[Vegan-commits] r1883 - pkg/vegan/tests/Examples
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sat Sep 24 19:33:17 CEST 2011
Author: jarioksa
Date: 2011-09-24 19:33:16 +0200 (Sat, 24 Sep 2011)
New Revision: 1883
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 2011-09-24 17:32:52 UTC (rev 1882)
+++ pkg/vegan/tests/Examples/vegan-Ex.Rout.save 2011-09-24 17:33:16 UTC (rev 1883)
@@ -161,7 +161,7 @@
Formula:
y ~ poly(x1, 1) + poly(x2, 1)
-<environment: 0x102618388>
+<environment: 0x102611008>
Total model degrees of freedom 3
GCV score: 0.0427924
@@ -584,11 +584,11 @@
with index richness, weights unif
statistic z 2.5% 50% 97.5% Pr(sim.)
-alpha.1 15.1143 -38.7550 22.0321 22.3000 22.608 0.05 *
+alpha.1 15.1143 -38.4304 22.0321 22.3000 22.608 0.05 *
alpha.2 29.7500 -27.1142 34.5000 34.7500 35.000 0.05 *
alpha.3 33.0000 0.0000 35.0000 35.0000 35.000 0.05 *
gamma 35.0000 0.0000 35.0000 35.0000 35.000 1.00
-beta.1 14.6357 9.0433 12.1629 12.4500 12.955 0.05 *
+beta.1 14.6357 9.1184 12.1629 12.4500 12.955 0.05 *
beta.2 3.2500 16.4371 0.0000 0.2500 0.500 0.05 *
beta.3 2.0000 0.0000 0.0000 0.0000 0.000 0.05 *
---
@@ -599,9 +599,9 @@
hiersimu with 19 simulations
statistic z 2.5% 50% 97.5% Pr(sim.)
-l1 0.76064 -65.47286 0.93511 0.93959 0.9437 0.05 *
-l2 0.89736 -127.77766 0.99635 0.99815 0.9989 0.05 *
-l3 0.92791 -516.33891 0.99921 0.99948 0.9997 0.05 *
+l1 0.76064 -72.78152 0.93511 0.93959 0.9424 0.05 *
+l2 0.89736 -117.34300 0.99619 0.99815 0.9989 0.05 *
+l3 0.92791 -462.37200 0.99914 0.99939 0.9997 0.05 *
l4 1.00000 0.00000 1.00000 1.00000 1.0000 1.00
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
@@ -611,9 +611,9 @@
hiersimu with 19 simulations
statistic z 2.5% 50% 97.5% Pr(sim.)
-l1 0.52070 4.98527 0.31016 0.36570 0.4227 0.05 *
-l2 0.60234 12.33099 0.11979 0.17096 0.2283 0.05 *
-l3 0.67509 19.37352 -0.24164 -0.16761 -0.0895 0.05 *
+l1 0.52070 5.05179 0.31808 0.36836 0.4227 0.05 *
+l2 0.60234 11.31794 0.10507 0.17096 0.2283 0.05 *
+l3 0.67509 16.06868 -0.27784 -0.19160 -0.0895 0.05 *
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
>
@@ -4081,13 +4081,13 @@
with index renyi, scales 1, global TRUE
statistic z 2.5% 50% 97.5% Pr(sim.)
