R help - Mar 2011 - 3 dimensional MDS plots

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. 
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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")

Hi Calla,

On Thu, Mar 10, 2011 at 3:38 PM, Calla Carbone <6cc4 at queensu.ca>
wrote:
> 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?
>
Assuming you are using metaMDS from the vegan package (it's important
to specify what package
you are using if your function is not in base R), the default option
is to use 2 dimensions. Since you
don't specify k, you only get 2 dimensions.

For NMDS, unlike most other ordination methods, you  need to choose
the number of dimensions
*first*.

mdsg.mds<- metaMDS(mdsg, k=3)

Sarah
> 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")
>
>
-- 
Sarah Goslee
http://www.functionaldiversity.org