[Vegan-commits] r1849 - pkg/vegan/tests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Sep 15 14:27:35 CEST 2011
Author: jarioksa
Date: 2011-09-15 14:27:35 +0200 (Thu, 15 Sep 2011)
New Revision: 1849
Modified:
pkg/vegan/tests/oecosimu-tests.R
pkg/vegan/tests/oecosimu-tests.Rout.save
Log:
permat*1 tests
Modified: pkg/vegan/tests/oecosimu-tests.R
===================================================================
--- pkg/vegan/tests/oecosimu-tests.R 2011-09-15 05:36:17 UTC (rev 1848)
+++ pkg/vegan/tests/oecosimu-tests.R 2011-09-15 12:27:35 UTC (rev 1849)
@@ -62,3 +62,83 @@
rm(list = ls())
### end commsimulator
+
+### set up permatfull/swap1 tests
+
+data(mite)
+data(mite.env)
+x <- as.matrix(subset(mite, mite.env$Topo == "Blanket"))
+x <- x[, colSums(x) > 0]
+gsum <- sum(x)
+rsum <- rowSums(x)
+csum <- colSums(x)
+fill <- sum(x>0)
+rfrq <- rowSums(x>0)
+cfrq <- colSums(x>0)
+
+margintest <-
+ function(x, gsum, rsum, csum, fill, rfrq, cfrq)
+{
+ cat("grand sum: ")
+ print(all.equal(sum(x), gsum, check.attributes = FALSE))
+ cat("row sums: ")
+ print(all.equal(rowSums(x), rsum, check.attributes = FALSE))
+ cat("col sums: ")
+ print(all.equal(colSums(x), csum, check.attributes = FALSE))
+ cat("fill: ")
+ print(all.equal(sum(x>0), fill, check.attributes = FALSE))
+ cat("row freqs: ")
+ print(all.equal(rowSums(x>0), rfrq, check.attributes = FALSE))
+ cat("col freqs: ")
+ print(all.equal(colSums(x), cfrq, check.attributes = FALSE))
+}
+
+### permatfull1
+
+set.seed(4711)
+margin <- c("none", "rows", "columns", "both")
+shuffle <- c("ind", "samp", "both")
+
+for(mar in margin) {
+ for(what in shuffle) {
+ cat("\n--> margin", mar, " shuffle", what, "<--\n")
+ m <- permatfull1(x, fixedmar = mar, shuffle = what, mtype = "count")
+ margintest(m, gsum, rsum, csum, fill, rfrq, cfrq)
+ print(m[,1:12])
+ }
+}
+
+### permatswap1
+set.seed(4711)
+methods <- c("swap", "quasiswap", "swsh", "abuswap")
+margins <- c("rows", "columns", "both")
+shuffle <- c("samp", "both")
+
+incompatible <- function(method, margin)
+{
+ (method == "swap" && margin != "both") ||
+ (method == "abuswap" && margin == "both") ||
+ (method %in% c("quasiswap", "swsh") && margin != "both")
+}
+
+for(method in methods) {
+ for(margin in margins) {
+ for(what in shuffle) {
+ if (incompatible(method = method, margin = margin))
+ next
+ cat("\n*** ", method, " ***\n")
