[Vegan-commits] r2827 - pkg/vegan/tests/Examples
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Jan 7 09:38:34 CET 2014
Author: jarioksa
Date: 2014-01-07 09:38:33 +0100 (Tue, 07 Jan 2014)
New Revision: 2827
Modified:
pkg/vegan/tests/Examples/vegan-Ex.Rout.save
Log:
community data were renamed and reorganized: examples change
Modified: pkg/vegan/tests/Examples/vegan-Ex.Rout.save
===================================================================
--- pkg/vegan/tests/Examples/vegan-Ex.Rout.save 2014-01-07 08:37:46 UTC (rev 2826)
+++ pkg/vegan/tests/Examples/vegan-Ex.Rout.save 2014-01-07 08:38:33 UTC (rev 2827)
@@ -1,6 +1,6 @@
-R Under development (unstable) (2013-11-15 r64218) -- "Unsuffered Consequences"
-Copyright (C) 2013 The R Foundation for Statistical Computing
+R Under development (unstable) (2014-01-07 r64685) -- "Unsuffered Consequences"
+Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -23,7 +23,7 @@
> library('vegan')
Loading required package: permute
Loading required package: lattice
-This is vegan 2.1-39
+This is vegan 2.1-41
>
> base::assign(".oldSearch", base::search(), pos = 'CheckExEnv')
> cleanEx()
@@ -155,14 +155,14 @@
> ordisurf(mod ~ pH, varechem, knots = 1, add = TRUE)
Loading required package: mgcv
Loading required package: nlme
-This is mgcv 1.7-26. For overview type 'help("mgcv-package")'.
+This is mgcv 1.7-27. For overview type 'help("mgcv-package")'.
Family: gaussian
Link function: identity
Formula:
y ~ poly(x1, 1) + poly(x2, 1)
-<environment: 0x280d1f8>
+<environment: 0x2dd2b28>
Total model degrees of freedom 3
REML score: -3.185099
@@ -395,26 +395,26 @@
Start: AIC=87.66
dune ~ 1
- Df AIC F N.Perm Pr(>F)
-+ Moisture 3 86.608 2.2536 199 0.010 **
-+ Management 3 86.935 2.1307 199 0.005 **
-+ A1 1 87.411 2.1400 199 0.020 *
-<none> 87.657
-+ Manure 4 88.832 1.5251 199 0.025 *
-+ Use 2 89.134 1.1431 99 0.250
+ Df AIC F Pr(>F)
++ Moisture 3 86.608 2.2536 0.005 **
++ Management 3 86.935 2.1307 0.005 **
++ A1 1 87.411 2.1400 0.025 *
+<none> 87.657
++ Manure 4 88.832 1.5251 0.045 *
++ Use 2 89.134 1.1431 0.295
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Step: AIC=86.61
dune ~ Moisture
- Df AIC F N.Perm Pr(>F)
-<none> 86.608
-+ Management 3 86.813 1.4565 199 0.020 *
-+ A1 1 86.992 1.2624 99 0.150
-+ Use 2 87.259 1.2760 199 0.120
-+ Manure 4 87.342 1.3143 199 0.090 .
-- Moisture 3 87.657 2.2536 199 0.005 **
+ Df AIC F Pr(>F)
+<none> 86.608
++ Management 3 86.813 1.4565 0.045 *
++ A1 1 86.992 1.2624 0.150
++ Use 2 87.259 1.2760 0.120
++ Manure 4 87.342 1.3143 0.040 *
+- Moisture 3 87.657 2.2536 0.010 **
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Call: cca(formula = dune ~ Moisture, data = dune.env)
@@ -446,40 +446,40 @@
> m0 <- rda(dune ~ 1, dune.env)
> ## -- manual selection and updating
> add1(m0, scope=formula(mbig), test="perm")
- Df AIC F N.Perm Pr(>F)
-<none> 89.620
-A1 1 89.591 1.9217 199 0.070 .
-Moisture 3 87.707 2.5883 199 0.005 **
-Management 3 87.082 2.8400 199 0.005 **
-Use 2 91.032 1.1741 99 0.180
-Manure 4 89.232 1.9539 199 0.010 **
+ Df AIC F Pr(>F)
+<none> 89.620
+A1 1 89.591 1.9217 0.060 .
+Moisture 3 87.707 2.5883 0.005 **
+Management 3 87.082 2.8400 0.005 **
+Use 2 91.032 1.1741 0.280
+Manure 4 89.232 1.9539 0.015 *
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
> m0 <- update(m0, . ~ . + Management)
> add1(m0, scope=formula(mbig), test="perm")
- Df AIC F N.Perm Pr(>F)
-<none> 87.082
-A1 1 87.424 1.2965 99 0.240
-Moisture 3 85.567 1.9764 199 0.005 **
-Use 2 88.284 1.0510 99 0.430
-Manure 3 87.517 1.3902 199 0.130
+ Df AIC F Pr(>F)
+<none> 87.082
+A1 1 87.424 1.2965 0.175
+Moisture 3 85.567 1.9764 0.005 **
+Use 2 88.284 1.0510 0.440
+Manure 3 87.517 1.3902 0.095 .
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
> m0 <- update(m0, . ~ . + Moisture)
> ## -- included variables still significant?
