[Vegan-commits] r2495 - in pkg/vegan: R inst man tests/Examples
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Apr 24 10:16:05 CEST 2013
Author: jarioksa
Date: 2013-04-24 10:16:04 +0200 (Wed, 24 Apr 2013)
New Revision: 2495
Modified:
pkg/vegan/R/oecosimu.R
pkg/vegan/R/print.oecosimu.R
pkg/vegan/inst/ChangeLog
pkg/vegan/man/oecosimu.Rd
pkg/vegan/tests/Examples/vegan-Ex.Rout.save
Log:
Fix twisted tests in oecosimu.
Change direction of one-sided tests to their opposite, and explain
the sidedness in comprehensible terms in printout.
Fixes issue #14 in GitHub (opened by jumanbar)
Modified: pkg/vegan/R/oecosimu.R
===================================================================
--- pkg/vegan/R/oecosimu.R 2013-04-21 08:16:02 UTC (rev 2494)
+++ pkg/vegan/R/oecosimu.R 2013-04-24 08:16:04 UTC (rev 2495)
@@ -104,8 +104,8 @@
z <- (indstat - means)/sd
if (any(sd < sqrt(.Machine$double.eps)))
z[sd < sqrt(.Machine$double.eps)] <- 0
- pless <- rowSums(indstat <= simind, na.rm = TRUE)
- pmore <- rowSums(indstat >= simind, na.rm = TRUE)
+ pless <- rowSums(indstat >= simind, na.rm = TRUE)
+ pmore <- rowSums(indstat <= simind, na.rm = TRUE)
if (any(is.na(simind))) {
warning("some simulated values were NA and were removed")
nsimul <- nsimul - rowSums(is.na(simind))
Modified: pkg/vegan/R/print.oecosimu.R
===================================================================
--- pkg/vegan/R/print.oecosimu.R 2013-04-21 08:16:02 UTC (rev 2494)
+++ pkg/vegan/R/print.oecosimu.R 2013-04-24 08:16:04 UTC (rev 2495)
@@ -13,10 +13,10 @@
cat("options: ", paste(names(att), att, collapse=", "))
}
alt.char <- switch(x$oecosimu$alternative,
- two.sided = "not equal to",
+ two.sided = "less or greater than",
less = "less than",
greater = "greater than")
- cat("\nalternative hypothesis: simulated median is", alt.char, "the statistic")
+ cat("\nalternative hypothesis: statistic is", alt.char, "simulated values")
## dim attribute is always there, but print all others
cat("\n\n")
Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog 2013-04-21 08:16:02 UTC (rev 2494)
+++ pkg/vegan/inst/ChangeLog 2013-04-24 08:16:04 UTC (rev 2495)
@@ -33,6 +33,12 @@
- The formula passed to `gam` is now built in greater detail. When
the model is printed the user can see exactly how the smoother was
constructed.
+
+ * oecosimu: the interpretation argument "alternative" was really
+ twisted. We now changed the test direction and have a much clearer
+ explanatory text in printed output. The issue was raised by Juan
+ Manual Barreneche (jumanbar) in GitHub (issue #14). NB. The
+ direction of the test changed from previous versions.