-alpha.1 8.05548 -50.70213 12.06155 12.17739 12.3400 0.05 *
-alpha.2 11.23526 -81.96187 14.03610 14.08098 14.1485 0.05 *
-alpha.3 12.00644 -352.92816 14.12822 14.13863 14.1485 0.05 *
+alpha.1 8.05548 -50.06937 12.06155 12.19041 12.3400 0.05 *
+alpha.2 11.23526 -91.66217 14.05255 14.08685 14.1485 0.05 *
+alpha.3 12.00644 -391.05300 14.13048 14.13932 14.1485 0.05 *
gamma 14.16027 0.00000 14.16027 14.16027 14.1603 1.00
-beta.1 1.35678 27.78084 1.14474 1.15859 1.1683 0.05 *
-beta.2 1.07103 28.03171 0.99912 1.00368 1.0067 0.05 *
-beta.3 1.17939 415.61573 1.00083 1.00153 1.0023 0.05 *
+beta.1 1.35678 27.32039 1.14474 1.15859 1.1683 0.05 *
+beta.2 1.07103 30.43075 0.99912 1.00340 1.0059 0.05 *
+beta.3 1.17939 460.54976 1.00083 1.00148 1.0021 0.05 *
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
> multipart(mite ~ ., levsm, index="renyi", scales=1, nsimul=19, relative=TRUE)
@@ -4095,13 +4095,13 @@
with index renyi, scales 1, global TRUE
statistic z 2.5% 50% 97.5% Pr(sim.)
-alpha.1 8.055481 -58.367006 12.114272 12.212001 12.3367 0.05 *
-alpha.2 11.235261 -101.405343 14.030529 14.092411 14.1193 0.05 *
-alpha.3 12.006443 -397.121850 14.130733 14.140903 14.1485 0.05 *
+alpha.1 8.055481 -66.642517 12.114272 12.212001 12.2910 0.05 *
+alpha.2 11.235261 -94.626473 14.024555 14.091674 14.1193 0.05 *
+alpha.3 12.006443 -355.962100 14.128270 14.137438 14.1485 0.05 *
gamma 14.160271 0.000000 14.160271 14.160271 14.1603 1.00
-beta.1 0.078594 24.964962 0.067424 0.068173 0.0688 0.05 *
-beta.2 0.535514 34.653906 0.500756 0.501720 0.5039 0.05 *
-beta.3 0.589695 467.673224 0.500417 0.500685 0.5010 0.05 *
+beta.1 0.078594 27.638115 0.067625 0.068160 0.0688 0.05 *
+beta.2 0.535514 33.422699 0.500756 0.501738 0.5039 0.05 *
+beta.3 0.589695 419.166208 0.500417 0.500808 0.5011 0.05 *
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
> multipart(mite ~ ., levsm, index="renyi", scales=1, nsimul=19, global=TRUE)
@@ -4109,13 +4109,13 @@
with index renyi, scales 1, global TRUE
statistic z 2.5% 50% 97.5% Pr(sim.)
-alpha.1 8.0555 -51.9567 12.0474 12.1983 12.3527 0.05 *
-alpha.2 11.2353 -97.0303 14.0328 14.0761 14.1247 0.05 *
-alpha.3 12.0064 -369.9941 14.1236 14.1345 14.1428 0.05 *
+alpha.1 8.0555 -53.5439 12.0712 12.1983 12.3689 0.05 *
+alpha.2 11.2353 -99.5061 14.0328 14.0761 14.1247 0.05 *
+alpha.3 12.0064 -343.9456 14.1236 14.1363 14.1438 0.05 *
gamma 14.1603 0.0000 14.1603 14.1603 14.1603 1.00
-beta.1 1.7578 78.6700 1.1463 1.1608 1.1754 0.05 *
-beta.2 1.2603 121.5731 1.0025 1.0060 1.0091 0.05 *
-beta.3 1.1794 435.4695 1.0012 1.0018 1.0026 0.05 *
+beta.1 1.7578 81.2944 1.1448 1.1608 1.1731 0.05 *
+beta.2 1.2603 124.6871 1.0025 1.0060 1.0091 0.05 *
+beta.3 1.1794 404.8142 1.0012 1.0017 1.0026 0.05 *
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
>
@@ -4156,7 +4156,7 @@
C-score (species mean): 2.258776
statistic z 2.5% 50% 97.5% Pr(sim.)
-statistic 2767.00000 0.73182 2569.80000 2680.00000 2905.1 0.49
+statistic 2767.00000 0.84129 2584.40000 2676.00000 2858.1 0.39
> ## Another Null model and standardized checkerboard score
> oecosimu(sipoo, nestedchecker, "r00", statistic = "C.score")
oecosimu with 99 simulations
@@ -4167,7 +4167,7 @@
C-score (species mean): 2.258776
statistic z 2.5% 50% 97.5% Pr(sim.)
