[Vegan-commits] r1910 - pkg/vegan/tests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Sep 28 17:42:23 CEST 2011
Author: jarioksa
Date: 2011-09-28 17:42:23 +0200 (Wed, 28 Sep 2011)
New Revision: 1910
Modified:
pkg/vegan/tests/oecosimu-tests.Rout.save
Log:
update for vegan at 1877
Modified: pkg/vegan/tests/oecosimu-tests.Rout.save
===================================================================
--- pkg/vegan/tests/oecosimu-tests.Rout.save 2011-09-28 15:41:03 UTC (rev 1909)
+++ pkg/vegan/tests/oecosimu-tests.Rout.save 2011-09-28 15:42:23 UTC (rev 1910)
@@ -577,7 +577,7 @@
>
> ### end commsimulator
>
-> ### set up permatfull/swap1 tests
+> ### set up permatfull/swap tests
>
> data(mite)
> data(mite.env)
@@ -607,7 +607,7 @@
+ print(all.equal(colSums(x>0), cfrq, check.attributes = FALSE))
+ }
>
-> ### permatfull1
+> ### permatfull
>
> set.seed(4711)
> margin <- c("none", "rows", "columns", "both")
@@ -617,7 +617,8 @@
+ for(what in shuffle) {
+ cat("\n--> margin", mar, " shuffle", what, "<--\n")
+ set.seed(4711)
-+ m <- permatfull1(x, fixedmar = mar, shuffle = what, mtype = "count")
++ m <- permatfull(x, fixedmar = mar, shuffle = what, mtype = "count",
++ times=1)$perm[[1]]
+ margintest(m, gsum, rsum, csum, fill, rfrq, cfrq)
+ print(m[,1:12])
+ }
@@ -1259,7 +1260,7 @@
[43,] 49 4 45 3 2 2 11 1 4 23 9 8
[44,] 8 0 10 1 0 0 0 1 2 2 3 1
>
-> ### permatswap1
+> ### permatswap
> set.seed(4711)
> methods <- c("swap", "quasiswap", "swsh", "abuswap")
> margins <- c("rows", "columns", "both")
@@ -1281,8 +1282,8 @@
+ cat("\n*** ", method, " ***\n")
+ cat("--> margin", margin, " shuffle", what, "<--\n")
+ set.seed(4711)
-+ m <- permatswap1(x, method = method, fixedmar = margin, shuffle = what,
-+ mtype = "count", thin=100)
++ m <- permatswap(x, method = method, fixedmar = margin, shuffle = what,
++ mtype = "count", thin=100, times=1)$perm[[1]]
+ margintest(m, gsum, rsum, csum,fill, rfrq, cfrq)
+ print(m[,1:12])
+ }
@@ -1508,218 +1509,218 @@
*** swsh ***
--> margin rows shuffle samp <--
grand sum: [1] TRUE