> drop1(m0, test="perm")
- Df AIC F N.Perm Pr(>F)
-<none> 85.567
-Management 3 87.707 2.1769 199 0.010 **
-Moisture 3 87.082 1.9764 199 0.015 *
+ Df AIC F Pr(>F)
+<none> 85.567
+Management 3 87.707 2.1769 0.010 **
+Moisture 3 87.082 1.9764 0.005 **
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
> add1(m0, scope=formula(mbig), test="perm")
- Df AIC F N.Perm Pr(>F)
-<none> 85.567
-A1 1 86.220 0.8359 99 0.72
-Use 2 86.842 0.8027 99 0.77
-Manure 3 85.762 1.1225 99 0.26
+ Df AIC F Pr(>F)
+<none> 85.567
+A1 1 86.220 0.8359 0.645
+Use 2 86.842 0.8027 0.700
+Manure 3 85.762 1.1225 0.320
>
>
>
@@ -638,8 +638,8 @@
Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
Management 3 1.4686 0.48953 3.2629 0.34161 0.01 **
-A1 1 0.4409 0.44089 2.9387 0.10256 0.02 *
-Management:A1 3 0.5892 0.19639 1.3090 0.13705 0.18
+A1 1 0.4409 0.44089 2.9387 0.10256 0.04 *
+Management:A1 3 0.5892 0.19639 1.3090 0.13705 0.23
Residuals 12 1.8004 0.15003 0.41878
Total 19 4.2990 1.00000
---
@@ -741,13 +741,13 @@
Dissimilarity: bray
ANOSIM statistic R: 0.2579
- Significance: 0.006
+ Significance: 0.017
Based on 999 permutations
Upper quantiles of permutations (null model):
90% 95% 97.5% 99%
-0.116 0.160 0.203 0.233
+0.121 0.174 0.222 0.276
Dissimilarity ranks between and within classes:
0% 25% 50% 75% 100% N
@@ -775,8 +775,7 @@
> ### Name: anova.cca
> ### Title: Permutation Test for Constrained Correspondence Analysis,
> ### Redundancy Analysis and Constrained Analysis of Principal Coordinates
-> ### Aliases: anova.cca anova.ccanull anova.ccabyaxis anova.ccabyterm
-> ### anova.ccabymargin anova.prc permutest permutest.default permutest.cca
+> ### Aliases: anova.cca permutest permutest.cca
> ### Keywords: multivariate htest
>
> ### ** Examples
@@ -787,94 +786,19 @@
> ## overall test
> anova(vare.cca)
Permutation test for cca under reduced model
+Permutation: free
+Number of permutations: 999
Model: cca(formula = varespec ~ Al + P + K, data = varechem)
- Df Chisq F N.Perm Pr(>F)
-Model 3 0.6441 2.9840 199 0.005 **
-Residual 20 1.4391
+ Df ChiSquare F Pr(>F)
+Model 3 0.64413 2.984 0.001 ***
+Residual 20 1.43906
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
-> ## Test for axes
-> anova(vare.cca, by="axis", perm.max=500)
-Model: cca(formula = varespec ~ Al + P + K, data = varechem)
- Df Chisq F N.Perm Pr(>F)
-CCA1 1 0.3616 5.0249 199 0.005 **
-CCA2 1 0.1700 2.3621 199 0.010 **
-CCA3 1 0.1126 1.5651 399 0.100 .
-Residual 20 1.4391
----
-Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
-> ## Sequential test for terms
-> anova(vare.cca, by="terms", permu=200)
-Permutation test for cca under reduced model
-Terms added sequentially (first to last)
-
-Model: cca(formula = varespec ~ Al + P + K, data = varechem)
- Df Chisq F N.Perm Pr(>F)
-Al 1 0.2982 4.1440 199 0.005 **
-P 1 0.1899 2.6393 199 0.015 *
-K 1 0.1561 2.1688 199 0.030 *
-Residual 20 1.4391
----
-Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
-> ## Marginal or Type III effects
-> anova(vare.cca, by="margin")
-Permutation test for cca under reduced model
-Marginal effects of terms
-
-Model: cca(formula = varespec ~ Al + P + K, data = varechem)
- Df Chisq F N.Perm Pr(>F)
-Al 1 0.3118 4.3340 199 0.00500 **
-P 1 0.1681 2.3362 199 0.01500 *
-K 1 0.1561 2.1688 599 0.02833 *
-Residual 20 1.4391
----
-Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
-> ## Marginal test knows 'scope'
-> anova(vare.cca, by = "m", scope="P")
-Permutation test for cca under reduced model
-Marginal effects of terms
-
-Model: cca(formula = varespec ~ Al + P + K, data = varechem)
- Df Chisq F N.Perm Pr(>F)
-P 1 0.1681 2.3362 199 0.015 *
-Residual 20 1.4391
----
-Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
>
>
>
> cleanEx()
-> nameEx("anovacca")
-> ### * anovacca
->
-> flush(stderr()); flush(stdout())
->
-> ### Name: anovacca
-> ### Title: Permutation Test for Constrained Correspondence Analysis,
-> ### Redundancy Analysis and Constrained Analysis of Principal Coordinates
-> ### Aliases: anovacca
-> ### Keywords: multivariate htest
->
-> ### ** Examples
->
-> data(varespec)
-> data(varechem)
-> vare.cca <- cca(varespec ~ Al + P + K, varechem)
-> ## overall test
-> anovacca(vare.cca)
-Permutation test for cca under reduced model
-
-Model: cca(formula = varespec ~ Al + P + K, data = varechem)
- Df Chisq F N.Perm Pr(>F)
-Model 3 0.6441 2.9840 999 0.001 ***
-Residual 20 1.4391
----
-Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
->
->
->
-> cleanEx()
> nameEx("as.mlm")
> ### * as.mlm
>
@@ -992,121 +916,121 @@
> boxplot(as.vector(x) ~ unlist(pa), xlab="Presence", ylab="Beals")
> ## Remove the bias of tarbet species: Yields lower values.