-C.score 2.2588 -26.3590 8.6760 9.2327 9.6403 0.01 **
+C.score 2.2588 -28.9196 8.6935 9.2384 9.6053 0.01 **
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
>
@@ -4326,24 +4326,9 @@
alternative hypothesis: true mean is not equal to the statistic
statistic z 2.5% 50% 97.5% Pr(sim.)
-statistic 0.64565 14.13820 0.44577 0.46758 0.4934 0.01 **
+statistic 0.64565 13.89665 0.44577 0.46758 0.4934 0.01 **
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
-> ## Define a custom function that shuffles
-> ## cells in each rows
-> f <- function(x) {
-+ apply(x, 2, function(z) sample(z, length(z)))
-+ }
-> mbc2 <- oecosimu(as.matrix(dune), meandist, f)
-> mbc2
-oecosimu with 99 simulations
-simulation method custom
-alternative hypothesis: true mean is not equal to the statistic
-
- statistic z 2.5% 50% 97.5% Pr(sim.)
-statistic 0.64565 3.13782 0.62989 0.63525 0.6424 0.01 **
----
-Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
>
>
>
@@ -4999,7 +4984,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x10649b800>
+<environment: 0x1074dd0a0>
Estimated degrees of freedom:
6.4351 total = 7.435071
@@ -5015,7 +5000,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x107d7ea78>
+<environment: 0x10696c9c8>
Estimated degrees of freedom:
6.1039 total = 7.103853
@@ -5171,7 +5156,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x106674b58>
+<environment: 0x1073b3118>
Estimated degrees of freedom:
8.9275 total = 9.927492
@@ -5184,7 +5169,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x106ce8200>
+<environment: 0x10715aa30>
Estimated degrees of freedom:
7.7529 total = 8.75294
@@ -5197,7 +5182,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x106d701f0>
+<environment: 0x107d26cd8>
Estimated degrees of freedom:
8.8962 total = 9.89616
@@ -5231,9 +5216,8 @@
> ### Name: permat
> ### Title: Matrix Permutation Algorithms for Presence-Absence and Count
> ### Data
-> ### Aliases: permatfull permatfull1 permatswap permatswap1 summary.permat
-> ### print.summary.permat print.permat plot.permat lines.permat
-> ### as.ts.permat as.mcmc.permat
+> ### Aliases: permatfull permatswap summary.permat print.summary.permat
+> ### print.permat plot.permat lines.permat as.ts.permat as.mcmc.permat
> ### Keywords: multivariate datagen
>
> ### ** Examples
@@ -5269,17 +5253,17 @@
Matrix fill retained: 100 %
Row sums retained: 100 %
Column sums retained: 100 %
-Row incidences retained: 9.09 %
-Column incidences retained: 7.07 %
+Row incidences retained: 2.02 %
+Column incidences retained: 6.06 %
Bray-Curtis dissimilarities among original and permuted matrices:
Min. 1st Qu. Median Mean 3rd Qu. Max.
- 0.2000 0.3667 0.4000 0.4229 0.5000 0.6333
+ 0.2000 0.3667 0.4333 0.4202 0.4667 0.6333
-Chi-squared for original matrix: 18.55)
+Chi-squared for original matrix: 18.55
Chi-squared values among expected and permuted matrices:
Min. 1st Qu. Median Mean 3rd Qu. Max.
- 15.75 19.64 20.93 21.41 23.25 29.87
+ 15.63 19.38 21.19 21.53 23.44 29.08
> ## Unrestricted permutation retaining
> ## row/columns sums but not matrix fill:
> x2 <- permatfull(m)
@@ -5299,20 +5283,20 @@
Number of permuted matrices: 99
Matrix sums retained: 100 %
-Matrix fill retained: 16.16 %
+Matrix fill retained: 18.18 %
Row sums retained: 100 %
Column sums retained: 100 %
-Row incidences retained: 1.01 %
+Row incidences retained: 0 %
Column incidences retained: 1.01 %
Bray-Curtis dissimilarities among original and permuted matrices:
Min. 1st Qu. Median Mean 3rd Qu. Max.
