[Vegan-commits] r2263 - pkg/vegan/tests/Examples
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun Sep 2 08:54:12 CEST 2012
Author: jarioksa
Date: 2012-09-02 08:54:12 +0200 (Sun, 02 Sep 2012)
New Revision: 2263
Modified:
pkg/vegan/tests/Examples/vegan-Ex.Rout.save
Log:
update examples
Modified: pkg/vegan/tests/Examples/vegan-Ex.Rout.save
===================================================================
--- pkg/vegan/tests/Examples/vegan-Ex.Rout.save 2012-09-02 06:20:32 UTC (rev 2262)
+++ pkg/vegan/tests/Examples/vegan-Ex.Rout.save 2012-09-02 06:54:12 UTC (rev 2263)
@@ -23,7 +23,7 @@
> options(warn = 1)
> library('vegan')
Loading required package: permute
-This is vegan 2.1-18
+This is vegan 2.1-19
>
> assign(".oldSearch", search(), pos = 'CheckExEnv')
> cleanEx()
@@ -161,7 +161,7 @@
Formula:
y ~ poly(x1, 1) + poly(x2, 1)
-<environment: 0x10246d238>
+<environment: 0x102470f90>
Total model degrees of freedom 3
GCV score: 0.0427924
@@ -684,32 +684,32 @@
> ordispider(mod, group=dat$field, lty=3, col="red")
>
> ### Correct hypothesis test (with strata)
-> adonis(Y ~ NO3, data=dat, strata=dat$field, perm=1e3)
+> adonis(Y ~ NO3, data=dat, strata=dat$field, perm=999)
Call:
-adonis(formula = Y ~ NO3, data = dat, permutations = 1000, strata = dat$field)
+adonis(formula = Y ~ NO3, data = dat, permutations = 999, strata = dat$field)
Terms added sequentially (first to last)
- Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
-NO3 1 0.055856 0.055856 4.0281 0.28714 0.008991 **
-Residuals 10 0.138667 0.013867 0.71286
-Total 11 0.194524 1.00000
+ Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
+NO3 1 0.055856 0.055856 4.0281 0.28714 0.009 **
+Residuals 10 0.138667 0.013867 0.71286
+Total 11 0.194524 1.00000
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
>
> ### Incorrect (no strata)
-> adonis(Y ~ NO3, data=dat, perm=1e3)
+> adonis(Y ~ NO3, data=dat, perm=999)
Call:
-adonis(formula = Y ~ NO3, data = dat, permutations = 1000)
+adonis(formula = Y ~ NO3, data = dat, permutations = 999)
Terms added sequentially (first to last)
- Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
-NO3 1 0.055856 0.055856 4.0281 0.28714 0.004995 **
-Residuals 10 0.138667 0.013867 0.71286
-Total 11 0.194524 1.00000
+ Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
+NO3 1 0.055856 0.055856 4.0281 0.28714 0.005 **
+Residuals 10 0.138667 0.013867 0.71286
+Total 11 0.194524 1.00000
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
>
@@ -1826,8 +1826,8 @@
>
> data(mite)
> data(mite.env)
-> x <- clamtest(mite, mite.env$Shrub=="None", alpha=0.005)
-> summary(x)
+> sol <- clamtest(mite, mite.env$Shrub=="None", alpha=0.005)
+> summary(sol)
Two Groups Species Classification Method (CLAM)
Specialization threshold = 0.6666667
@@ -1846,7 +1846,7 @@
Specialist_FALSE 14 0.400
Specialist_TRUE 4 0.114
Too_rare 7 0.200
-> head(x)
+> head(sol)
Species Total_FALSE Total_TRUE Classes
1 Brachy 534 77 Generalist
2 PHTH 89 0 Specialist_FALSE
@@ -1854,7 +1854,7 @@
4 RARD 85 0 Specialist_FALSE
5 SSTR 22 0 Too_rare
6 Protopl 26 0 Too_rare
-> plot(x)
+> plot(sol)
>
>
>
@@ -3434,10 +3434,10 @@
> mite.hel.resid <- resid(lm(as.matrix(mite.hel) ~ ., data=mite.xy))
>
> # Compute the detrended species distance matrix
-> mite.hel.D = dist(mite.hel.resid)
+> mite.hel.D <- dist(mite.hel.resid)
>
> # Compute Mantel correlogram with cutoff, Pearson statistic
