+ ![]()
+
+
+
+
+ Add New Points to NMDS ordination
+ +MDSaddpoints.Rd
+
+
+
+ Usage
+MDSaddpoints(nmds, dis, neighbors = 5, maxit = 200)
+
+dist2xy(dist, pick, type = c("xy", "xx"), invert = FALSE)
+
+ Arguments
+- nmds +
Result object from
metaMDSor +monoMDS. The configuration of points is fixed, + but new points are added.
+
+
+- dis +
Rectangular non-symmetric dissimilarity matrix among new + points (rows) and old fixed points (columns). Such matrix can be + extracted from complete dissimilarities of both old and new points + with
dist2xy, or calculated withdesigndist2.
+
+
+- neighbors +
Number of nearest points used to get the starting + locations for new points.
+
+
+- maxit +
Maximum number of iterations.
+
+
+- dist +
Input dissimilarities.
+
+
+- pick +
Indices (integers) of selected observations or a logical + vector that is
TRUEfor picked items. The output will be + in the original order and will not be reordered by this argument.
+
+
+- type +
"xy"returns rectangular data of picked against + not picked observations, and"xx"a subset of symmetric + dissimilarities.
+
+
+- invert +
Invert
pick: drop elements listed.
+
+
+
+ Value
+ + +Function return a list of class "nmds" (there are no other
+objects of that type in vegan) with following elements
- points +
Coordinates of all points, the first being fixed and the + last the new points.
+
+ - newpoints +
Coordinates of added new points; the same as the last + ones in the previous item.
+
+ - stress +
Stress as estimated here (but needs checking).
+
+ - iters +
Number of iterations.
+
+ - cause +
Cause of termination of iterations (numeric).
+
+ - seeds +
Starting coordinates for new points.
+
+
+
+
+
+ Details
+ + +Function provides an interface to monoMDS Fortran code to add new
+points to an existing ordination that will be regarded as fixed. The
+function has a similar role as predict functions with
+newdata in Euclidean ordination (e.g. predict.cca).
+Input data must be a rectangular matrix of distances among new added
+points (rows) and all fixed old points (columns). Such matrices can be
+extracted from complete dissimilarities with helper function
+dist2xy. Function designdist2 can directly
+calculate such rectangular dissimilarity matrices between sampling units
+(rows) in two matries. In addition, analogue has distance
+function that can calculate dissimilarities among two matrices,
+including functions that cannot be specified in
+designdist2.
Great care is needed in preparing the dissimilarities for the +input. The dissimilarity index must be exactly the same as in the +fixed ordination, and columns must match old fixed points, and rows +added new points.
+
+
+
+ Examples
+## Cross-validation: remove a point when performing NMDS and add as
+## a new points
+data(dune)
+d <- vegdist(dune)
+## remove point 3 from ordination
+mod3 <- metaMDS(dist2xy(d, 3, "xx", invert = TRUE), trace=0)
+## add point 3 to the result
+MDSaddpoints(mod3, dist2xy(d, 3))
+#> $nobj
+#> [1] 20
+#>
+#> $nfix
+#> [1] 19
+#>
+#> $ndim
+#> [1] 2
