[Vegan-commits] r2084 - in pkg/vegan: . R man tests/Examples
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun Feb 12 08:38:29 CET 2012
Author: jarioksa
Date: 2012-02-12 08:38:29 +0100 (Sun, 12 Feb 2012)
New Revision: 2084
Modified:
pkg/vegan/NAMESPACE
pkg/vegan/R/simper.R
pkg/vegan/man/simper.Rd
pkg/vegan/tests/Examples/vegan-Ex.Rout.save
Log:
simper: S3 method/generic consistency, NAMESPACE, example, tests
Modified: pkg/vegan/NAMESPACE
===================================================================
--- pkg/vegan/NAMESPACE 2012-02-12 07:20:01 UTC (rev 2083)
+++ pkg/vegan/NAMESPACE 2012-02-12 07:38:29 UTC (rev 2084)
@@ -307,6 +307,7 @@
S3method(print, radline)
S3method(print, specaccum)
S3method(print, simmat)
+S3method(print, simper)
S3method(print, summary.bioenv)
S3method(print, summary.cca)
S3method(print, summary.clamtest)
@@ -384,6 +385,7 @@
S3method(summary, prc)
S3method(summary, procrustes)
S3method(summary, radfit.frame)
+S3method(summary, simper)
S3method(summary, specaccum)
S3method(summary, taxondive)
# tail: utils
Modified: pkg/vegan/R/simper.R
===================================================================
--- pkg/vegan/R/simper.R 2012-02-12 07:20:01 UTC (rev 2083)
+++ pkg/vegan/R/simper.R 2012-02-12 07:38:29 UTC (rev 2084)
@@ -74,15 +74,15 @@
}
`print.simper` <-
- function(object)
+ function(x, ...)
{
- out <- lapply(object, function(x) t(x[x$cum <= 70 ,"cum", drop = FALSE]))
+ out <- lapply(x, function(z) t(z[z$cum <= 70 ,"cum", drop = FALSE]))
print(out)
- invisible(object)
+ invisible(x)
}
`summary.simper` <-
- function(object)
+ function(object, ...)
{
class(object) <- "summary.simper"
object
Modified: pkg/vegan/man/simper.Rd
===================================================================
--- pkg/vegan/man/simper.Rd 2012-02-12 07:20:01 UTC (rev 2083)
+++ pkg/vegan/man/simper.Rd 2012-02-12 07:38:29 UTC (rev 2084)
@@ -33,6 +33,10 @@
The \code{simper} functions performs pairwise comparisons of groups
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).
+
}
\value{
@@ -47,7 +51,8 @@
\examples{
data(dune)
data(dune.env)
-with(dune.env, simper(dune, Management))
+(sim <- with(dune.env, simper(dune, Management)))
+summary(sim)
}
\author{
Eduard Szöcs \email{szoe8822 at uni-landau.de}
Modified: pkg/vegan/tests/Examples/vegan-Ex.Rout.save
===================================================================
--- pkg/vegan/tests/Examples/vegan-Ex.Rout.save 2012-02-12 07:20:01 UTC (rev 2083)
+++ pkg/vegan/tests/Examples/vegan-Ex.Rout.save 2012-02-12 07:38:29 UTC (rev 2084)
@@ -23,7 +23,7 @@
> options(warn = 1)
> library('vegan')
Loading required package: permute
-This is vegan 2.1-11
+This is vegan 2.1-12
>
> assign(".oldSearch", search(), pos = 'CheckExEnv')
> cleanEx()
@@ -161,7 +161,7 @@
Formula:
y ~ poly(x1, 1) + poly(x2, 1)
-<environment: 0x102131ae8>
+<environment: 0x102139710>
Total model degrees of freedom 3
GCV score: 0.0427924
@@ -4730,7 +4730,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x10abb98a0>
+<environment: 0x10ab0b478>
Estimated degrees of freedom:
6.4351 total = 7.435071
@@ -4746,7 +4746,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x1097e0438>
+<environment: 0x109904a78>
Estimated degrees of freedom:
6.1039 total = 7.103853
