[Vegan-commits] r2092 - in pkg/vegan: R man tests/Examples
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Feb 17 14:47:58 CET 2012
Author: jarioksa
Date: 2012-02-17 14:47:58 +0100 (Fri, 17 Feb 2012)
New Revision: 2092
Modified:
pkg/vegan/R/simper.R
pkg/vegan/man/simper.Rd
pkg/vegan/tests/Examples/vegan-Ex.Rout.save
Log:
merge from simper fixes
Modified: pkg/vegan/R/simper.R
===================================================================
--- pkg/vegan/R/simper.R 2012-02-16 14:10:36 UTC (rev 2091)
+++ pkg/vegan/R/simper.R 2012-02-17 13:47:58 UTC (rev 2092)
@@ -1,15 +1,24 @@
`simper` <-
- function(comm, group, permutations = 0)
+ function(comm, group, permutations = 0, trace = FALSE, ...)
{
comm <- as.matrix(comm)
comp <- t(combn(unique(as.character(group)), 2))
outlist <- NULL
+ ## data parameters
+ P <- ncol(comm)
+ nobs <- nrow(comm)
+ ## Make permutation matrix
+ if (length(permutations) == 1) {
+ perm <- shuffleSet(nobs, permutations, ...)
+ }
+ nperm <- nrow(perm)
+ if (nperm > 0)
+ perm.contr <- matrix(nrow=P, ncol=nperm)
for (i in 1:nrow(comp)) {
group.a <- comm[group == comp[i, 1], ]
group.b <- comm[group == comp[i, 2], ]
n.a <- nrow(group.a)
n.b <- nrow(group.b)
- P <- ncol(comm)
contr <- matrix(ncol = P, nrow = n.a * n.b)
for (j in 1:n.b) {
for (k in 1:n.a) {
@@ -20,14 +29,12 @@
}
average <- colMeans(contr) * 100
- if(permutations != 0){
- cat("Permuting", paste(comp[i,1], "_", comp[i,2], sep = ""), "\n")
- nobs <- length(group)
- perm.contr <- matrix(nrow=P, ncol=permutations)
+ if(nperm > 0){
+ if (trace)
+ cat("Permuting", paste(comp[i,1], comp[i,2], sep = "_"), "\n")
contrp <- matrix(ncol = P, nrow = n.a * n.b)
- for(p in 1:permutations){
- perm <- shuffle(nobs)
- groupp <- group[perm]
+ for(p in 1:nperm){
+ groupp <- group[perm[p,]]
ga <- comm[groupp == comp[i, 1], ]
gb <- comm[groupp == comp[i, 2], ]
for(j in 1:n.b) {
@@ -68,7 +75,8 @@
for (i in 1:length(cusum)) {
names(cusum[[i]]) <- spec[[i]]
}
- out <- lapply(cusum, function(z) z[z <= 70])
+ ## this probably fails with empty or identical groups that have 0/0 = NaN
+ out <- lapply(cusum, function(z) z[seq_len(min(which(z >= 70)))])
print(out)
invisible(x)
}
@@ -76,7 +84,7 @@
`summary.simper` <-
function(object, ordered = TRUE, ...)
{
- if (ordered == TRUE) {
+ if (ordered) {
out <- lapply(object, function(z) data.frame(contr = z$average, sd = z$sd, ratio = z$ratio, av.a = z$ava, av.b = z$avb)[z$ord, ])
cusum <- lapply(object, function(z) z$cusum)
for(i in 1:length(out)) {
Modified: pkg/vegan/man/simper.Rd
===================================================================
--- pkg/vegan/man/simper.Rd 2012-02-16 14:10:36 UTC (rev 2091)
+++ pkg/vegan/man/simper.Rd 2012-02-17 13:47:58 UTC (rev 2092)
@@ -10,18 +10,27 @@
}
\usage{
- simper(comm, group, permutations = 0)
+ simper(comm, group, permutations = 0, trace = FALSE, ...)
\method{summary}{simper}(object, ordered = TRUE, ...)
