[Vegan-commits] r2578 - in pkg/vegan: R inst tests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Aug 1 15:43:24 CEST 2013
Author: jarioksa
Date: 2013-08-01 15:43:23 +0200 (Thu, 01 Aug 2013)
New Revision: 2578
Modified:
pkg/vegan/R/make.commsim.R
pkg/vegan/inst/ChangeLog
pkg/vegan/tests/oecosimu-tests.Rout.save
Log:
replace indshuffle with much faster stats::rmultinom in make.commsim
Modified: pkg/vegan/R/make.commsim.R
===================================================================
--- pkg/vegan/R/make.commsim.R 2013-07-28 05:04:40 UTC (rev 2577)
+++ pkg/vegan/R/make.commsim.R 2013-08-01 13:43:23 UTC (rev 2578)
@@ -199,10 +199,7 @@
mode="integer",
fun=function(x, n, nr, nc, cs, rs, rf, cf, s, fill, thin) {
indshuffle <- function(x) {
- out <- integer(length(x))
- tmp <- table(sample.int(length(x), sum(x), replace = TRUE))
- out[as.integer(names(tmp))] <- as.integer(tmp)
- out
+ drop(rmultinom(1, sum(x), rep(1, length(x))))
}
nz <- as.integer(x[x > 0])
out <- array(unlist(r2dtable(fill, rf, cf)), c(nr, nc, n))
@@ -256,10 +253,7 @@
mode="integer",
fun=function(x, n, nr, nc, cs, rs, rf, cf, s, fill, thin) {
indshuffle <- function(x) {
- out <- integer(length(x))
- tmp <- table(sample.int(length(x), sum(x), replace = TRUE))
- out[as.integer(names(tmp))] <- as.integer(tmp)
- out
+ drop(rmultinom(1, sum(x), rep(1, length(x))))
}
I <- seq_len(nr)
out <- array(unlist(r2dtable(fill, rf, cf)), c(nr, nc, n))
@@ -281,10 +275,7 @@
mode="integer",
fun=function(x, n, nr, nc, cs, rs, rf, cf, s, fill, thin) {
indshuffle <- function(x) {
- out <- integer(length(x))
- tmp <- table(sample.int(length(x), sum(x), replace = TRUE))
- out[as.integer(names(tmp))] <- as.integer(tmp)
- out
+ drop(rmultinom(1, sum(x), rep(1, length(x))))
}
J <- seq_len(nc)
out <- array(unlist(r2dtable(fill, rf, cf)), c(nr, nc, n))
@@ -357,10 +348,7 @@
mode="integer",
fun=function(x, n, nr, nc, rs, cs, rf, cf, s, fill, thin) {
indshuffle <- function(x) {
- out <- integer(length(x))
- tmp <- table(sample.int(length(x), sum(x), replace = TRUE))
- out[as.integer(names(tmp))] <- as.integer(tmp)
- out
+ drop(rmultinom(1, sum(x), rep(1, length(x))))
}
out <- matrix(0L, nr * nc, n)
for (k in seq_len(n))
@@ -372,10 +360,7 @@
mode="integer",
