[Vegan-commits] r2579 - in pkg/vegan: R tests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Aug 2 07:29:42 CEST 2013
Author: jarioksa
Date: 2013-08-02 07:29:41 +0200 (Fri, 02 Aug 2013)
New Revision: 2579
Modified:
pkg/vegan/R/make.commsim.R
pkg/vegan/tests/oecosimu-tests.Rout.save
Log:
remove redundant sample() of random vectors
Modified: pkg/vegan/R/make.commsim.R
===================================================================
--- pkg/vegan/R/make.commsim.R 2013-08-01 13:43:23 UTC (rev 2578)
+++ pkg/vegan/R/make.commsim.R 2013-08-02 05:29:41 UTC (rev 2579)
@@ -207,7 +207,7 @@
for (k in seq_len(n)) {
out[,,k] <- .C("quasiswap",
m = out[,,k], nr, nc, PACKAGE = "vegan")$m
- out[,,k][out[,,k] > 0] <- sample(indshuffle(nz - 1L) + 1L) # we assume that length(nz)>1
+ out[,,k][out[,,k] > 0] <- indshuffle(nz - 1L) + 1L # we assume that length(nz)>1
}
out
}),
@@ -266,7 +266,7 @@
if (length(nz) == 1)
out[i,,k][out[i,,k] > 0] <- nz
if (length(nz) > 1)
- out[i,,k][out[i,,k] > 0] <- sample(indshuffle(nz - 1L) + 1L)
+ out[i,,k][out[i,,k] > 0] <- indshuffle(nz - 1L) + 1L
}
}
out
@@ -288,7 +288,7 @@
if (length(nz) == 1)
out[,j,k][out[,j,k] > 0] <- nz
if (length(nz) > 1)
- out[,j,k][out[,j,k] > 0] <- sample(indshuffle(nz - 1L) + 1L)
+ out[,j,k][out[,j,k] > 0] <- indshuffle(nz - 1L) + 1L
}
}
out
Modified: pkg/vegan/tests/oecosimu-tests.Rout.save
===================================================================
--- pkg/vegan/tests/oecosimu-tests.Rout.save 2013-08-01 13:43:23 UTC (rev 2578)
+++ pkg/vegan/tests/oecosimu-tests.Rout.save 2013-08-02 05:29:41 UTC (rev 2579)
@@ -1564,55 +1564,55 @@
--> margin rows shuffle both <--
grand sum: [1] TRUE
row sums: [1] TRUE
-col sums: [1] "Mean relative difference: 0.7018816"
+col sums: [1] "Mean relative difference: 0.677024"
fill: [1] TRUE
row freqs: [1] TRUE
col freqs: [1] TRUE
Brachy PHTH HPAV RARD SSTR Protopl MEGR MPRO TVIE HMIN HMIN2 NPRA