+ cat("--> margin", margin, " shuffle", what, "<--\n")
+ m <- permatswap1(x, method = method, fixedmar = margin, shuffle = what,
+ mtype = "count", thin=100)
+ margintest(m, gsum, rsum, csum,fill, rfrq, cfrq)
+ print(m[,1:12])
+ }
+ }
+}
+### end permatswap1
+
+### clean
+rm(list = ls())
+
+## end permatfull1/swap1
+
Modified: pkg/vegan/tests/oecosimu-tests.Rout.save
===================================================================
--- pkg/vegan/tests/oecosimu-tests.Rout.save 2011-09-15 05:36:17 UTC (rev 1848)
+++ pkg/vegan/tests/oecosimu-tests.Rout.save 2011-09-15 12:27:35 UTC (rev 1849)
@@ -577,3 +577,1259 @@
>
> ### end commsimulator
>
+> ### set up permatfull/swap1 tests
+>
+> data(mite)
+> data(mite.env)
+> x <- as.matrix(subset(mite, mite.env$Topo == "Blanket"))
+> x <- x[, colSums(x) > 0]
+> gsum <- sum(x)
+> rsum <- rowSums(x)
+> csum <- colSums(x)
+> fill <- sum(x>0)
+> rfrq <- rowSums(x>0)
+> cfrq <- colSums(x>0)
+>
+> margintest <-
++ function(x, gsum, rsum, csum, fill, rfrq, cfrq)
++ {
++ cat("grand sum: ")
++ print(all.equal(sum(x), gsum, check.attributes = FALSE))
++ cat("row sums: ")
++ print(all.equal(rowSums(x), rsum, check.attributes = FALSE))
++ cat("col sums: ")
++ print(all.equal(colSums(x), csum, check.attributes = FALSE))
++ cat("fill: ")
++ print(all.equal(sum(x>0), fill, check.attributes = FALSE))
++ cat("row freqs: ")
++ print(all.equal(rowSums(x>0), rfrq, check.attributes = FALSE))
++ cat("col freqs: ")
++ print(all.equal(colSums(x), cfrq, check.attributes = FALSE))
++ }
+>
+> ### permatfull1
+>
+> set.seed(4711)
+> margin <- c("none", "rows", "columns", "both")
+> shuffle <- c("ind", "samp", "both")
+>
+> for(mar in margin) {
++ for(what in shuffle) {
++ cat("\n--> margin", mar, " shuffle", what, "<--\n")
++ m <- permatfull1(x, fixedmar = mar, shuffle = what, mtype = "count")
++ margintest(m, gsum, rsum, csum, fill, rfrq, cfrq)
++ print(m[,1:12])
++ }
++ }
+
+--> 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: 0.8950457"
+ [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12]
+ [1,] 3 2 3 9 0 1 5 6 3 4 5 0
+ [2,] 3 3 4 3 4 5 4 7 4 5 2 2
+ [3,] 4 2 7 3 2 2 4 4 6 3 3 7
+ [4,] 2 5 6 2 6 1 3 5 2 4 2 3
+ [5,] 2 0 6 1 5 2 2 1 2 5 4 4
+ [6,] 2 3 6 10 5 3 2 2 1 4 3 2
+ [7,] 6 3 5 4 3 4 5 2 2 1 6 2
+ [8,] 9 3 1 5 6 3 4 7 6 4 3 4
+ [9,] 5 0 3 3 3 6 5 5 3 4 2 9
+[10,] 4 5 1 5 5 1 1 6 4 3 4 4
+[11,] 4 2 6 7 4 5 6 6 5 2 6 3