fun=function(x, n, nr, nc, rs, cs, rf, cf, s, fill, thin) {
indshuffle <- function(x) {
- out <- integer(length(x))
- tmp <- table(sample.int(length(x), sum(x), replace = TRUE))
- out[as.integer(names(tmp))] <- as.integer(tmp)
- out
+ drop(rmultinom(1, sum(x), rep(1, length(x))))
}
out <- array(0L, c(nr, nc, n))
J <- seq_len(nc)
@@ -388,10 +373,7 @@
mode="integer",
fun=function(x, n, nr, nc, rs, cs, rf, cf, s, fill, thin) {
indshuffle <- function(x) {
- out <- integer(length(x))
- tmp <- table(sample.int(length(x), sum(x), replace = TRUE))
- out[as.integer(names(tmp))] <- as.integer(tmp)
- out
+ drop(rmultinom(1, sum(x), rep(1, length(x))))
}
out <- array(0L, c(nr, nc, n))
I <- seq_len(nr)
@@ -404,10 +386,7 @@
mode="integer",
fun=function(x, n, nr, nc, rs, cs, rf, cf, s, fill, thin) {
indshuffle <- function(x) {
- out <- integer(length(x))
- tmp <- table(sample.int(length(x), sum(x), replace = TRUE))
- out[as.integer(names(tmp))] <- as.integer(tmp)
- out
+ drop(rmultinom(1, sum(x), rep(1, length(x))))
}
out <- matrix(0L, nr * nc, n)
for (k in seq_len(n)) {
@@ -421,10 +400,7 @@
mode="integer",
fun=function(x, n, nr, nc, rs, cs, rf, cf, s, fill, thin) {
indshuffle <- function(x) {
- out <- integer(length(x))
- tmp <- table(sample.int(length(x), sum(x), replace = TRUE))
- out[as.integer(names(tmp))] <- as.integer(tmp)
- out
+ drop(rmultinom(1, sum(x), rep(1, length(x))))
}
out <- array(0L, c(nr, nc, n))
J <- seq_len(nc)
@@ -439,10 +415,7 @@
mode="integer",
fun=function(x, n, nr, nc, rs, cs, rf, cf, s, fill, thin) {
indshuffle <- function(x) {
- out <- integer(length(x))
- tmp <- table(sample.int(length(x), sum(x), replace = TRUE))
- out[as.integer(names(tmp))] <- as.integer(tmp)
- out
+ drop(rmultinom(1, sum(x), rep(1, length(x))))
}
out <- array(0L, c(nr, nc, n))
I <- seq_len(nr)
Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog 2013-07-28 05:04:40 UTC (rev 2577)
+++ pkg/vegan/inst/ChangeLog 2013-08-01 13:43:23 UTC (rev 2578)
@@ -13,6 +13,14 @@
Ecology Progress Series_, 320, 11–27. The basic development was
made in github.com and merged to R-Forge.
+ * nullmodel: replaced internal indshuffle() function in
+ make.commsim() with much faster stats::rmultinom(). The
+ rmultinom() function takes argument 'n' for the number of random