-8 3 0 8 0 7 4 0 0 0 0 4 3
-9 12 0 5 5 0 13 10 0 0 0 0 6
-11 12 0 8 11 0 0 5 7 5 9 0 9
-14 13 12 13 0 0 0 0 0 12 14 13 8
-15 3 0 10 0 0 0 0 0 6 2 0 5
-19 9 0 7 0 0 0 0 4 0 8 3 0
-25 5 7 6 0 0 0 0 0 6 6 0 0
-30 4 2 5 0 0 0 0 2 2 0 3 6
-32 8 8 8 0 0 0 0 0 2 0 0 6
-33 9 0 11 0 0 7 0 0 0 0 0 10
-34 11 0 7 8 0 8 6 0 4 7 4 10
-35 3 4 4 0 0 0 0 0 0 9 4 7
-36 6 0 6 0 3 8 8 6 0 0 0 8
-37 9 11 7 0 11 0 0 0 0 0 0 5
-38 19 0 11 0 0 16 15 0 0 0 0 11
-39 9 0 6 0 0 0 10 0 0 0 0 8
-40 21 0 11 0 0 0 16 0 14 0 0 0
-41 0 10 6 0 0 0 0 0 0 0 0 9
-42 17 0 18 0 0 16 0 0 0 0 0 0
-43 12 0 13 0 0 0 14 0 16 15 0 0
-44 0 0 15 0 0 0 0 0 0 0 0 11
-45 6 0 12 0 0 0 10 0 0 0 0 0
-46 11 0 9 0 0 0 0 12 4 8 0 0
-47 0 0 11 0 0 0 8 0 0 0 0 6
-48 9 0 12 0 0 0 0 0 0 0 0 0
-49 8 0 10 0 0 0 10 0 0 0 0 0
-50 13 0 9 0 0 0 0 0 0 0 0 14
-51 11 0 7 0 0 0 0 0 0 0 0 0
-52 13 0 11 0 0 0 0 0 0 5 0 0
-53 4 0 10 0 0 0 11 0 0 9 11 8
-54 7 0 4 0 0 0 0 0 0 5 0 0
-55 0 0 5 0 0 0 6 0 0 7 0 8
-56 9 0 7 0 0 0 0 0 0 0 0 7
-57 0 0 1 0 0 0 0 0 0 0 0 0
-58 0 0 13 0 0 0 8 0 0 5 0 0
-59 14 0 0 0 0 0 11 0 0 0 0 0
-60 9 0 0 0 0 0 0 0 11 0 0 7
-61 4 0 7 5 0 0 0 0 0 0 0 4
-62 1 0 0 0 0 0 0 0 2 0 0 0
-63 6 3 10 0 0 0 9 0 8 1 0 4
-64 8 0 0 0 0 0 12 0 6 0 0 6
-66 17 0 6 4 0 0 8 0 7 9 9 9
-67 0 0 136 0 0 0 0 0 0 135 0 0
-68 11 0 9 0 0 0 0 0 4 0 6 8
+8 8 0 3 0 5 14 0 0 0 0 5 5
+9 7 0 4 12 0 10 10 0 0 0 0 4
+11 6 0 8 13 0 0 8 8 12 8 0 9
+14 14 11 9 0 0 0 0 0 15 15 13 10
+15 5 0 6 0 0 0 0 0 5 5 0 7
+19 5 0 5 0 0 0 0 4 0 4 6 0
+25 5 6 5 0 0 0 0 0 9 6 0 0
+30 5 5 1 0 0 0 0 6 2 0 3 5
+32 6 4 3 0 0 0 0 0 8 0 0 3
+33 7 0 4 0 0 8 0 0 0 0 0 13
+34 9 0 11 10 0 7 11 0 6 13 12 9
+35 6 5 10 0 0 0 0 0 0 10 3 10
+36 8 0 7 0 13 6 4 4 0 0 0 9
+37 14 11 7 0 8 0 0 0 0 0 0 8
+38 17 0 14 0 0 20 12 0 0 0 0 12
+39 7 0 8 0 0 0 8 0 0 0 0 10
+40 14 0 10 0 0 0 12 0 15 0 0 0
+41 0 4 8 0 0 0 0 0 0 0 0 8
+42 15 0 14 0 0 15 0 0 0 0 0 0
+43 12 0 17 0 0 0 11 0 11 15 0 0
+44 0 0 9 0 0 0 0 0 0 0 0 15