+[12,] 5 9 5 6 2 5 3 4 7 3 2 3
+[13,] 3 2 5 5 0 5 3 1 1 8 4 3
+[14,] 7 2 5 7 8 2 3 2 4 3 6 3
+[15,] 2 7 4 3 7 3 4 1 3 4 6 3
+[16,] 3 4 4 2 1 3 3 4 0 2 6 4
+[17,] 3 4 2 6 3 2 5 3 3 3 5 2
+[18,] 2 3 3 3 5 4 5 3 6 4 2 6
+[19,] 7 4 3 3 5 5 3 4 5 4 1 4
+[20,] 4 4 2 3 5 6 2 7 7 3 2 7
+[21,] 5 6 4 3 4 1 6 2 5 5 2 8
+[22,] 3 4 4 2 4 6 2 0 2 4 6 6
+[23,] 1 3 6 5 2 3 2 4 0 5 2 6
+[24,] 5 2 3 5 5 1 6 5 4 4 0 3
+[25,] 2 7 2 5 6 7 3 2 2 3 1 5
+[26,] 5 2 4 4 4 4 4 1 4 7 3 3
+[27,] 3 6 2 7 2 1 10 2 3 5 2 3
+[28,] 2 5 7 2 4 8 6 1 3 1 2 5
+[29,] 2 2 0 1 2 5 3 3 3 2 3 3
+[30,] 3 6 6 5 4 5 5 6 4 8 1 4
+[31,] 7 3 1 5 1 2 4 4 8 4 2 9
+[32,] 5 3 6 8 1 5 1 3 5 4 6 6
+[33,] 4 3 4 5 3 4 3 6 5 5 4 4
+[34,] 2 3 2 0 6 6 1 8 5 3 3 1
+[35,] 4 6 4 6 5 4 1 6 6 5 7 3
+[36,] 2 5 6 2 3 6 5 6 6 5 4 5
+[37,] 1 2 2 1 3 5 5 6 6 3 5 2
+[38,] 2 1 2 3 3 3 4 2 1 5 4 6
+[39,] 7 6 2 2 0 0 2 3 2 5 1 4
+[40,] 8 2 6 4 3 0 3 4 6 5 7 5
+[41,] 0 4 6 1 6 8 3 4 3 0 4 6
+[42,] 3 8 2 7 3 4 4 7 6 0 3 1
+[43,] 6 3 1 3 3 1 3 6 3 5 9 5
+[44,] 5 4 8 6 4 1 0 6 2 5 4 1
+
+--> margin none shuffle samp <--
+grand sum: [1] TRUE
+row sums: [1] "Mean relative difference: 0.6269636"
+col sums: [1] "Mean relative difference: 1.136544"
+fill: [1] TRUE
+row freqs: [1] "Mean relative difference: 0.365812"
+col freqs: [1] "Mean relative difference: 0.8950457"
+ [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12]
+ [1,] 5 0 0 0 0 0 0 0 14 0 3 11
+ [2,] 18 2 2 22 0 0 0 0 4 0 1 0
+ [3,] 2 0 0 4 0 0 0 0 2 1 0 0
+ [4,] 0 16 0 0 0 1 0 0 0 0 2 0
+ [5,] 0 8 0 0 5 2 0 9 1 0 25 0
+ [6,] 5 1 0 3 0 0 2 4 0 0 0 1
+ [7,] 0 1 0 7 4 0 0 0 0 0 2 5
+ [8,] 0 12 0 2 0 0 0 0 0 0 0 0
+ [9,] 0 5 0 3 0 0 0 0 0 0 0 0
+[10,] 0 2 15 4 0 2 5 4 9 33 0 0
+[11,] 2 0 6 1 0 7 0 3 8 0 0 0
+[12,] 0 0 2 1 2 5 20 4 0 1 0 0
+[13,] 0 3 0 0 0 44 0 1 0 1 57 0
+[14,] 6 1 0 0 6 0 0 0 0 0 3 0
+[15,] 0 0 1 0 0 0 0 15 0 1 0 3
+[16,] 0 20 723 2 0 9 0 0 7 20 1 0
+[17,] 24 1 0 2 0 0 0 0 0 0 0 5
+[18,] 1 0 0 1 2 0 0 2 0 1 1 0
+[19,] 0 1 0 0 0 0 0 1 2 0 1 0
+[20,] 5 2 2 0 2 4 0 0 1 1 0 0
+[21,] 0 0 0 0 0 0 32 0 0 0 11 0
+[22,] 0 0 4 0 0 0 0 0 1 0 0 0
+[23,] 1 25 0 0 0 0 0 0 6 0 0 0
+[24,] 0 0 0 0 0 0 0 0 24 31 15 1
+[25,] 2 8 1 2 2 0 2 0 0 1 0 0
+[26,] 5 2 4 0 2 2 0 1 0 0 0 0
+[27,] 0 19 0 0 26 2 0 38 2 0 9 5
+[28,] 0 20 0 0 0 0 0 0 7 0 0 0
+[29,] 0 5 0 5 0 1 2 11 0 0 0 0
+[30,] 0 20 0 1 1 44 2 1 0 0 0 9
+[31,] 0 0 0 0 0 0 0 0 0 2 0 1