+#>
+#> $ndis
+#> [1] 190
+#>
+#> $ngrp
+#> [1] 1
+#>
+#> $diss
+#> [1] 0.2272727 0.2289157 0.2705882 0.2771084 0.2941176 0.2962963 0.2967033
+#> [8] 0.3170732 0.3186813 0.3220339 0.3250000 0.3414634 0.3414634 0.3437500
+#> [15] 0.3488372 0.3506494 0.3529412 0.3563218 0.3571429 0.3617021 0.3698630
+#> [22] 0.3793103 0.4117647 0.4117647 0.4133333 0.4133333 0.4246575 0.4246575
+#> [29] 0.4285714 0.4390244 0.4400000 0.4400000 0.4444444 0.4482759 0.4500000
+#> [36] 0.4545455 0.4666667 0.4698795 0.4698795 0.4750000 0.4761905 0.4772727
+#> [43] 0.4857143 0.4878049 0.4929577 0.4933333 0.5000000 0.5058824 0.5058824
+#> [50] 0.5111111 0.5128205 0.5238095 0.5250000 0.5250000 0.5277778 0.5365854
+#> [57] 0.5405405 0.5421687 0.5428571 0.5438596 0.5517241 0.5517241 0.5522388
+#> [64] 0.5555556 0.5555556 0.5600000 0.5625000 0.5652174 0.5681818 0.5737705
+#> [71] 0.5844156 0.5882353 0.5909091 0.5942029 0.5945946 0.6000000 0.6000000
+#> [78] 0.6000000 0.6000000 0.6060606 0.6119403 0.6206897 0.6206897 0.6206897
+#> [85] 0.6266667 0.6266667 0.6344086 0.6363636 0.6385542 0.6385542 0.6393443
+#> [92] 0.6417910 0.6438356 0.6491228 0.6533333 0.6551724 0.6615385 0.6666667
+#> [99] 0.6666667 0.6712329 0.6716418 0.6727273 0.6785714 0.6811594 0.6825397
+#> [106] 0.6842105 0.6896552 0.6923077 0.6949153 0.6969697 0.6969697 0.6986301
+#> [113] 0.7021277 0.7027027 0.7027027 0.7142857 0.7142857 0.7179487 0.7187500
+#> [120] 0.7200000 0.7215190 0.7352941 0.7368421 0.7419355 0.7419355 0.7454545
+#> [127] 0.7464789 0.7464789 0.7500000 0.7530864 0.7538462 0.7575758 0.7611940
+#> [134] 0.7619048 0.7631579 0.7746479 0.7777778 0.7777778 0.7808219 0.7878788
+#> [141] 0.7894737 0.7971014 0.8000000 0.8028169 0.8055556 0.8082192 0.8095238
+#> [148] 0.8125000 0.8214286 0.8245614 0.8309859 0.8412698 0.8431373 0.8431373
+#> [155] 0.8481013 0.8484848 0.8484848 0.8518519 0.8545455 0.8666667 0.8750000
+#> [162] 0.8750000 0.8769231 0.8787879 0.8805970 0.8873239 0.8904110 0.8909091
+#> [169] 0.8909091 0.8918919 0.8918919 0.8933333 0.8947368 0.8947368 0.8947368
+#> [176] 0.8947368 0.8974359 0.9000000 0.9062500 0.9076923 0.9130435 0.9200000
+#> [183] 0.9215686 0.9245283 0.9452055 1.0000000 1.0000000 1.0000000 1.0000000
+#> [190] 1.0000000
+#>
+#> $iidx
+#> [1] 6 6 20 9 9 19 5 8 9 17 20 20 20 19 9 11 12 3 15 14 12 8 4 7 12
+#> [26] 10 20 15 14 6 11 20 10 20 10 19 2 20 20 20 8 9 17 8 19 17 4 6 8 5
+#> [51] 12 3 11 7 10 7 10 9 17 15 18 6 17 18 20 10 13 18 20 9 10 15 7 17 10
+#> [76] 9 8 12 8 15 20 14 16 16 10 11 5 5 7 11 4 17 12 13 15 7 14 17 15 20
+#> [101] 11 16 14 17 16 12 19 11 13 19 18 19 16 18 18 11 20 11 19 17 18 14 12 17 19
+#> [126] 14 18 18 20 12 12 13 13 17 19 20 18 17 18 13 18 13 17 14 13 18 19 18 13 16
+#> [151] 20 14 17 12 19 14 14 15 18 17 13 16 15 16 13 19 15 20 16 19 19 15 15 15 16
+#> [176] 16 16 16 18 14 19 16 15 11 19 18 14 19 13 16
+#>
+#> $jidx
+#> [1] 5 4 3 6 2 14 4 7 5 10 7 8 2 15 4 8 11 2 14 13 7 3 2 3 8
+#> [26] 9 12 7 7 2 7 11 6 1 5 13 1 4 9 6 2 3 9 6 7 5 3 3 4 2
+#> [51] 3 1 3 6 7 2 2 7 4 13 17 1 6 10 10 1 7 16 5 1 3 11 5 2 8
