wascores: Weighted Averages Scores for Species
In vegan: Community Ecology Package
Description
Usage
Arguments
Details
Value
Author(s)
See Also
Examples
Description
Computes Weighted Averages scores of species for ordination
configuration or for environmental variables.
Usage
1
2
Arguments
x
Environmental variables or ordination scores.
w
Weights: species abundances.
expand
Expand weighted averages so that they have the same
weighted variance as the corresponding environmental variables.
Details
Function wascores computes weighted averages. Weighted averages
‘shrink’: they cannot be more extreme than values used for calculating
the averages. With expand = TRUE, the function ‘dehsrinks’ the
weighted averages by making their biased weighted variance equal to
the biased weighted variance of the corresponding environmental
variable. Function eigengrad returns the inverses of squared
expansion factors or the attribute shrinkage of the
wascores result for each environmental gradient. This is equal
to the constrained eigenvalue of cca when only this one
gradient was used as a constraint, and describes the strength of the
gradient.
Value
Function wascores returns a matrix where species define rows
and ordination axes or environmental variables define columns. If
expand = TRUE, attribute shrinkage has the inverses of
squared expansion factors or cca eigenvalues for the
variable. Function eigengrad returns only the shrinkage
attribute.
Author(s)
Jari Oksanen
See Also
Examples
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
data(varespec)
data(varechem)
vare.dist <- vegdist(wisconsin(varespec))
vare.mds <- monoMDS(vare.dist)
vare.points <- postMDS(vare.mds$points, vare.dist)
vare.wa <- wascores(vare.points, varespec)
plot(scores(vare.points), pch="+", asp=1)
text(vare.wa, rownames(vare.wa), cex=0.8, col="blue")
## Omit rare species (frequency <= 4)
freq <- apply(varespec>0, 2, sum)
plot(scores(vare.points), pch="+", asp=1)
text(vare.wa[freq > 4,], rownames(vare.wa)[freq > 4],cex=0.8,col="blue")
## Works for environmental variables, too.
wascores(varechem, varespec)
## And the strengths of these variables are:
eigengrad(varechem, varespec)
Example output
Loading required package: permute
Loading required package: lattice
This is vegan 2.4-4
N P K Ca Mg S Al
Callvulg 25.12401 41.66188 246.92383 572.3431 99.40828 49.10552 245.15751
Empenigr 21.61371 44.17350 158.92517 580.8403 89.20628 35.75327 107.05670
Rhodtome 22.34553 40.35530 162.31108 643.8819 95.07712 30.84303 28.83159
Vaccmyrt 24.96352 49.80649 189.70177 656.4179 96.75529 34.55190 32.75705
Vaccviti 21.14028 45.86984 162.12372 613.2126 94.30084 37.26975 116.14656
Pinusylv 18.37299 44.24818 163.60195 670.9387 93.52214 37.02238 150.45523
Descflex 22.24089 54.74804 212.20357 771.0159 114.15179 38.00000 24.64143
Betupube 21.51034 28.86552 112.28276 513.5586 75.15172 23.55172 33.12414
Vacculig 28.00729 33.48758 114.90230 372.9653 70.89954 29.32378 202.89008
Diphcomp 22.34228 39.71049 127.44259 446.1565 80.16173 32.32963 122.31574