}
\arguments{
\item{comm}{Community data matrix.}
- \item{group}{Factor describing the group structure. Must have at least 2 levels.}
- \item{permutations}{Number of permutations for assessing the \dQuote{significance} of the average contribution. Default is set to 0 (no permutation test), since computations may take long time.}
+ \item{group}{Factor describing the group structure. Must have at
+ least 2 levels.}
+ \item{permutations}{Number of permutations or a permutation matrix
+ such as produced by \code{\link[permute]{shuffleSet}} for assessing
+ the \dQuote{significance} of the average contribution. Default is
+ set to 0 (no permutation test), since computations may take long
+ time.}
+ \item{trace}{Trace permutations.}
\item{object}{an object returned by \code{simper}.}
- \item{ordered}{Logical; Should the species be ordered by their average contribution?}
- \item{...}{Parameters passed to other functions}
+ \item{ordered}{Logical; Should the species be ordered by their
+ average contribution?}
+ \item{...}{Parameters passed to other functions. In \code{simper} the
+ extra parameters are passed to \code{\link[permute]{shuffleSet}} if
+ permutations are used.}
}
\details{ Similarity percentage, \code{simper} (Clarke 1993) is based
@@ -41,27 +50,37 @@
of sampling units and finds the average percentage contributions
of each species to the average overall Bray-Curtis dissimilarity.
- The function displays most important species for each contrast. The
- complete results can be seen with \code{summary} (see Examples).
+ The function displays most important species for each pair of
+ \code{groups}. These species contribute at least to 70 \% of the
+ differences between groups. The function returns much more
+ extensive results which can be accessed directly from the result
+ object (see section Value). Function \code{summary} transforms the
+ result to a list of data frames. With argument \code{ordered =
+ TRUE} the data frames also include the cumulative contributions and
+ are ordered by species contribution.
}
\value{
- A list of dataframes for every factor-combination.
- \item{contr}{average contribution to overall
- dissimilarity.}
- \item{sd}{standard deviation of
- contribution.}
+ A list of class \code{"simper"} with following items:
+ \item{species}{The species names.}
+ \item{average}{average contribution to overall dissimilarity.}
+ \item{overall}{The overall between-group dissimilarity (times 100).}
+ \item{sd}{standard deviation of contribution.}
\item{ratio}{mean to sd ratio.}
- \item{av_}{average abundance per group.}
- \item{cumsum}{cumulative per cent contribution.}
- \item{p}{permutation p-value. Probability of getting a larger or equal average contribution in random permutation of the group factor.}
+ \item{ava, avb}{average abundances per group.}
+ \item{ord}{An index vector to order vectors by their contribution or
+ order \code{cusum} back to the original data order.}