+ vectors, and using this could be still faster, but we only
+ generate one vector in time. Using 'n' would require better
+ analysis of individual nullmodels. The commit changes random
+ sequences, but passes tests.
+
* oecosimu: Gained argument 'batchsize' to set the maximum size of
simulated nullmodels (in Mb). If a larger object would be
produced, the analysis is broken into several batches to avoid
Modified: pkg/vegan/tests/oecosimu-tests.Rout.save
===================================================================
--- pkg/vegan/tests/oecosimu-tests.Rout.save 2013-07-28 05:04:40 UTC (rev 2577)
+++ pkg/vegan/tests/oecosimu-tests.Rout.save 2013-08-01 13:43:23 UTC (rev 2578)
@@ -1,8 +1,8 @@
-R Under development (unstable) (2013-01-31 r61792) -- "Unsuffered Consequences"
+R version 2.15.3 (2013-03-01) -- "Security Blanket"
Copyright (C) 2013 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
-Platform: x86_64-unknown-linux-gnu (64-bit)
+Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
@@ -626,56 +626,56 @@
--> margin none shuffle ind <--
grand sum: [1] TRUE
-row sums: [1] "Mean relative difference: 0.3935785"
-col sums: [1] "Mean relative difference: 1.181426"
-fill: [1] "Mean relative difference: 0.5952064"
-row freqs: [1] "Mean relative difference: 0.5952064"
-col freqs: [1] "Mean relative difference: 0.5952064"
+row sums: [1] "Mean relative difference: 0.4053168"
+col sums: [1] "Mean relative difference: 1.1797"
+fill: [1] "Mean relative difference: 0.5960133"
+row freqs: [1] "Mean relative difference: 0.5960133"
+col freqs: [1] "Mean relative difference: 0.6122867"
Brachy PHTH HPAV RARD SSTR Protopl MEGR MPRO TVIE HMIN HMIN2 NPRA
-8 3 2 3 9 0 1 5 6 3 4 5 0
-9 3 3 4 3 4 5 4 7 4 5 2 2
-11 4 2 7 3 2 2 4 4 6 3 3 7
-14 2 5 6 2 6 1 3 5 2 4 2 3
-15 2 0 6 1 5 2 2 1 2 5 4 4
-19 2 3 6 10 5 3 2 2 1 4 3 2
-25 6 3 5 4 3 4 5 2 2 1 6 2
-30 9 3 1 5 6 3 4 7 6 4 3 4
-32 5 0 3 3 3 6 5 5 3 4 2 9
-33 4 5 1 5 5 1 1 6 4 3 4 4
-34 4 2 6 7 4 5 6 6 5 2 6 3
-35 5 9 5 6 2 5 3 4 7 3 2 3
-36 3 2 5 5 0 5 3 1 1 8 4 3
-37 7 2 5 7 8 2 3 2 4 3 6 3
-38 2 7 4 3 7 3 4 1 3 4 6 3
-39 3 4 4 2 1 3 3 4 0 2 6 4
-40 3 4 2 6 3 2 5 3 3 3 5 2
-41 2 3 3 3 5 4 5 3 6 4 2 6
-42 7 4 3 3 5 5 3 4 5 4 1 4
-43 4 4 2 3 5 6 2 7 7 3 2 7