-row sums: [1] "Mean relative difference: 0.5330571"
-col sums: [1] "Mean relative difference: 0.799931"
+row sums: [1] TRUE
+col sums: [1] "Mean relative difference: 0.8285862"
fill: [1] TRUE
row freqs: [1] TRUE
col freqs: [1] TRUE
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12]
- [1,] 1 0 1 0 0 0 5 0 23 0 0 15
- [2,] 6 0 6 61 0 0 0 0 0 5 1 1
- [3,] 1 7 6 3 0 0 1 0 2 14 0 1
- [4,] 1 3 1 0 0 1 0 0 1 9 0 7
- [5,] 2 0 2 0 0 1 0 1 0 29 0 0
- [6,] 4 0 0 0 0 1 6 0 1 3 1 4
- [7,] 1 0 2 0 0 4 2 0 1 0 0 5
- [8,] 2 0 2 0 0 4 0 0 12 2 0 2
- [9,] 14 0 2 0 0 12 1 8 0 0 0 1
-[10,] 0 2 0 7 0 0 5 0 0 2 0 3
-[11,] 1 0 17 0 0 0 4 0 1 38 5 37
-[12,] 5 1 18 0 0 0 1 0 1 0 0 4
-[13,] 9 0 8 0 0 0 3 1 0 8 0 1
-[14,] 9 1 20 0 0 0 1 0 0 0 0 4
-[15,] 3 1 3 0 0 73 13 0 0 3 0 0
-[16,] 2 0 3 0 0 0 0 0 0 0 0 0
-[17,] 4 0 3 0 3 0 1 0 0 0 0 19
-[18,] 31 0 8 0 0 0 0 0 1 0 0 2
-[19,] 9 0 0 0 0 0 0 0 15 0 0 0
-[20,] 18 0 2 0 0 0 0 0 0 20 0 0
-[21,] 6 0 1 0 0 0 0 0 0 0 0 0
-[22,] 0 0 1 0 0 0 1 0 0 2 1 1
-[23,] 4 0 17 0 0 0 0 0 0 0 1 5
-[24,] 25 0 5 0 0 0 28 0 3 4 0 10
-[25,] 1 0 4 0 0 0 0 0 0 0 0 2
-[26,] 1 0 1 0 0 0 0 0 0 0 1 0
-[27,] 1 0 1 0 0 0 0 0 0 0 0 0
-[28,] 16 0 2 0 0 0 0 18 0 0 0 0
-[29,] 3 89 6 0 21 0 5 0 0 0 0 0
-[30,] 2 0 3 110 0 0 0 0 2 3 0 20
-[31,] 3 1 6 0 0 0 0 0 0 0 0 24
-[32,] 0 0 6 0 0 0 0 0 0 4 0 0
-[33,] 0 0 6 0 0 0 0 10 4 0 0 0
-[34,] 20 0 2 0 0 0 0 0 0 0 0 0
-[35,] 0 0 16 0 0 0 0 0 0 0 0 11
-[36,] 0 0 4 0 0 0 2 0 0 0 0 0
-[37,] 10 0 0 0 0 0 36 0 2 0 1 0
-[38,] 2 0 9 0 0 0 0 0 0 4 0 5
-[39,] 0 0 14 0 0 0 0 0 0 0 0 1
-[40,] 1 0 4 2 0 0 0 0 3 4 0 0
-[41,] 1 0 5 0 1 0 0 0 0 0 1 1
-[42,] 31 0 4 0 0 0 5 0 0 0 0 6
-[43,] 1 0 2 0 0 0 0 0 0 0 0 0
-[44,] 1 0 1 0 0 0 0 0 29 0 3 1
+ [1,] 2 0 8 0 1 1 0 0 0 0 3 6
+ [2,] 3 0 2 19 0 7 3 0 0 0 0 8
+ [3,] 3 0 17 42 0 0 1 15 2 5 0 1
+ [4,] 8 8 2 0 0 0 0 0 3 2 24 19
+ [5,] 2 0 1 0 0 0 0 0 1 1 0 7
+ [6,] 10 0 5 0 0 0 0 1 0 1 4 0
+ [7,] 15 1 4 0 0 0 0 0 5 2 0 0
+ [8,] 1 1 6 0 0 0 0 2 1 0 1 7
+ [9,] 5 2 9 0 0 0 0 0 4 0 0 2
+[10,] 2 0 2 0 0 38 0 0 0 0 0 1
+[11,] 14 0 2 1 0 22 39 0 56 1 2 11
+[12,] 26 3 2 0 0 0 0 0 0 1 2 6
