405
+Run 13 stress 0.2341085
+Run 14 stress 0.1955872
+Run 15 stress 0.2137414
+Run 16 stress 0.2109643
+Run 17 stress 0.1825664
... New best solution
-... procrustes: rmse 0.1701481 max resid 0.3710944
-Run 2 stress 0.2313238
-Run 3 stress 0.1974421
-... New best solution
-... procrustes: rmse 0.1031564 max resid 0.2251109
-Run 4 stress 0.1858424
-... New best solution
-... procrustes: rmse 0.1299653 max resid 0.5189456
-Run 5 stress 0.1948436
-Run 6 stress 0.2265718
-Run 7 stress 0.2225085
-Run 8 stress 0.2023228
-Run 9 stress 0.2673177
-Run 10 stress 0.1976154
-Run 11 stress 0.1852405
-... New best solution
-... procrustes: rmse 0.06229216 max resid 0.150469
-Run 12 stress 0.2341085
-Run 13 stress 0.1955872
-Run 14 stress 0.2137414
-Run 15 stress 0.2109643
-Run 16 stress 0.1825664
-... New best solution
-... procrustes: rmse 0.03764707 max resid 0.1441352
-Run 17 stress 0.1843199
-Run 18 stress 0.2570123
-Run 19 stress 0.3760596
-Run 20 stress 0.202883
+... procrustes: rmse 0.0421789 max resid 0.1544029
+Run 18 stress 0.1843199
+Run 19 stress 0.2570123
+Run 20 stress 0.3760596
> plot(ord, type = "t")
> ## Fit environmental variables
> ef <- envfit(ord, varechem)
@@ -7423,17 +7394,17 @@
NMDS1 NMDS2 r2 Pr(>r)
N 0.056188 0.998420 0.2542 0.046 *
-P -0.618628 -0.785684 0.1936 0.102
-K -0.765142 -0.643862 0.1809 0.142
+P -0.618628 -0.785684 0.1936 0.103
+K -0.765142 -0.643862 0.1809 0.143
Ca -0.683985 -0.729496 0.4120 0.008 **
Mg -0.631457 -0.775411 0.4273 0.004 **
-S -0.190091 -0.981767 0.1754 0.139
+S -0.190091 -0.981767 0.1754 0.140
Al 0.872443 -0.488715 0.5270 0.001 ***
Fe 0.937013 -0.349294 0.4452 0.002 **
Mn -0.799058 0.601253 0.5228 0.001 ***
-Zn -0.616932 -0.787017 0.1878 0.124
+Zn -0.616932 -0.787017 0.1878 0.125
Mo 0.903112 -0.429406 0.0609 0.539
-Baresoil -0.926090 0.377302 0.2509 0.039 *
+Baresoil -0.926090 0.377302 0.2509 0.038 *
Humdepth -0.933540 0.358473 0.5198 0.002 **
pH 0.648970 -0.760814 0.2306 0.060 .
---
@@ -7491,9 +7462,9 @@
Permutation test for rda under reduced model
Model: rda(formula = dune ~ A1 + Moisture + Management + Use + Manure, data = dune.env)
- Df Var F N.Perm Pr(>F)
-Model 12 63.206 1.7627 199 0.015 *
-Residual 7 20.917
+ Df Var F N.Perm Pr(>F)
+Model 12 63.206 1.7627 199 0.005 **
+Residual 7 20.917
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
> ## Permutation test for terms added sequentially
@@ -7506,8 +7477,8 @@
A1 1 8.1148 2.7156 99 0.01 **
Moisture 3 21.6497 2.4150 99 0.01 **
Management 3 19.1153 2.1323 99 0.02 *
-Use 2 4.7007 0.7865 99 0.78
-Manure 3 9.6257 1.0737 99 0.35
+Use 2 4.7007 0.7865 99 0.70
+Manure 3 9.6257 1.0737 99 0.40
Residual 7 20.9175
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
@@ -7520,8 +7491,8 @@
+ Management 3 87.082 2.8400 199 0.005 **
+ Moisture 3 87.707 2.5883 199 0.005 **
+ Manure 4 89.232 1.9539 199 0.005 **
-+ A1 1 89.591 1.9217 999 0.043 *
-+ Use 2 91.032 1.1741 99 0.300
++ A1 1 89.591 1.9217 999 0.040 *
++ Use 2 91.032 1.1741 99 0.250
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
@@ -7534,24 +7505,24 @@
Df AIC F N.Perm Pr(>F)
+ Moisture 3 85.567 1.9764 199 0.01 **
-+ Manure 3 87.517 1.3902 399 0.09 .
-+ A1 1 87.424 1.2965 99 0.18
-+ Use 2 88.284 1.0510 99 0.39
++ Manure 3 87.517 1.3902 99 0.18
++ A1 1 87.424 1.2965 99 0.24
++ Use 2 88.284 1.0510 99 0.37
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Step: dune ~ Management + Moisture
Df AIC F N.Perm Pr(>F)
-- Moisture 3 87.082 1.9764 99 0.02 *
+- Moisture 3 87.082 1.9764 99 0.01 **
- Management 3 87.707 2.1769 99 0.01 **
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Df AIC F N.Perm Pr(>F)
-+ Manure 3 85.762 1.1225 99 0.32
-+ A1 1 86.220 0.8359 99 0.64
-+ Use 2 86.842 0.8027 99 0.75
++ Manure 3 85.762 1.1225 99 0.27
++ A1 1 86.220 0.8359 99 0.70
++ Use 2 86.842 0.8027 99 0.77
> mod
Call: rda(formula = dune ~ Management + Moisture, data = dune.env)
@@ -7582,7 +7553,7 @@
Model: rda(formula = dune ~ Management + Moisture, data = dune.env)
Df Var F N.Perm Pr(>F)
Management 3 18.938 2.1769 199 0.005 **
-Moisture 3 17.194 1.9764 199 0.010 **
+Moisture 3 17.194 1.9764 199 0.005 **
Residual 13 37.699
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
@@ -7603,7 +7574,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x10802f698>
+<environment: 0x1080d9440>
Estimated degrees of freedom:
2 total = 3
@@ -7616,14 +7587,14 @@
Call:
adonis(formula = dune ~ ., data = dune.env)
- Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
-A1 1 0.7230 0.72295 5.2038 0.16817 0.003 **
-Moisture 3 1.1871 0.39569 2.8482 0.27613 0.007 **
-Management 3 0.9036 0.30121 2.1681 0.21019 0.045 *
-Use 2 0.0921 0.04606 0.3315 0.02143 0.971
-Manure 3 0.4208 0.14026 1.0096 0.09787 0.468
-Residuals 7 0.9725 0.13893 0.22621
-Total 19 4.2990 1.00000
+ Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
+A1 1 0.7230 0.72295 5.2038 0.16817 0.001 ***
+Moisture 3 1.1871 0.39569 2.8482 0.27613 0.004 **
+Management 3 0.9036 0.30121 2.1681 0.21019 0.028 *
+Use 2 0.0921 0.04606 0.3315 0.02143 0.973
+Manure 3 0.4208 0.14026 1.0096 0.09787 0.489
+Residuals 7 0.9725 0.13893 0.22621
+Total 19 4.2990 1.00000
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
> adonis(dune ~ Management + Moisture, dune.env)
@@ -8080,7 +8051,7 @@
> ### * <FOOTER>
> ###
> cat("Time elapsed: ", proc.time() - get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed: 111.852 1.255 113.956 0 0
+Time elapsed: 108.803 1.165 111.255 0 0
> grDevices::dev.off()
null device
1
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