-44 5 6 4 3 4 1 6 2 5 5 2 8
-45 3 4 4 2 4 6 2 0 2 4 6 6
-46 1 3 6 5 2 3 2 4 0 5 2 6
-47 5 2 3 5 5 1 6 5 4 4 0 3
-48 2 7 2 5 6 7 3 2 2 3 1 5
-49 5 2 4 4 4 4 4 1 4 7 3 3
-50 3 6 2 7 2 1 10 2 3 5 2 3
-51 2 5 7 2 4 8 6 1 3 1 2 5
-52 2 2 0 1 2 5 3 3 3 2 3 3
-53 3 6 6 5 4 5 5 6 4 8 1 4
-54 7 3 1 5 1 2 4 4 8 4 2 9
-55 5 3 6 8 1 5 1 3 5 4 6 6
-56 4 3 4 5 3 4 3 6 5 5 4 4
-57 2 3 2 0 6 6 1 8 5 3 3 1
-58 4 6 4 6 5 4 1 6 6 5 7 3
-59 2 5 6 2 3 6 5 6 6 5 4 5
-60 1 2 2 1 3 5 5 6 6 3 5 2
-61 2 1 2 3 3 3 4 2 1 5 4 6
-62 7 6 2 2 0 0 2 3 2 5 1 4
-63 8 2 6 4 3 0 3 4 6 5 7 5
-64 0 4 6 1 6 8 3 4 3 0 4 6
-66 3 8 2 7 3 4 4 7 6 0 3 1
-67 6 3 1 3 3 1 3 6 3 5 9 5
-68 5 4 8 6 4 1 0 6 2 5 4 1
+8 8 6 5 2 5 2 3 2 3 4 1 6
+9 4 3 4 11 2 5 3 4 3 2 6 3
+11 7 3 5 2 2 4 3 3 6 5 2 2
+14 2 7 1 3 5 1 4 5 7 6 8 6
+15 6 1 4 6 1 2 6 2 3 4 1 3
+19 4 6 2 5 5 8 4 7 3 5 3 3
+25 3 4 8 4 3 2 5 1 2 4 5 4
+30 2 5 4 3 1 4 2 8 5 2 2 1
+32 2 2 5 3 5 4 5 4 4 4 4 5
+33 1 4 3 2 2 7 4 1 3 3 2 1
+34 1 3 1 4 4 2 4 7 2 5 5 2
+35 4 5 3 8 10 6 2 6 5 1 6 3
+36 5 2 3 5 5 4 2 5 2 2 3 5
+37 2 5 5 5 5 1 6 5 3 3 1 2
+38 2 5 5 4 2 3 2 8 2 4 5 3
+39 2 8 7 2 2 4 5 5 6 2 1 5
+40 4 4 3 4 3 3 4 0 2 1 4 5
+41 5 7 5 3 4 3 2 2 6 4 2 6
+42 5 7 1 6 3 5 2 2 0 5 4 5
+43 8 7 2 4 1 1 4 2 2 1 7 3
+44 2 6 3 4 7 4 1 8 1 2 4 9
+45 6 4 3 1 5 3 3 3 3 1 6 5
+46 1 3 2 9 2 2 0 6 3 4 4 2
+47 5 7 5 4 3 8 2 4 1 5 5 5
+48 4 2 3 8 3 5 3 7 5 1 4 3
+49 6 4 1 3 5 4 3 3 3 3 6 2
+50 4 2 0 4 4 3 1 3 6 2 2 2
+51 1 1 3 2 4 1 3 5 2 5 6 5
+52 4 3 5 3 5 5 2 6 3 2 4 5
+53 3 4 9 5 2 0 2 5 3 3 2 2
+54 7 0 6 3 4 6 4 6 4 6 2 5
+55 0 5 2 8 5 3 4 6 2 4 3 2
+56 3 1 5 5 1 2 5 2 6 3 2 4
+57 3 5 5 2 1 4 4 5 4 3 5 2
+58 4 7 5 6 3 3 2 1 2 3 1 7
+59 2 3 1 0 5 5 2 6 4 5 6 6
+60 3 1 4 5 4 8 6 3 2 6 3 5
+61 4 4 2 4 4 6 6 6 6 4 6 4
+62 6 4 4 0 5 1 3 4 3 7 0 5
+63 4 5 2 3 2 3 4 4 2 3 3 2
+64 5 3 3 4 5 3 4 2 3 3 3 4
+66 2 6 3 4 2 4 1 5 2 1 5 5
+67 4 1 2 4 3 3 4 4 1 5 2 1
+68 3 5 6 3 6 4 4 4 1 6 1 1
--> margin none shuffle samp <--
grand sum: [1] TRUE
@@ -732,109 +732,109 @@
--> margin none shuffle both <--
grand sum: [1] TRUE
-row sums: [1] "Mean relative difference: 0.4619368"
-col sums: [1] "Mean relative difference: 1.228379"
+row sums: [1] "Mean relative difference: 0.4389986"
+col sums: [1] "Mean relative difference: 1.20342"
fill: [1] TRUE