+[13,] 12 0 1 0 1 2 3 2 0 0 0 4
+[14,] 22 5 1 0 1 0 0 0 0 0 0 3
+[15,] 110 0 2 0 0 1 9 0 0 0 0 18
+[16,] 1 0 40 0 0 0 3 0 0 0 0 18
+[17,] 6 0 26 0 0 0 10 0 1 0 0 0
+[18,] 0 1 13 0 0 0 0 0 0 0 0 44
+[19,] 12 0 3 0 0 1 0 0 0 0 0 0
+[20,] 1 0 2 0 0 0 4 0 1 5 0 0
+[21,] 0 0 24 0 0 0 0 0 0 0 0 1
+[22,] 6 0 52 0 0 0 3 0 0 0 0 0
+[23,] 12 0 3 0 0 0 0 1 28 22 0 0
+[24,] 0 0 34 0 0 0 20 0 0 0 0 2
+[25,] 3 0 1 0 0 0 0 0 0 0 0 0
+[26,] 3 0 5 0 0 0 7 0 0 0 0 0
+[27,] 3 0 37 0 0 0 0 0 0 0 0 4
+[28,] 31 0 5 0 0 0 0 0 0 0 0 0
+[29,] 31 0 5 0 0 0 0 0 0 9 0 0
+[30,] 6 0 2 0 0 0 1 0 0 5 25 1
+[31,] 1 0 2 0 0 0 0 0 0 1 0 0
+[32,] 0 0 18 0 0 0 6 0 0 3 0 1
+[33,] 16 0 54 0 0 0 0 0 0 0 0 5
+[34,] 0 0 1 0 0 0 0 0 0 0 0 0
+[35,] 0 0 20 0 0 0 57 0 0 2 0 0
+[36,] 1 0 0 0 0 0 54 0 0 0 0 0
+[37,] 2 0 0 0 0 0 0 0 1 0 0 1
+[38,] 1 0 9 1 0 0 0 0 0 0 0 3
+[39,] 1 0 0 0 0 0 0 0 5 0 0 0
+[40,] 2 1 2 0 0 0 2 0 5 14 0 2
+[41,] 3 0 0 0 0 0 3 0 4 0 0 2
+[42,] 1 0 21 12 0 0 4 0 25 18 1 8
+[43,] 0 0 3 0 0 0 0 0 0 7 0 0
+[44,] 3 0 1 0 0 0 0 0 9 0 3 4
*** swsh ***
--> margin rows shuffle both <--
grand sum: [1] TRUE
-row sums: [1] "Mean relative difference: 0.3711844"
-col sums: [1] "Mean relative difference: 0.7871569"
+row sums: [1] TRUE
+col sums: [1] "Mean relative difference: 0.6853099"
fill: [1] TRUE
row freqs: [1] TRUE
col freqs: [1] TRUE
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12]
- [1,] 15 0 12 0 0 0 7 0 9 0 0 9
- [2,] 6 0 11 7 0 0 0 0 0 9 12 6
- [3,] 12 12 7 11 0 0 8 0 6 15 0 9
- [4,] 9 11 10 0 0 9 0 0 8 7 0 7
- [5,] 10 0 11 0 0 6 0 9 0 9 0 0
- [6,] 8 0 0 0 0 11 9 0 10 5 5 4
- [7,] 6 0 9 0 0 15 7 0 10 0 0 13
- [8,] 7 0 8 0 0 9 0 0 6 8 0 14
- [9,] 9 0 5 0 0 8 15 12 0 0 0 9
-[10,] 0 14 0 10 0 0 6 0 0 7 0 8
-[11,] 12 0 10 0 0 0 6 0 15 6 6 8
-[12,] 13 9 6 0 0 0 11 0 14 0 0 4
-[13,] 8 0 12 0 0 0 8 9 0 7 0 13
-[14,] 14 13 5 0 0 0 10 0 0 0 0 10
-[15,] 7 8 10 0 0 9 13 0 0 12 0 0
-[16,] 10 0 10 0 0 0 0 0 0 0 0 0
-[17,] 9 0 7 0 7 0 11 0 0 0 0 6
-[18,] 12 0 9 0 0 0 0 0 18 0 0 11
-[19,] 4 0 0 0 0 0 0 0 12 0 0 0
-[20,] 13 0 8 0 0 0 0 0 0 12 0 0