Dicrsp 21.33007 60.03758 185.04563 828.0544 148.67509 46.75427 90.42294
Dicrfusc 23.45681 39.14575 162.91954 578.2309 77.81648 33.48086 60.66890
Dicrpoly 20.65446 43.87409 150.51485 665.5845 115.22112 36.17079 90.16733
Hylosple 26.10599 67.88980 245.78681 779.6520 111.96685 42.27433 24.92738
Pleuschr 22.60476 54.22534 199.96241 712.6278 109.23425 40.01132 70.43900
Polypili 23.17377 43.75902 144.82623 724.9738 85.42623 30.58525 145.73115
Polyjuni 22.89480 47.98022 154.81906 643.3864 87.27819 33.63863 53.24888
Polycomm 21.73521 41.17042 154.91549 631.8704 101.84789 32.17324 46.80986
Pohlnuta 19.99885 48.59198 169.68855 678.3813 104.31641 39.94427 132.05458
Ptilcili 21.27880 33.44211 127.08522 564.5652 85.96417 27.11720 56.60692
Barbhatc 21.17461 27.93323 113.13542 497.9138 77.50564 23.72288 42.09749
Cladarbu 23.56127 38.04952 142.03073 454.9019 74.00779 33.81002 173.12698
Cladrang 24.28421 38.60534 135.31177 463.2750 70.54209 32.53349 183.79979
Cladstel 19.28049 46.71060 158.00576 540.4904 80.19153 40.29106 225.89526
Cladunci 21.41240 45.49844 163.40402 621.9100 98.35538 40.00734 119.59481
Cladcocc 21.72473 42.80681 156.32330 557.9007 80.95448 36.25161 149.82616
Cladcorn 22.11640 47.06656 160.36881 623.5185 95.17781 36.75273 104.71463
Cladgrac 22.51887 44.06576 156.50214 583.1558 94.10292 36.93930 134.13424
Cladfimb 21.77980 41.82652 153.29444 512.4646 78.28232 35.62323 128.96061
Cladcris 20.88795 44.12262 171.04016 574.5672 92.52169 38.24003 116.03507
Cladchlo 19.51207 45.39655 150.93190 571.0233 95.77586 39.50862 156.81983
Cladbotr 22.97660 38.89574 167.20000 590.8021 99.57234 34.79362 87.75957
Cladamau 25.07143 35.84286 105.07857 395.2214 68.18571 27.11429 95.91429
Cladsp 19.21923 47.37308 168.49231 526.7654 79.54423 45.15385 215.33846
Cetreric 21.00944 47.76972 165.07972 579.6322 99.14944 42.25472 163.46000
Cetrisla 18.36552 42.73695 151.78374 626.2813 89.77833 35.33498 132.68227
Flavniva 18.56110 61.18194 207.67705 502.9203 60.91755 50.22532 396.82405
Nepharct 23.33099 49.10019 146.84715 618.1601 64.27319 29.95760 31.72300
Stersp 28.19743 32.84800 94.33459 389.5143 53.25377 24.22175 95.39326
Peltapht 21.08553 54.45395 193.38816 886.5487 119.35132 37.92500 106.16447
Icmaeric 28.88636 27.00000 87.86818 307.0500 40.48182 22.17273 89.94091
Cladcerv 20.25000 56.79000 192.36000 519.2300 62.10000 45.18000 314.92000
Claddefo 22.19198 45.22981 167.73069 583.7983 92.01320 38.51369 100.46139
Cladphyl 15.73750 54.56875 180.39375 775.4500 99.65625 43.35000 208.55000
Fe Mn Zn Mo Baresoil Humdepth pH
Callvulg 75.457843 52.38247 8.281074 0.4734635 27.241036 2.187819 2.845108
Empenigr 38.146102 53.49357 7.159938 0.3289657 27.324317 2.367439 2.888078
Rhodtome 5.560906 70.48260 7.444100 0.2251490 37.325030 2.689154 2.895352
Vaccmyrt 5.589213 75.17221 7.838533 0.2666732 31.404171 2.798935 2.855216
Vaccviti 37.586067 51.81515 7.617213 0.3680289 26.307701 2.307879 2.923128
Pinusylv 39.121898 35.22311 7.733333 0.3485401 17.762968 1.996350 3.049148
Descflex 6.066429 110.87232 9.526607 0.2316071 22.740179 2.834821 2.822857