@@ -4902,7 +4902,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x10acb8a28>
+<environment: 0x10a92adc0>
Estimated degrees of freedom:
8.9275 total = 9.927492
@@ -4915,7 +4915,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x109f4be98>
+<environment: 0x109825c40>
Estimated degrees of freedom:
7.7529 total = 8.75294
@@ -4928,7 +4928,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x10a85bdf8>
+<environment: 0x109a64110>
Estimated degrees of freedom:
8.8962 total = 9.89616
@@ -5994,205 +5994,244 @@
>
> data(dune)
> data(dune.env)
-> with(dune.env, simper(dune, Management))
+> (sim <- with(dune.env, simper(dune, Management)))
$BF_SF
- contr sd contr/sd av_BF av_SF cum
-Agrsto 6.1373875 0.034193273 0.005571308 0.0000000 4.6666667 9.824271
-Alogen 5.2667124 0.036475863 0.006925737 0.6666667 4.3333333 18.254830
-Lolper 4.8116494 0.039445076 0.008197828 6.0000000 3.0000000 25.956958
-Trirep 4.6297215 0.025525394 0.005513376 4.6666667 1.3333333 33.367870
-Poatri 4.6020231 0.033801137 0.007344843 3.6666667 4.6666667 40.734444
-Leoaut 4.3697453 0.024922188 0.005703350 4.3333333 1.3333333 47.729205
-Brohor 3.3677364 0.025859567 0.007678620 2.6666667 0.5000000 53.120026
-Achmil 3.0151964 0.020820614 0.006905226 2.3333333 0.1666667 57.946526
-Plalan 2.8585347 0.021548975 0.007538469 2.0000000 0.0000000 62.522255
-Elyrep 2.8074412 0.029777588 0.010606665 1.3333333 2.0000000 67.016196
-Brarut 2.5500549 0.023901903 0.009373093 2.0000000 2.0000000 71.098133
-Poapra 2.5128826 0.023967065 0.009537678 4.0000000 2.5000000 75.120568
-Sagpro 2.4325600 0.022148544 0.009105035 0.6666667 1.8333333 79.014428
-Belper 1.9858984 0.017087515 0.008604426 1.6666667 0.6666667 82.193305
-Elepal 1.8611486 0.042957616 0.023081239 0.0000000 1.3333333 85.172493
-Antodo 1.7542572 0.025803830 0.014709263 1.3333333 0.0000000 87.980576
-Junbuf 1.6031063 0.023707975 0.014788773 0.0000000 1.1666667 90.546709
-Viclat 1.4671255 0.013306461 0.009069750 1.0000000 0.0000000 92.895173
-Hyprad 1.0285612 0.015197764 0.014775751 0.6666667 0.0000000 94.541617
-Ranfla 0.9305743 0.013595007 0.014609265 0.0000000 0.6666667 96.031211
-Junart 0.6979307 0.016109106 0.023081239 0.0000000 0.5000000 97.148406
-Calcus 0.6979307 0.016109106 0.023081239 0.0000000 0.5000000 98.265601
-Rumace 0.4525878 0.010444461 0.023077206 0.0000000 0.3333333 98.990070
-Cirarv 0.3982767 0.009184791 0.023061332 0.0000000 0.3333333 99.627602
-Chealb 0.2326436 0.005369702 0.023081239 0.0000000 0.1666667 100.000000
-Empnig 0.0000000 0.000000000 NaN 0.0000000 0.0000000 100.000000
-Airpra 0.0000000 0.000000000 NaN 0.0000000 0.0000000 100.000000
-Potpal 0.0000000 0.000000000 NaN 0.0000000 0.0000000 100.000000
-Tripra 0.0000000 0.000000000 NaN 0.0000000 0.0000000 100.000000
-Salrep 0.0000000 0.000000000 NaN 0.0000000 0.0000000 100.000000
+ 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
$BF_HF
- contr sd contr/sd av_BF av_HF cum
-Rumace 3.8666202 0.02605967 0.006739652 0.0000000 3.2 8.163219
-Poatri 3.3301297 0.02579295 0.007745329 3.6666667 4.8 15.193797
-Plalan 3.1851684 0.01830432 0.005746736 2.0000000 3.0 21.918333
-Brohor 2.8651195 0.01799001 0.006278973 2.6666667 0.8 27.967181
-Lolper 2.8431092 0.02215330 0.007791927 6.0000000 4.0 33.969561