Version 2.1-28 (closed April 19, 2013)
Modified: pkg/vegan/man/oecosimu.Rd
===================================================================
--- pkg/vegan/man/oecosimu.Rd 2013-04-21 08:16:02 UTC (rev 2494)
+++ pkg/vegan/man/oecosimu.Rd 2013-04-24 08:16:04 UTC (rev 2495)
@@ -237,7 +237,7 @@
oecosimu(sipoo, nestedchecker, "r0")
## sequential model, one-sided test, a vector statistic
out <- oecosimu(sipoo, decorana, "swap", burnin=100, thin=10,
- statistic="evals", alt = "less")
+ statistic="evals", alt = "greater")
out
## Inspect the swap sequence as a time series object
plot(as.ts(out))
Modified: pkg/vegan/tests/Examples/vegan-Ex.Rout.save
===================================================================
--- pkg/vegan/tests/Examples/vegan-Ex.Rout.save 2013-04-21 08:16:02 UTC (rev 2494)
+++ pkg/vegan/tests/Examples/vegan-Ex.Rout.save 2013-04-24 08:16:04 UTC (rev 2495)
@@ -1,8 +1,8 @@
-R version 2.15.3 (2013-03-01) -- "Security Blanket"
-Copyright (C) 2013 The R Foundation for Statistical Computing
+R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
+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-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
@@ -161,7 +161,7 @@
Formula:
y ~ poly(x1, 1) + poly(x2, 1)
-<environment: 0x10242dc98>
+<environment: 0x1db31c0>
Total model degrees of freedom 3
REML score: -3.185099
@@ -529,7 +529,7 @@
nullmodel method ‘r2dtable’ with 19 simulations
options: index richness, weights unif
-alternative hypothesis: simulated median is not equal to the statistic
+alternative hypothesis: statistic is less or greater than simulated values
statistic z mean 2.5% 50% 97.5% Pr(sim.)
alpha.1 15.114 -38.43 22.344 22.032 22.300 22.608 0.05 *
@@ -545,7 +545,7 @@
nullmodel method ‘r2dtable’ with 19 simulations
options: index richness, weights unif
-alternative hypothesis: simulated median is not equal to the statistic
+alternative hypothesis: statistic is less or greater than simulated values
statistic z mean 2.5% 50% 97.5% Pr(sim.)
alpha.1 15.114 -46.2370 22.39624 22.12571 22.44286 22.6236 0.05 *
@@ -566,7 +566,7 @@
nullmodel method ‘r2dtable’ with 19 simulations
-alternative hypothesis: simulated median is not equal to the statistic
+alternative hypothesis: statistic is less or greater than simulated values
statistic z mean 2.5% 50% 97.5% Pr(sim.)
level_1 0.76064 -71.195 0.93904 0.93487 0.93856 0.9444 0.05 *
@@ -581,7 +581,7 @@
nullmodel method ‘r2dtable’ with 19 simulations
-alternative hypothesis: simulated median is not equal to the statistic
+alternative hypothesis: statistic is less or greater than simulated values
statistic z mean 2.5% 50% 97.5% Pr(sim.)
l1 0.76064 -75.139 0.93833 0.93389 0.93819 0.9427 0.05 *
@@ -600,7 +600,7 @@
nullmodel method ‘r2dtable’ with 19 simulations
-alternative hypothesis: simulated median is not equal to the statistic
+alternative hypothesis: statistic is less or greater than simulated values
statistic z mean 2.5% 50% 97.5% Pr(sim.)
l1 0.52070 8.5216 0.353253 0.322624 0.351073 0.3848 0.05 *
@@ -675,7 +675,7 @@
Run 1 stress 0.1560544
Run 2 stress 0.08556586
... New best solution
-... procrustes: rmse 1.094365e-06 max resid 1.88838e-06
+... procrustes: rmse 1.09439e-06 max resid 1.88838e-06
*** Solution reached
> plot(mod)
> ### Hulls show treatment
@@ -3685,7 +3685,7 @@
Run 0 stress 0.1067169
Run 1 stress 0.1067169
... New best solution
-... procrustes: rmse 1.234853e-05 max resid 2.993581e-05
+... procrustes: rmse 1.234853e-05 max resid 2.993582e-05
*** Solution reached
> sol
@@ -3889,7 +3889,7 @@
> plot(dune.ord <- metaMDS(dune), type="text", display="sites" )
Run 0 stress 0.1192678
Run 1 stress 0.119268
-... procrustes: rmse 8.18569e-05 max resid 0.0001982896
+... procrustes: rmse 8.185687e-05 max resid 0.0001982896
*** Solution reached
> ordihull(dune.ord, dune.env$Management)
>
@@ -4080,7 +4080,7 @@
nullmodel method ‘r2dtable’ with 19 simulations
options: index renyi, scales 1, global FALSE
-alternative hypothesis: simulated median is not equal to the statistic
+alternative hypothesis: statistic is less or greater than simulated values
statistic z mean 2.5% 50% 97.5% Pr(sim.)