+45 13 0 12 0 0 0 6 0 0 0 0 0
+46 10 0 10 0 0 0 0 8 8 15 0 0
+47 0 0 12 0 0 0 8 0 0 0 0 8
+48 12 0 9 0 0 0 0 0 0 0 0 0
+49 7 0 13 0 0 0 7 0 0 0 0 0
+50 12 0 8 0 0 0 0 0 0 0 0 16
+51 2 0 7 0 0 0 0 0 0 0 0 0
+52 4 0 8 0 0 0 0 0 0 11 0 0
+53 11 0 6 0 0 0 10 0 0 9 7 7
+54 7 0 6 0 0 0 0 0 0 4 0 0
+55 0 0 5 0 0 0 6 0 0 2 0 7
+56 10 0 10 0 0 0 0 0 0 0 0 10
+57 0 0 2 0 0 0 0 0 0 0 0 0
+58 0 0 10 0 0 0 10 0 0 5 0 0
+59 15 0 0 0 0 0 13 0 0 0 0 0
+60 3 0 0 0 0 0 0 0 9 0 0 8
+61 4 0 5 6 0 0 0 0 0 0 0 5
+62 3 0 0 0 0 0 0 0 3 0 0 0
+63 6 5 4 0 0 0 7 0 3 4 0 10
+64 8 0 0 0 0 0 5 0 7 0 0 7
+66 8 0 7 10 0 0 11 0 5 7 7 9
+67 0 0 119 0 0 0 0 0 0 134 0 0
+68 11 0 7 0 0 0 0 0 7 0 7 12
*** swsh ***
--> margin columns shuffle samp <--
@@ -1671,56 +1671,56 @@
*** swsh ***
--> margin columns shuffle both <--
grand sum: [1] TRUE
-row sums: [1] "Mean relative difference: 0.378733"
+row sums: [1] "Mean relative difference: 0.3752805"
col sums: [1] TRUE
fill: [1] TRUE
row freqs: [1] TRUE
col freqs: [1] TRUE
Brachy PHTH HPAV RARD SSTR Protopl MEGR MPRO TVIE HMIN HMIN2 NPRA
-8 8 0 9 0 1 1 0 0 0 0 3 4
-9 6 0 10 7 0 1 5 0 0 0 0 3
-11 8 0 19 1 0 0 4 2 3 10 0 3
-14 12 2 9 0 0 0 0 0 2 11 9 1
-15 7 0 10 0 0 0 0 0 1 12 0 4
-19 5 0 11 0 0 0 0 1 0 13 6 0
-25 8 2 10 0 0 0 0 0 3 9 0 0
-30 7 3 7 0 0 0 0 1 2 0 7 5
-32 8 3 14 0 0 0 0 0 2 0 0 1
-33 9 0 8 0 0 2 0 0 0 0 0 1
-34 11 0 14 5 0 1 5 0 2 10 6 2
-35 8 7 14 0 0 0 0 0 0 8 6 2
-36 11 0 7 0 1 2 5 1 0 0 0 3
-37 7 2 10 0 2 0 0 0 0 0 0 2
-38 13 0 12 0 0 1 6 0 0 0 0 5
-39 8 0 8 0 0 0 4 0 0 0 0 3
-40 8 0 7 0 0 0 9 0 2 0 0 0
-41 0 4 11 0 0 0 0 0 0 0 0 4
-42 5 0 13 0 0 1 0 0 0 0 0 0
-43 10 0 8 0 0 0 6 0 2 11 0 0
-44 0 0 8 0 0 0 0 0 0 0 0 5
-45 6 0 11 0 0 0 7 0 0 0 0 0
-46 6 0 10 0 0 0 0 1 4 12 0 0
-47 0 0 17 0 0 0 6 0 0 0 0 6
-48 13 0 8 0 0 0 0 0 0 0 0 0
-49 6 0 8 0 0 0 3 0 0 0 0 0
-50 9 0 6 0 0 0 0 0 0 0 0 5
-51 5 0 15 0 0 0 0 0 0 0 0 0
-52 11 0 13 0 0 0 0 0 0 10 0 0