- 0.2000 0.3333 0.3667 0.3848 0.4333 0.5333
+ 0.1667 0.3333 0.4000 0.3754 0.4333 0.5667
-Chi-squared for original matrix: 18.55)
+Chi-squared for original matrix: 18.55
Chi-squared values among expected and permuted matrices:
Min. 1st Qu. Median Mean 3rd Qu. Max.
- 5.076 12.730 15.190 15.810 18.830 26.120
+ 7.857 12.640 15.650 16.410 20.240 33.150
> ## Unrestricted permutation of presence-absence type
> ## not retaining row/columns sums:
> x3 <- permatfull(m, "none", mtype="prab")
@@ -5340,19 +5324,19 @@
Matrix sums retained: 100 %
Matrix fill retained: 100 %
-Row sums retained: 3.03 %
+Row sums retained: 2.02 %
Column sums retained: 0 %
-Row incidences retained: 3.03 %
+Row incidences retained: 2.02 %
Column incidences retained: 0 %
Bray-Curtis dissimilarities among original and permuted matrices:
Min. 1st Qu. Median Mean 3rd Qu. Max.
- 0.2000 0.3333 0.4000 0.3805 0.4000 0.5333
+ 0.2000 0.3333 0.4000 0.3643 0.4000 0.5333
-Chi-squared for original matrix: 8.4)
+Chi-squared for original matrix: 8.4
Chi-squared values among expected and permuted matrices:
Min. 1st Qu. Median Mean 3rd Qu. Max.
- 9.188 13.620 15.730 15.420 17.340 20.830
+ 8.354 13.340 15.060 15.280 17.180 21.330
> ## Restricted permutation,
> ## check sums within strata:
> x4 <- permatfull(m, strata=c(1,1,2,2))
@@ -5372,21 +5356,21 @@
Number of permuted matrices: 99
Matrix sums retained: 100 %
-Matrix fill retained: 38.38 %
+Matrix fill retained: 49.49 %
Row sums retained: 100 %
Column sums retained: 100 %
-Row incidences retained: 2.02 %
-Column incidences retained: 5.05 %
+Row incidences retained: 7.07 %
+Column incidences retained: 3.03 %
Sums within strata retained: 100 %
Bray-Curtis dissimilarities among original and permuted matrices:
Min. 1st Qu. Median Mean 3rd Qu. Max.
-0.06667 0.20000 0.20000 0.21750 0.26670 0.33330
+0.06667 0.20000 0.20000 0.21950 0.26670 0.40000
-Chi-squared for original matrix: 18.55)
+Chi-squared for original matrix: 18.55
Chi-squared values among expected and permuted matrices:
Min. 1st Qu. Median Mean 3rd Qu. Max.
- 14.21 18.20 21.27 21.18 23.45 37.88
+ 14.21 18.28 19.84 20.85 23.01 32.63
>
> ## NOTE: 'times' argument usually needs to be >= 99
> ## here much lower value is used for demonstration
@@ -5417,17 +5401,17 @@
Coefficients:
ar1 intercept
- 0.9918 0.1835
-s.e. 0.0116 0.1364
+ 0.9914 0.1847
+s.e. 0.0122 0.1343
-sigma^2 estimated as 0.0003259: log likelihood = 47.26, aic = -88.51
+sigma^2 estimated as 0.0003348: log likelihood = 47.03, aic = -88.06
> ## Ljung-Box test of residuals
> Box.test(mar$residuals)
Box-Pierce test
data: mar$residuals
-X-squared = 0.1905, df = 1, p-value = 0.6625
+X-squared = 0.0011, df = 1, p-value = 0.9739
> ## Graphical diagnostics
> tsdiag(mar)
@@ -6871,27 +6855,27 @@
simulation method r0
alternative hypothesis: true mean is not equal to the statistic
- statistic z 2.5% 50% 97.5% Pr(sim.)