alpha.1 8.0555 -50.069 12.19396 12.06155 12.19041 12.3400 0.05 *
@@ -4100,7 +4100,7 @@
nullmodel method ‘r2dtable’ with 19 simulations
options: index renyi, scales 1, global FALSE
-alternative hypothesis: simulated median is not equal to the statistic
+alternative hypothesis: statistic is less or greater than simulated values
statistic z mean 2.5% 50% 97.5% Pr(sim.)
alpha.1 8.0555 -66.643 12.2056 12.1143 12.2120 12.2910 0.05 *
@@ -4120,7 +4120,7 @@
nullmodel method ‘r2dtable’ with 19 simulations
options: index renyi, scales 1, global FALSE
-alternative hypothesis: simulated median is not equal to the statistic
+alternative hypothesis: statistic is less or greater than simulated values
statistic z mean 2.5% 50% 97.5% Pr(sim.)
alpha.1 8.055481 -53.544 12.204883 12.071168 12.198307 12.3689 0.05 *
@@ -4140,7 +4140,7 @@
nullmodel method ‘r2dtable’ with 19 simulations
options: index renyi, scales 1, global TRUE
-alternative hypothesis: simulated median is not equal to the statistic
+alternative hypothesis: statistic is less or greater than simulated values
statistic z mean 2.5% 50% 97.5% Pr(sim.)
alpha.1 8.0555 -69.630 12.19342 12.09434 12.18504 12.3160 0.05 *
@@ -4189,7 +4189,7 @@
nullmodel method ‘quasiswap’ with 99 simulations
-alternative hypothesis: simulated median is not equal to the statistic
+alternative hypothesis: statistic is less or greater than simulated values
Checkerboard Units : 2767
C-score (species mean): 2.258776
@@ -4205,7 +4205,7 @@
nullmodel method ‘r00’ with 99 simulations
-alternative hypothesis: simulated median is not equal to the statistic
+alternative hypothesis: statistic is less or greater than simulated values
Checkerboard Units : 2767
C-score (species mean): 2.258776
@@ -4333,7 +4333,7 @@
nullmodel method ‘r0’ with 99 simulations
-alternative hypothesis: simulated median is not equal to the statistic
+alternative hypothesis: statistic is less or greater than simulated values
Checkerboard Units : 2767
C-score (species mean): 2.258776
@@ -4344,16 +4344,16 @@
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
> ## sequential model, one-sided test, a vector statistic
> out <- oecosimu(sipoo, decorana, "swap", burnin=100, thin=10,
-+ statistic="evals", alt = "less")
++ statistic="evals", alt = "greater")
> out
oecosimu object
Call: oecosimu(comm = sipoo, nestfun = decorana, method = "swap",
-burnin = 100, thin = 10, statistic = "evals", alternative = "less")
+burnin = 100, thin = 10, statistic = "evals", alternative = "greater")
nullmodel method ‘swap’ with 99 simulations
options: thin 10, burnin 100
-alternative hypothesis: simulated median is less than the statistic
+alternative hypothesis: statistic is greater than simulated values
Call:
@@ -4368,11 +4368,11 @@
Axis lengths 2.9197 2.5442 2.7546 1.78074
- statistic z mean 0% 50% 95% Pr(sim.)
-DCA1 0.382249 1.8658 0.324042 0.230869 0.323729 0.3726 0.02 *
-DCA2 0.261208 1.5772 0.219388 0.149703 0.216169 0.2637 0.09 .