+#> [76] 8 5 2 1 12 17 11 9 4 4 6 3 1 4 5 1 7 6 12 8 1 8 3 3 15
+#> [101] 10 6 12 8 5 4 17 4 11 11 11 8 10 9 4 2 14 9 12 14 5 3 9 11 18
+#> [126] 10 6 7 13 5 10 8 9 16 3 19 14 1 8 2 3 3 12 5 5 2 10 12 10 2
+#> [151] 18 6 13 1 5 9 4 5 13 15 6 12 10 1 4 6 6 16 7 9 4 2 9 4 8
+#> [176] 14 13 3 15 2 16 11 1 1 2 1 1 1 1 15
+#>
+#> $xinit
+#> [1] -0.405368146 -0.236708966 -0.058703386 -0.274157895 -0.217031243
+#> [6] -0.232004049 0.134364792 0.036636789 -0.238585114 -0.151580664
+#> [11] 0.188406642 0.177125449 0.423394465 0.394969745 0.475715820
+#> [16] -0.379548925 -0.075451265 -0.022182004 0.460707955 0.005468966
+#> [21] -0.313546164 -0.184459571 -0.241995341 -0.044835263 0.036997524
+#> [26] -0.037019338 -0.081122689 -0.203676519 0.008214549 0.144277770
+#> [31] -0.179685738 -0.269829677 0.194591853 0.082322189 -0.092833780
+#> [36] 0.425357514 0.227403910 0.435343132 0.094495638 -0.194768568
+#>
+#> $istart
+#> [1] 1
+#>
+#> $isform
+#> [1] 1
+#>
+#> $ities
+#> [1] 1
+#>
+#> $iregn
+#> [1] 1
+#>
+#> $iscal
+#> [1] 0
+#>
+#> $maxits
+#> [1] 200
+#>
+#> $sratmx
+#> [1] 0.999999
+#>
+#> $strmin
+#> [1] 1e-04
+#>
+#> $sfgrmn
+#> [1] 1e-07
+#>
+#> $dist
+#> [1] 0.07551610 0.04287231 0.04087889 0.04571012 0.19268325 0.06685585
+#> [7] 0.09980010 0.15674886 0.03595871 0.11271930 0.21621639 0.08014858
+#> [13] 0.19418816 0.18792963 0.06387257 0.15365431 0.09084710 0.18707312
+#> [19] 0.19287183 0.11581210 0.19349109 0.10275252 0.14455923 0.25130725
+#> [25] 0.15528459 0.16150224 0.23023492 0.34155186 0.30761855 0.14751528
+#> [31] 0.11240639 0.23319329 0.19833447 0.37806252 0.12566952 0.10682485
+#> [37] 0.21238942 0.28025982 0.28828423 0.25184723 0.27402042 0.30815974
+#> [43] 0.27323365 0.31613686 0.37059635 0.23727512 0.29204921 0.26841811
+#> [49] 0.34903278 0.22232962 0.23746576 0.35397172 0.25484476 0.36901387
+#> [55] 0.36410187 0.38519378 0.33958072 0.38350068 0.33704375 0.29214897
+#> [61] 0.21465399 0.32637738 0.30729209 0.31853266 0.36470180 0.52346045
+#> [67] 0.39944544 0.35750640 0.29700254 0.36241763 0.39728215 0.30014967
+#> [73] 0.37071763 0.44230710 0.39559828 0.34733978 0.34967337 0.42254820
+#> [79] 0.45545549 0.34710770 0.43262898 0.33364123 0.44031699 0.48185944
+#> [85] 0.22536396 0.44395816 0.32078767 0.39793425 0.41013115 0.45970808
+#> [91] 0.29903458 0.37311049 0.47073092 0.52567650 0.45285374 0.58764982
+#> [97] 0.45847330 0.46969793 0.55484508 0.53100305 0.46962083 0.48534714
+#> [103] 0.41408583 0.44541449 0.42099344 0.50426099 0.55238693 0.48182009
+#> [109] 0.44193098 0.38642390 0.65008314 0.51840427 0.36190517 0.47882056
+#> [115] 0.54227589 0.42514241 0.52370902 0.46650668 0.46168385 0.49228511
+#> [121] 0.44344723 0.55767479 0.50012385 0.48512161 0.59106660 0.55005076
+#> [127] 0.51686709 0.53967012 0.61393121 0.49950218 0.52870851 0.55515691
+#> [133] 0.68771612 0.36285123 0.61888151 0.58597172 0.54647906 0.63361828
+#> [139] 0.64172094 0.76119414 0.67832236 0.65040504 0.55770623 0.61367706
+#> [145] 0.65953094 0.65587896 0.61430905 0.73279748 0.57717234 0.62632270