-[21,] 14 0 10 0 0 0 0 0 0 0 0 0
-[22,] 0 0 10 0 0 0 6 0 0 11 7 4
-[23,] 9 0 10 0 0 0 0 0 0 0 11 12
-[24,] 8 0 7 0 0 0 14 0 9 11 0 5
-[25,] 4 0 16 0 0 0 0 0 0 0 0 11
-[26,] 13 0 6 0 0 0 0 0 0 0 16 0
-[27,] 15 0 9 0 0 0 0 0 0 0 0 0
-[28,] 12 0 9 0 0 0 0 12 0 0 0 0
-[29,] 14 10 11 0 19 0 8 0 0 0 0 0
-[30,] 12 0 9 16 0 0 0 0 12 8 0 11
-[31,] 10 7 5 0 0 0 0 0 0 0 0 12
-[32,] 0 0 8 0 0 0 0 0 0 10 0 0
-[33,] 0 0 17 0 0 0 0 9 10 0 0 0
-[34,] 12 0 7 0 0 0 0 0 0 0 0 0
-[35,] 0 0 15 0 0 0 0 0 0 0 0 10
-[36,] 0 0 10 0 0 0 8 0 0 0 0 0
-[37,] 16 0 0 0 0 0 4 0 9 0 11 0
-[38,] 10 0 8 0 0 0 0 0 0 9 0 11
-[39,] 0 0 4 0 0 0 0 0 0 0 0 13
-[40,] 7 0 3 12 0 0 0 0 5 10 0 0
-[41,] 16 0 8 0 10 0 0 0 0 0 11 8
-[42,] 14 0 8 0 0 0 8 0 0 0 0 6
-[43,] 11 0 8 0 0 0 0 0 0 0 0 0
-[44,] 8 0 15 0 0 0 0 0 13 0 11 7
+ [1,] 4 0 9 0 6 3 0 0 0 0 5 4
+ [2,] 9 0 6 3 0 7 6 0 0 0 0 12
+ [3,] 14 0 10 12 0 0 6 7 3 10 0 7
+ [4,] 10 14 15 0 0 0 0 0 8 11 12 12
+ [5,] 10 0 3 0 0 0 0 0 5 8 0 5
+ [6,] 5 0 4 0 0 0 0 5 0 5 6 0
+ [7,] 8 5 9 0 0 0 0 0 8 8 0 0
+ [8,] 8 2 6 0 0 0 0 5 2 0 3 4
+ [9,] 5 7 6 0 0 0 0 0 6 0 0 5
+[10,] 8 0 9 0 0 7 0 0 0 0 0 16
+[11,] 10 0 8 5 0 6 12 0 12 14 10 8
+[12,] 9 5 8 0 0 0 0 0 0 8 5 6
+[13,] 3 0 8 0 7 6 15 8 0 0 0 5
+[14,] 10 5 6 0 6 0 0 0 0 0 0 7
+[15,] 13 0 7 0 0 9 11 0 0 0 0 13
+[16,] 11 0 9 0 0 0 8 0 0 0 0 9
+[17,] 8 0 18 0 0 0 12 0 15 0 0 0
+[18,] 0 8 5 0 0 0 0 0 0 0 0 12
+[19,] 11 0 20 0 0 17 0 0 0 0 0 0
+[20,] 10 0 14 0 0 0 11 0 18 12 0 0
+[21,] 0 0 14 0 0 0 0 0 0 0 0 11
+[22,] 8 0 8 0 0 0 7 0 0 0 0 0
+[23,] 16 0 5 0 0 0 0 14 9 7 0 0
+[24,] 0 0 8 0 0 0 12 0 0 0 0 6
+[25,] 8 0 6 0 0 0 0 0 0 0 0 0
+[26,] 7 0 7 0 0 0 11 0 0 0 0 0
+[27,] 12 0 8 0 0 0 0 0 0 0 0 11
+[28,] 4 0 4 0 0 0 0 0 0 0 0 0
+[29,] 8 0 12 0 0 0 0 0 0 9 0 0
+[30,] 5 0 17 0 0 0 6 0 0 6 6 10
+[31,] 8 0 3 0 0 0 0 0 0 6 0 0
+[32,] 0 0 4 0 0 0 8 0 0 8 0 4
+[33,] 10 0 10 0 0 0 0 0 0 0 0 11
+[34,] 0 0 1 0 0 0 0 0 0 0 0 0
+[35,] 0 0 10 0 0 0 15 0 0 9 0 0
+[36,] 11 0 0 0 0 0 15 0 0 0 0 0
+[37,] 8 0 0 0 0 0 0 0 14 0 0 7
+[38,] 5 0 9 6 0 0 0 0 0 0 0 5
+[39,] 1 0 0 0 0 0 0 0 2 0 0 0