-Elyrep 2.7821948 0.02958641 0.010634198 1.3333333 2.0 39.843338
-Trirep 2.5837719 0.01655977 0.006409144 4.6666667 2.8 45.298204
-Antodo 2.3582034 0.02042340 0.008660576 1.3333333 1.8 50.276849
-Achmil 2.3426457 0.01474036 0.006292186 2.3333333 1.2 55.222648
-Brarut 2.2732759 0.01801781 0.007925922 2.0000000 2.8 60.021994
-Alogen 2.1610138 0.02308107 0.010680667 0.6666667 1.6 64.584333
-Tripra 2.1514461 0.02207334 0.010259767 0.0000000 1.8 69.126471
-Junart 2.0084049 0.02555374 0.012723400 0.0000000 1.6 73.366621
-Leoaut 1.9318258 0.01356486 0.007021783 4.3333333 2.8 77.445097
-Belper 1.8289995 0.01486414 0.008126925 1.6666667 0.4 81.306485
-Agrsto 1.7605184 0.02284119 0.012974130 0.0000000 1.4 85.023296
-Junbuf 1.4999755 0.02066084 0.013774115 0.0000000 1.2 88.190049
-Viclat 1.2848484 0.01139618 0.008869669 1.0000000 0.0 90.902624
-Sagpro 1.1684667 0.01297192 0.011101662 0.6666667 0.8 93.369494
-Elepal 1.0168588 0.02110771 0.020757761 0.0000000 0.8 95.516289
-Hyprad 0.8949950 0.01311558 0.014654358 0.6666667 0.0 97.405805
-Poapra 0.7203468 0.01009842 0.014018831 4.0000000 3.4 98.926603
-Ranfla 0.5084294 0.01055386 0.020757761 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
+ 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
$BF_NM
- contr sd contr/sd av_BF av_NM cum
-Lolper 9.0680890 0.02644343 0.002916097 6.0000000 0.3333333 12.42718
-Poatri 5.4684115 0.04464645 0.008164428 3.6666667 0.0000000 19.92126
-Poapra 5.2511240 0.01812886 0.003452376 4.0000000 0.6666667 27.11756
-Trirep 5.1287027 0.02755807 0.005373302 4.6666667 1.8333333 34.14609
-Brohor 3.9689114 0.02920386 0.007358154 2.6666667 0.0000000 39.58520
-Brarut 3.5722867 0.02868949 0.008031129 2.0000000 2.8333333 44.48077
-Elepal 3.3759250 0.03572888 0.010583433 0.0000000 2.1666667 49.10724
-Agrsto 3.3446318 0.03473296 0.010384687 0.0000000 2.1666667 53.69083
-Achmil 3.3189820 0.02337698 0.007043419 2.3333333 0.3333333 58.23926
-Leoaut 3.1356499 0.02025675 0.006460144 4.3333333 3.1666667 62.53645
-Antodo 2.8059604 0.03294714 0.011741840 1.3333333 1.3333333 66.38182
-Plalan 2.7319482 0.02192961 0.008027095 2.0000000 0.8333333 70.12577
-Salrep 2.6770230 0.02927399 0.010935277 0.0000000 1.8333333 73.79444
-Belper 2.3528522 0.01909409 0.008115295 1.6666667 0.3333333 77.01886
-Hyprad 2.1720695 0.02450331 0.011281089 0.6666667 1.1666667 79.99553
-Ranfla 2.0313589 0.02275206 0.011200412 0.0000000 1.3333333 82.77937
-Elyrep 1.9993334 0.02926048 0.014635117 1.3333333 0.0000000 85.51931
-Calcus 1.7832867 0.02680560 0.015031571 0.0000000 1.1666667 87.96318
-Junart 1.7694138 0.02599948 0.014693836 0.0000000 1.1666667 90.38804
-Viclat 1.5772799 0.01446762 0.009172510 1.0000000 0.1666667 92.54959
-Sagpro 1.5432494 0.01857093 0.012033654 0.6666667 0.5000000 94.66451
-Airpra 1.3409953 0.01969485 0.014686741 0.0000000 0.8333333 96.50225
-Potpal 1.0739109 0.01571113 0.014629824 0.0000000 0.6666667 97.97397
-Alogen 0.9996667 0.01463024 0.014635117 0.6666667 0.0000000 99.34394
-Empnig 0.4787240 0.01105165 0.023085641 0.0000000 0.3333333 100.00000
-Junbuf 0.0000000 0.00000000 NaN 0.0000000 0.0000000 100.00000
-Rumace 0.0000000 0.00000000 NaN 0.0000000 0.0000000 100.00000
-Cirarv 0.0000000 0.00000000 NaN 0.0000000 0.0000000 100.00000