-row freqs: [1] "Mean relative difference: 0.3531599"
-col freqs: [1] "Mean relative difference: 0.6381579"
+row freqs: [1] "Mean relative difference: 0.3670669"
+col freqs: [1] "Mean relative difference: 0.5723684"
Brachy PHTH HPAV RARD SSTR Protopl MEGR MPRO TVIE HMIN HMIN2 NPRA
-8 0 0 0 14 0 0 9 16 7 5 0 0
-9 0 11 0 0 0 6 0 0 10 0 0 0
-11 5 0 0 13 0 0 0 0 0 12 0 0
-14 0 0 0 12 0 0 6 11 19 0 0 0
-15 0 0 0 6 0 6 0 0 7 0 13 9
-19 0 0 11 0 16 0 9 0 0 0 0 0
-25 0 12 5 0 0 0 0 0 13 0 0 0
-30 0 0 0 7 8 0 6 0 5 9 0 12
-32 6 14 0 11 0 10 12 0 12 0 8 0
-33 7 0 0 0 0 12 8 0 0 0 8 0
-34 9 0 0 0 0 10 0 0 0 0 0 11
-35 0 0 8 5 12 8 0 0 0 0 0 0
-36 0 0 0 0 0 7 0 0 0 11 10 0
-37 0 0 0 0 6 13 0 0 5 0 0 0
-38 7 9 0 0 0 0 15 6 0 11 8 0
-39 0 0 0 0 0 0 0 9 0 11 0 0
-40 11 0 0 6 6 11 0 8 0 0 0 11
-41 0 0 0 10 0 0 0 7 0 0 0 14
-42 0 14 0 7 0 0 12 10 10 0 6 0
-43 8 13 0 4 0 11 8 0 0 0 0 0
-44 11 7 8 11 0 12 11 16 0 0 0 0
-45 0 8 0 0 0 8 0 14 0 9 0 0
-46 0 0 0 2 14 9 0 0 12 14 0 0
-47 0 0 0 0 0 0 0 0 0 0 6 0
-48 0 9 0 11 0 0 11 0 7 0 0 0
-49 0 11 0 0 4 0 12 10 0 8 0 0
-50 0 9 0 0 16 0 0 0 0 0 0 0
-51 0 0 9 10 0 8 8 0 8 15 0 8
-52 0 0 0 10 11 3 11 10 0 10 0 0
-53 12 7 0 0 0 8 8 0 7 0 6 9
-54 8 6 8 9 0 0 0 6 6 0 11 0
-55 0 0 0 14 10 8 0 0 10 0 0 0
-56 11 0 0 0 0 0 0 0 0 0 0 0
-57 0 7 11 0 0 0 10 10 8 0 0 5
-58 9 0 0 8 0 11 14 0 0 0 0 10
-59 13 0 0 0 0 10 7 9 8 0 9 6
-60 6 0 0 0 0 11 9 0 10 0 0 6
-61 9 0 0 7 0 0 0 0 8 19 5 0
-62 0 0 0 0 0 0 0 6 0 16 0 10
-63 0 0 0 0 13 0 0 10 0 0 11 12
-64 0 0 0 0 0 6 13 13 10 0 0 8
-66 0 0 0 0 0 9 7 0 0 0 8 0
-67 0 0 0 0 0 0 0 0 0 0 13 8
-68 0 0 9 0 0 7 14 9 6 9 0 0
+8 0 7 9 7 6 12 0 10 0 0 0 0
+9 10 0 12 0 11 0 8 0 7 0 7 0
+11 6 14 9 0 6 0 12 0 0 7 0 11
+14 0 13 7 0 0 0 0 0 0 0 0 10
+15 15 0 0 0 9 0 11 0 16 11 0 0
+19 0 8 9 8 0 0 11 12 9 0 12 0
+25 0 12 7 10 0 7 12 0 0 10 0 12
+30 7 0 0 8 0 10 0 8 9 0 0 0
+32 8 0 0 0 0 0 11 0 0 0 0 0
+33 11 6 0 8 0 9 0 0 0 0 0 0
+34 0 15 9 7 0 13 5 7 0 11 0 0
+35 11 0 0 0 0 9 0 0 5 0 0 0
+36 0 0 10 9 9 0 0 9 0 7 4 0
+37 9 0 0 13 0 8 0 0 0 0 0 0
+38 10 7 10 9 10 0 10 0 14 11 6 0
+39 8 0 0 9 0 0 0 0 0 10 0 8
+40 0 8 0 0 0 0 12 0 0 0 11 0
+41 0 0 11 0 13 0 5 10 13 0 0 13
+42 0 7 7 0 0 11 16 11 11 14 0 7
+43 9 11 0 0 6 0 0 0 0 0 11 13
+44 9 0 0 7 14 8 0 7 10 0 7 0