+ \item{cusum}{Ordered cumulative per cent contribution.}
+ \item{p}{permutation \eqn{p}-value. Probability of getting a larger
+ or equal average contribution in random permutation of the group
+ factor.}
}
\examples{
data(dune)
data(dune.env)
-(sim <- with(dune.env, simper(dune, Management, permutations = 0)))
+(sim <- with(dune.env, simper(dune, Management)))
summary(sim)
}
\author{
Modified: pkg/vegan/tests/Examples/vegan-Ex.Rout.save
===================================================================
--- pkg/vegan/tests/Examples/vegan-Ex.Rout.save 2012-02-16 14:10:36 UTC (rev 2091)
+++ pkg/vegan/tests/Examples/vegan-Ex.Rout.save 2012-02-17 13:47:58 UTC (rev 2092)
@@ -161,7 +161,7 @@
Formula:
y ~ poly(x1, 1) + poly(x2, 1)
-<environment: 0x102139710>
+<environment: 0x1021396d8>
Total model degrees of freedom 3
GCV score: 0.0427924
@@ -4730,7 +4730,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x10ab0b478>
+<environment: 0x109c72cd8>
Estimated degrees of freedom:
6.4351 total = 7.435071
@@ -4746,7 +4746,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x109904a78>
+<environment: 0x10969d268>
Estimated degrees of freedom:
6.1039 total = 7.103853
@@ -4902,7 +4902,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x10a92adc0>
+<environment: 0x109ddf588>
Estimated degrees of freedom:
8.9275 total = 9.927492
@@ -4915,7 +4915,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x109825c40>
+<environment: 0x1094cc2e8>
Estimated degrees of freedom:
7.7529 total = 8.75294
@@ -4928,7 +4928,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x109a64110>
+<environment: 0x10916cb58>
Estimated degrees of freedom:
8.8962 total = 9.89616
@@ -5987,7 +5987,7 @@
>
> ### Name: simper
> ### Title: Similarity Percentages
-> ### Aliases: simper
+> ### Aliases: simper summary.simper
> ### Keywords: multivariate
>
> ### ** Examples
@@ -5995,45 +5995,47 @@
> data(dune)
> data(dune.env)
> (sim <- with(dune.env, simper(dune, Management)))
+cumulative contributions of most influential species:
+
$BF_SF
- Agrsto Alogen Lolper Trirep Poatri Leoaut Brohor Achmil
-cum 9.824271 18.25483 25.95696 33.36787 40.73444 47.72921 53.12003 57.94653
- Plalan Elyrep
-cum 62.52225 67.0162
+ Agrsto Alogen Lolper Trirep Poatri Leoaut Brohor Achmil
+ 9.824271 18.254830 25.956958 33.367870 40.734444 47.729205 53.120026 57.946526
+ Plalan Elyrep Brarut
+62.522255 67.016196 71.098133
$BF_HF
- Rumace Poatri Plalan Brohor Lolper Elyrep Trirep Antodo
-cum 8.163219 15.1938 21.91833 27.96718 33.96956 39.84334 45.2982 50.27685
- Achmil Brarut Alogen Tripra
-cum 55.22265 60.02199 64.58433 69.12647
+ Rumace Poatri Plalan Brohor Lolper Elyrep Trirep Antodo
+ 8.163219 15.193797 21.918333 27.967181 33.969561 39.843338 45.298204 50.276849
+ Achmil Brarut Alogen Tripra Junart
+55.222648 60.021994 64.584333 69.126471 73.366621
$BF_NM
- Lolper Poatri Poapra Trirep Brohor Brarut Elepal Agrsto