-Tripra 0.0000000 0.00000000 NaN 0.0000000 0.0000000 100.00000
-Chealb 0.0000000 0.00000000 NaN 0.0000000 0.0000000 100.00000
+ 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
$SF_HF
- contr sd contr/sd av_SF av_HF cum
-Agrsto 4.7380081 0.031272715 0.006600393 4.6666667 1.4 8.350879
-Alogen 4.6433015 0.032896891 0.007084806 4.3333333 1.6 16.534834
-Lolper 4.1985660 0.027006718 0.006432367 3.0000000 4.0 23.934930
-Plalan 3.9197607 0.033208288 0.008472019 0.0000000 3.0 30.843624
-Rumace 3.8992342 0.027368676 0.007018988 0.3333333 3.2 37.716139
-Elyrep 3.1876647 0.029550307 0.009270206 2.0000000 2.0 43.334492
-Poatri 2.8466256 0.021521731 0.007560436 4.6666667 4.8 48.351753
-Brarut 2.5260809 0.021044097 0.008330729 2.0000000 2.8 52.804045
-Elepal 2.4974367 0.038876909 0.015566724 1.3333333 0.8 57.205850
-Poapra 2.3932257 0.019179734 0.008014177 2.5000000 3.4 61.423981
-Antodo 2.3408728 0.021430212 0.009154796 0.0000000 1.8 65.549838
-Sagpro 2.3143518 0.020478964 0.008848682 1.8333333 0.8 69.628951
-Tripra 2.3079782 0.023431610 0.010152440 0.0000000 1.8 73.696831
-Junart 2.2849877 0.025676555 0.011237065 0.5000000 1.6 77.724189
-Trirep 2.2382699 0.019486710 0.008706148 1.3333333 2.8 81.669205
-Junbuf 2.1642678 0.022237444 0.010274812 1.1666667 1.2 85.483791
-Leoaut 2.0509314 0.016422027 0.008007107 1.3333333 2.8 89.098618
-Achmil 1.5183100 0.011393329 0.007503955 0.1666667 1.2 91.774684
-Brohor 1.3375437 0.014503626 0.010843479 0.5000000 0.8 94.132144
-Ranfla 1.0660700 0.013386946 0.012557287 0.6666667 0.4 96.011124
-Belper 0.9990990 0.012570517 0.012581853 0.6666667 0.4 97.772065
-Calcus 0.6623417 0.015076322 0.022762152 0.5000000 0.0 98.939462
-Cirarv 0.3809333 0.008669044 0.022757383 0.3333333 0.0 99.610868
-Chealb 0.2207806 0.005025441 0.022762152 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
+ 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
$SF_NM
- contr sd contr/sd av_SF av_NM cum
-Poatri 7.8284148 0.040947182 0.005230584 4.6666667 0.0000000 10.13601
-Alogen 7.1219425 0.046958337 0.006593473 4.3333333 0.0000000 19.35731
-Agrsto 5.6508187 0.044176062 0.007817639 4.6666667 2.1666667 26.67383
-Lolper 5.4851012 0.059913861 0.010923018 3.0000000 0.3333333 33.77578
-Elepal 4.8027074 0.047168454 0.009821222 1.3333333 2.1666667 39.99419
-Poapra 4.0724386 0.031790183 0.007806179 2.5000000 0.6666667 45.26707
-Brarut 4.0008412 0.034397513 0.008597570 2.0000000 2.8333333 50.44725
-Elyrep 3.5598394 0.038515239 0.010819375 2.0000000 0.0000000 55.05643
-Leoaut 3.2474710 0.034813104 0.010720066 1.3333333 3.1666667 59.26117
-Trirep 3.0429642 0.031634061 0.010395804 1.3333333 1.8333333 63.20111
-Sagpro 3.0303946 0.030476566 0.010056963 1.8333333 0.5000000 67.12478
-Salrep 2.9275366 0.032014215 0.010935547 0.0000000 1.8333333 70.91528
-Antodo 2.4541140 0.036694444 0.014952216 0.0000000 1.3333333 74.09279
-Calcus 2.2762575 0.029443338 0.012934977 0.5000000 1.1666667 77.04003
-Ranfla 2.2566173 0.022818681 0.010111897 0.6666667 1.3333333 79.96183
-Junart 2.2542858 0.028597560 0.012685863 0.5000000 1.1666667 82.88062
-Hyprad 2.0108243 0.031290623 0.015561092 0.0000000 1.1666667 85.48418
-Junbuf 1.9859538 0.029033704 0.014619526 1.1666667 0.0000000 88.05554