> beals(dune, type =3, include = FALSE)
- Belper Empnig Junbuf Junart Airpra Elepal Rumace
-2 0.4917791 0.01829337 0.2070478 0.13017869 0.03361524 0.08656209 0.3031318
-13 0.2939740 0.01840390 0.3339728 0.28204736 0.02191119 0.22437598 0.3107471
-4 0.4398775 0.02527165 0.2318440 0.21320122 0.02876960 0.16112450 0.2610006
-16 0.1516354 0.00742115 0.1776781 0.54304667 0.00742115 0.51523810 0.1508409
-6 0.3696613 0.03093489 0.2166255 0.11631772 0.05967771 0.08784329 0.4330705
-1 0.4935662 0.00000000 0.1987270 0.14794933 0.01157407 0.05592045 0.3160963
-8 0.2720122 0.02102222 0.2323566 0.33219882 0.02588333 0.29777644 0.2331043
-5 0.4322142 0.03029752 0.2164230 0.10406655 0.06632771 0.05419613 0.3979230
-17 0.3129358 0.21968254 0.1038156 0.03333333 0.29233391 0.02777778 0.2913631
-15 0.1420251 0.02215971 0.1370235 0.51561767 0.02538032 0.53973883 0.1459458
-10 0.4705094 0.03425596 0.1678040 0.09080902 0.07349127 0.07787078 0.3226025
-11 0.3713794 0.07310076 0.1656396 0.13478872 0.10259239 0.11146095 0.2753878
-9 0.3292320 0.01838883 0.2675624 0.23134366 0.02213662 0.19018562 0.3464870
-18 0.3676424 0.06763669 0.1376386 0.18956922 0.08535723 0.17341352 0.2668100
-3 0.4033301 0.01074444 0.2544828 0.22291082 0.01520046 0.16099072 0.2909068
-20 0.1450721 0.05905666 0.1192488 0.53056145 0.06144615 0.58476297 0.1098600
-14 0.1682755 0.01989756 0.1206518 0.46685537 0.02298398 0.55982776 0.1241545
-19 0.2237843 0.26011417 0.1127832 0.13543701 0.35137675 0.12592768 0.1831168
-12 0.2802946 0.03413656 0.3231724 0.27306206 0.03625297 0.19518888 0.3507140
-7 0.4051777 0.02304603 0.2110045 0.11293676 0.05329633 0.06694311 0.4113622
- Viclat Brarut Ranfla Cirarv Hyprad Leoaut Potpal
-2 0.18494940 0.7415172 0.13042865 0.08570299 0.07454127 0.9349640 0.026548839
-13 0.06604026 0.7465509 0.33309468 0.07905124 0.04250245 0.9255312 0.056084315
-4 0.12550967 0.7919786 0.21909541 0.12920228 0.06985986 0.9204237 0.039859621
-16 0.03353260 0.8029953 0.66893881 0.05184498 0.01731602 0.8131968 0.201352298
-6 0.18035860 0.8387650 0.10909966 0.03223112 0.11463153 0.9590466 0.030347896
-1 0.17244420 0.7476589 0.08105273 0.09504980 0.07702746 0.8898317 0.000000000
-8 0.10213052 0.8109194 0.40134447 0.06688407 0.06550319 0.8755515 0.100703044
-5 0.16693075 0.8079786 0.08063087 0.05520104 0.10245961 0.9576838 0.015892090
-17 0.20728700 0.7635487 0.03549383 0.01049383 0.36492870 0.9839744 0.009876543
-15 0.07370069 0.7997141 0.64449081 0.04022968 0.05040404 0.8430677 0.198176675
-10 0.23383453 0.7660374 0.10355742 0.06037513 0.13692492 0.9568824 0.029746617
-11 0.24317802 0.8182692 0.13269569 0.05778318 0.18108995 0.9442707 0.035740922
-9 0.08630413 0.7972178 0.26006489 0.07647268 0.05343787 0.9145996 0.045830682
-18 0.26222869 0.8397471 0.18805395 0.04454602 0.17491099 0.9554011 0.042890320
-3 0.12833142 0.7666969 0.22632936 0.08967477 0.05562332 0.9036443 0.031898812
-20 0.09111967 0.8397124 0.62796060 0.03453783 0.07795311 0.8457313 0.185726965
-14 0.07857237 0.7238162 0.64674225 0.03618335 0.04665747 0.8477706 0.241811837
-19 0.18188455 0.8161275 0.14551892 0.03668466 0.39145281 0.9902041 0.031845637
-12 0.08049055 0.8061715 0.29873222 0.07799259 0.06777311 0.9377963 0.045375827
-7 0.19027523 0.8089116 0.10541081 0.04706743 0.10837376 0.9550487 0.017083997
- Poapra Calcus Tripra Trirep Antodo Salrep Achmil
-2 0.8972046 0.034597921 0.20673650 0.9125666 0.34723984 0.05983781 0.47083676
-13 0.7063028 0.122856392 0.11199114 0.8841739 0.16737280 0.06572594 0.21850759
-4 0.7940926 0.081110164 0.12896524 0.8943213 0.21542662 0.07579199 0.30816435