-cum 12.42718 19.92126 27.11756 34.14609 39.5852 44.48077 49.10724 53.69083
- Achmil Leoaut Antodo
-cum 58.23926 62.53645 66.38182
+ Lolper Poatri Poapra Trirep Brohor Brarut Elepal Agrsto
+12.42718 19.92126 27.11756 34.14609 39.58520 44.48077 49.10724 53.69083
+ Achmil Leoaut Antodo Plalan
+58.23926 62.53645 66.38182 70.12577
$SF_HF
- Agrsto Alogen Lolper Plalan Rumace Elyrep Poatri Brarut
-cum 8.350879 16.53483 23.93493 30.84362 37.71614 43.33449 48.35175 52.80404
- Elepal Poapra Antodo Sagpro
-cum 57.20585 61.42398 65.54984 69.62895
+ Agrsto Alogen Lolper Plalan Rumace Elyrep Poatri Brarut
+ 8.350879 16.534834 23.934930 30.843624 37.716139 43.334492 48.351753 52.804045
+ Elepal Poapra Antodo Sagpro Tripra
+57.205850 61.423981 65.549838 69.628951 73.696831
$SF_NM
- Poatri Alogen Agrsto Lolper Elepal Poapra Brarut Elyrep
-cum 10.13601 19.35731 26.67383 33.77578 39.99419 45.26707 50.44725 55.05643
- Leoaut Trirep Sagpro
-cum 59.26117 63.20111 67.12478
+ Poatri Alogen Agrsto Lolper Elepal Poapra Brarut Elyrep
+10.13601 19.35731 26.67383 33.77578 39.99419 45.26707 50.44725 55.05643
+ Leoaut Trirep Sagpro Salrep
+59.26117 63.20111 67.12478 70.91528
$HF_NM
- Poatri Lolper Rumace Poapra Plalan Brarut Elepal Agrsto
-cum 9.913221 17.46846 23.91719 29.70133 35.46931 40.36549 44.80485 49.22655
- Trirep Elyrep Antodo Junart Tripra
-cum 53.43447 57.56466 61.54324 65.3413 68.9217
+ Poatri Lolper Rumace Poapra Plalan Brarut Elepal Agrsto
+ 9.913221 17.468460 23.917190 29.701331 35.469313 40.365488 44.804851 49.226546
+ Trirep Elyrep Antodo Junart Tripra Salrep
+53.434466 57.564661 61.543243 65.341300 68.921695 72.432408
> summary(sim)
$BF_SF
- contr sd contr/sd av_BF av_SF cum
+ contr sd ratio av.a av.b cumsum
Agrsto 6.1373875 0.034193273 179.49108 0.0000000 4.6666667 9.824271
Alogen 5.2667124 0.036475863 144.38897 0.6666667 4.3333333 18.254830
Lolper 4.8116494 0.039445076 121.98353 6.0000000 3.0000000 25.956958
@@ -6066,40 +6068,40 @@
Salrep 0.0000000 0.000000000 NaN 0.0000000 0.0000000 100.000000
$BF_HF
- contr sd contr/sd av_BF av_HF cum
-Rumace 3.8666202 0.02605967 148.37562 0.0000000 3.2 8.163219
-Poatri 3.3301297 0.02579295 129.11008 3.6666667 4.8 15.193797
-Plalan 3.1851684 0.01830432 174.01181 2.0000000 3.0 21.918333
-Brohor 2.8651195 0.01799001 159.26170 2.6666667 0.8 27.967181
-Lolper 2.8431092 0.02215330 128.33796 6.0000000 4.0 33.969561
-Elyrep 2.7821948 0.02958641 94.03624 1.3333333 2.0 39.843338
-Trirep 2.5837719 0.01655977 156.02708 4.6666667 2.8 45.298204
-Antodo 2.3582034 0.02042340 115.46577 1.3333333 1.8 50.276849
-Achmil 2.3426457 0.01474036 158.92727 2.3333333 1.2 55.222648
-Brarut 2.2732759 0.01801781 126.16829 2.0000000 2.8 60.021994
-Alogen 2.1610138 0.02308107 93.62711 0.6666667 1.6 64.584333
-Tripra 2.1514461 0.02207334 97.46810 0.0000000 1.8 69.126471
-Junart 2.0084049 0.02555374 78.59534 0.0000000 1.6 73.366621
-Leoaut 1.9318258 0.01356486 142.41397 4.3333333 2.8 77.445097