+[32,] 20 0 0 24 21 0 0 6 0 3 0 0
+[33,] 9 0 0 11 0 0 0 3 0 3 0 1
+[34,] 3 0 0 0 0 1 0 0 0 1 0 4
+[35,] 8 0 0 0 0 0 0 5 12 0 5 13
+[36,] 0 0 0 0 1 3 5 1 0 0 0 0
+[37,] 0 0 20 53 1 0 11 0 0 0 2 1
+[38,] 0 14 0 0 4 0 0 0 6 0 2 9
+[39,] 0 0 0 4 0 0 2 0 0 0 1 0
+[40,] 1 2 0 2 0 0 4 0 0 0 0 0
+[41,] 2 1 1 1 0 0 0 0 0 1 6 5
+[42,] 0 0 0 61 0 0 1 37 0 1 0 0
+[43,] 12 3 0 0 8 0 0 0 0 0 0 2
+[44,] 0 28 0 29 0 0 7 0 4 0 0 6
+
+--> margin none shuffle both <--
+grand sum: [1] TRUE
+row sums: [1] "Mean relative difference: 0.4682944"
+col sums: [1] "Mean relative difference: 1.192474"
+fill: [1] TRUE
+row freqs: [1] "Mean relative difference: 0.3378378"
+col freqs: [1] "Mean relative difference: 0.8950457"
+ [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12]
+ [1,] 0 0 14 0 0 0 0 0 0 0 0 8
+ [2,] 0 15 12 0 0 5 0 9 0 0 6 5
+ [3,] 0 13 8 0 0 7 0 0 0 0 11 0
+ [4,] 17 12 0 0 0 10 0 0 21 0 13 10
+ [5,] 0 11 0 10 0 10 10 0 0 0 0 0
+ [6,] 14 0 10 0 0 12 10 12 0 0 8 0
+ [7,] 0 7 0 16 0 7 11 0 0 0 11 10
+ [8,] 0 0 0 0 0 0 8 0 11 0 0 0
+ [9,] 0 9 0 0 0 12 0 0 0 0 11 8
+[10,] 0 13 10 11 0 14 10 0 9 0 7 0
+[11,] 11 0 10 14 11 0 11 0 12 6 0 0
+[12,] 9 12 5 0 15 0 11 9 0 0 0 0
+[13,] 0 0 0 0 9 0 0 9 4 12 0 0
+[14,] 0 0 0 0 0 0 12 0 0 0 0 0
+[15,] 0 6 0 0 0 7 0 10 0 11 13 10
+[16,] 11 12 16 0 0 10 5 6 11 0 11 0
+[17,] 8 12 0 0 0 0 0 13 7 11 0 0
+[18,] 0 0 9 0 10 0 7 7 10 0 2 0
+[19,] 10 0 0 0 0 0 0 9 0 0 0 0
+[20,] 0 0 12 17 0 9 10 4 0 0 14 0
+[21,] 0 0 0 0 9 11 0 13 0 10 10 0
+[22,] 11 10 7 0 0 5 0 0 0 8 9 0
+[23,] 9 0 11 0 0 10 0 0 6 0 9 0
+[24,] 0 0 12 0 13 0 0 0 0 6 0 0
+[25,] 0 0 8 5 0 0 0 9 0 0 0 0
+[26,] 0 7 0 8 0 0 7 0 0 0 0 0
+[27,] 0 0 0 0 0 13 0 9 0 0 8 10
+[28,] 0 7 0 10 0 0 0 0 7 0 0 8
+[29,] 0 17 0 0 0 0 11 9 0 9 12 0
+[30,] 6 0 8 0 0 0 0 0 0 0 0 0
+[31,] 0 11 0 11 6 0 0 0 13 0 9 8
+[32,] 5 7 0 0 7 0 0 9 0 13 0 0
+[33,] 0 6 0 0 0 0 0 12 8 0 8 0
+[34,] 12 0 13 0 8 0 12 9 0 0 0 0
+[35,] 0 7 0 0 9 0 0 0 0 8 0 0
+[36,] 0 11 7 0 11 0 11 0 0 0 0 11
+[37,] 0 0 0 7 9 0 8 7 0 0 13 0
+[38,] 6 0 0 13 0 8 12 9 0 7 0 7
+[39,] 6 14 0 0 0 0 0 9 0 7 0 0
+[40,] 0 10 6 7 0 6 12 0 4 0 12 8
+[41,] 0 0 8 9 15 0 0 0 0 0 0 0
+[42,] 0 0 0 0 9 0 9 0 8 0 0 0
+[43,] 0 0 0 6 0 0 0 9 0 7 7 0
+[44,] 6 10 0 7 11 0 0 0 0 7 12 0
+
+--> margin rows shuffle ind <--
+grand sum: [1] TRUE
+row sums: [1] TRUE
+col sums: [1] "Mean relative difference: 1.161747"
