Hi, I am trying to create 3 mds plots: one with axis 1 vs axis 2, one with axis 2 vs axis 3, and one with axis 1 vs axis 3. When inputting my code, I only end up with one diagram and when inputting mdsg.mds$dims, the program returns 2 for 2 dimensions. How can I create the other two plots?
Any help would be greatly appreciated, Calla Carbone The table I use is number of each taxa on each surface and is attached.
Below is a copy of my work: >mdsg=read.csv(file.choose(), header=TRUE, row.names=1, sep=",") > mdsg.mds<- metaMDS(sp.rich) Error in metaMDS(sp.rich) : object 'sp.rich' not found > mdsg.mds<- metaMDS(mdsg) Square root transformation Wisconsin double standardization Run 0 stress 10.62813 Run 1 stress 14.73774 Run 2 stress 11.19939 Run 3 stress 10.61520 ... New best solution ... procrustes: rmse 0.005646588 max resid 0.009332332 Run 4 stress 10.61520 ... New best solution ... procrustes: rmse 0.0001009763 max resid 0.0001754211 *** Solution reached > mdsg.mds.ALT<- metaMDS(mdsg, distance="euclidean", k=3, trymax=50, > autotransform=FALSE) Run 0 stress 3.020817 Run 1 stress 0.00673153 ... New best solution ... procrustes: rmse 0.09349157 max resid 0.2443702 Run 2 stress 0.008861757 ... procrustes: rmse 0.08275172 max resid 0.1932439 Run 3 stress 0.006908548 ... procrustes: rmse 0.0447681 max resid 0.1093436 Run 4 stress 0.007621072 ... procrustes: rmse 0.05445531 max resid 0.1437309 Run 5 stress 0.005675308 ... New best solution ... procrustes: rmse 0.1021018 max resid 0.2694876 Run 6 stress 0.008473566 ... procrustes: rmse 0.1411485 max resid 0.3583789 Run 7 stress 0.008235768 ... procrustes: rmse 0.05178896 max resid 0.1487678 Run 8 stress 0.009192125 ... procrustes: rmse 0.1135218 max resid 0.3126878 Run 9 stress 0.00984179 ... procrustes: rmse 0.1117180 max resid 0.3110542 Run 10 stress 0.00942402 ... procrustes: rmse 0.08053243 max resid 0.2261970 Run 11 stress 0.008956116 ... procrustes: rmse 0.06461741 max resid 0.1729917 Run 12 stress 0.00871519 ... procrustes: rmse 0.08382491 max resid 0.2297745 Run 13 stress 0.006883284 ... procrustes: rmse 0.05259355 max resid 0.1339228 Run 14 stress 0.007745699 ... procrustes: rmse 0.1032920 max resid 0.2410554 Run 15 stress 0.009062592 ... procrustes: rmse 0.07324642 max resid 0.2127011 Run 16 stress 0.006311344 ... procrustes: rmse 0.1242246 max resid 0.3201084 Run 17 stress 0.00679012 ... procrustes: rmse 0.05894517 max resid 0.1699838 Run 18 stress 0.00892886 ... procrustes: rmse 0.0886889 max resid 0.2505874 Run 19 stress 0.007831356 ... procrustes: rmse 0.04815574 max resid 0.1443481 Run 20 stress 0.008307666 ... procrustes: rmse 0.08109922 max resid 0.2286835 Run 21 stress 0.009738125 ... procrustes: rmse 0.04494221 max resid 0.0853707 Run 22 stress 0.006648893 ... procrustes: rmse 0.0714659 max resid 0.180198 Run 23 stress 0.008319666 ... procrustes: rmse 0.1326991 max resid 0.3451491 Run 24 stress 0.007369039 ... procrustes: rmse 0.1406218 max resid 0.3560638 Run 25 stress 0.006693668 ... procrustes: rmse 0.06047182 max resid 0.1445884 Run 26 stress 0.007021456 ... procrustes: rmse 0.06223025 max resid 0.1552082 Run 27 stress 0.008450277 ... procrustes: rmse 0.06290812 max resid 0.1474387 Run 28 stress 0.007949867 ... procrustes: rmse 0.06185912 max resid 0.1779437 Run 29 stress 0.007607591 ... procrustes: rmse 0.0791691 max resid 0.2204299 Run 30 stress 0.007450255 ... procrustes: rmse 0.1027691 max resid 0.2798933 Run 31 stress 0.006476469 ... procrustes: rmse 0.02180973 max resid 0.04587615 Run 32 stress 0.008423953 ... procrustes: rmse 0.05009894 max resid 0.1326238 Run 33 stress 0.009818617 ... procrustes: rmse 0.1293366 max resid 0.3352202 Run 34 stress 0.009782313 ... procrustes: rmse 0.02056321 max resid 0.04534656 Run 35 stress 0.007691246 ... procrustes: rmse 0.06954554 max resid 0.1907627 Run 36 stress 0.009071507 ... procrustes: rmse 0.03511019 max resid 0.08272775 Run 37 stress 0.00867032 ... procrustes: rmse 0.03915756 max resid 0.08640346 Run 38 stress 0.008109802 ... procrustes: rmse 0.04896411 max resid 0.09568495 Run 39 stress 0.0065526 ... procrustes: rmse 0.07546078 max resid 0.1902766 Run 40 stress 0.007617851 ... procrustes: rmse 0.02149247 max resid 0.0493953 Run 41 stress 0.007433552 ... procrustes: rmse 0.03954261 max resid 0.07601604 Run 42 stress 0.008697543 ... procrustes: rmse 0.1110775 max resid 0.2855709 Run 43 stress 0.006243913 ... procrustes: rmse 0.0806811 max resid 0.2283781 Run 44 stress 0.008474417 ... procrustes: rmse 0.1519882 max resid 0.3552259 Run 45 stress 0.0083211 ... procrustes: rmse 0.0727077 max resid 0.1767035 Run 46 stress 0.008051925 ... procrustes: rmse 0.06954848 max resid 0.172751 Run 47 stress 0.009271762 ... procrustes: rmse 0.09332512 max resid 0.2182002 Run 48 stress 0.009197149 ... procrustes: rmse 0.104169 max resid 0.2856122 Run 49 stress 0.00656145 ... procrustes: rmse 0.04243012 max resid 0.1266379 Run 50 stress 0.006636944 ... procrustes: rmse 0.09853805 max resid 0.2584870 > names(mdsg.mds) [1] "points" "dims" "stress" "data" "distance" "converged" [7] "tries" "species" "call" > mdsg.mds$points [,1] [,2] Disc -0.75970137 0.82615812 Johns 1.09698866 -0.42726075 LBW -0.69603453 -0.21063881 Spbay -0.11433730 -0.03734453 BC 0.80952315 0.09556815 D 0.50518560 -0.24053747 E 0.22159986 0.04797842 G -0.40841770 -0.27384498 LMP 0.23686884 1.23858885 PC -0.87625155 -0.64825212 SH -0.01542367 -0.37041488 attr(,"centre") [1] TRUE attr(,"pc") [1] TRUE attr(,"halfchange") [1] TRUE > mdsg.mds$dims [1] 2 > mdsg.mds$stress [1] 10.61520 > mdsg.mds$data [1] "wisconsin(sqrt(mdsg))" > mdsg.mds$distance [1] "bray" > mdsg.mds$converged [1] TRUE > mdsg.mds$tries [1] 4 > mdsg.mds$species [,1] [,2] Charnia -0.64803962 -0.25570377 Charniodiscus -0.29435409 0.05427335 Ivesheadia -0.31324619 -0.33485080 Thectardis -0.90038964 -0.63829244 Tree.Frond -0.52192114 -0.15500003 Fractofusus 0.77371091 -0.11631453 Bradgatia -0.04960810 -0.21083582 Pectinifrons 0.04014456 -0.32244681 Aspidella -0.45120914 0.39904260 Hapsidophylla 0.50383940 -0.17459408 Heimalora -0.10441330 0.62593841 Ostrich.Feather 0.28843372 1.46582729 Feather.Duster 0.01804479 -0.02227495 Tulip.Frond 0.66742592 0.73062070 Trepassia 0.28843372 1.46582729 Beothukis 0.73931198 -0.08363615 Primocandelabrum -0.92508363 0.97772972 Hadryniscala -0.92508363 0.97772972 Blackbrookia 1.33579627 -0.50564841 Frondophyllas 0.28843372 1.46582729 Parviscopa -0.92508363 0.97772972 attr(,"shrinkage") [1] 0.6744097 0.7139844 attr(,"centre") [1] 1.788934e-18 -3.794708e-19 attr(,"old.wa") [1] FALSE > mdsg.mds$call metaMDS(comm = mdsg) > mds1.mds Call: metaMDS(comm = mds1) Nonmetric Multidimensional Scaling using isoMDS (MASS package) Data: wisconsin(sqrt(mds1)) Distance: bray Dimensions: 2 Stress: 9.804838 Two convergent solutions found after 3 tries Scaling: centring, PC rotation, halfchange scaling Species: expanded scores based on ‘wisconsin(sqrt(mds1))’ > variableScores<- mds1.mds$species > sampleScores<- mds1.mds$points > plot(mds1.mds) > plot(mds1.mds, type="n") > text(mds1.mds, display=c("sites"), choices=c(1,2), col="blue", cex=0.7) > points(mds1.mds, display=c("species"), choices=c(1,2), pch=3, col="red")
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