-Belper 1.8289995 0.01486414 123.04777 1.6666667 0.4 81.306485
-Agrsto 1.7605184 0.02284119 77.07646 0.0000000 1.4 85.023296
-Junbuf 1.4999755 0.02066084 72.59994 0.0000000 1.2 88.190049
-Viclat 1.2848484 0.01139618 112.74378 1.0000000 0.0 90.902624
-Sagpro 1.1684667 0.01297192 90.07661 0.6666667 0.8 93.369494
-Elepal 1.0168588 0.02110771 48.17475 0.0000000 0.8 95.516289
-Hyprad 0.8949950 0.01311558 68.23909 0.6666667 0.0 97.405805
-Poapra 0.7203468 0.01009842 71.33262 4.0000000 3.4 98.926603
-Ranfla 0.5084294 0.01055386 48.17475 0.0000000 0.4 100.000000
-Empnig 0.0000000 0.00000000 NaN 0.0000000 0.0 100.000000
-Airpra 0.0000000 0.00000000 NaN 0.0000000 0.0 100.000000
-Cirarv 0.0000000 0.00000000 NaN 0.0000000 0.0 100.000000
-Potpal 0.0000000 0.00000000 NaN 0.0000000 0.0 100.000000
-Calcus 0.0000000 0.00000000 NaN 0.0000000 0.0 100.000000
-Salrep 0.0000000 0.00000000 NaN 0.0000000 0.0 100.000000
-Chealb 0.0000000 0.00000000 NaN 0.0000000 0.0 100.000000
+ contr sd ratio av.a av.b cumsum
+Rumace 3.8666202 0.02605967 148.37562 0.0000000 3.2 8.163219
+Poatri 3.3301297 0.02579295 129.11008 3.6666667 4.8 15.193797
+Plalan 3.1851684 0.01830432 174.01181 2.0000000 3.0 21.918333
+Brohor 2.8651195 0.01799001 159.26170 2.6666667 0.8 27.967181
+Lolper 2.8431092 0.02215330 128.33796 6.0000000 4.0 33.969561
+Elyrep 2.7821948 0.02958641 94.03624 1.3333333 2.0 39.843338
+Trirep 2.5837719 0.01655977 156.02708 4.6666667 2.8 45.298204
+Antodo 2.3582034 0.02042340 115.46577 1.3333333 1.8 50.276849
+Achmil 2.3426457 0.01474036 158.92727 2.3333333 1.2 55.222648
+Brarut 2.2732759 0.01801781 126.16829 2.0000000 2.8 60.021994
+Alogen 2.1610138 0.02308107 93.62711 0.6666667 1.6 64.584333
+Tripra 2.1514461 0.02207334 97.46810 0.0000000 1.8 69.126471
+Junart 2.0084049 0.02555374 78.59534 0.0000000 1.6 73.366621
+Leoaut 1.9318258 0.01356486 142.41397 4.3333333 2.8 77.445097
+Belper 1.8289995 0.01486414 123.04777 1.6666667 0.4 81.306485
+Agrsto 1.7605184 0.02284119 77.07646 0.0000000 1.4 85.023296
+Junbuf 1.4999755 0.02066084 72.59994 0.0000000 1.2 88.190049
+Viclat 1.2848484 0.01139618 112.74378 1.0000000 0.0 90.902624
+Sagpro 1.1684667 0.01297192 90.07661 0.6666667 0.8 93.369494
+Elepal 1.0168588 0.02110771 48.17475 0.0000000 0.8 95.516289
+Hyprad 0.8949950 0.01311558 68.23909 0.6666667 0.0 97.405805
+Poapra 0.7203468 0.01009842 71.33262 4.0000000 3.4 98.926603
+Ranfla 0.5084294 0.01055386 48.17475 0.0000000 0.4 100.000000
+Empnig 0.0000000 0.00000000 NaN 0.0000000 0.0 100.000000
+Airpra 0.0000000 0.00000000 NaN 0.0000000 0.0 100.000000
+Cirarv 0.0000000 0.00000000 NaN 0.0000000 0.0 100.000000
+Potpal 0.0000000 0.00000000 NaN 0.0000000 0.0 100.000000
+Calcus 0.0000000 0.00000000 NaN 0.0000000 0.0 100.000000
+Salrep 0.0000000 0.00000000 NaN 0.0000000 0.0 100.000000
+Chealb 0.0000000 0.00000000 NaN 0.0000000 0.0 100.000000
$BF_NM
- contr sd contr/sd av_BF av_NM cum
+ contr sd ratio av.a av.b cumsum
Lolper 9.0680890 0.02644343 342.92411 6.0000000 0.3333333 12.42718