+fill: [1] "Mean relative difference: 0.5733333"
+row freqs: [1] "Mean relative difference: 0.5733333"
+col freqs: [1] "Mean relative difference: 0.8950457"
+ [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12]
+ [1,] 0 6 3 5 5 4 9 2 2 2 4 1
+ [2,] 10 4 3 5 2 5 3 4 2 3 3 4
+ [3,] 3 8 10 8 8 7 2 7 2 9 6 7
+ [4,] 11 7 6 10 10 10 10 10 11 9 11 5
+ [5,] 4 2 4 3 3 3 2 3 3 0 6 2
+ [6,] 3 1 1 4 6 3 2 5 3 2 3 0
+ [7,] 5 2 1 6 3 2 6 2 5 5 5 1
+ [8,] 5 4 5 6 3 2 1 2 5 3 3 2
+ [9,] 4 0 10 3 3 2 1 3 4 2 3 2
+[10,] 3 1 6 4 8 4 7 4 6 0 2 2
+[11,] 4 10 3 6 7 8 12 13 5 10 4 2
+[12,] 3 6 1 3 3 5 3 4 2 2 4 5
+[13,] 1 4 3 6 4 5 3 4 0 2 4 4
+[14,] 6 2 3 1 3 4 7 2 3 6 3 6
+[15,] 4 4 2 4 5 3 4 7 4 6 10 12
+[16,] 4 3 2 4 2 2 3 3 2 4 7 4
+[17,] 9 2 3 4 6 7 6 2 5 3 6 3
+[18,] 4 5 3 5 3 2 6 2 1 5 3 1
+[19,] 3 6 2 5 7 1 4 5 7 0 3 6
+[20,] 6 3 5 6 2 7 7 1 4 8 4 3
+[21,] 3 1 2 2 2 0 0 1 2 1 1 3
+[22,] 9 4 2 4 3 6 4 6 1 4 6 5
+[23,] 8 12 2 1 3 3 4 4 5 3 9 4
+[24,] 4 3 3 4 4 1 3 0 3 2 1 6
+[25,] 4 3 4 5 2 4 1 5 1 3 4 6
+[26,] 5 0 0 2 2 2 3 5 3 5 5 4
+[27,] 0 4 9 4 2 4 4 3 2 1 3 6
+[28,] 2 2 2 4 2 4 2 2 3 2 3 2
+[29,] 2 4 3 3 2 2 5 3 1 3 3 3
+[30,] 6 5 5 7 3 5 6 5 4 7 3 4
+[31,] 0 2 1 0 1 2 4 2 2 0 3 0
+[32,] 3 3 1 3 1 2 2 0 1 0 1 2
+[33,] 1 2 5 5 2 3 3 3 2 3 2 3
+[34,] 0 0 0 0 1 0 0 1 0 0 0 1
+[35,] 5 3 2 6 3 3 1 2 4 4 4 3
+[36,] 2 2 3 3 0 1 1 5 0 1 6 4
+[37,] 4 3 9 1 8 6 0 1 5 3 5 3
+[38,] 1 1 2 1 0 2 1 0 2 0 4 2
+[39,] 1 0 0 0 1 0 1 0 0 0 1 3
+[40,] 1 4 0 3 1 3 6 0 2 1 1 0
+[41,] 6 0 6 1 1 0 2 4 2 3 2 4
+[42,] 6 7 3 5 1 3 0 3 2 5 3 2
+[43,] 25 23 28 21 19 21 24 22 22 20 20 18
+[44,] 4 5 6 1 6 3 5 4 5 3 2 1
+
+--> margin rows shuffle samp <--
+grand sum: [1] TRUE
+row sums: [1] TRUE
+col sums: [1] "Mean relative difference: 1.316775"
+fill: [1] TRUE
+row freqs: [1] TRUE
+col freqs: [1] "Mean relative difference: 0.8950457"
+ [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12]
+ [1,] 4 10 1 12 0 8 0 0 0 2 1 4
+ [2,] 0 0 3 2 0 0 1 9 0 0 0 0
+ [3,] 1 2 0 0 1 0 3 0 6 4 42 1
+ [4,] 2 0 19 17 0 24 8 2 5 0 12 7
+ [5,] 0 0 1 1 0 0 1 29 0 0 0 0
+ [6,] 0 0 3 12 16 8 5 0 0 0 0 0
+ [7,] 0 0 1 0 1 2 1 0 2 0 1 0
+ [8,] 2 1 12 0 0 0 0 1 1 2 20 1
+ [9,] 0 9 0 18 2 0 0 0 4 0 4 0
+[10,] 2 0 0 0 2 0 1 0 0 0 0 0
+[11,] 0 2 0 0 5 1 9 2 0 4 56 1
+[12,] 1 0 0 4 0 0 0 3 1 0 1 0
+[13,] 0 1 20 1 2 3 0 4 3 12 0 0
+[14,] 1 2 0 3 0 2 0 0 2 0 0 0
+[15,] 0 0 8 110 0 1 1 0 0 0 0 0