+45 0 0 0 0 0 0 7 0 11 0 0 0
+46 9 9 0 0 0 9 7 0 0 0 0 0
+47 0 7 0 7 10 0 7 10 11 0 0 0
+48 9 7 0 9 12 0 12 8 7 10 10 0
+49 0 0 8 0 0 6 0 0 0 0 0 0
+50 0 0 9 11 8 15 0 0 15 9 0 7
+51 0 0 0 0 0 10 0 0 0 6 0 17
+52 0 8 0 0 3 0 0 10 8 0 0 10
+53 0 0 0 0 0 0 12 7 0 0 10 8
+54 9 6 10 0 6 6 0 0 7 14 0 0
+55 7 0 0 0 0 9 0 0 12 0 0 0
+56 0 0 8 0 0 17 10 8 0 0 0 0
+57 0 13 0 0 17 11 16 0 0 8 8 11
+58 0 4 12 0 6 0 0 0 0 15 12 8
+59 0 7 0 0 0 0 9 0 0 10 0 12
+60 0 10 0 0 0 7 0 0 0 0 0 0
+61 0 0 16 7 0 10 0 6 0 0 0 0
+62 11 0 4 0 5 9 11 8 0 12 0 9
+63 0 0 0 0 6 0 0 0 9 11 0 0
+64 0 0 2 7 0 0 0 0 10 3 0 0
+66 0 0 0 0 5 0 11 0 0 0 0 8
+67 0 0 0 11 0 0 9 0 6 0 8 0
+68 13 0 0 0 0 0 9 0 0 0 0 10
--> margin rows shuffle ind <--
grand sum: [1] TRUE
row sums: [1] TRUE
-col sums: [1] "Mean relative difference: 1.181426"
-fill: [1] "Mean relative difference: 0.5700141"
-row freqs: [1] "Mean relative difference: 0.5700141"
-col freqs: [1] "Mean relative difference: 0.5909753"
+col sums: [1] "Mean relative difference: 1.1797"
+fill: [1] "Mean relative difference: 0.5715292"
+row freqs: [1] "Mean relative difference: 0.5715292"
+col freqs: [1] "Mean relative difference: 0.6076233"
Brachy PHTH HPAV RARD SSTR Protopl MEGR MPRO TVIE HMIN HMIN2 NPRA
-8 4 4 7 3 3 3 2 3 3 4 4 4
-9 3 1 3 6 6 1 5 4 1 4 3 1
-11 5 6 5 10 5 5 9 12 6 4 7 9
-14 7 7 6 10 5 2 7 8 9 6 10 9
-15 4 1 2 3 1 0 3 1 1 4 2 2
-19 3 3 6 3 6 4 2 5 7 2 3 3
-25 6 3 2 5 5 5 3 3 6 3 2 4
-30 2 5 2 3 1 3 1 3 3 1 5 3
-32 0 2 1 1 1 4 4 3 1 1 3 3
-33 7 7 4 5 4 2 5 3 1 3 5 7
-34 5 11 3 8 6 6 2 9 2 4 7 5
-35 3 2 2 6 2 4 8 4 4 3 2 6
-36 8 4 4 4 3 2 6 3 3 1 4 5
-37 5 3 6 6 4 4 1 4 5 3 4 5
-38 4 6 6 4 4 8 7 6 1 5 6 6
-39 1 4 1 2 2 6 2 1 3 2 3 4
-40 4 7 2 2 7 4 5 4 9 4 4 5
-41 0 3 3 1 0 2 2 2 3 5 0 2
-42 3 0 6 1 7 3 4 8 5 4 3 4
-43 5 8 3 5 4 6 7 3 7 8 4 2
-44 0 3 2 1 0 0 1 2 1 0 2 4
-45 1 4 5 4 5 3 3 4 5 4 3 8
-46 7 3 4 4 6 7 1 3 1 4 5 5
-47 6 1 1 5 3 2 6 3 4 5 2 4
-48 4 1 2 4 1 1 3 6 6 9 4 4
-49 2 2 4 3 3 5 5 3 1 4 3 6
-50 3 6 4 6 10 9 4 5 2 5 6 4
-51 4 1 1 3 3 2 2 3 2 3 0 4
-52 4 5 3 3 5 3 1 5 6 3 3 1
-53 4 4 7 6 3 2 4 2 6 5 5 0
-54 3 1 3 1 2 2 0 2 0 1 1 1
-55 2 1 1 3 0 0 0 2 2 2 2 1
-56 4 4 9 3 2 3 4 3 3 3 2 2
-57 0 0 0 0 0 0 1 0 0 1 0 1
-58 6 3 3 2 1 3 4 5 5 0 6 3
-59 4 2 6 3 2 0 2 4 5 1 3 1