Poatri 5.4684115 0.04464645 122.48255 3.6666667 0.0000000 19.92126
Poapra 5.2511240 0.01812886 289.65557 4.0000000 0.6666667 27.11756
@@ -6132,40 +6134,40 @@
Chealb 0.0000000 0.00000000 NaN 0.0000000 0.0000000 100.00000
$SF_HF
- contr sd contr/sd av_SF av_HF cum
-Agrsto 4.7380081 0.031272715 151.50613 4.6666667 1.4 8.350879
-Alogen 4.6433015 0.032896891 141.14712 4.3333333 1.6 16.534834
-Lolper 4.1985660 0.027006718 155.46377 3.0000000 4.0 23.934930
-Plalan 3.9197607 0.033208288 118.03562 0.0000000 3.0 30.843624
-Rumace 3.8992342 0.027368676 142.47069 0.3333333 3.2 37.716139
-Elyrep 3.1876647 0.029550307 107.87247 2.0000000 2.0 43.334492
-Poatri 2.8466256 0.021521731 132.26750 4.6666667 4.8 48.351753
-Brarut 2.5260809 0.021044097 120.03751 2.0000000 2.8 52.804045
-Elepal 2.4974367 0.038876909 64.23959 1.3333333 0.8 57.205850
-Poapra 2.3932257 0.019179734 124.77888 2.5000000 3.4 61.423981
-Antodo 2.3408728 0.021430212 109.23237 0.0000000 1.8 65.549838
-Sagpro 2.3143518 0.020478964 113.01118 1.8333333 0.8 69.628951
-Tripra 2.3079782 0.023431610 98.49849 0.0000000 1.8 73.696831
-Junart 2.2849877 0.025676555 88.99121 0.5000000 1.6 77.724189
-Trirep 2.2382699 0.019486710 114.86135 1.3333333 2.8 81.669205
-Junbuf 2.1642678 0.022237444 97.32538 1.1666667 1.2 85.483791
-Leoaut 2.0509314 0.016422027 124.88905 1.3333333 2.8 89.098618
-Achmil 1.5183100 0.011393329 133.26307 0.1666667 1.2 91.774684
-Brohor 1.3375437 0.014503626 92.22133 0.5000000 0.8 94.132144
-Ranfla 1.0660700 0.013386946 79.63504 0.6666667 0.4 96.011124
-Belper 0.9990990 0.012570517 79.47955 0.6666667 0.4 97.772065
-Calcus 0.6623417 0.015076322 43.93258 0.5000000 0.0 98.939462
-Cirarv 0.3809333 0.008669044 43.94178 0.3333333 0.0 99.610868
-Chealb 0.2207806 0.005025441 43.93258 0.1666667 0.0 100.000000
-Empnig 0.0000000 0.000000000 NaN 0.0000000 0.0 100.000000
-Airpra 0.0000000 0.000000000 NaN 0.0000000 0.0 100.000000
-Viclat 0.0000000 0.000000000 NaN 0.0000000 0.0 100.000000
-Hyprad 0.0000000 0.000000000 NaN 0.0000000 0.0 100.000000
-Potpal 0.0000000 0.000000000 NaN 0.0000000 0.0 100.000000
-Salrep 0.0000000 0.000000000 NaN 0.0000000 0.0 100.000000
+ contr sd ratio av.a av.b cumsum
+Agrsto 4.7380081 0.031272715 151.50613 4.6666667 1.4 8.350879
+Alogen 4.6433015 0.032896891 141.14712 4.3333333 1.6 16.534834
+Lolper 4.1985660 0.027006718 155.46377 3.0000000 4.0 23.934930
+Plalan 3.9197607 0.033208288 118.03562 0.0000000 3.0 30.843624
+Rumace 3.8992342 0.027368676 142.47069 0.3333333 3.2 37.716139
+Elyrep 3.1876647 0.029550307 107.87247 2.0000000 2.0 43.334492
+Poatri 2.8466256 0.021521731 132.26750 4.6666667 4.8 48.351753
+Brarut 2.5260809 0.021044097 120.03751 2.0000000 2.8 52.804045
+Elepal 2.4974367 0.038876909 64.23959 1.3333333 0.8 57.205850
+Poapra 2.3932257 0.019179734 124.77888 2.5000000 3.4 61.423981
+Antodo 2.3408728 0.021430212 109.23237 0.0000000 1.8 65.549838