Betupube 5.417241 37.53448 5.637931 0.2068966 51.496552 2.527586 2.979310
Vacculig 93.963929 37.73062 4.593824 0.3780552 21.410710 2.041196 3.006965
Diphcomp 73.281173 46.88025 4.593827 0.3725309 31.836574 2.103704 2.856790
Dicrsp 22.504617 65.35020 13.060765 0.5610370 23.182889 2.232247 2.954272
Dicrfusc 13.922252 61.40958 6.922859 0.3218816 26.918674 2.484399 2.806431
Dicrpoly 20.973927 33.28779 9.110561 0.3892739 37.304043 2.228713 3.015842
Hylosple 4.729157 115.14606 9.885976 0.2851996 20.956264 2.925000 2.807594
Pleuschr 19.113811 77.12277 9.007860 0.3405945 24.584979 2.596881 2.858446
Polypili 51.993443 36.74754 8.045902 0.2204918 17.368852 1.493443 3.227869
Polyjuni 12.885704 82.56274 7.945126 0.2760289 28.116303 2.615523 2.874729
Polycomm 7.895775 68.22535 7.843662 0.2591549 38.687324 2.926761 2.860563
Pohlnuta 33.089313 42.02290 8.452290 0.3935115 24.709351 2.147328 2.985496
Ptilcili 14.036188 33.93547 5.906924 0.2303712 48.941884 2.502498 2.973376
Barbhatc 8.199687 31.11379 5.550784 0.2084639 54.331975 2.514734 2.986834
Cladarbu 65.470394 38.28429 6.387500 0.4464046 22.592997 2.048540 2.937879
Cladrang 76.612752 34.86010 6.616452 0.3903501 17.270158 1.799128 3.022346
Cladstel 84.639467 33.27903 7.287216 0.4054879 9.854042 1.851973 3.052167
Cladunci 27.463504 40.10322 9.108102 0.5120114 28.312376 2.362687 2.858564
Cladcocc 46.653763 43.53584 7.269176 0.3698925 19.972222 2.025090 2.974194
Cladcorn 32.916238 53.38441 7.518489 0.3639871 26.620868 2.399518 2.890997
Cladgrac 45.758366 44.63911 7.702724 0.4244163 25.546654 2.230350 2.933658
Cladfimb 41.710354 47.83687 6.815152 0.3887626 24.763889 2.239394 2.902778
Cladcris 34.729585 44.75984 6.933735 0.3746988 29.711352 2.400000 2.841633
Cladchlo 42.089655 35.13276 7.908621 0.3814655 22.319655 2.075000 3.022414
Cladbotr 23.374468 46.54255 7.263830 0.3106383 45.725532 2.580851 2.904255
Cladamau 68.971429 41.98571 4.928571 0.3214286 27.592857 1.857143 2.914286
Cladsp 47.913462 49.61923 8.421154 0.6173077 16.864423 2.213462 2.921154
Cetreric 42.614167 36.96694 9.516389 0.5687500 21.452639 2.058056 2.923889
Cetrisla 29.617734 33.24138 7.518227 0.3192118 26.417980 2.027586 3.065025
Flavniva 94.339916 37.03232 9.116371 0.9987764 19.692312 1.799241 2.923629
Nepharct 12.910837 115.15684 7.743536 0.2180608 23.135932 2.541065 2.918251
Stersp 30.226998 31.97061 7.635502 0.2828767 15.844007 1.477740 3.038756
Peltapht 37.598684 56.64079 7.652632 0.2046053 28.321053 2.286842 3.026316
Icmaeric 24.236364 23.95909 6.618182 0.2863636 18.727273 1.568182 2.968182
Cladcerv 111.090000 52.04000 8.530000 0.6800000 15.393000 1.870000 2.900000
Claddefo 25.116325 48.81105 7.599609 0.4096285 33.814545 2.468133 2.823656
Cladphyl 50.475000 35.28125 8.568750 0.2812500 7.728125 1.575000 3.231250
N P K Ca Mg S Al
0.13000842 0.18880078 0.16246365 0.15722067 0.16359171 0.13391967 0.29817406
Fe Mn Zn Mo Baresoil Humdepth pH
0.20766831 0.27254480 0.16783834 0.09542514 0.20931501 0.25051326 0.14583161
vegan documentation built on May 2, 2019, 5:51 p.m.