+[16,] 0 0 0 0 1 12 0 0 0 3 0 40
+[17,] 2 26 10 3 1 0 0 0 6 0 0 1
+[18,] 0 1 0 0 0 1 1 0 0 0 2 0
+[19,] 0 0 0 0 0 31 0 1 0 0 0 7
+[20,] 1 3 0 14 0 5 0 1 0 0 4 0
+[21,] 0 0 0 0 0 0 0 0 1 0 28 0
+[22,] 0 1 0 4 0 0 11 0 1 0 3 0
+[23,] 0 0 0 4 0 0 28 4 0 0 0 0
+[24,] 8 0 1 0 1 0 0 1 0 0 0 0
+[25,] 0 1 0 29 6 0 10 0 0 3 1 0
+[26,] 4 0 7 25 7 2 0 14 0 0 10 7
+[27,] 0 0 0 0 1 0 0 14 0 0 0 0
+[28,] 0 0 3 0 0 0 0 1 1 0 4 3
+[29,] 0 31 0 0 3 0 0 0 3 0 0 0
+[30,] 17 0 0 0 1 9 2 44 0 0 0 0
+[31,] 0 0 0 0 0 21 0 1 1 0 1 0
+[32,] 0 0 0 0 0 0 0 0 18 5 0 0
+[33,] 0 0 0 3 1 0 0 2 16 0 1 0
+[34,] 0 0 0 0 0 0 2 0 0 0 0 0
+[35,] 0 0 0 0 0 0 2 1 0 0 0 0
+[36,] 0 0 1 0 0 0 0 0 2 0 0 1
+[37,] 0 7 0 0 55 1 0 28 0 0 1 0
+[38,] 6 3 0 9 0 0 2 0 0 1 0 0
+[39,] 0 0 1 0 2 0 0 0 0 0 0 0
+[40,] 0 0 2 13 2 0 0 5 0 0 0 2
+[41,] 0 0 4 0 0 0 4 0 0 0 1 0
+[42,] 0 0 0 0 18 0 0 4 1 9 0 0
+[43,] 0 0 0 0 0 0 0 0 3 0 0 0
+[44,] 7 17 0 0 0 32 0 0 1 3 0 1
+
+--> margin rows shuffle both <--
+grand sum: [1] TRUE
+row sums: [1] TRUE
+col sums: [1] "Mean relative difference: 1.170378"
+fill: [1] TRUE
+row freqs: [1] TRUE
+col freqs: [1] "Mean relative difference: 0.8950457"
+ [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12]
+ [1,] 2 6 9 0 5 0 0 10 11 4 0 4
+ [2,] 0 0 0 8 3 0 0 7 0 5 12 5
+ [3,] 0 12 4 9 9 9 0 11 5 9 0 0
+ [4,] 7 14 9 0 11 11 0 11 11 0 10 16
+ [5,] 5 6 0 7 0 6 0 5 6 0 0 6
+ [6,] 8 5 0 6 3 0 8 0 4 6 0 6
+ [7,] 0 5 0 4 10 0 0 5 8 0 7 8
+ [8,] 0 4 3 0 0 5 0 8 5 3 4 3
+ [9,] 0 3 5 0 5 0 0 0 0 11 4 0
+[10,] 13 0 5 0 0 0 0 8 0 0 0 0
+[11,] 0 0 0 11 12 0 0 12 0 6 0 9
+[12,] 4 0 5 7 0 0 0 0 3 8 4 0
+[13,] 9 6 0 10 2 12 6 0 0 14 5 0
+[14,] 9 0 9 5 0 8 3 0 10 15 0 0
+[15,] 13 23 0 0 17 0 0 0 20 0 0 0
+[16,] 0 7 0 0 0 0 11 0 0 0 9 9
+[17,] 0 0 10 0 0 10 14 0 19 11 16 0
+[18,] 0 12 0 11 0 5 7 0 0 0 10 0
+[19,] 17 0 0 0 12 0 0 0 0 0 0 0
+[20,] 11 10 0 0 12 15 19 0 0 0 8 0
+[21,] 0 0 0 17 0 0 0 0 0 0 0 0
+[22,] 8 10 10 6 15 0 17 8 13 0 6 0
+[23,] 0 7 0 0 8 0 10 4 15 12 0 9
+[24,] 0 0 0 0 10 11 6 8 0 0 11 12
+[25,] 0 6 0 0 0 12 0 8 0 14 0 0
+[26,] 6 0 10 0 0 0 0 0 0 5 0 0
+[27,] 0 16 0 0 16 0 16 0 0 0 0 0
+[28,] 0 0 0 8 9 9 0 4 0 0 0 7
+[29,] 0 0 0 7 0 0 9 0 0 0 0 0
+[30,] 0 0 10 0 0 15 0 0 6 0 0 10
+[31,] 10 0 0 4 0 0 0 0 0 0 5 0
+[32,] 0 0 0 0 0 7 10 0 0 10 0 0
+[33,] 12 0 0 0 9 0 0 11 0 12 0 9
+[34,] 0 0 0 0 0 0 0 1 0 0 0 0
+[35,] 0 5 0 0 0 21 6 0 14 0 0 0
+[36,] 0 0 0 12 0 0 10 0 0 0 0 0