-> mite.correlog = mantel.correlog(mite.hel.D, XY=mite.xy, nperm=49)
+> mite.correlog <- mantel.correlog(mite.hel.D, XY=mite.xy, nperm=49)
> summary(mite.correlog)
Length Class Mode
mantel.res 65 -none- numeric
@@ -3475,34 +3475,8 @@
> plot(mite.correlog)
>
> # Compute Mantel correlogram without cutoff, Spearman statistic
-> mite.correlog2 = mantel.correlog(mite.hel.D, XY=mite.xy, cutoff=FALSE,
-+ r.type="spearman", nperm=49)
-Warning in cor.test.default(as.vector(xdis), ydis, method = method) :
- Cannot compute exact p-values with ties
-Warning in cor.test.default(as.vector(xdis), ydis, method = method) :
- Cannot compute exact p-values with ties
-Warning in cor.test.default(as.vector(xdis), ydis, method = method) :
- Cannot compute exact p-values with ties
-Warning in cor.test.default(as.vector(xdis), ydis, method = method) :
- Cannot compute exact p-values with ties
-Warning in cor.test.default(as.vector(xdis), ydis, method = method) :
- Cannot compute exact p-values with ties
-Warning in cor.test.default(as.vector(xdis), ydis, method = method) :
- Cannot compute exact p-values with ties
-Warning in cor.test.default(as.vector(xdis), ydis, method = method) :
- Cannot compute exact p-values with ties
-Warning in cor.test.default(as.vector(xdis), ydis, method = method) :
- Cannot compute exact p-values with ties
-Warning in cor.test.default(as.vector(xdis), ydis, method = method) :
- Cannot compute exact p-values with ties
-Warning in cor.test.default(as.vector(xdis), ydis, method = method) :
- Cannot compute exact p-values with ties
-Warning in cor.test.default(as.vector(xdis), ydis, method = method) :
- Cannot compute exact p-values with ties
-Warning in cor.test.default(as.vector(xdis), ydis, method = method) :
- Cannot compute exact p-values with ties
-Warning in cor.test.default(as.vector(xdis), ydis, method = method) :
- Cannot compute exact p-values with ties
+> mite.correlog2 <- mantel.correlog(mite.hel.D, XY=mite.xy, cutoff=FALSE,
++ r.type="spearman", nperm=49)
> summary(mite.correlog2)
Length Class Mode
mantel.res 65 -none- numeric
@@ -4905,7 +4879,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x10a815200>
+<environment: 0x10aafba40>
Estimated degrees of freedom:
6.4351 total = 7.435071
@@ -4921,7 +4895,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x10acdc078>
+<environment: 0x1093858d8>
Estimated degrees of freedom:
6.1039 total = 7.103853
@@ -5077,7 +5051,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x107b67040>
+<environment: 0x10708cb78>
Estimated degrees of freedom:
8.9275 total = 9.927492
@@ -5090,7 +5064,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x10af199f8>
+<environment: 0x10b37eb48>
Estimated degrees of freedom:
7.7529 total = 8.75294
@@ -5103,7 +5077,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x10a096db8>
+<environment: 0x109042d90>
Estimated degrees of freedom:
8.8962 total = 9.89616
@@ -7647,7 +7621,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x10aec3f08>
+<environment: 0x108774e98>
Estimated degrees of freedom:
2 total = 3
@@ -8127,7 +8101,7 @@
> ### * <FOOTER>
> ###
> cat("Time elapsed: ", proc.time() - get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed: 153.286 4.277 466.257 0 0
+Time elapsed: 88.33 1.663 90.694 0 0
> grDevices::dev.off()
null device
1
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