+#> [151] 0.63974319 0.63823079 0.49992369 0.58413176 0.68017384 0.63787436
+#> [157] 0.68110265 0.70480824 0.50645786 0.63744594 0.69511938 0.89060181
+#> [163] 0.67061372 0.73935464 0.73749891 0.70508589 0.70991737 0.71349023
+#> [169] 0.72154661 0.70459579 0.74795783 0.71829267 0.72141291 0.75140831
+#> [175] 0.75425086 0.84708465 0.83544651 0.74047397 0.72586024 0.68570438
+#> [181] 0.90305105 0.82984990 0.90830772 0.60867653 0.75113672 0.84122934
+#> [187] 0.89288997 0.95738494 0.97213770 1.00000000
+#>
+#> $dhat
+#> [1] 0.05124435 0.05124435 0.05124435 0.05124435 0.11040935 0.11040935
+#> [7] 0.11040935 0.11040935 0.11040935 0.11271930 0.14097953 0.14097953
+#> [13] 0.14097953 0.14097953 0.14097953 0.14097953 0.14097953 0.15609331
+#> [19] 0.15609331 0.15609331 0.15609331 0.15609331 0.15609331 0.18936469
+#> [25] 0.18936469 0.18936469 0.21761828 0.21761828 0.21761828 0.21761828
+#> [31] 0.21761828 0.21761828 0.21761828 0.21761828 0.21761828 0.21761828
+#> [37] 0.21761828 0.27346376 0.27346376 0.27346376 0.27402042 0.28746972
+#> [43] 0.28746972 0.28746972 0.28746972 0.28746972 0.28746972 0.28746972
+#> [49] 0.28746972 0.28746972 0.28746972 0.30440824 0.30440824 0.33067634
+#> [55] 0.33067634 0.33067634 0.33067634 0.33067634 0.33067634 0.33067634
+#> [61] 0.33067634 0.33067634 0.33067634 0.33067634 0.36470180 0.37599774
+#> [67] 0.37599774 0.37599774 0.37599774 0.37599774 0.37599774 0.37599774
+#> [73] 0.37599774 0.38372963 0.38372963 0.38372963 0.38372963 0.38957242
+#> [79] 0.38957242 0.38957242 0.38957242 0.38957242 0.38957242 0.38957242
+#> [85] 0.38957242 0.38957242 0.38957242 0.38957242 0.38957242 0.38957242
+#> [91] 0.38957242 0.38957242 0.47073092 0.48132259 0.48132259 0.48132259
+#> [97] 0.48132259 0.48132259 0.48132259 0.48132259 0.48132259 0.48132259
+#> [103] 0.48132259 0.48132259 0.48132259 0.48132259 0.48132259 0.48132259
+#> [109] 0.48132259 0.48132259 0.48766030 0.48766030 0.48766030 0.48766030
+#> [115] 0.48766030 0.48766030 0.48766030 0.48766030 0.48766030 0.48766030
+#> [121] 0.48766030 0.51430675 0.51430675 0.51430675 0.54455207 0.54455207
+#> [127] 0.54455207 0.54455207 0.54455207 0.54455207 0.54455207 0.54455207
+#> [133] 0.54455207 0.54455207 0.58377743 0.58377743 0.58377743 0.63321676
+#> [139] 0.63321676 0.63321676 0.63321676 0.63321676 0.63321676 0.63321676
+#> [145] 0.63321676 0.63321676 0.63321676 0.63321676 0.63321676 0.63321676
+#> [151] 0.63321676 0.63321676 0.63321676 0.63321676 0.64131048 0.64131048
+#> [157] 0.64131048 0.64131048 0.64131048 0.64131048 0.69511938 0.73169736
+#> [163] 0.73169736 0.73169736 0.73169736 0.73169736 0.73169736 0.73169736
+#> [169] 0.73169736 0.73169736 0.73169736 0.73169736 0.73169736 0.75140831
+#> [175] 0.75425086 0.76691395 0.76691395 0.76691395 0.76691395 0.76691395
+#> [181] 0.80020438 0.80020438 0.80020438 0.80020438 0.80020438 0.84122934
+#> [187] 0.89288997 0.95738494 0.97213770 1.00000000
+#>
+#> $points
+#> [,1] [,2]
+#> [1,] -0.40536815 -0.313546164
+#> [2,] -0.23670897 -0.184459571