+[40,] 5 5 5 0 0 0 4 0 8 8 0 7
+[41,] 8 0 0 0 0 0 9 0 6 0 0 7
+[42,] 7 0 10 10 0 0 8 0 10 11 6 8
+[43,] 0 0 129 0 0 0 0 0 0 126 0 0
+[44,] 9 0 15 0 0 0 0 0 9 0 8 8
*** swsh ***
--> margin columns shuffle samp <--
grand sum: [1] TRUE
-row sums: [1] "Mean relative difference: 0.5330571"
-col sums: [1] "Mean relative difference: 0.799931"
+row sums: [1] "Mean relative difference: 0.5289142"
+col sums: [1] TRUE
fill: [1] TRUE
row freqs: [1] TRUE
col freqs: [1] TRUE
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12]
- [1,] 1 0 1 0 0 0 5 0 23 0 0 15
- [2,] 6 0 6 61 0 0 0 0 0 5 1 1
- [3,] 1 7 6 3 0 0 1 0 2 14 0 1
- [4,] 1 3 1 0 0 1 0 0 1 9 0 7
- [5,] 2 0 2 0 0 1 0 1 0 29 0 0
- [6,] 4 0 0 0 0 1 6 0 1 3 1 4
- [7,] 1 0 2 0 0 4 2 0 1 0 0 5
- [8,] 2 0 2 0 0 4 0 0 12 2 0 2
- [9,] 14 0 2 0 0 12 1 8 0 0 0 1
-[10,] 0 2 0 7 0 0 5 0 0 2 0 3
-[11,] 1 0 17 0 0 0 4 0 1 38 5 37
-[12,] 5 1 18 0 0 0 1 0 1 0 0 4
-[13,] 9 0 8 0 0 0 3 1 0 8 0 1
-[14,] 9 1 20 0 0 0 1 0 0 0 0 4
-[15,] 3 1 3 0 0 73 13 0 0 3 0 0
-[16,] 2 0 3 0 0 0 0 0 0 0 0 0
-[17,] 4 0 3 0 3 0 1 0 0 0 0 19
-[18,] 31 0 8 0 0 0 0 0 1 0 0 2
-[19,] 9 0 0 0 0 0 0 0 15 0 0 0
-[20,] 18 0 2 0 0 0 0 0 0 20 0 0
-[21,] 6 0 1 0 0 0 0 0 0 0 0 0
-[22,] 0 0 1 0 0 0 1 0 0 2 1 1
-[23,] 4 0 17 0 0 0 0 0 0 0 1 5
-[24,] 25 0 5 0 0 0 28 0 3 4 0 10
-[25,] 1 0 4 0 0 0 0 0 0 0 0 2
-[26,] 1 0 1 0 0 0 0 0 0 0 1 0
-[27,] 1 0 1 0 0 0 0 0 0 0 0 0
-[28,] 16 0 2 0 0 0 0 18 0 0 0 0
-[29,] 3 89 6 0 21 0 5 0 0 0 0 0
-[30,] 2 0 3 110 0 0 0 0 2 3 0 20
-[31,] 3 1 6 0 0 0 0 0 0 0 0 24
-[32,] 0 0 6 0 0 0 0 0 0 4 0 0
-[33,] 0 0 6 0 0 0 0 10 4 0 0 0
-[34,] 20 0 2 0 0 0 0 0 0 0 0 0
-[35,] 0 0 16 0 0 0 0 0 0 0 0 11
-[36,] 0 0 4 0 0 0 2 0 0 0 0 0
-[37,] 10 0 0 0 0 0 36 0 2 0 1 0
-[38,] 2 0 9 0 0 0 0 0 0 4 0 5
-[39,] 0 0 14 0 0 0 0 0 0 0 0 1
-[40,] 1 0 4 2 0 0 0 0 3 4 0 0
-[41,] 1 0 5 0 1 0 0 0 0 0 1 1
-[42,] 31 0 4 0 0 0 5 0 0 0 0 6
-[43,] 1 0 2 0 0 0 0 0 0 0 0 0
-[44,] 1 0 1 0 0 0 0 0 29 0 3 1
+ [1,] 6 0 14 0 1 1 0 0 0 0 5 4
+ [2,] 6 0 8 1 0 2 2 0 0 0 0 3
+ [3,] 8 0 17 9 0 0 5 1 3 18 0 9
+ [4,] 3 1 5 0 0 0 0 0 4 1 3 2