-60 7 3 1 1 2 5 3 4 5 5 2 2
-61 2 0 1 1 1 0 2 2 2 2 1 1
-62 0 0 0 0 1 0 0 1 0 0 1 0
-63 2 1 2 3 3 2 3 0 3 4 0 2
-64 0 1 8 1 1 1 3 4 3 2 2 3
-66 5 5 5 4 3 4 1 1 3 7 1 6
-67 15 23 23 30 24 28 16 21 19 26 22 25
-68 3 2 2 3 3 2 4 3 4 4 2 2
+8 7 4 6 2 6 4 2 2 2 1 1 4
+9 4 2 2 4 5 4 5 1 4 3 5 3
+11 5 6 4 2 6 6 1 8 2 9 11 5
+14 9 12 6 9 4 6 6 7 5 10 7 4
+15 4 4 3 2 2 2 3 7 4 3 3 1
+19 0 2 4 4 4 3 4 2 2 4 1 5
+25 5 1 3 4 0 1 3 5 4 4 5 2
+30 3 0 3 2 1 7 4 3 2 1 4 0
+32 4 3 3 1 1 4 1 4 3 1 1 3
+33 4 4 2 4 3 5 2 7 1 8 4 1
+34 3 7 3 8 4 9 5 6 4 7 5 5
+35 3 1 4 3 5 2 2 3 4 2 5 4
+36 2 3 4 2 1 4 6 1 2 1 4 6
+37 2 9 1 4 6 2 4 2 5 6 3 2
+38 4 8 1 4 5 7 3 3 9 5 3 9
+39 1 4 4 1 4 1 3 1 6 5 3 2
+40 3 3 5 9 1 4 7 5 7 6 1 2
+41 4 3 3 3 3 2 2 0 3 1 4 2
+42 4 4 6 3 1 5 3 2 6 4 3 3
+43 3 3 6 2 8 4 6 4 4 5 1 4
+44 2 2 0 1 2 2 3 0 2 1 2 3
+45 6 7 3 8 3 2 2 4 5 8 1 4
+46 5 4 7 2 2 5 3 7 6 7 3 4
+47 4 4 3 3 1 5 2 3 4 6 5 4
+48 5 4 4 4 3 1 3 4 0 4 2 4
+49 2 6 1 1 0 1 6 5 3 2 1 2
+50 3 4 6 4 6 1 6 6 4 5 5 4
+51 0 2 2 7 3 3 4 5 7 4 3 5
+52 2 3 8 1 7 2 4 3 3 5 2 3
+53 5 7 3 5 3 5 3 6 7 4 4 5
+54 1 0 3 1 0 2 3 1 1 1 1 0
+55 0 1 2 2 3 5 0 1 2 0 2 3
+56 2 4 2 2 2 2 2 3 7 1 3 5
+57 0 1 0 0 0 0 1 0 0 1 0 0
+58 5 3 3 4 2 5 9 3 4 3 3 2
+59 7 2 2 2 4 3 0 1 2 1 3 3
+60 5 7 3 4 6 2 3 3 7 1 6 2
+61 2 0 1 1 1 1 1 1 1 2 1 4
+62 0 0 0 0 0 0 1 0 0 1 0 1
+63 3 2 0 3 3 2 2 1 1 0 4 1
+64 2 3 6 3 2 3 2 1 2 1 0 1
+66 2 1 6 2 4 2 2 4 5 1 1 2
+67 15 24 21 18 36 22 25 21 18 21 19 28
+68 6 4 4 2 0 4 6 1 1 1 4 6
--> margin rows shuffle samp <--
grand sum: [1] TRUE
@@ -892,108 +892,108 @@
--> margin rows shuffle both <--
grand sum: [1] TRUE
row sums: [1] TRUE
-col sums: [1] "Mean relative difference: 1.223546"
+col sums: [1] "Mean relative difference: 1.251856"
fill: [1] TRUE
row freqs: [1] TRUE
-col freqs: [1] "Mean relative difference: 0.6239168"
+col freqs: [1] "Mean relative difference: 0.6503497"
Brachy PHTH HPAV RARD SSTR Protopl MEGR MPRO TVIE HMIN HMIN2 NPRA
-8 3 6 0 5 4 6 0 4 0 8 11 3
-9 7 0 7 0 5 0 0 0 10 0 0 7
-11 11 9 9 7 0 6 0 7 9 0 13 6
-14 0 11 17 11 12 11 0 8 12 0 19 11
-15 0 0 5 6 3 6 3 5 5 0 10 0
-19 6 0 4 0 6 0 0 5 0 0 3 0
-25 0 0 4 6 5 0 0 0 0 6 0 0
-30 3 6 2 6 4 4 3 0 0 7 4 2
-32 0 0 8 0 0 4 8 8 2 0 4 0
-33 0 0 8 8 0 0 8 8 0 0 10 6