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Description Usage Arguments Details Value Author(s) See Also Examples
Description
Computes Weighted Averages scores of species for ordination configuration or for environmental variables.
Usage
1 2 |
Arguments
x |
Environmental variables or ordination scores. |
w |
Weights: species abundances. |
expand |
Expand weighted averages so that they have the same weighted variance as the corresponding environmental variables. |
Details
Function wascores computes weighted averages. Weighted averages
‘shrink’: they cannot be more extreme than values used for calculating
the averages. With expand = TRUE, the function ‘dehsrinks’ the
weighted averages by making their biased weighted variance equal to
the biased weighted variance of the corresponding environmental
variable. Function eigengrad returns the inverses of squared
expansion factors or the attribute shrinkage of the
wascores result for each environmental gradient. This is equal
to the constrained eigenvalue of cca when only this one
gradient was used as a constraint, and describes the strength of the
gradient.
Value
Function wascores returns a matrix where species define rows
and ordination axes or environmental variables define columns. If
expand = TRUE, attribute shrinkage has the inverses of
squared expansion factors or cca eigenvalues for the
variable. Function eigengrad returns only the shrinkage
attribute.
Author(s)
Jari Oksanen
See Also
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | data(varespec)
data(varechem)
vare.dist <- vegdist(wisconsin(varespec))
vare.mds <- monoMDS(vare.dist)
vare.points <- postMDS(vare.mds$points, vare.dist)
vare.wa <- wascores(vare.points, varespec)
plot(scores(vare.points), pch="+", asp=1)
text(vare.wa, rownames(vare.wa), cex=0.8, col="blue")
## Omit rare species (frequency <= 4)
freq <- apply(varespec>0, 2, sum)
plot(scores(vare.points), pch="+", asp=1)
text(vare.wa[freq > 4,], rownames(vare.wa)[freq > 4],cex=0.8,col="blue")
## Works for environmental variables, too.
wascores(varechem, varespec)
## And the strengths of these variables are:
eigengrad(varechem, varespec)
|
Example output
Loading required package: permute
Loading required package: lattice
This is vegan 2.4-4
N P K Ca Mg S Al
Callvulg 25.12401 41.66188 246.92383 572.3431 99.40828 49.10552 245.15751
Empenigr 21.61371 44.17350 158.92517 580.8403 89.20628 35.75327 107.05670
Rhodtome 22.34553 40.35530 162.31108 643.8819 95.07712 30.84303 28.83159
Vaccmyrt 24.96352 49.80649 189.70177 656.4179 96.75529 34.55190 32.75705
Vaccviti 21.14028 45.86984 162.12372 613.2126 94.30084 37.26975 116.14656
Pinusylv 18.37299 44.24818 163.60195 670.9387 93.52214 37.02238 150.45523
Descflex 22.24089 54.74804 212.20357 771.0159 114.15179 38.00000 24.64143
Betupube 21.51034 28.86552 112.28276 513.5586 75.15172 23.55172 33.12414
Vacculig 28.00729 33.48758 114.90230 372.9653 70.89954 29.32378 202.89008
Diphcomp 22.34228 39.71049 127.44259 446.1565 80.16173 32.32963 122.31574