-16 0.4124222 0.364128496 0.03916718 0.6776273 0.05538377 0.15783292 0.06335463
-6 0.8666677 0.040981168 0.35423465 0.9110822 0.53154426 0.08921540 0.58819821
-1 0.9863946 0.003527337 0.21701279 0.8782576 0.30827883 0.02729885 0.49590853
-8 0.6160461 0.201958942 0.09897600 0.8002526 0.16247716 0.11569906 0.21230502
-5 0.9035899 0.023129027 0.34808957 0.9142360 0.48876285 0.07589611 0.59949785
-17 0.7434618 0.009876543 0.27593101 0.8141660 0.69331132 0.25651777 0.55254140
-15 0.4078219 0.381379395 0.05831084 0.7170446 0.10117099 0.17750323 0.09168815
-10 0.8915882 0.033527777 0.26807372 0.9003730 0.42671693 0.09037489 0.54083871
-11 0.8062720 0.043950322 0.19982976 0.8979262 0.38766111 0.16465286 0.40509331
-9 0.7523318 0.092982775 0.16269563 0.8714833 0.21896113 0.07351827 0.30323659
-18 0.7368632 0.109959916 0.20461193 0.8600701 0.36918166 0.17191937 0.37751017
-3 0.8083020 0.075789630 0.14654749 0.8817430 0.21609954 0.06065155 0.34063019
-20 0.3662817 0.397924041 0.03708580 0.6350394 0.10738280 0.21674174 0.05429986
-14 0.3817081 0.347514804 0.06176123 0.6485949 0.12128973 0.15917563 0.13570397
-19 0.5548077 0.082361157 0.11966159 0.8147968 0.51929869 0.36429493 0.29826049
-12 0.6932541 0.100954127 0.13849854 0.9079979 0.20078932 0.08041977 0.21008725
-7 0.8925059 0.024070054 0.32489503 0.9171688 0.48010987 0.07094548 0.56496165
- Poatri Chealb Elyrep Sagpro Plalan Agrsto Lolper
-2 0.8288385 0.043866562 0.4407282 0.3302063 0.40700777 0.39501120 0.8272395
-13 0.7993754 0.122547745 0.3511708 0.5131337 0.18153869 0.68239707 0.5714581
-4 0.8197302 0.057970906 0.4399661 0.4191908 0.25797285 0.51198853 0.7197924
-16 0.6071083 0.056246994 0.1832397 0.3480368 0.07269979 0.87877202 0.3561752
-6 0.7782619 0.021256367 0.3138879 0.2539380 0.58765018 0.26299306 0.8000021
-1 0.8826329 0.025132275 0.4667439 0.3371121 0.40103107 0.38333415 0.9226190
-8 0.7101299 0.063278453 0.3046956 0.4009544 0.20596764 0.66906674 0.5403355
-5 0.8094632 0.026434737 0.3575948 0.2612828 0.52628928 0.27622698 0.8380779
-17 0.5036834 0.007716049 0.1929470 0.3292030 0.59641331 0.07330247 0.5858415
-15 0.5263520 0.035609053 0.1462975 0.3151199 0.13523214 0.79412733 0.3689922
-10 0.7543592 0.025686639 0.3736128 0.2732735 0.52588347 0.26902092 0.8102783
-11 0.6404351 0.021234732 0.2884798 0.3673397 0.47012501 0.31656550 0.7180948
-9 0.8247374 0.069879277 0.3523460 0.4531178 0.25274756 0.59744543 0.6874068
-18 0.5859071 0.014640428 0.2651538 0.3154533 0.45087176 0.34451209 0.7124388
-3 0.8383185 0.065338638 0.4137888 0.4204104 0.27933493 0.52738394 0.7205525
-20 0.4523029 0.037623741 0.1168700 0.3105433 0.13059496 0.76675441 0.3262685
-14 0.5090703 0.042990591 0.1428372 0.2528665 0.14342002 0.76284476 0.3356311
-19 0.3605827 0.019591245 0.1422725 0.4798245 0.40784415 0.25952255 0.4289185
-12 0.8199960 0.103543341 0.3354080 0.5122033 0.22110550 0.66278454 0.5875943
-7 0.8018775 0.038467708 0.3586644 0.2954682 0.51905808 0.29412293 0.8053380
- Alogen Brohor
-2 0.4718807 0.42000984
-13 0.6404427 0.24942466
-4 0.5971801 0.35732610
-16 0.5232448 0.09458531
-6 0.2700508 0.39760652
-1 0.4923280 0.43263047
-8 0.5187956 0.21219877
-5 0.3349203 0.44309579
-17 0.1013889 0.34982363
-15 0.4505613 0.09794548
-10 0.3372958 0.42934344
-11 0.3185489 0.31413659
-9 0.5792855 0.28613526
-18 0.2838834 0.30478244
-3 0.5309152 0.33010938
-20 0.4063662 0.06706410
-14 0.4107645 0.13757552
-19 0.1934048 0.18074796
-12 0.5753377 0.22974415
-7 0.3403047 0.40471531
+ Achimill Agrostol Airaprae Alopgeni Anthodor Bellpere Bromhord