-DCA3 0.166788 0.5209 0.155941 0.105269 0.155716 0.1859 0.30
-DCA4 0.087226 -1.9822 0.130151 0.066742 0.126492 0.1649 0.99
+ statistic z mean 5% 50% 100% Pr(sim.)
+DCA1 0.382249 1.8658 0.32404 0.27338 0.32373 0.3918 0.02 *
+DCA2 0.261208 1.5772 0.21939 0.17891 0.21617 0.2899 0.09 .
+DCA3 0.166788 0.5209 0.15594 0.12380 0.15572 0.2361 0.30
+DCA4 0.087226 -1.9822 0.13015 0.10335 0.12649 0.2011 0.99
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
> ## Inspect the swap sequence as a time series object
@@ -4395,7 +4395,7 @@
nullmodel method ‘r2dtable’ with 99 simulations
-alternative hypothesis: simulated median is not equal to the statistic
+alternative hypothesis: statistic is less or greater than simulated values
statistic z mean 2.5% 50% 97.5% Pr(sim.)
statistic 0.64565 14.66 0.46734 0.44069 0.46760 0.4903 0.01 **
@@ -4419,7 +4419,7 @@
nullmodel method ‘myshuffle’ with 99 simulations
-alternative hypothesis: simulated median is not equal to the statistic
+alternative hypothesis: statistic is less or greater than simulated values
statistic z mean 2.5% 50% 97.5% Pr(sim.)
statistic 0.64565 3.1832 0.63514 0.63016 0.63441 0.6419 0.03 *
@@ -4960,7 +4960,7 @@
Formula:
y ~ s(x1, x2, k = 10, bs = "tp", fx = FALSE)
-<environment: 0x10b539600>
+<environment: 0x8fd4ae0>
Estimated degrees of freedom:
5.63 total = 6.63
@@ -4977,7 +4977,7 @@
Formula:
y ~ s(x1, x2, k = 10, bs = "tp", fx = FALSE)
-<environment: 0x108c2ba38>
+<environment: 0x84775b0>
Estimated degrees of freedom:
6.45 total = 7.45
@@ -4991,9 +4991,9 @@
1 2 3 4 5 6 7 8
21.253963 5.675210 3.679486 3.898355 9.643787 7.698255 7.729282 9.758092
9 10 11 12 13 14 15 16
- 2.743202 29.700505 11.971987 8.310916 5.390556 24.906203 11.006871 25.330571
+ 2.743203 29.700504 11.971986 8.310916 5.390556 24.906203 11.006871 25.330570
17 18 19 20 21 22 23 24
- 6.520735 9.410672 4.519645 4.090900 11.558075 4.314814 11.693769 14.244150
+ 6.520735 9.410672 4.519645 4.090901 11.558075 4.314814 11.693769 14.244150
>
> ## Variable selection via additional shrinkage penalties
> ## This allows non-significant smooths to be selected out
@@ -5008,7 +5008,7 @@
Formula:
y ~ s(x1, x2, k = 10, bs = "tp", fx = FALSE)
-<environment: 0x10af55c40>
+<environment: 0x8f8c7c8>
Estimated degrees of freedom:
5.63 total = 6.63
@@ -5023,7 +5023,7 @@
Formula:
y ~ s(x1, x2, k = 10, bs = "ts", fx = FALSE)
-<environment: 0x1097c4cd0>
+<environment: 0x81b54f8>
Estimated degrees of freedom:
4.43 total = 5.43
@@ -5049,7 +5049,7 @@
Formula:
y ~ s(x1, x2, k = 10, bs = "ds", fx = FALSE)
-<environment: 0x10b7a61b8>
+<environment: 0x90eebb8>
Estimated degrees of freedom:
5.63 total = 6.63
@@ -5065,7 +5065,7 @@
Formula:
y ~ s(x1, x2, k = 4, bs = "tp", fx = TRUE)
-<environment: 0x10aa42df0>