+Sagpro 2.3143518 0.020478964 113.01118 1.8333333 0.8 69.628951
+Tripra 2.3079782 0.023431610 98.49849 0.0000000 1.8 73.696831
+Junart 2.2849877 0.025676555 88.99121 0.5000000 1.6 77.724189
+Trirep 2.2382699 0.019486710 114.86135 1.3333333 2.8 81.669205
+Junbuf 2.1642678 0.022237444 97.32538 1.1666667 1.2 85.483791
+Leoaut 2.0509314 0.016422027 124.88905 1.3333333 2.8 89.098618
+Achmil 1.5183100 0.011393329 133.26307 0.1666667 1.2 91.774684
+Brohor 1.3375437 0.014503626 92.22133 0.5000000 0.8 94.132144
+Ranfla 1.0660700 0.013386946 79.63504 0.6666667 0.4 96.011124
+Belper 0.9990990 0.012570517 79.47955 0.6666667 0.4 97.772065
+Calcus 0.6623417 0.015076322 43.93258 0.5000000 0.0 98.939462
+Cirarv 0.3809333 0.008669044 43.94178 0.3333333 0.0 99.610868
+Chealb 0.2207806 0.005025441 43.93258 0.1666667 0.0 100.000000
+Empnig 0.0000000 0.000000000 NaN 0.0000000 0.0 100.000000
+Airpra 0.0000000 0.000000000 NaN 0.0000000 0.0 100.000000
+Viclat 0.0000000 0.000000000 NaN 0.0000000 0.0 100.000000
+Hyprad 0.0000000 0.000000000 NaN 0.0000000 0.0 100.000000
+Potpal 0.0000000 0.000000000 NaN 0.0000000 0.0 100.000000
+Salrep 0.0000000 0.000000000 NaN 0.0000000 0.0 100.000000
$SF_NM
- contr sd contr/sd av_SF av_NM cum
+ contr sd ratio av.a av.b cumsum
Poatri 7.8284148 0.040947182 191.18324 4.6666667 0.0000000 10.13601
Alogen 7.1219425 0.046958337 151.66513 4.3333333 0.0000000 19.35731
Agrsto 5.6508187 0.044176062 127.91585 4.6666667 2.1666667 26.67383
@@ -6198,37 +6200,37 @@
Tripra 0.0000000 0.000000000 NaN 0.0000000 0.0000000 100.00000
$HF_NM
- contr sd contr/sd av_HF av_NM cum
-Poatri 7.1552962 0.013680801 523.01735 4.8 0.0000000 9.913221
-Lolper 5.4533212 0.029624608 184.08079 4.0 0.3333333 17.468460
-Rumace 4.6546497 0.030806132 151.09491 3.2 0.0000000 23.917190
-Poapra 4.1749543 0.018851704 221.46297 3.4 0.6666667 29.701331
-Plalan 4.1632907 0.029559966 140.84220 3.0 0.8333333 35.469313
-Brarut 3.5340259 0.020103791 175.78903 2.8 2.8333333 40.365488
-Elepal 3.2043023 0.032314877 99.15873 0.8 2.1666667 44.804851
-Agrsto 3.1915495 0.028887302 110.48278 1.4 2.1666667 49.226546
-Trirep 3.0372486 0.022871293 132.79742 2.8 1.8333333 53.434466
-Elyrep 2.9811469 0.038675842 77.08033 2.0 0.0000000 57.564661
-Antodo 2.8717143 0.024799203 115.79865 1.8 1.3333333 61.543243
-Junart 2.7414119 0.028536540 96.06672 1.6 1.1666667 65.341300
-Tripra 2.5843049 0.025971573 99.50514 1.8 0.0000000 68.921695
-Salrep 2.5340091 0.027291287 92.85048 0.0 1.8333333 72.432408
-Alogen 2.4459371 0.032399067 75.49406 1.6 0.0000000 75.821103
-Leoaut 2.0703325 0.014124614 146.57622 2.8 3.1666667 78.689420
-Ranfla 1.9284693 0.019938840 96.71923 0.4 1.3333333 81.361196
-Junbuf 1.8180949 0.024648229 73.76168 1.2 0.0000000 83.880054
-Hyprad 1.7141357 0.026547931 64.56758 0.0 1.1666667 86.254883
-Calcus 1.6832709 0.024900688 67.59937 0.0 1.1666667 88.586951
-Achmil 1.6555393 0.014899781 111.11165 1.2 0.3333333 90.880598
-Sagpro 1.5282469 0.016534777 92.42622 0.8 0.5000000 92.997890
