wascores: Weighted Averages Scores for Species

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

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wascores(x, w, expand=FALSE)
eigengrad(x, w)

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

monoMDS, cca.

Examples

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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.