+ [5,] 3 0 12 0 0 0 0 0 2 16 0 1
+ [6,] 8 0 2 0 0 0 0 1 0 26 4 0
+ [7,] 4 7 12 0 0 0 0 0 1 1 0 0
+ [8,] 4 1 31 0 0 0 0 1 3 0 5 6
+ [9,] 3 2 3 0 0 0 0 0 2 0 0 2
+[10,] 3 0 16 0 0 1 0 0 0 0 0 10
+[11,] 36 0 4 2 0 1 2 0 2 20 2 1
+[12,] 2 3 6 0 0 0 0 0 0 12 20 7
+[13,] 12 0 10 0 1 1 12 2 0 0 0 2
+[14,] 1 5 18 0 2 0 0 0 0 0 0 1
+[15,] 6 0 4 0 0 1 7 0 0 0 0 2
+[16,] 1 0 5 0 0 0 2 0 0 0 0 1
+[17,] 3 0 6 0 0 0 3 0 2 0 0 0
+[18,] 0 4 8 0 0 0 0 0 0 0 0 2
+[19,] 5 0 2 0 0 2 0 0 0 0 0 0
+[20,] 20 0 16 0 0 0 2 0 3 11 0 0
+[21,] 0 0 2 0 0 0 0 0 0 0 0 3
+[22,] 2 0 14 0 0 0 2 0 0 0 0 0
+[23,] 4 0 10 0 0 0 0 1 4 1 0 0
+[24,] 0 0 9 0 0 0 5 0 0 0 0 1
+[25,] 5 0 5 0 0 0 0 0 0 0 0 0
+[26,] 1 0 3 0 0 0 3 0 0 0 0 0
+[27,] 3 0 3 0 0 0 0 0 0 0 0 1
+[28,] 19 0 2 0 0 0 0 0 0 0 0 0
+[29,] 3 0 9 0 0 0 0 0 0 1 0 0
+[30,] 4 0 2 0 0 0 16 0 0 24 9 4
+[31,] 41 0 16 0 0 0 0 0 0 5 0 0
+[32,] 0 0 35 0 0 0 5 0 0 1 0 2
+[33,] 2 0 37 0 0 0 0 0 0 0 0 5
+[34,] 0 0 3 0 0 0 0 0 0 0 0 0
+[35,] 0 0 7 0 0 0 1 0 0 36 0 0
+[36,] 3 0 0 0 0 0 1 0 0 0 0 0
+[37,] 10 0 0 0 0 0 0 0 1 0 0 1
+[38,] 11 0 15 2 0 0 0 0 0 0 0 1
+[39,] 12 0 0 0 0 0 0 0 3 0 0 0
+[40,] 5 4 17 0 0 0 4 0 7 3 0 1
+[41,] 1 0 0 0 0 0 15 0 1 0 0 2
+[42,] 1 0 8 2 0 0 1 0 1 2 6 1
+[43,] 0 0 22 0 0 0 0 0 0 1 0 0
+[44,] 38 0 12 0 0 0 0 0 2 0 4 1
*** swsh ***
--> margin columns shuffle both <--
grand sum: [1] TRUE
-row sums: [1] "Mean relative difference: 0.3711844"
-col sums: [1] "Mean relative difference: 0.7871569"
+row sums: [1] "Mean relative difference: 0.3683756"
+col sums: [1] TRUE
fill: [1] TRUE
row freqs: [1] TRUE
col freqs: [1] TRUE
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12]
- [1,] 15 0 12 0 0 0 7 0 9 0 0 9
- [2,] 6 0 11 7 0 0 0 0 0 9 12 6
- [3,] 12 12 7 11 0 0 8 0 6 15 0 9
- [4,] 9 11 10 0 0 9 0 0 8 7 0 7
- [5,] 10 0 11 0 0 6 0 9 0 9 0 0
- [6,] 8 0 0 0 0 11 9 0 10 5 5 4
- [7,] 6 0 9 0 0 15 7 0 10 0 0 13
- [8,] 7 0 8 0 0 9 0 0 6 8 0 14
- [9,] 9 0 5 0 0 8 15 12 0 0 0 9
-[10,] 0 14 0 10 0 0 6 0 0 7 0 8
-[11,] 12 0 10 0 0 0 6 0 15 6 6 8
-[12,] 13 9 6 0 0 0 11 0 14 0 0 4