-Plalan 1.5420359 0.022769128 0.014765628 0.0000000 0.8333333 90.05212
-Airpra 1.4883128 0.021880904 0.014701818 0.0000000 0.8333333 91.97915
-Belper 1.2317474 0.015920540 0.012925167 0.6666667 0.3333333 93.57398
-Potpal 1.1882720 0.017406896 0.014648916 0.0000000 0.6666667 95.11252
-Achmil 0.9293657 0.014931384 0.016066209 0.1666667 0.3333333 96.31584
-Brohor 0.7172498 0.016333288 0.022772104 0.5000000 0.0000000 97.24451
-Rumace 0.5590144 0.012750682 0.022809219 0.3333333 0.0000000 97.96831
-Empnig 0.5225116 0.012000618 0.022967182 0.0000000 0.3333333 98.64484
-Cirarv 0.4781666 0.010888859 0.022772104 0.3333333 0.0000000 99.26396
-Chealb 0.2893083 0.006601805 0.022819268 0.1666667 0.0000000 99.63855
-Viclat 0.2791635 0.006424596 0.023013743 0.0000000 0.1666667 100.00000
-Tripra 0.0000000 0.000000000 NaN 0.0000000 0.0000000 100.00000
+ 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
$HF_NM
- contr sd contr/sd av_HF av_NM cum
-Poatri 7.1552962 0.013680801 0.001911982 4.8 0.0000000 9.913221
-Lolper 5.4533212 0.029624608 0.005432397 4.0 0.3333333 17.468460
-Rumace 4.6546497 0.030806132 0.006618357 3.2 0.0000000 23.917190
-Poapra 4.1749543 0.018851704 0.004515427 3.4 0.6666667 29.701331
-Plalan 4.1632907 0.029559966 0.007100145 3.0 0.8333333 35.469313
-Brarut 3.5340259 0.020103791 0.005688637 2.8 2.8333333 40.365488
-Elepal 3.2043023 0.032314877 0.010084840 0.8 2.1666667 44.804851
-Agrsto 3.1915495 0.028887302 0.009051184 1.4 2.1666667 49.226546
-Trirep 3.0372486 0.022871293 0.007530267 2.8 1.8333333 53.434466
-Elyrep 2.9811469 0.038675842 0.012973478 2.0 0.0000000 57.564661
-Antodo 2.8717143 0.024799203 0.008635679 1.8 1.3333333 61.543243
-Junart 2.7414119 0.028536540 0.010409432 1.6 1.1666667 65.341300
-Tripra 2.5843049 0.025971573 0.010049732 1.8 0.0000000 68.921695
-Salrep 2.5340091 0.027291287 0.010770004 0.0 1.8333333 72.432408
-Alogen 2.4459371 0.032399067 0.013246075 1.6 0.0000000 75.821103
-Leoaut 2.0703325 0.014124614 0.006822389 2.8 3.1666667 78.689420
-Ranfla 1.9284693 0.019938840 0.010339205 0.4 1.3333333 81.361196
-Junbuf 1.8180949 0.024648229 0.013557174 1.2 0.0000000 83.880054
-Hyprad 1.7141357 0.026547931 0.015487648 0.0 1.1666667 86.254883
-Calcus 1.6832709 0.024900688 0.014793037 0.0 1.1666667 88.586951
-Achmil 1.6555393 0.014899781 0.008999956 1.2 0.3333333 90.880598
-Sagpro 1.5282469 0.016534777 0.010819441 0.8 0.5000000 92.997890
-Airpra 1.2605398 0.018242589 0.014472046 0.0 0.8333333 94.744290
-Brohor 1.2093682 0.015168791 0.012542740 0.8 0.0000000 96.419795
-Potpal 1.0105496 0.014556161 0.014404201 0.0 0.6666667 97.819849
-Belper 0.8801475 0.013732352 0.015602330 0.4 0.3333333 99.039239
-Empnig 0.4535959 0.010325282 0.022763173 0.0 0.3333333 99.667668
-Viclat 0.2398752 0.005460872 0.022765475 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
+ 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
+> summary(sim)
+$BF_SF
+ contr sd contr/sd av_BF av_SF cum
+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
+Trirep 4.6297215 0.025525394 181.37708 4.6666667 1.3333333 33.367870
+Poatri 4.6020231 0.033801137 136.14995 3.6666667 4.6666667 40.734444
+Leoaut 4.3697453 0.024922188 175.33554 4.3333333 1.3333333 47.729205
+Brohor 3.3677364 0.025859567 130.23174 2.6666667 0.5000000 53.120026