+1 0.49590853 0.38333415 0.01157407 0.4923280 0.30827883 0.4935662 0.43263047
+2 0.47083676 0.39501120 0.03361524 0.4718807 0.34723984 0.4917791 0.42000984
+3 0.34063019 0.52738394 0.01520046 0.5309152 0.21609954 0.4033301 0.33010938
+4 0.30816435 0.51198853 0.02876960 0.5971801 0.21542662 0.4398775 0.35732610
+5 0.59949785 0.27622698 0.06632771 0.3349203 0.48876285 0.4322142 0.44309579
+6 0.58819821 0.26299306 0.05967771 0.2700508 0.53154426 0.3696613 0.39760652
+7 0.56496165 0.29412293 0.05329633 0.3403047 0.48010987 0.4051777 0.40471531
+8 0.21230502 0.66906674 0.02588333 0.5187956 0.16247716 0.2720122 0.21219877
+9 0.30323659 0.59744543 0.02213662 0.5792855 0.21896113 0.3292320 0.28613526
+10 0.54083871 0.26902092 0.07349127 0.3372958 0.42671693 0.4705094 0.42934344
+11 0.40509331 0.31656550 0.10259239 0.3185489 0.38766111 0.3713794 0.31413659
+12 0.21008725 0.66278454 0.03625297 0.5753377 0.20078932 0.2802946 0.22974415
+13 0.21850759 0.68239707 0.02191119 0.6404427 0.16737280 0.2939740 0.24942466
+14 0.13570397 0.76284476 0.02298398 0.4107645 0.12128973 0.1682755 0.13757552
+15 0.09168815 0.79412733 0.02538032 0.4505613 0.10117099 0.1420251 0.09794548
+16 0.06335463 0.87877202 0.00742115 0.5232448 0.05538377 0.1516354 0.09458531
+17 0.55254140 0.07330247 0.29233391 0.1013889 0.69331132 0.3129358 0.34982363
+18 0.37751017 0.34451209 0.08535723 0.2838834 0.36918166 0.3676424 0.30478244
+19 0.29826049 0.25952255 0.35137675 0.1934048 0.51929869 0.2237843 0.18074796
+20 0.05429986 0.76675441 0.06144615 0.4063662 0.10738280 0.1450721 0.06706410
+ Chenalbu Cirsarve Comapalu Eleopalu Elymrepe Empenigr
+1 0.025132275 0.09504980 0.000000000 0.05592045 0.4667439 0.00000000
+2 0.043866562 0.08570299 0.026548839 0.08656209 0.4407282 0.01829337
+3 0.065338638 0.08967477 0.031898812 0.16099072 0.4137888 0.01074444
+4 0.057970906 0.12920228 0.039859621 0.16112450 0.4399661 0.02527165
+5 0.026434737 0.05520104 0.015892090 0.05419613 0.3575948 0.03029752
+6 0.021256367 0.03223112 0.030347896 0.08784329 0.3138879 0.03093489
+7 0.038467708 0.04706743 0.017083997 0.06694311 0.3586644 0.02304603
+8 0.063278453 0.06688407 0.100703044 0.29777644 0.3046956 0.02102222
+9 0.069879277 0.07647268 0.045830682 0.19018562 0.3523460 0.01838883
+10 0.025686639 0.06037513 0.029746617 0.07787078 0.3736128 0.03425596
+11 0.021234732 0.05778318 0.035740922 0.11146095 0.2884798 0.07310076
+12 0.103543341 0.07799259 0.045375827 0.19518888 0.3354080 0.03413656
+13 0.122547745 0.07905124 0.056084315 0.22437598 0.3511708 0.01840390
+14 0.042990591 0.03618335 0.241811837 0.55982776 0.1428372 0.01989756
+15 0.035609053 0.04022968 0.198176675 0.53973883 0.1462975 0.02215971
+16 0.056246994 0.05184498 0.201352298 0.51523810 0.1832397 0.00742115
+17 0.007716049 0.01049383 0.009876543 0.02777778 0.1929470 0.21968254
+18 0.014640428 0.04454602 0.042890320 0.17341352 0.2651538 0.06763669
+19 0.019591245 0.03668466 0.031845637 0.12592768 0.1422725 0.26011417
+20 0.037623741 0.03453783 0.185726965 0.58476297 0.1168700 0.05905666
+ Hyporadi Juncarti Juncbufo Lolipere Planlanc Poaprat Poatriv
+1 0.07702746 0.14794933 0.1987270 0.9226190 0.40103107 0.9863946 0.8826329
+2 0.07454127 0.13017869 0.2070478 0.8272395 0.40700777 0.8972046 0.8288385
+3 0.05562332 0.22291082 0.2544828 0.7205525 0.27933493 0.8083020 0.8383185
+4 0.06985986 0.21320122 0.2318440 0.7197924 0.25797285 0.7940926 0.8197302
+5 0.10245961 0.10406655 0.2164230 0.8380779 0.52628928 0.9035899 0.8094632
+6 0.11463153 0.11631772 0.2166255 0.8000021 0.58765018 0.8666677 0.7782619