Dicrsp 21.33007 60.03758 185.04563 828.0544 148.67509 46.75427 90.42294
Dicrfusc 23.45681 39.14575 162.91954 578.2309 77.81648 33.48086 60.66890
Dicrpoly 20.65446 43.87409 150.51485 665.5845 115.22112 36.17079 90.16733
Hylosple 26.10599 67.88980 245.78681 779.6520 111.96685 42.27433 24.92738
Pleuschr 22.60476 54.22534 199.96241 712.6278 109.23425 40.01132 70.43900
Polypili 23.17377 43.75902 144.82623 724.9738 85.42623 30.58525 145.73115
Polyjuni 22.89480 47.98022 154.81906 643.3864 87.27819 33.63863 53.24888
Polycomm 21.73521 41.17042 154.91549 631.8704 101.84789 32.17324 46.80986
Pohlnuta 19.99885 48.59198 169.68855 678.3813 104.31641 39.94427 132.05458
Ptilcili 21.27880 33.44211 127.08522 564.5652 85.96417 27.11720 56.60692
Barbhatc 21.17461 27.93323 113.13542 497.9138 77.50564 23.72288 42.09749
Cladarbu 23.56127 38.04952 142.03073 454.9019 74.00779 33.81002 173.12698
Cladrang 24.28421 38.60534 135.31177 463.2750 70.54209 32.53349 183.79979
Cladstel 19.28049 46.71060 158.00576 540.4904 80.19153 40.29106 225.89526
Cladunci 21.41240 45.49844 163.40402 621.9100 98.35538 40.00734 119.59481
Cladcocc 21.72473 42.80681 156.32330 557.9007 80.95448 36.25161 149.82616
Cladcorn 22.11640 47.06656 160.36881 623.5185 95.17781 36.75273 104.71463
Cladgrac 22.51887 44.06576 156.50214 583.1558 94.10292 36.93930 134.13424
Cladfimb 21.77980 41.82652 153.29444 512.4646 78.28232 35.62323 128.96061
Cladcris 20.88795 44.12262 171.04016 574.5672 92.52169 38.24003 116.03507
Cladchlo 19.51207 45.39655 150.93190 571.0233 95.77586 39.50862 156.81983
Cladbotr 22.97660 38.89574 167.20000 590.8021 99.57234 34.79362 87.75957
Cladamau 25.07143 35.84286 105.07857 395.2214 68.18571 27.11429 95.91429
Cladsp 19.21923 47.37308 168.49231 526.7654 79.54423 45.15385 215.33846
Cetreric 21.00944 47.76972 165.07972 579.6322 99.14944 42.25472 163.46000
Cetrisla 18.36552 42.73695 151.78374 626.2813 89.77833 35.33498 132.68227
Flavniva 18.56110 61.18194 207.67705 502.9203 60.91755 50.22532 396.82405
Nepharct 23.33099 49.10019 146.84715 618.1601 64.27319 29.95760 31.72300
Stersp 28.19743 32.84800 94.33459 389.5143 53.25377 24.22175 95.39326
Peltapht 21.08553 54.45395 193.38816 886.5487 119.35132 37.92500 106.16447
Icmaeric 28.88636 27.00000 87.86818 307.0500 40.48182 22.17273 89.94091
Cladcerv 20.25000 56.79000 192.36000 519.2300 62.10000 45.18000 314.92000
Claddefo 22.19198 45.22981 167.73069 583.7983 92.01320 38.51369 100.46139
Cladphyl 15.73750 54.56875 180.39375 775.4500 99.65625 43.35000 208.55000
Fe Mn Zn Mo Baresoil Humdepth pH
Callvulg 75.457843 52.38247 8.281074 0.4734635 27.241036 2.187819 2.845108
Empenigr 38.146102 53.49357 7.159938 0.3289657 27.324317 2.367439 2.888078
Rhodtome 5.560906 70.48260 7.444100 0.2251490 37.325030 2.689154 2.895352
Vaccmyrt 5.589213 75.17221 7.838533 0.2666732 31.404171 2.798935 2.855216
Vaccviti 37.586067 51.81515 7.617213 0.3680289 26.307701 2.307879 2.923128
Pinusylv 39.121898 35.22311 7.733333 0.3485401 17.762968 1.996350 3.049148
Descflex 6.066429 110.87232 9.526607 0.2316071 22.740179 2.834821 2.822857