-2 411.98157 -2.99423 478.34101 575.57604 673.73 0.01 **
-13 548.84793 -0.51412 473.54839 574.19355 678.29 0.57
-4 606.91244 -1.28888 569.12442 694.00922 791.24 0.23
-16 479.26267 -0.15414 364.51613 491.70507 591.24 0.93
-6 572.35023 -0.84373 502.18894 619.81567 711.45 0.51
-1 249.30876 -2.28880 267.74194 367.28111 444.70 0.05 *
-8 692.16590 0.95083 552.53456 642.39631 744.19 0.33
-5 640.09217 -1.68020 627.14286 724.88479 798.69 0.09 .
-17 341.93548 -2.06383 362.67281 441.47465 544.19 0.03 *
-15 599.53917 2.12165 384.23963 493.08756 575.07 0.03 *
-10 563.59447 -1.61592 545.27650 650.69124 739.63 0.15
-11 564.05530 0.54226 436.86636 535.02304 647.42 0.77
-9 625.80645 -1.24238 596.26728 693.08756 795.81 0.27
-18 543.31797 0.16005 431.29032 543.31797 622.12 1.00
-3 489.40092 -1.54810 488.47926 565.89862 649.26 0.11
-20 578.80184 1.71999 393.54839 493.08756 575.07 0.07 .
-14 547.92627 2.07286 362.67281 448.38710 539.63 0.05 *
-19 593.08756 1.02914 431.29032 543.31797 622.12 0.49
-12 572.35023 0.73286 426.72811 543.31797 622.12 0.51
-7 646.54378 -0.67463 581.15207 683.41014 776.11 0.65
+ statistic z 2.5% 50% 97.5% Pr(sim.)
+2 411.981567 -3.174838 462.373272 577.880184 673.73 0.01 **
+13 548.847926 -0.391605 464.447005 565.898618 664.40 0.71
+4 606.912442 -1.670683 584.493088 694.009217 791.24 0.13
+16 479.262673 -0.364249 364.516129 502.304147 591.24 0.53
+6 572.350230 -0.652353 510.253456 609.216590 717.05 0.63
+1 249.308756 -2.584802 264.700461 367.281106 435.37 0.05 *
+8 692.165899 0.891185 550.276498 643.778802 747.93 0.45
+5 640.092166 -1.331165 613.870968 724.884793 830.41 0.25
+17 341.935484 -2.279642 373.271889 441.474654 538.59 0.03 *
+15 599.539171 1.874784 395.852535 491.705069 599.54 0.09 .
+10 563.594470 -1.618219 553.801843 660.829493 723.46 0.11
+11 564.055300 0.531521 418.433180 536.405530 634.15 0.77
+9 625.806452 -1.015424 548.387097 694.009217 778.80 0.31
+18 543.317972 0.090292 411.820276 543.317972 626.68 1.00
+3 489.400922 -1.486983 460.483871 567.281106 673.73 0.15
+20 578.801843 1.595836 408.709677 495.391705 585.65 0.11
+14 547.926267 1.912479 370.967742 462.211982 544.19 0.07 .
+19 593.087558 0.978571 439.170507 527.188940 642.86 0.49
+12 572.350230 0.797098 425.460829 527.188940 642.86 0.33
+7 646.543779 -0.606963 576.152074 681.566820 770.51 0.53
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
> ## Clustering of tree distances
@@ -7457,7 +7441,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x107d8ac00>
+<environment: 0x1072c38d0>
Estimated degrees of freedom:
2 total = 3
@@ -7933,7 +7917,7 @@
> ### * <FOOTER>
> ###
> cat("Time elapsed: ", proc.time() - get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed: 119.899 1.399 124.377 0 0
+Time elapsed: 110.662 1.469 112.859 0 0
> grDevices::dev.off()
null device
1
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