-Airpra 1.2605398 0.018242589 69.09873 0.0 0.8333333 94.744290
-Brohor 1.2093682 0.015168791 79.72739 0.8 0.0000000 96.419795
-Potpal 1.0105496 0.014556161 69.42419 0.0 0.6666667 97.819849
-Belper 0.8801475 0.013732352 64.09299 0.4 0.3333333 99.039239
-Empnig 0.4535959 0.010325282 43.93061 0.0 0.3333333 99.667668
-Viclat 0.2398752 0.005460872 43.92616 0.0 0.1666667 100.000000
-Cirarv 0.0000000 0.000000000 NaN 0.0 0.0000000 100.000000
-Chealb 0.0000000 0.000000000 NaN 0.0 0.0000000 100.000000
+ contr sd ratio av.a av.b cumsum
+Poatri 7.1552962 0.013680801 523.01735 4.8 0.0000000 9.913221
+Lolper 5.4533212 0.029624608 184.08079 4.0 0.3333333 17.468460
+Rumace 4.6546497 0.030806132 151.09491 3.2 0.0000000 23.917190
+Poapra 4.1749543 0.018851704 221.46297 3.4 0.6666667 29.701331
+Plalan 4.1632907 0.029559966 140.84220 3.0 0.8333333 35.469313
+Brarut 3.5340259 0.020103791 175.78903 2.8 2.8333333 40.365488
+Elepal 3.2043023 0.032314877 99.15873 0.8 2.1666667 44.804851
+Agrsto 3.1915495 0.028887302 110.48278 1.4 2.1666667 49.226546
+Trirep 3.0372486 0.022871293 132.79742 2.8 1.8333333 53.434466
+Elyrep 2.9811469 0.038675842 77.08033 2.0 0.0000000 57.564661
+Antodo 2.8717143 0.024799203 115.79865 1.8 1.3333333 61.543243
+Junart 2.7414119 0.028536540 96.06672 1.6 1.1666667 65.341300
+Tripra 2.5843049 0.025971573 99.50514 1.8 0.0000000 68.921695
+Salrep 2.5340091 0.027291287 92.85048 0.0 1.8333333 72.432408
+Alogen 2.4459371 0.032399067 75.49406 1.6 0.0000000 75.821103
+Leoaut 2.0703325 0.014124614 146.57622 2.8 3.1666667 78.689420
+Ranfla 1.9284693 0.019938840 96.71923 0.4 1.3333333 81.361196
+Junbuf 1.8180949 0.024648229 73.76168 1.2 0.0000000 83.880054
+Hyprad 1.7141357 0.026547931 64.56758 0.0 1.1666667 86.254883
+Calcus 1.6832709 0.024900688 67.59937 0.0 1.1666667 88.586951
+Achmil 1.6555393 0.014899781 111.11165 1.2 0.3333333 90.880598
+Sagpro 1.5282469 0.016534777 92.42622 0.8 0.5000000 92.997890
+Airpra 1.2605398 0.018242589 69.09873 0.0 0.8333333 94.744290
+Brohor 1.2093682 0.015168791 79.72739 0.8 0.0000000 96.419795
+Potpal 1.0105496 0.014556161 69.42419 0.0 0.6666667 97.819849
+Belper 0.8801475 0.013732352 64.09299 0.4 0.3333333 99.039239
+Empnig 0.4535959 0.010325282 43.93061 0.0 0.3333333 99.667668
+Viclat 0.2398752 0.005460872 43.92616 0.0 0.1666667 100.000000
+Cirarv 0.0000000 0.000000000 NaN 0.0 0.0000000 100.000000
+Chealb 0.0000000 0.000000000 NaN 0.0 0.0000000 100.000000
attr(,"class")
[1] "summary.simper"
@@ -7461,7 +7463,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x109e96b50>
+<environment: 0x109f0bf90>
Estimated degrees of freedom:
2 total = 3
@@ -7941,7 +7943,7 @@
> ### * <FOOTER>
> ###
> cat("Time elapsed: ", proc.time() - get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed: 102.327 1.858 104.737 0 0
+Time elapsed: 81.254 1.591 83.713 0 0
> grDevices::dev.off()
null device
1
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