+<environment: 0x93068f8>
Estimated degrees of freedom:
3 total = 4
@@ -5082,7 +5082,7 @@
Formula:
y ~ te(x1, x2, k = c(4, 4), bs = c("cr", "cr"), fx = c(FALSE,
FALSE))
-<environment: 0x10b831308>
+<environment: 0x878fdd0>
Estimated degrees of freedom:
2.99 total = 3.99
@@ -5101,7 +5101,7 @@
Formula:
y ~ te(x1, x2, k = c(3, 4), bs = c("cs", "cs"), fx = c(TRUE,
TRUE))
-<environment: 0x1096b7828>
+<environment: 0x9324410>
Estimated degrees of freedom:
11 total = 12
@@ -5248,7 +5248,7 @@
Formula:
y ~ s(x1, x2, k = 10, bs = "tp", fx = FALSE)
-<environment: 0x10b9719b8>
+<environment: 0x70d43c8>
Estimated degrees of freedom:
8.71 total = 9.71
@@ -5261,7 +5261,7 @@
Formula:
y ~ s(x1, x2, k = 10, bs = "tp", fx = FALSE)
-<environment: 0x10a84cc60>
+<environment: 0x8def7e8>
Estimated degrees of freedom:
7.18 total = 8.18
@@ -5274,7 +5274,7 @@
Formula:
y ~ s(x1, x2, k = 10, bs = "tp", fx = FALSE)
-<environment: 0x10b84f910>
+<environment: 0x8f33320>
Estimated degrees of freedom:
8.32 total = 9.32
@@ -6025,7 +6025,7 @@
0.7398422
Quantiles of Procrustes errors:
Min 1Q Median 3Q Max
-0.02033237 0.27686842 0.34124239 0.64358542 2.23460568
+0.02033237 0.27686842 0.34124239 0.64358542 2.23460567
Rotation matrix:
[,1] [,2]
@@ -6033,8 +6033,8 @@
[2,] 0.1154641 0.9933117
Translation of averages:
- [,1] [,2]
-[1,] -9.421394e-19 -8.582272e-18
+ [,1] [,2]
+[1,] 3.038945e-17 1.218602e-17
Scaling of target:
[1] 0.6727804
@@ -6045,9 +6045,9 @@
18 15 24 27 23 19 22
0.28003467 0.13180094 1.72990690 0.63953155 0.37177564 0.11807007 0.38558576
16 28 13 14 20 25 7
-0.28008712 1.22839229 0.65574702 0.26736966 0.02033237 0.35725398 0.28654874
+0.28008711 1.22839229 0.65574702 0.26736966 0.02033237 0.35725398 0.28654874
5 6 3 4 2 9 12
-0.69324047 0.20264726 0.29744269 0.50070811 2.23460568 0.31901411 0.21727135
+0.69324047 0.20264726 0.29744269 0.50070811 2.23460567 0.31901411 0.21727135
10 11 21
0.32523080 0.56506437 0.78179902
>
@@ -7232,7 +7232,7 @@
nullmodel method ‘r0’ with 99 simulations
-alternative hypothesis: simulated median is not equal to the statistic
+alternative hypothesis: statistic is less or greater than simulated values
statistic z mean 2.5% 50% 97.5% Pr(sim.)
2 411.98 -3.174838 580.78 462.37 577.88 673.73 0.01 **
@@ -7830,7 +7830,7 @@
Formula:
y ~ s(x1, x2, k = 10, bs = "tp", fx = FALSE)
-<environment: 0x10b4b0158>
+<environment: 0x90ccd10>
Estimated degrees of freedom:
1.28 total = 2.28
@@ -8382,7 +8382,7 @@
> ### * <FOOTER>
> ###
> cat("Time elapsed: ", proc.time() - get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed: 87.513 1.918 100.236 0 0
+Time elapsed: 27.085 0.14 27.323 0 0
> grDevices::dev.off()
null device
1
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