+7 0.10837376 0.11293676 0.2110045 0.8053380 0.51905808 0.8925059 0.8018775
+8 0.06550319 0.33219882 0.2323566 0.5403355 0.20596764 0.6160461 0.7101299
+9 0.05343787 0.23134366 0.2675624 0.6874068 0.25274756 0.7523318 0.8247374
+10 0.13692492 0.09080902 0.1678040 0.8102783 0.52588347 0.8915882 0.7543592
+11 0.18108995 0.13478872 0.1656396 0.7180948 0.47012501 0.8062720 0.6404351
+12 0.06777311 0.27306206 0.3231724 0.5875943 0.22110550 0.6932541 0.8199960
+13 0.04250245 0.28204736 0.3339728 0.5714581 0.18153869 0.7063028 0.7993754
+14 0.04665747 0.46685537 0.1206518 0.3356311 0.14342002 0.3817081 0.5090703
+15 0.05040404 0.51561767 0.1370235 0.3689922 0.13523214 0.4078219 0.5263520
+16 0.01731602 0.54304667 0.1776781 0.3561752 0.07269979 0.4124222 0.6071083
+17 0.36492870 0.03333333 0.1038156 0.5858415 0.59641331 0.7434618 0.5036834
+18 0.17491099 0.18956922 0.1376386 0.7124388 0.45087176 0.7368632 0.5859071
+19 0.39145281 0.13543701 0.1127832 0.4289185 0.40784415 0.5548077 0.3605827
+20 0.07795311 0.53056145 0.1192488 0.3262685 0.13059496 0.3662817 0.4523029
+ Ranuflam Rumeacet Sagiproc Salirepe Scorautu Trifprat Trifrepe
+1 0.08105273 0.3160963 0.3371121 0.02729885 0.8898317 0.21701279 0.8782576
+2 0.13042865 0.3031318 0.3302063 0.05983781 0.9349640 0.20673650 0.9125666
+3 0.22632936 0.2909068 0.4204104 0.06065155 0.9036443 0.14654749 0.8817430
+4 0.21909541 0.2610006 0.4191908 0.07579199 0.9204237 0.12896524 0.8943213
+5 0.08063087 0.3979230 0.2612828 0.07589611 0.9576838 0.34808957 0.9142360
+6 0.10909966 0.4330705 0.2539380 0.08921540 0.9590466 0.35423465 0.9110822
+7 0.10541081 0.4113622 0.2954682 0.07094548 0.9550487 0.32489503 0.9171688
+8 0.40134447 0.2331043 0.4009544 0.11569906 0.8755515 0.09897600 0.8002526
+9 0.26006489 0.3464870 0.4531178 0.07351827 0.9145996 0.16269563 0.8714833
+10 0.10355742 0.3226025 0.2732735 0.09037489 0.9568824 0.26807372 0.9003730
+11 0.13269569 0.2753878 0.3673397 0.16465286 0.9442707 0.19982976 0.8979262
+12 0.29873222 0.3507140 0.5122033 0.08041977 0.9377963 0.13849854 0.9079979
+13 0.33309468 0.3107471 0.5131337 0.06572594 0.9255312 0.11199114 0.8841739
+14 0.64674225 0.1241545 0.2528665 0.15917563 0.8477706 0.06176123 0.6485949
+15 0.64449081 0.1459458 0.3151199 0.17750323 0.8430677 0.05831084 0.7170446
+16 0.66893881 0.1508409 0.3480368 0.15783292 0.8131968 0.03916718 0.6776273
+17 0.03549383 0.2913631 0.3292030 0.25651777 0.9839744 0.27593101 0.8141660
+18 0.18805395 0.2668100 0.3154533 0.17191937 0.9554011 0.20461193 0.8600701
+19 0.14551892 0.1831168 0.4798245 0.36429493 0.9902041 0.11966159 0.8147968
+20 0.62796060 0.1098600 0.3105433 0.21674174 0.8457313 0.03708580 0.6350394
+ Vicilath Bracruta Callcusp
+1 0.17244420 0.7476589 0.003527337
+2 0.18494940 0.7415172 0.034597921
+3 0.12833142 0.7666969 0.075789630
+4 0.12550967 0.7919786 0.081110164
+5 0.16693075 0.8079786 0.023129027
+6 0.18035860 0.8387650 0.040981168
+7 0.19027523 0.8089116 0.024070054
+8 0.10213052 0.8109194 0.201958942
+9 0.08630413 0.7972178 0.092982775
+10 0.23383453 0.7660374 0.033527777
+11 0.24317802 0.8182692 0.043950322
+12 0.08049055 0.8061715 0.100954127
+13 0.06604026 0.7465509 0.122856392
+14 0.07857237 0.7238162 0.347514804
+15 0.07370069 0.7997141 0.381379395
+16 0.03353260 0.8029953 0.364128496
+17 0.20728700 0.7635487 0.009876543
+18 0.26222869 0.8397471 0.109959916
+19 0.18188455 0.8161275 0.082361157
+20 0.09111967 0.8397124 0.397924041
> ## Uses abundance information.
> ## Vector with beals smoothing values corresponding to the first species
> ## in dune.