+#> [3,] -0.05870339 -0.241995341
+#> [4,] -0.27415789 -0.044835263
+#> [5,] -0.21703124 0.036997524
+#> [6,] -0.23200405 -0.037019338
+#> [7,] 0.13436479 -0.081122689
+#> [8,] 0.03663679 -0.203676519
+#> [9,] -0.23858511 0.008214549
+#> [10,] -0.15158066 0.144277770
+#> [11,] 0.18840664 -0.179685738
+#> [12,] 0.17712545 -0.269829677
+#> [13,] 0.42339446 0.194591853
+#> [14,] 0.39496974 0.082322189
+#> [15,] 0.47571582 -0.092833780
+#> [16,] -0.37954892 0.425357514
+#> [17,] -0.07545126 0.227403910
+#> [18,] -0.02218200 0.435343132
+#> [19,] 0.46070796 0.094495638
+#> [20,] -0.04351094 -0.204044409
+#>
+#> $stress
+#> [1] 0.1191559
+#>
+#> $strs
+#> [1] 0.1191559
+#>
+#> $iters
+#> [1] 16
+#>
+#> $cause
+#> [1] 4
+#>
+#> $newpoints
+#> [,1] [,2]
+#> [1,] -0.04351094 -0.2040444
+#>
+#> $seeds
+#> [,1] [,2]
+#> [1,] 0.005468966 -0.1947686
+#>
+#> attr(,"class")
+#> [1] "nmds"
+## Use designdist2
+d15 <- designdist(dune[1:15,])
+m15 <- metaMDS(d15, trace=0)
+MDSaddpoints(m15, designdist2(dune[1:15,], dune[16:20,]))
+#> $nobj
+#> [1] 20
+#>
+#> $nfix
+#> [1] 15
+#>
+#> $ndim
+#> [1] 2
+#>
+#> $ndis
+#> [1] 180
+#>
+#> $ngrp
+#> [1] 1
+#>
+#> $diss
+#> [1] 0.08333333 0.11111111 0.12000000 0.13043478 0.15384615 0.18181818
+#> [7] 0.20000000 0.20000000 0.20000000 0.20000000 0.21739130 0.21739130
+#> [13] 0.21739130 0.22222222 0.23076923 0.23809524 0.25000000 0.25000000
+#> [19] 0.26315789 0.27272727 0.27272727 0.27272727 0.28000000 0.30000000
+#> [25] 0.30000000 0.30434783 0.33333333 0.33333333 0.33333333 0.33333333
+#> [31] 0.33333333 0.33333333 0.36000000 0.36363636 0.36363636 0.36842105
+#> [37] 0.36842105 0.37500000 0.38461538 0.39130435 0.39130435 0.39130435
+#> [43] 0.39130435 0.40000000 0.40000000 0.40000000 0.40000000 0.40740741
+#> [49] 0.41666667 0.42857143 0.42857143 0.42857143 0.44444444 0.44444444
+#> [55] 0.45454545 0.45454545 0.45454545 0.45454545 0.45454545 0.45454545
+#> [61] 0.45454545 0.46153846 0.46666667 0.46666667 0.47368421 0.47368421
+#> [67] 0.47368421 0.47368421 0.47368421 0.47826087 0.47826087 0.47826087
+#> [73] 0.50000000 0.50000000 0.50000000 0.50000000 0.50000000 0.50000000
+#> [79] 0.50000000 0.52000000 0.52000000 0.52380952 0.52380952 0.52380952
+#> [85] 0.52380952 0.52941176 0.52941176 0.52941176 0.52941176 0.53846154
+#> [91] 0.54545455 0.55555556 0.55555556 0.55555556 0.55555556 0.55555556
+#> [97] 0.55555556 0.55555556 0.55555556 0.55555556 0.56521739 0.56521739
+#> [103] 0.57894737 0.57894737 0.57894737 0.60000000 0.61904762 0.61904762
+#> [109] 0.61904762 0.61904762 0.61904762 0.61904762 0.61904762 0.62500000
+#> [115] 0.63636364 0.63636364 0.63636364 0.63636364 0.64705882 0.64705882
+#> [121] 0.64705882 0.64705882 0.64705882 0.64705882 0.64705882 0.65217391
+#> [127] 0.66666667 0.66666667 0.66666667 0.66666667 0.66666667 0.68421053
+#> [133] 0.68421053 0.68421053 0.68421053 0.70000000 0.70000000 0.70000000
+#> [139] 0.71428571 0.71428571 0.71428571 0.71428571 0.72727273 0.73333333
+#> [145] 0.75000000 0.75000000 0.75000000 0.76470588 0.76470588 0.76470588