-[13,] 8 0 12 0 0 0 8 9 0 7 0 13
-[14,] 14 13 5 0 0 0 10 0 0 0 0 10
-[15,] 7 8 10 0 0 9 13 0 0 12 0 0
-[16,] 10 0 10 0 0 0 0 0 0 0 0 0
-[17,] 9 0 7 0 7 0 11 0 0 0 0 6
-[18,] 12 0 9 0 0 0 0 0 18 0 0 11
-[19,] 4 0 0 0 0 0 0 0 12 0 0 0
-[20,] 13 0 8 0 0 0 0 0 0 12 0 0
-[21,] 14 0 10 0 0 0 0 0 0 0 0 0
-[22,] 0 0 10 0 0 0 6 0 0 11 7 4
-[23,] 9 0 10 0 0 0 0 0 0 0 11 12
-[24,] 8 0 7 0 0 0 14 0 9 11 0 5
-[25,] 4 0 16 0 0 0 0 0 0 0 0 11
-[26,] 13 0 6 0 0 0 0 0 0 0 16 0
-[27,] 15 0 9 0 0 0 0 0 0 0 0 0
-[28,] 12 0 9 0 0 0 0 12 0 0 0 0
-[29,] 14 10 11 0 19 0 8 0 0 0 0 0
-[30,] 12 0 9 16 0 0 0 0 12 8 0 11
-[31,] 10 7 5 0 0 0 0 0 0 0 0 12
-[32,] 0 0 8 0 0 0 0 0 0 10 0 0
-[33,] 0 0 17 0 0 0 0 9 10 0 0 0
-[34,] 12 0 7 0 0 0 0 0 0 0 0 0
-[35,] 0 0 15 0 0 0 0 0 0 0 0 10
-[36,] 0 0 10 0 0 0 8 0 0 0 0 0
-[37,] 16 0 0 0 0 0 4 0 9 0 11 0
-[38,] 10 0 8 0 0 0 0 0 0 9 0 11
-[39,] 0 0 4 0 0 0 0 0 0 0 0 13
-[40,] 7 0 3 12 0 0 0 0 5 10 0 0
-[41,] 16 0 8 0 10 0 0 0 0 0 11 8
-[42,] 14 0 8 0 0 0 8 0 0 0 0 6
-[43,] 11 0 8 0 0 0 0 0 0 0 0 0
-[44,] 8 0 15 0 0 0 0 0 13 0 11 7
+ [1,] 7 0 11 0 2 2 0 0 0 0 3 2
+ [2,] 10 0 8 2 0 2 6 0 0 0 0 3
+ [3,] 13 0 11 5 0 0 2 2 2 12 0 3
+ [4,] 4 4 5 0 0 0 0 0 3 9 4 2
+ [5,] 10 0 6 0 0 0 0 0 4 15 0 3
+ [6,] 12 0 13 0 0 0 0 1 0 13 11 0
+ [7,] 5 3 11 0 0 0 0 0 2 12 0 0
+ [8,] 11 4 10 0 0 0 0 1 3 0 10 3
+ [9,] 1 3 9 0 0 0 0 0 3 0 0 3
+[10,] 14 0 10 0 0 1 0 0 0 0 0 5
+[11,] 8 0 8 2 0 1 4 0 5 10 6 2
+[12,] 6 4 10 0 0 0 0 0 0 6 7 3
+[13,] 10 0 12 0 1 1 5 1 0 0 0 2
+[14,] 11 3 8 0 1 0 0 0 0 0 0 3
+[15,] 8 0 9 0 0 1 7 0 0 0 0 2
+[16,] 9 0 9 0 0 0 5 0 0 0 0 3
+[17,] 5 0 12 0 0 0 4 0 2 0 0 0
+[18,] 0 1 7 0 0 0 0 0 0 0 0 4
+[19,] 7 0 23 0 0 1 0 0 0 0 0 0
+[20,] 6 0 15 0 0 0 6 0 2 9 0 0
+[21,] 0 0 9 0 0 0 0 0 0 0 0 2
+[22,] 7 0 16 0 0 0 2 0 0 0 0 0
+[23,] 7 0 14 0 0 0 0 1 3 10 0 0
+[24,] 0 0 10 0 0 0 4 0 0 0 0 1
+[25,] 12 0 11 0 0 0 0 0 0 0 0 0
+[26,] 6 0 18 0 0 0 6 0 0 0 0 0
+[27,] 13 0 12 0 0 0 0 0 0 0 0 4
+[28,] 7 0 14 0 0 0 0 0 0 0 0 0
+[29,] 6 0 8 0 0 0 0 0 0 12 0 0
+[30,] 6 0 12 0 0 0 1 0 0 9 7 3
+[31,] 6 0 12 0 0 0 0 0 0 11 0 0