Betupube 5.417241 37.53448 5.637931 0.2068966 51.496552 2.527586 2.979310
Vacculig 93.963929 37.73062 4.593824 0.3780552 21.410710 2.041196 3.006965
Diphcomp 73.281173 46.88025 4.593827 0.3725309 31.836574 2.103704 2.856790
Dicrsp 22.504617 65.35020 13.060765 0.5610370 23.182889 2.232247 2.954272
Dicrfusc 13.922252 61.40958 6.922859 0.3218816 26.918674 2.484399 2.806431
Dicrpoly 20.973927 33.28779 9.110561 0.3892739 37.304043 2.228713 3.015842
Hylosple 4.729157 115.14606 9.885976 0.2851996 20.956264 2.925000 2.807594
Pleuschr 19.113811 77.12277 9.007860 0.3405945 24.584979 2.596881 2.858446
Polypili 51.993443 36.74754 8.045902 0.2204918 17.368852 1.493443 3.227869
Polyjuni 12.885704 82.56274 7.945126 0.2760289 28.116303 2.615523 2.874729
Polycomm 7.895775 68.22535 7.843662 0.2591549 38.687324 2.926761 2.860563
Pohlnuta 33.089313 42.02290 8.452290 0.3935115 24.709351 2.147328 2.985496
Ptilcili 14.036188 33.93547 5.906924 0.2303712 48.941884 2.502498 2.973376
Barbhatc 8.199687 31.11379 5.550784 0.2084639 54.331975 2.514734 2.986834
Cladarbu 65.470394 38.28429 6.387500 0.4464046 22.592997 2.048540 2.937879
Cladrang 76.612752 34.86010 6.616452 0.3903501 17.270158 1.799128 3.022346
Cladstel 84.639467 33.27903 7.287216 0.4054879 9.854042 1.851973 3.052167
Cladunci 27.463504 40.10322 9.108102 0.5120114 28.312376 2.362687 2.858564
Cladcocc 46.653763 43.53584 7.269176 0.3698925 19.972222 2.025090 2.974194
Cladcorn 32.916238 53.38441 7.518489 0.3639871 26.620868 2.399518 2.890997
Cladgrac 45.758366 44.63911 7.702724 0.4244163 25.546654 2.230350 2.933658
Cladfimb 41.710354 47.83687 6.815152 0.3887626 24.763889 2.239394 2.902778
Cladcris 34.729585 44.75984 6.933735 0.3746988 29.711352 2.400000 2.841633
Cladchlo 42.089655 35.13276 7.908621 0.3814655 22.319655 2.075000 3.022414
Cladbotr 23.374468 46.54255 7.263830 0.3106383 45.725532 2.580851 2.904255
Cladamau 68.971429 41.98571 4.928571 0.3214286 27.592857 1.857143 2.914286
Cladsp 47.913462 49.61923 8.421154 0.6173077 16.864423 2.213462 2.921154
Cetreric 42.614167 36.96694 9.516389 0.5687500 21.452639 2.058056 2.923889
Cetrisla 29.617734 33.24138 7.518227 0.3192118 26.417980 2.027586 3.065025
Flavniva 94.339916 37.03232 9.116371 0.9987764 19.692312 1.799241 2.923629
Nepharct 12.910837 115.15684 7.743536 0.2180608 23.135932 2.541065 2.918251
Stersp 30.226998 31.97061 7.635502 0.2828767 15.844007 1.477740 3.038756
Peltapht 37.598684 56.64079 7.652632 0.2046053 28.321053 2.286842 3.026316
Icmaeric 24.236364 23.95909 6.618182 0.2863636 18.727273 1.568182 2.968182
Cladcerv 111.090000 52.04000 8.530000 0.6800000 15.393000 1.870000 2.900000
Claddefo 25.116325 48.81105 7.599609 0.4096285 33.814545 2.468133 2.823656
Cladphyl 50.475000 35.28125 8.568750 0.2812500 7.728125 1.575000 3.231250
N P K Ca Mg S Al
0.13000842 0.18880078 0.16246365 0.15722067 0.16359171 0.13391967 0.29817406
Fe Mn Zn Mo Baresoil Humdepth pH
0.20766831 0.27254480 0.16783834 0.09542514 0.20931501 0.25051326 0.14583161
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