-53 4 0 11 0 0 0 5 0 0 10 7 1
-54 6 0 10 0 0 0 0 0 0 9 0 0
-55 0 0 11 0 0 0 4 0 0 7 0 4
-56 6 0 8 0 0 0 0 0 0 0 0 2
-57 0 0 8 0 0 0 0 0 0 0 0 0
-58 0 0 14 0 0 0 2 0 0 8 0 0
-59 5 0 0 0 0 0 1 0 0 0 0 0
-60 5 0 0 0 0 0 0 0 3 0 0 2
-61 4 0 12 1 0 0 0 0 0 0 0 1
-62 9 0 0 0 0 0 0 0 1 0 0 0
-63 17 4 19 0 0 0 7 0 6 18 0 1
-64 8 0 0 0 0 0 3 0 5 0 0 3
-66 13 0 11 2 0 0 6 0 1 10 7 1
-67 0 0 8 0 0 0 0 0 0 11 0 0
-68 7 0 11 0 0 0 0 0 2 0 7 2
+8 11 0 9 0 2 1 0 0 0 0 5 3
+9 5 0 10 3 0 2 3 0 0 0 0 6
+11 7 0 9 3 0 0 3 1 4 10 0 1
+14 17 3 5 0 0 0 0 0 2 14 7 3
+15 7 0 13 0 0 0 0 0 2 14 0 1
+19 8 0 16 0 0 0 0 1 0 8 10 0
+25 5 5 7 0 0 0 0 0 5 11 0 0
+30 9 3 6 0 0 0 0 1 1 0 7 1
+32 7 3 16 0 0 0 0 0 2 0 0 4
+33 8 0 10 0 0 1 0 0 0 0 0 1
+34 4 0 15 3 0 1 7 0 2 11 4 5
+35 9 5 10 0 0 0 0 0 0 13 7 3
+36 6 0 15 0 1 1 2 1 0 0 0 5
+37 8 3 10 0 1 0 0 0 0 0 0 2
+38 6 0 11 0 0 2 5 0 0 0 0 7
+39 5 0 11 0 0 0 5 0 0 0 0 1
+40 9 0 13 0 0 0 4 0 4 0 0 0
+41 0 3 10 0 0 0 0 0 0 0 0 1
+42 8 0 8 0 0 1 0 0 0 0 0 0
+43 8 0 14 0 0 0 4 0 2 11 0 0
+44 0 0 14 0 0 0 0 0 0 0 0 5
+45 13 0 12 0 0 0 4 0 0 0 0 0
+46 8 0 9 0 0 0 0 2 3 11 0 0
+47 0 0 8 0 0 0 6 0 0 0 0 1
+48 4 0 9 0 0 0 0 0 0 0 0 0
+49 13 0 11 0 0 0 3 0 0 0 0 0
+50 11 0 15 0 0 0 0 0 0 0 0 1
+51 11 0 10 0 0 0 0 0 0 0 0 0
+52 5 0 6 0 0 0 0 0 0 4 0 0
+53 13 0 15 0 0 0 6 0 0 13 6 2
+54 6 0 11 0 0 0 0 0 0 6 0 0
+55 0 0 10 0 0 0 11 0 0 8 0 1
+56 7 0 7 0 0 0 0 0 0 0 0 3
+57 0 0 9 0 0 0 0 0 0 0 0 0
+58 0 0 17 0 0 0 10 0 0 11 0 0
+59 10 0 0 0 0 0 3 0 0 0 0 0
+60 6 0 0 0 0 0 0 0 1 0 0 5
+61 6 0 9 4 0 0 0 0 0 0 0 4
+62 6 0 0 0 0 0 0 0 2 0 0 0
+63 8 2 6 0 0 0 3 0 1 10 0 4
+64 12 0 0 0 0 0 6 0 4 0 0 2
+66 5 0 13 3 0 0 3 0 4 13 6 3
+67 0 0 10 0 0 0 0 0 0 11 0 0
+68 8 0 11 0 0 0 0 0 2 0 6 1
*** abuswap ***
--> margin rows shuffle samp <--
@@ -1979,4 +1979,4 @@
>
> proc.time()
user system elapsed
- 2.390 0.228 2.623
+ 2.317 0.220 2.504
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