-34 10 4 12 0 0 0 0 7 7 0 8 0
-35 0 5 7 4 0 0 0 9 8 3 8 0
-36 5 0 0 0 6 9 8 0 9 8 0 5
-37 10 16 8 0 0 11 0 11 8 0 0 5
-38 0 0 12 0 0 0 13 0 11 15 0 0
-39 8 10 0 5 8 0 4 12 6 0 0 0
-40 9 0 0 8 0 0 0 20 0 14 11 0
-41 3 9 9 0 0 0 0 7 8 0 0 0
-42 0 0 0 0 13 18 0 0 0 18 0 12
-43 16 14 0 0 0 0 11 0 0 0 12 15
-44 0 0 0 0 0 0 10 0 0 0 0 0
-45 7 0 0 0 0 16 10 0 0 0 7 0
-46 0 14 0 0 9 6 0 0 0 0 0 0
-47 8 15 0 0 0 9 0 10 0 0 10 0
-48 0 0 0 0 0 0 12 0 0 0 9 8
-49 0 8 0 8 0 0 0 0 0 0 7 0
-50 0 0 0 0 0 0 0 0 0 0 0 9
-51 0 0 0 7 0 0 0 0 0 7 9 0
-52 11 7 7 0 0 6 0 6 0 0 12 12
-53 0 8 8 0 13 14 11 10 0 0 0 0
-54 5 0 0 0 0 0 0 2 7 0 6 0
-55 0 0 7 0 4 7 0 0 3 0 0 0
-56 9 0 13 9 0 0 12 0 11 0 0 0
-57 1 0 0 0 0 1 0 0 2 0 0 0
-58 0 0 0 0 9 10 0 11 0 0 11 0
-59 0 0 0 0 0 15 14 0 9 0 8 0
-60 0 8 0 0 9 0 0 14 0 0 16 0
-61 0 4 0 0 0 0 0 4 0 0 0 0
-62 0 0 0 0 0 3 0 0 0 0 0 0
-63 0 0 0 0 5 0 0 5 6 5 8 0
-64 7 12 0 8 0 9 0 8 3 7 0 8
-66 0 10 0 0 0 0 0 0 3 0 0 0
-67 0 0 0 0 0 0 0 0 0 139 0 0
-68 0 6 0 0 0 0 0 0 12 0 0 7
+8 6 0 6 0 0 9 4 0 0 4 0 10
+9 0 6 8 3 9 0 0 0 0 0 9 6
+11 5 6 0 0 10 0 4 5 7 0 11 0
+14 9 0 12 8 13 0 0 13 13 13 15 0
+15 0 6 0 4 0 6 2 0 0 0 8 7
+19 4 0 0 6 2 8 3 0 0 0 3 4
+25 0 0 5 0 3 7 9 7 4 0 0 0
+30 4 3 0 3 0 0 5 6 5 5 3 8
+32 0 8 0 0 3 8 0 2 0 11 0 6
+33 11 0 0 0 0 0 0 0 8 12 0 7
+34 10 9 0 0 9 8 12 0 0 0 10 0
+35 6 5 0 9 0 2 0 0 4 0 0 0
+36 6 5 8 0 0 0 6 0 0 0 4 12
+37 0 0 0 7 8 0 0 12 10 0 13 0
+38 0 8 14 15 14 0 0 13 12 0 0 0
+39 9 0 0 4 8 0 8 0 9 0 0 13
+40 0 0 0 0 10 14 0 0 0 0 0 0
+41 0 3 9 0 0 0 0 0 0 9 7 0
+42 21 0 0 0 12 17 0 0 15 0 15 0
+43 0 0 0 0 0 13 17 0 12 0 0 13
+44 0 13 0 0 0 0 0 0 0 17 0 0
+45 0 0 6 10 9 8 0 8 6 16 0 9
+46 0 0 0 8 9 13 0 12 0 7 0 4
+47 13 5 13 9 0 0 9 0 0 0 6 7
+48 0 0 8 0 0 0 0 0 12 11 12 0
+49 0 7 0 10 0 0 0 8 14 0 7 8
+50 0 0 0 10 13 11 0 0 0 0 18 13
+51 0 5 0 7 0 6 0 0 5 7 0 11
+52 0 0 0 0 5 12 0 0 0 0 0 0
+53 9 0 5 0 7 0 0 8 0 0 0 12
+54 0 0 0 11 0 0 0 0 6 4 5 0
+55 0 0 6 3 0 0 7 8 0 0 9 0
+56 13 0 14 0 0 0 7 0 13 9 0 0
+57 0 0 0 0 0 0 0 1 0 0 0 0
+58 16 0 0 10 10 0 0 9 0 0 0 0
+59 0 0 18 0 13 0 0 0 0 0 0 13
+60 0 0 0 9 0 10 13 0 0 0 0 15
+61 0 0 3 8 0 0 0 0 5 0 0 0
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/vegan -r 2578
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