+[37,] 8 6 0 9 11 0 12 14 0 9 0 0
+[38,] 0 0 0 0 6 2 0 0 0 6 0 0
+[39,] 0 0 0 0 0 0 0 2 0 0 0 0
+[40,] 0 11 7 5 5 4 2 5 0 0 0 0
+[41,] 0 7 0 0 0 0 5 7 0 8 5 0
+[42,] 0 7 8 0 0 10 0 10 9 8 0 0
+[43,] 0 0 116 0 0 0 0 0 0 0 0 0
+[44,] 0 7 0 0 0 0 0 8 0 0 9 0
+
+--> margin columns shuffle ind <--
+grand sum: [1] TRUE
+row sums: [1] "Mean relative difference: 0.4001381"
+col sums: [1] TRUE
+fill: [1] "Mean relative difference: 0.360673"
+row freqs: [1] "Mean relative difference: 0.3812095"
+col freqs: [1] "Mean relative difference: 0.8950457"
+ [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12]
+ [1,] 5 1 6 0 0 0 3 1 0 3 2 2
+ [2,] 7 1 17 0 0 0 1 0 0 3 0 1
+ [3,] 8 0 6 0 0 0 2 0 1 1 0 2
+ [4,] 11 1 5 0 0 0 1 0 3 6 2 2
+ [5,] 5 1 9 1 0 1 2 0 3 9 0 3
+ [6,] 11 0 6 0 0 2 0 0 1 7 0 4
+ [7,] 8 0 6 0 0 0 2 0 0 6 1 3
+ [8,] 5 0 6 2 0 0 4 1 2 5 2 1
+ [9,] 5 0 9 0 1 0 2 0 1 2 1 2
+[10,] 5 1 6 0 0 0 1 0 1 5 2 2
+[11,] 10 1 12 0 0 0 1 1 0 4 1 4
+[12,] 8 1 11 0 1 0 3 1 1 3 1 1
+[13,] 12 0 6 0 0 0 5 1 1 4 2 3
+[14,] 3 1 7 0 0 0 3 0 0 7 2 2
+[15,] 7 0 8 0 0 0 1 0 0 5 1 1
+[16,] 9 2 9 0 0 0 2 0 1 3 3 0
+[17,] 6 2 11 0 1 1 1 0 2 4 0 0
+[18,] 4 0 13 0 1 0 1 0 2 2 2 3
+[19,] 4 1 7 0 0 1 2 0 1 3 0 0
+[20,] 3 1 11 0 0 1 3 0 0 3 0 4
+[21,] 5 0 8 0 0 0 1 0 1 3 4 1
+[22,] 4 0 12 1 0 0 3 0 1 2 1 1
+[23,] 4 1 10 1 0 0 2 0 2 6 1 1
+[24,] 12 2 10 3 0 0 2 0 1 4 0 0
+[25,] 9 1 6 0 0 2 1 0 0 2 3 1
+[26,] 7 1 11 0 0 0 2 0 0 3 2 1
+[27,] 4 0 7 1 0 0 0 0 1 6 2 2
+[28,] 7 0 16 0 0 0 3 0 1 6 2 2
+[29,] 11 0 14 0 0 0 2 0 0 3 0 2
+[30,] 8 0 12 0 0 0 0 0 1 5 2 1
+[31,] 6 0 9 1 0 0 1 1 1 3 0 0
+[32,] 3 1 14 1 0 1 1 0 0 2 1 4
+[33,] 7 0 12 0 0 0 3 0 2 5 1 2
+[34,] 8 1 7 0 0 0 2 0 2 3 5 2
+[35,] 9 0 9 2 0 0 3 0 1 3 2 0
+[36,] 3 0 11 0 0 0 1 0 2 3 0 0
+[37,] 8 0 9 0 0 0 2 0 2 7 3 0
+[38,] 7 1 15 0 0 0 4 0 1 4 1 2
+[39,] 2 2 11 0 0 0 4 0 0 2 1 2
+[40,] 9 0 11 0 0 0 3 0 1 6 1 5
+[41,] 5 0 11 0 0 0 0 0 0 4 0 0
+[42,] 10 1 8 1 0 0 2 0 1 2 1 1
+[43,] 7 1 9 2 0 0 3 0 0 4 2 2
+[44,] 8 1 17 0 0 0 3 0 0 6 1 4
+
+--> margin columns shuffle samp <--
+grand sum: [1] TRUE
+row sums: [1] "Mean relative difference: 0.5156635"
+col sums: [1] TRUE
+fill: [1] TRUE
+row freqs: [1] "Mean relative difference: 0.3597122"
+col freqs: [1] "Mean relative difference: 0.8950457"
+ [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12]
+ [1,] 0 0 0 0 0 0 15 0 0 0 4 0