> beals(dune, species=1, include=TRUE)
- 2 13 4 16 6 1 8 5
-0.5291758 0.2239377 0.5030290 0.1616186 0.3707875 0.4816850 0.2560592 0.4675235
- 17 15 10 11 9 18 3 20
-0.2789116 0.1552083 0.5009997 0.3564815 0.3030290 0.4887566 0.4596520 0.1500000
- 14 19 12 7
-0.1297619 0.2056878 0.2604599 0.3752818
+ 1 2 3 4 5 6 7 8
+0.5923077 0.5032372 0.3499038 0.3306953 0.5944041 0.5928780 0.5824352 0.2082532
+ 9 10 11 12 13 14 15 16
+0.2960799 0.5462492 0.3659392 0.2610043 0.1982372 0.0922619 0.1140625 0.1066506
+ 17 18 19 20
+0.6020408 0.3844577 0.2865741 0.0750000
>
>
>
@@ -1183,9 +1107,10 @@
Number of permutations requested: 999
Max. number of permutations allowed: 9999
Evaluate all permutations?: No. Activation limit: 99
+
Response: Distances
Df Sum Sq Mean Sq F N.Perm Pr(>F)
-Groups 1 0.07931 0.079306 4.6156 999 0.05 *
+Groups 1 0.07931 0.079306 4.6156 1000 0.05 *
Residuals 22 0.37801 0.017182
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
@@ -1350,12 +1275,13 @@
Permutation type: free
Permutation details:
- Number of permutations requested: 100
+ Number of permutations requested: 999
Max. number of permutations allowed: 9999
Evaluate all permutations?: No. Activation limit: 99
+
Response: Distances
Df Sum Sq Mean Sq F N.Perm Pr(>F)
-Groups 1 0.039979 0.039979 2.4237 100 0.1584
+Groups 1 0.039979 0.039979 2.4237 1000 0.115
Residuals 18 0.296910 0.016495
> anova(mod2)
Analysis of Variance Table
@@ -1406,13 +1332,14 @@
Permutation type: free
Permutation details:
- Number of permutations requested: 100
+ Number of permutations requested: 999
Max. number of permutations allowed: 9999
Evaluate all permutations?: No. Activation limit: 99
+
Response: Distances
- Df Sum Sq Mean Sq F N.Perm Pr(>F)
-Groups 1 0.033468 0.033468 3.1749 100 0.06931 .
-Residuals 18 0.189749 0.010542
+ Df Sum Sq Mean Sq F N.Perm Pr(>F)
+Groups 1 0.033468 0.033468 3.1749 1000 0.084 .
+Residuals 18 0.189749 0.010542
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
> anova(mod3)
@@ -1659,16 +1586,20 @@
> plot(vare.cap)
> anova(vare.cap)
Permutation test for capscale under reduced model
+Permutation: free
+Number of permutations: 999
Model: capscale(formula = varespec ~ N + P + K + Condition(Al), data = varechem, distance = "bray")
- Df Var F N.Perm Pr(>F)
-Model 3 0.99717 2.2324 199 0.005 **
-Residual 19 2.82904
+ Df Variance F Pr(>F)
+Model 3 0.99717 2.2324 0.002 **
+Residual 19 2.82904
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
> ## Avoid negative eigenvalues with additive constant
> capscale(varespec ~ N + P + K + Condition(Al), varechem,
+ dist="bray", add =TRUE)
+Warning in cmdscale(X, k = k, eig = TRUE, add = add) :
+ only 22 of the first 23 eigenvalues are > 0
Call: capscale(formula = varespec ~ N + P + K + Condition(Al), data =
varechem, distance = "bray", add = TRUE)
@@ -1900,8 +1831,8 @@
> mod <- cca(dune[1:15,] ~ ., dune.env[1:15,])
> # Look at the names of missing species
> attr(mod$CCA$v, "na.action")
-Empnig
- 2
+Airaprae Empenigr Salirepe
+ 3 13 24
attr(,"class")
[1] "exclude"
> # Look at the names of the aliased variables:
@@ -2164,51 +2095,51 @@
Species scores:
- DCA1 DCA2 DCA3 DCA4 Totals
-Cal.vul 0.04119 -1.53268 -2.55101 1.32277 45.07
-Emp.nig 0.09019 0.82274 0.20569 0.30631 151.99
-Led.pal 1.34533 2.47141 -0.34970 -1.13823 8.39
-Vac.myr 1.86298 1.71424 -0.60535 -0.40205 50.71
-Vac.vit 0.16641 0.71095 0.00313 -0.55801 275.03
-Pin.syl -0.73490 1.62050 -1.60275 -2.10199 4.11
-Des.fle 1.97061 1.81651 1.74896 -0.91463 5.60
-Bet.pub 0.79745 3.36374 -0.94546 -1.01741 0.29
-Vac.uli -0.08912 -1.17478 2.86624 0.87025 15.22
-Dip.mon -0.82669 -0.44195 2.58579 -0.38459 3.24
-Dic.sp 2.37743 -0.27373 -0.47099 -1.89036 40.50
-Dic.fus 1.58267 -1.33770 -1.33563 1.47417 113.52
-Dic.pol 0.86689 2.39519 -0.82064 -3.41534 6.06