+Achmil 3.0151964 0.020820614 144.81785 2.3333333 0.1666667 57.946526
+Plalan 2.8585347 0.021548975 132.65293 2.0000000 0.0000000 62.522255
+Elyrep 2.8074412 0.029777588 94.28034 1.3333333 2.0000000 67.016196
+Brarut 2.5500549 0.023901903 106.68837 2.0000000 2.0000000 71.098133
+Poapra 2.5128826 0.023967065 104.84732 4.0000000 2.5000000 75.120568
+Sagpro 2.4325600 0.022148544 109.82934 0.6666667 1.8333333 79.014428
+Belper 1.9858984 0.017087515 116.21926 1.6666667 0.6666667 82.193305
+Elepal 1.8611486 0.042957616 43.32523 0.0000000 1.3333333 85.172493
+Antodo 1.7542572 0.025803830 67.98437 1.3333333 0.0000000 87.980576
+Junbuf 1.6031063 0.023707975 67.61886 0.0000000 1.1666667 90.546709
+Viclat 1.4671255 0.013306461 110.25663 1.0000000 0.0000000 92.895173
+Hyprad 1.0285612 0.015197764 67.67845 0.6666667 0.0000000 94.541617
+Ranfla 0.9305743 0.013595007 68.44971 0.0000000 0.6666667 96.031211
+Junart 0.6979307 0.016109106 43.32523 0.0000000 0.5000000 97.148406
+Calcus 0.6979307 0.016109106 43.32523 0.0000000 0.5000000 98.265601
+Rumace 0.4525878 0.010444461 43.33280 0.0000000 0.3333333 98.990070
+Cirarv 0.3982767 0.009184791 43.36263 0.0000000 0.3333333 99.627602
+Chealb 0.2326436 0.005369702 43.32523 0.0000000 0.1666667 100.000000
+Empnig 0.0000000 0.000000000 NaN 0.0000000 0.0000000 100.000000
+Airpra 0.0000000 0.000000000 NaN 0.0000000 0.0000000 100.000000
+Potpal 0.0000000 0.000000000 NaN 0.0000000 0.0000000 100.000000
+Tripra 0.0000000 0.000000000 NaN 0.0000000 0.0000000 100.000000
+Salrep 0.0000000 0.000000000 NaN 0.0000000 0.0000000 100.000000
+
+$BF_HF
+ contr sd contr/sd av_BF av_HF cum
+Rumace 3.8666202 0.02605967 148.37562 0.0000000 3.2 8.163219
+Poatri 3.3301297 0.02579295 129.11008 3.6666667 4.8 15.193797
+Plalan 3.1851684 0.01830432 174.01181 2.0000000 3.0 21.918333
+Brohor 2.8651195 0.01799001 159.26170 2.6666667 0.8 27.967181
+Lolper 2.8431092 0.02215330 128.33796 6.0000000 4.0 33.969561
+Elyrep 2.7821948 0.02958641 94.03624 1.3333333 2.0 39.843338
+Trirep 2.5837719 0.01655977 156.02708 4.6666667 2.8 45.298204
+Antodo 2.3582034 0.02042340 115.46577 1.3333333 1.8 50.276849
+Achmil 2.3426457 0.01474036 158.92727 2.3333333 1.2 55.222648
+Brarut 2.2732759 0.01801781 126.16829 2.0000000 2.8 60.021994
+Alogen 2.1610138 0.02308107 93.62711 0.6666667 1.6 64.584333
+Tripra 2.1514461 0.02207334 97.46810 0.0000000 1.8 69.126471
+Junart 2.0084049 0.02555374 78.59534 0.0000000 1.6 73.366621
+Leoaut 1.9318258 0.01356486 142.41397 4.3333333 2.8 77.445097
+Belper 1.8289995 0.01486414 123.04777 1.6666667 0.4 81.306485
+Agrsto 1.7605184 0.02284119 77.07646 0.0000000 1.4 85.023296
+Junbuf 1.4999755 0.02066084 72.59994 0.0000000 1.2 88.190049
+Viclat 1.2848484 0.01139618 112.74378 1.0000000 0.0 90.902624
+Sagpro 1.1684667 0.01297192 90.07661 0.6666667 0.8 93.369494
+Elepal 1.0168588 0.02110771 48.17475 0.0000000 0.8 95.516289
+Hyprad 0.8949950 0.01311558 68.23909 0.6666667 0.0 97.405805
+Poapra 0.7203468 0.01009842 71.33262 4.0000000 3.4 98.926603
+Ranfla 0.5084294 0.01055386 48.17475 0.0000000 0.4 100.000000
+Empnig 0.0000000 0.00000000 NaN 0.0000000 0.0 100.000000
+Airpra 0.0000000 0.00000000 NaN 0.0000000 0.0 100.000000
+Cirarv 0.0000000 0.00000000 NaN 0.0000000 0.0 100.000000