+ [2,] 12 0 10 0 0 0 5 0 0 16 0 0
+ [3,] 19 0 3 0 0 0 0 0 2 26 3 1
+ [4,] 0 0 0 0 0 1 16 0 2 20 2 1
+ [5,] 1 0 4 0 0 0 0 0 0 24 0 0
+ [6,] 12 0 4 0 0 2 0 0 0 0 0 2
+ [7,] 0 0 7 0 0 0 0 0 2 12 0 1
+ [8,] 1 0 6 0 0 1 0 0 1 2 0 2
+ [9,] 3 0 3 2 0 0 3 0 0 1 5 7
+[10,] 6 0 37 0 0 0 0 0 4 0 0 3
+[11,] 0 0 10 0 0 0 5 1 1 3 0 2
+[12,] 20 5 5 0 0 1 0 0 0 0 0 0
+[13,] 5 4 6 0 0 0 1 0 1 1 0 0
+[14,] 38 0 35 2 0 0 1 0 0 0 0 0
+[15,] 3 0 14 0 0 0 5 0 0 0 5 0
+[16,] 41 0 2 0 0 0 0 0 3 0 0 2
+[17,] 8 0 18 0 0 0 0 0 0 1 0 1
+[18,] 1 0 15 0 1 0 3 1 0 0 0 5
+[19,] 6 0 16 0 0 0 0 0 0 0 4 1
+[20,] 0 0 22 0 0 0 0 0 0 0 0 6
+[21,] 8 0 3 0 0 0 2 0 0 0 0 0
+[22,] 3 0 2 0 0 0 0 0 0 0 0 0
+[23,] 0 0 3 0 0 0 0 0 0 0 0 2
+[24,] 4 0 8 0 0 0 2 0 7 0 0 9
+[25,] 1 0 0 0 0 0 1 0 0 1 20 0
+[26,] 3 0 2 0 0 0 0 0 0 1 0 0
+[27,] 5 1 2 0 1 0 12 2 3 0 0 3
+[28,] 5 0 14 0 2 1 2 1 0 0 6 1
+[29,] 2 4 12 0 0 0 0 0 4 0 0 1
+[30,] 6 0 31 9 0 0 0 0 2 0 0 1
+[31,] 3 3 9 1 0 1 0 0 0 0 0 1
+[32,] 1 0 0 0 0 0 0 0 0 1 0 0
+[33,] 4 7 17 0 0 2 0 1 1 0 0 4
+[34,] 2 2 5 0 0 0 0 0 0 0 0 1
+[35,] 36 0 12 0 0 0 2 0 0 5 0 0
+[36,] 4 0 9 0 0 0 2 0 0 0 0 0
+[37,] 3 0 12 0 0 0 4 0 0 36 0 0
+[38,] 3 0 16 0 0 0 0 0 0 11 0 1
+[39,] 11 0 2 2 0 0 0 0 0 0 0 10
+[40,] 4 0 5 0 0 0 0 0 0 0 9 2
+[41,] 3 0 8 0 0 0 7 0 3 0 0 4
+[42,] 2 1 8 0 0 0 0 0 0 18 0 0
+[43,] 10 0 16 0 0 0 0 0 2 0 0 0
+[44,] 0 0 17 0 0 0 0 0 3 0 0 2
+
+--> margin columns shuffle both <--
+grand sum: [1] TRUE
+row sums: [1] "Mean relative difference: 0.419817"
+col sums: [1] TRUE
+fill: [1] TRUE
+row freqs: [1] "Mean relative difference: 0.3198653"
+col freqs: [1] "Mean relative difference: 0.8950457"
+ [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12]
+ [1,] 7 0 11 0 2 1 0 0 1 13 0 2
+ [2,] 0 0 13 0 0 0 8 1 0 12 0 6
+ [3,] 10 0 8 0 0 0 0 0 3 5 0 3
+ [4,] 8 4 11 0 0 1 0 0 0 0 0 2
+ [5,] 4 0 10 0 0 0 0 0 3 12 2 0
+ [6,] 5 0 11 0 0 0 5 1 4 0 8 1
+ [7,] 11 4 7 0 0 0 6 0 0 9 0 0
+ [8,] 8 4 9 0 1 0 6 0 0 0 0 4
+ [9,] 5 0 5 0 0 0 6 0 0 0 0 0
+[10,] 8 0 8 0 0 0 0 0 0 8 9 0
+[11,] 9 0 19 3 0 0 0 0 0 0 0 0
+[12,] 8 0 15 0 0 0 7 0 0 0 0 0
+[13,] 0 0 0 0 0 0 2 0 2 0 0 0
+[14,] 9 1 16 0 0 0 0 0 2 0 0 0
+[15,] 5 0 14 3 0 1 0 0 0 0 0 2
+[16,] 7 0 16 0 0 1 0 0 1 14 0 1
+[17,] 0 0 12 0 0 2 7 1 0 0 0 4
+[18,] 10 0 11 0 0 0 3 0 0 12 0 0
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/vegan -r 1849
More information about the Vegan-commits
mailing list