-Hyl.spl 2.66242 1.19669 1.48288 -0.69978 18.04
-Ple.sch 1.64098 0.15607 0.30044 -0.26717 377.97
-Pol.pil -0.56213 0.14009 0.25198 0.49177 0.61
-Pol.jun 1.22244 -0.89173 0.61287 3.60066 13.85
-Pol.com 1.01545 2.08388 0.06402 0.84199 0.71
-Poh.nut -0.00712 1.09704 -0.82126 -1.59862 2.62
-Pti.cil 0.48093 2.86420 -0.71801 -1.02698 14.01
-Bar.lyc 0.58303 3.71792 -0.84212 -1.88837 3.19
-Cla.arb -0.18554 -1.18973 0.68113 0.55399 255.05
-Cla.ran -0.83427 -0.78085 0.90603 0.70057 388.71
-Cla.ste -1.67768 0.98907 -0.83789 -0.60206 486.71
-Cla.unc 0.97686 -1.70859 -1.68281 -2.26756 56.28
-Cla.coc -0.27221 -0.76713 -0.63836 0.66927 2.79
-Cla.cor 0.29068 -0.97039 0.50414 0.95738 6.22
-Cla.gra 0.21778 -0.41879 0.06530 -0.31472 5.14
-Cla.fim 0.00889 -0.23922 -0.26505 0.33123 3.96
-Cla.cri 0.37774 -1.09161 -0.55627 0.23868 7.47
-Cla.chl -0.91983 1.54955 -0.58109 -1.48643 1.16
-Cla.bot 0.66438 2.19584 -0.90331 -0.91391 0.47
-Cla.ama -0.96418 -0.98992 2.71458 0.52352 0.14
-Cla.sp -1.12318 -0.15330 -0.69833 0.44040 0.52
-Cet.eri 0.27163 -1.28867 -0.81682 -1.93935 3.60
-Cet.isl -0.50158 2.22098 -1.16461 -1.89349 2.03
-Cet.niv -1.67937 -3.67985 4.15644 3.18919 11.85
-Nep.arc 2.18561 -0.82837 0.71958 5.81930 5.26
-Ste.sp -0.78699 -2.01214 2.31212 2.03946 17.52
-Pel.aph 0.45763 -0.34395 0.09916 1.34695 0.76
-Ich.eri 0.04950 -1.97605 1.41509 2.10154 0.22
-Cla.cer -1.21585 -2.30519 2.55186 3.41532 0.10
-Cla.def 0.60517 -1.19771 -0.33388 0.22585 10.23
-Cla.phy -1.53959 1.48574 -1.43209 -1.52387 0.80
+ DCA1 DCA2 DCA3 DCA4 Totals
+Callvulg 0.04119 -1.53268 -2.55101 1.32277 45.07
+Empenigr 0.09019 0.82274 0.20569 0.30631 151.99
+Rhodtome 1.34533 2.47141 -0.34970 -1.13823 8.39
+Vaccmyrt 1.86298 1.71424 -0.60535 -0.40205 50.71
+Vaccviti 0.16641 0.71095 0.00313 -0.55801 275.03
+Pinusylv -0.73490 1.62050 -1.60275 -2.10199 4.11
+Descflex 1.97061 1.81651 1.74896 -0.91463 5.60
+Betupube 0.79745 3.36374 -0.94546 -1.01741 0.29
+Vacculig -0.08912 -1.17478 2.86624 0.87025 15.22
+Diphcomp -0.82669 -0.44195 2.58579 -0.38459 3.24
+Dicrsp 2.37743 -0.27373 -0.47099 -1.89036 40.50
+Dicrfusc 1.58267 -1.33770 -1.33563 1.47417 113.52
+Dicrpoly 0.86689 2.39519 -0.82064 -3.41534 6.06
+Hylosple 2.66242 1.19669 1.48288 -0.69978 18.04
+Pleuschr 1.64098 0.15607 0.30044 -0.26717 377.97
+Polypili -0.56213 0.14009 0.25198 0.49177 0.61
+Polyjuni 1.22244 -0.89173 0.61287 3.60066 13.85
+Polycomm 1.01545 2.08388 0.06402 0.84199 0.71
+Pohlnuta -0.00712 1.09704 -0.82126 -1.59862 2.62
+Ptilcili 0.48093 2.86420 -0.71801 -1.02698 14.01
+Barbhatc 0.58303 3.71792 -0.84212 -1.88837 3.19
+Cladarbu -0.18554 -1.18973 0.68113 0.55399 255.05
+Cladrang -0.83427 -0.78085 0.90603 0.70057 388.71
+Cladstel -1.67768 0.98907 -0.83789 -0.60206 486.71
+Cladunci 0.97686 -1.70859 -1.68281 -2.26756 56.28
+Cladcocc -0.27221 -0.76713 -0.63836 0.66927 2.79
+Cladcorn 0.29068 -0.97039 0.50414 0.95738 6.22
+Cladgrac 0.21778 -0.41879 0.06530 -0.31472 5.14
+Cladfimb 0.00889 -0.23922 -0.26505 0.33123 3.96
+Cladcris 0.37774 -1.09161 -0.55627 0.23868 7.47
+Cladchlo -0.91983 1.54955 -0.58109 -1.48643 1.16
+Cladbotr 0.66438 2.19584 -0.90331 -0.91391 0.47
+Cladamau -0.96418 -0.98992 2.71458 0.52352 0.14
+Cladsp -1.12318 -0.15330 -0.69833 0.44040 0.52
+Cetreric 0.27163 -1.28867 -0.81682 -1.93935 3.60
+Cetrisla -0.50158 2.22098 -1.16461 -1.89349 2.03
+Flavniva -1.67937 -3.67985 4.15644 3.18919 11.85
+Nepharct 2.18561 -0.82837 0.71958 5.81930 5.26
+Stersp -0.78699 -2.01214 2.31212 2.03946 17.52
+Peltapht 0.45763 -0.34395 0.09916 1.34695 0.76
+Icmaeric 0.04950 -1.97605 1.41509 2.10154 0.22
+Cladcerv -1.21585 -2.30519 2.55186 3.41532 0.10
+Claddefo 0.60517 -1.19771 -0.33388 0.22585 10.23
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/vegan -r 2827
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