+Potpal 0.0000000 0.00000000 NaN 0.0000000 0.0 100.000000
+Calcus 0.0000000 0.00000000 NaN 0.0000000 0.0 100.000000
+Salrep 0.0000000 0.00000000 NaN 0.0000000 0.0 100.000000
+Chealb 0.0000000 0.00000000 NaN 0.0000000 0.0 100.000000
+
+$BF_NM
+ contr sd contr/sd av_BF av_NM cum
+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
+Trirep 5.1287027 0.02755807 186.10529 4.6666667 1.8333333 34.14609
+Brohor 3.9689114 0.02920386 135.90364 2.6666667 0.0000000 39.58520
+Brarut 3.5722867 0.02868949 124.51550 2.0000000 2.8333333 44.48077
+Elepal 3.3759250 0.03572888 94.48730 0.0000000 2.1666667 49.10724
+Agrsto 3.3446318 0.03473296 96.29563 0.0000000 2.1666667 53.69083
+Achmil 3.3189820 0.02337698 141.97651 2.3333333 0.3333333 58.23926
+Leoaut 3.1356499 0.02025675 154.79531 4.3333333 3.1666667 62.53645
+Antodo 2.8059604 0.03294714 85.16553 1.3333333 1.3333333 66.38182
+Plalan 2.7319482 0.02192961 124.57807 2.0000000 0.8333333 70.12577
+Salrep 2.6770230 0.02927399 91.44715 0.0000000 1.8333333 73.79444
+Belper 2.3528522 0.01909409 123.22410 1.6666667 0.3333333 77.01886
+Hyprad 2.1720695 0.02450331 88.64393 0.6666667 1.1666667 79.99553
+Ranfla 2.0313589 0.02275206 89.28243 0.0000000 1.3333333 82.77937
+Elyrep 1.9993334 0.02926048 68.32880 1.3333333 0.0000000 85.51931
+Calcus 1.7832867 0.02680560 66.52664 0.0000000 1.1666667 87.96318
+Junart 1.7694138 0.02599948 68.05575 0.0000000 1.1666667 90.38804
+Viclat 1.5772799 0.01446762 109.02141 1.0000000 0.1666667 92.54959
+Sagpro 1.5432494 0.01857093 83.10028 0.6666667 0.5000000 94.66451
+Airpra 1.3409953 0.01969485 68.08862 0.0000000 0.8333333 96.50225
+Potpal 1.0739109 0.01571113 68.35352 0.0000000 0.6666667 97.97397
+Alogen 0.9996667 0.01463024 68.32880 0.6666667 0.0000000 99.34394
+Empnig 0.4787240 0.01105165 43.31697 0.0000000 0.3333333 100.00000
+Junbuf 0.0000000 0.00000000 NaN 0.0000000 0.0000000 100.00000
+Rumace 0.0000000 0.00000000 NaN 0.0000000 0.0000000 100.00000
+Cirarv 0.0000000 0.00000000 NaN 0.0000000 0.0000000 100.00000
+Tripra 0.0000000 0.00000000 NaN 0.0000000 0.0000000 100.00000
+Chealb 0.0000000 0.00000000 NaN 0.0000000 0.0000000 100.00000
+
+$SF_HF
+ contr sd contr/sd av_SF av_HF cum
+Agrsto 4.7380081 0.031272715 151.50613 4.6666667 1.4 8.350879
+Alogen 4.6433015 0.032896891 141.14712 4.3333333 1.6 16.534834
+Lolper 4.1985660 0.027006718 155.46377 3.0000000 4.0 23.934930
+Plalan 3.9197607 0.033208288 118.03562 0.0000000 3.0 30.843624
+Rumace 3.8992342 0.027368676 142.47069 0.3333333 3.2 37.716139
+Elyrep 3.1876647 0.029550307 107.87247 2.0000000 2.0 43.334492
+Poatri 2.8466256 0.021521731 132.26750 4.6666667 4.8 48.351753
+Brarut 2.5260809 0.021044097 120.03751 2.0000000 2.8 52.804045
+Elepal 2.4974367 0.038876909 64.23959 1.3333333 0.8 57.205850
+Poapra 2.3932257 0.019179734 124.77888 2.5000000 3.4 61.423981
+Antodo 2.3408728 0.021430212 109.23237 0.0000000 1.8 65.549838
+Sagpro 2.3143518 0.020478964 113.01118 1.8333333 0.8 69.628951
+Tripra 2.3079782 0.023431610 98.49849 0.0000000 1.8 73.696831
+Junart 2.2849877 0.025676555 88.99121 0.5000000 1.6 77.724189
+Trirep 2.2382699 0.019486710 114.86135 1.3333333 2.8 81.669205
+Junbuf 2.1642678 0.022237444 97.32538 1.1666667 1.2 85.483791
+Leoaut 2.0509314 0.016422027 124.88905 1.3333333 2.8 89.098618