+[32,] 0 0 7 0 0 0 4 0 0 9 0 3
+[33,] 10 0 8 0 0 0 0 0 0 0 0 1
+[34,] 0 0 13 0 0 0 0 0 0 0 0 0
+[35,] 0 0 12 0 0 0 5 0 0 11 0 0
+[36,] 7 0 0 0 0 0 5 0 0 0 0 0
+[37,] 9 0 0 0 0 0 0 0 2 0 0 3
+[38,] 7 0 10 2 0 0 0 0 0 0 0 6
+[39,] 11 0 0 0 0 0 0 0 3 0 0 0
+[40,] 4 5 8 0 0 0 5 0 3 8 0 2
+[41,] 10 0 0 0 0 0 9 0 1 0 0 2
+[42,] 3 0 13 5 0 0 8 0 1 10 4 2
+[43,] 0 0 13 0 0 0 0 0 0 13 0 0
+[44,] 11 0 3 0 0 0 0 0 2 0 6 4
*** abuswap ***
--> margin rows shuffle samp <--
@@ -1936,12 +1937,32 @@
[42,] 8 0 6 0 1 0 0 0 4 0 0 9
[43,] 4 0 3 0 0 0 0 0 0 0 0 0
[44,] 6 0 16 0 0 0 0 0 3 0 0 4
-> ### end permatswap1
+Warning messages:
+1: In permatswap(x, method = method, fixedmar = margin, shuffle = what, :
+ quantitative swap method may not yield random null models, use only to study its properties
+2: In permatswap(x, method = method, fixedmar = margin, shuffle = what, :
+ quantitative swap method may not yield random null models, use only to study its properties
+3: In simulate.nullmodel(nullmodel(m, ALGO), nsim = times, burnin = burnin, :
+ non-sequential model: 'thin' set to 1
+4: In simulate.nullmodel(nullmodel(m, ALGO), nsim = times, burnin = burnin, :
+ non-sequential model: 'thin' set to 1
+5: In simulate.nullmodel(nullmodel(m, ALGO), nsim = times, burnin = burnin, :
+ non-sequential model: 'thin' set to 1
+6: In simulate.nullmodel(nullmodel(m, ALGO), nsim = times, burnin = burnin, :
+ non-sequential model: 'thin' set to 1
+7: In simulate.nullmodel(nullmodel(m, ALGO), nsim = times, burnin = burnin, :
+ non-sequential model: 'thin' set to 1
+8: In simulate.nullmodel(nullmodel(m, ALGO), nsim = times, burnin = burnin, :
+ non-sequential model: 'thin' set to 1
+> ### end permatswap
>
+> nm=nullmodel(m,"abuswap_c")
+> sm<-simulate(nm,nsim=100,thin=100,burnin=100)
+>
> ### clean
> rm(list = ls())
>
-> ## end permatfull1/swap1
+> ## end permatfull/swap
>
> ## The following vegan functions depend on *oecosimu*: adipart
> ## hiersimu multipart raupcrick. The following functions directly
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