+Achmil 1.5183100 0.011393329 133.26307 0.1666667 1.2 91.774684
+Brohor 1.3375437 0.014503626 92.22133 0.5000000 0.8 94.132144
+Ranfla 1.0660700 0.013386946 79.63504 0.6666667 0.4 96.011124
+Belper 0.9990990 0.012570517 79.47955 0.6666667 0.4 97.772065
+Calcus 0.6623417 0.015076322 43.93258 0.5000000 0.0 98.939462
+Cirarv 0.3809333 0.008669044 43.94178 0.3333333 0.0 99.610868
+Chealb 0.2207806 0.005025441 43.93258 0.1666667 0.0 100.000000
+Empnig 0.0000000 0.000000000 NaN 0.0000000 0.0 100.000000
+Airpra 0.0000000 0.000000000 NaN 0.0000000 0.0 100.000000
+Viclat 0.0000000 0.000000000 NaN 0.0000000 0.0 100.000000
+Hyprad 0.0000000 0.000000000 NaN 0.0000000 0.0 100.000000
+Potpal 0.0000000 0.000000000 NaN 0.0000000 0.0 100.000000
+Salrep 0.0000000 0.000000000 NaN 0.0000000 0.0 100.000000
+
+$SF_NM
+ contr sd contr/sd av_SF av_NM cum
+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
+Lolper 5.4851012 0.059913861 91.54979 3.0000000 0.3333333 33.77578
+Elepal 4.8027074 0.047168454 101.82033 1.3333333 2.1666667 39.99419
+Poapra 4.0724386 0.031790183 128.10365 2.5000000 0.6666667 45.26707
+Brarut 4.0008412 0.034397513 116.31193 2.0000000 2.8333333 50.44725
+Elyrep 3.5598394 0.038515239 92.42678 2.0000000 0.0000000 55.05643
+Leoaut 3.2474710 0.034813104 93.28301 1.3333333 3.1666667 59.26117
+Trirep 3.0429642 0.031634061 96.19265 1.3333333 1.8333333 63.20111
+Sagpro 3.0303946 0.030476566 99.43360 1.8333333 0.5000000 67.12478
+Salrep 2.9275366 0.032014215 91.44490 0.0000000 1.8333333 70.91528
+Antodo 2.4541140 0.036694444 66.87972 0.0000000 1.3333333 74.09279
+Calcus 2.2762575 0.029443338 77.30976 0.5000000 1.1666667 77.04003
+Ranfla 2.2566173 0.022818681 98.89341 0.6666667 1.3333333 79.96183
+Junart 2.2542858 0.028597560 78.82791 0.5000000 1.1666667 82.88062
+Hyprad 2.0108243 0.031290623 64.26284 0.0000000 1.1666667 85.48418
+Junbuf 1.9859538 0.029033704 68.40167 1.1666667 0.0000000 88.05554
+Plalan 1.5420359 0.022769128 67.72486 0.0000000 0.8333333 90.05212
+Airpra 1.4883128 0.021880904 68.01880 0.0000000 0.8333333 91.97915
+Belper 1.2317474 0.015920540 77.36844 0.6666667 0.3333333 93.57398
+Potpal 1.1882720 0.017406896 68.26444 0.0000000 0.6666667 95.11252
+Achmil 0.9293657 0.014931384 62.24244 0.1666667 0.3333333 96.31584
+Brohor 0.7172498 0.016333288 43.91338 0.5000000 0.0000000 97.24451
+Rumace 0.5590144 0.012750682 43.84192 0.3333333 0.0000000 97.96831
+Empnig 0.5225116 0.012000618 43.54039 0.0000000 0.3333333 98.64484
+Cirarv 0.4781666 0.010888859 43.91338 0.3333333 0.0000000 99.26396
+Chealb 0.2893083 0.006601805 43.82261 0.1666667 0.0000000 99.63855
+Viclat 0.2791635 0.006424596 43.45230 0.0000000 0.1666667 100.00000
+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
+
+attr(,"class")
+[1] "summary.simper"
>
>
>
@@ -7422,7 +7461,7 @@
Formula:
y ~ s(x1, x2, k = knots)
-<environment: 0x10b0e19f0>
+<environment: 0x109e96b50>
Estimated degrees of freedom:
2 total = 3
@@ -7902,7 +7941,7 @@
> ### * <FOOTER>
> ###
> cat("Time elapsed: ", proc.time() - get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed: 84.542 1.578 86.391 0 0
+Time elapsed: 102.327 1.858 104.737 0 0
> grDevices::dev.off()
null device
1
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