+#> [151] 0.76470588 0.77777778 0.77777778 0.77777778 0.78947368 0.78947368
+#> [157] 0.78947368 0.78947368 0.78947368 0.80000000 0.80000000 0.80000000
+#> [163] 0.80000000 0.80000000 0.80952381 0.80952381 0.80952381 0.81818182
+#> [169] 0.81818182 0.84615385 0.85714286 0.85714286 0.86666667 0.87500000
+#> [175] 0.88235294 0.88888889 1.00000000 1.00000000 1.00000000 1.00000000
+#>
+#> $iidx
+#> [1] 7 7 6 4 10 12 9 10 3 15 10 4 9 18 9 18 20 5 13 13 8 10 8 15 16
+#> [26] 13 12 2 20 5 5 11 10 10 12 12 18 16 9 13 18 9 7 18 11 13 20 9 9 6
+#> [51] 6 11 19 17 18 11 11 8 12 11 18 7 16 3 5 17 11 14 18 7 11 8 6 17 12
+#> [76] 13 10 17 6 10 8 17 15 18 16 15 10 14 16 8 18 16 12 15 19 4 7 16 15 9
+#> [101] 12 13 12 11 13 19 12 19 16 15 13 20 19 14 19 19 13 19 20 15 19 14 8 17 18
+#> [126] 19 18 20 13 17 20 18 19 19 15 14 14 15 18 11 20 15 15 13 14 19 18 20 17 14
+#> [151] 17 16 15 14 17 19 16 20 14 17 17 16 14 20 16 20 14 16 20 16 12 17 17 17 16
+#> [176] 20 15 19 14 20
+#>
+#> $jidx
+#> [1] 6 5 5 3 5 9 8 7 2 14 6 2 3 11 4 10 15 2 12 8 3 2 4 8 8
+#> [26] 9 8 1 14 3 4 10 4 3 4 3 3 15 7 4 5 2 2 6 6 3 8 5 6 3
+#> [51] 2 8 11 6 7 7 9 2 7 4 4 4 14 1 1 10 3 8 2 3 5 6 4 7 6
+#> [76] 2 8 11 1 9 7 5 9 8 9 12 1 13 12 5 9 13 11 13 12 1 1 3 3 1
+#> [101] 5 7 2 2 11 6 10 8 4 4 6 9 10 12 9 7 10 4 12 11 15 3 1 2 15
+#> [126] 5 12 13 5 1 3 13 3 13 6 9 4 10 1 1 4 7 5 1 11 14 14 11 3 2
+#> [151] 13 2 2 6 8 2 6 6 10 9 4 10 7 10 7 7 5 5 5 1 1 14 15 12 11
+#> [176] 2 1 1 1 1
+#>
+#> $xinit
+#> [1] -0.431379499 -0.172959102 -0.040336607 -0.017821489 -0.253447574
+#> [6] -0.205202334 -0.218680998 0.143973781 0.052907706 -0.263705403
+#> [11] -0.017157615 0.189777261 0.225280096 0.558393337 0.450358440
+#> [16] 0.283256615 -0.192099439 -0.152999810 -0.024459699 0.321225779
+#> [21] -0.236404729 -0.168632467 -0.112016592 -0.124133678 0.077985334
+#> [26] 0.121879257 0.143016694 0.008071928 0.023413697 0.048729150
+#> [31] 0.298290799 0.139972520 -0.161993480 -0.093752241 0.035573808
+#> [36] 0.019571976 0.137270818 0.094374124 0.137988191 0.009941098
+#>
+#> $istart
+#> [1] 1
+#>
+#> $isform
+#> [1] 1
+#>
+#> $ities
+#> [1] 1
+#>
+#> $iregn
+#> [1] 1
+#>
+#> $iscal
+#> [1] 0
+#>
+#> $maxits
+#> [1] 200
+#>
+#> $sratmx
+#> [1] 0.999999
+#>
+#> $strmin
+#> [1] 1e-04
+#>
+#> $sfgrmn
+#> [1] 1e-07
+#>
+#> $dist
+#> [1] 0.02506922 0.07374139 0.06522484 0.02556862 0.03100238 0.17977551
+#> [7] 0.09234934 0.10448607 0.14420154 0.16851340 0.09366722 0.16139337
+#> [13] 0.16442587 0.09742131 0.16362410 0.30311819 0.19688976 0.25942000
+#> [19] 0.30404591 0.18850188 0.21998084 0.23554397 0.20894026 0.30761650
+#> [25] 0.42521099 0.25315620 0.13962709 0.26715947 0.27063936 0.28551185
+#> [31] 0.31043799 0.35080882 0.30056689 0.27519595 0.33593054 0.34124904
+#> [37] 0.43036911 0.34309032 0.29675798 0.24603200 0.27267841 0.29647520
+#> [43] 0.31498522 0.21110169 0.25784074 0.27027749 0.47558379 0.31117780
+#> [49] 0.27625398 0.28616075 0.29229555 0.33194927 0.24692227 0.35628525
+#> [55] 0.19905133 0.25440464 0.28366630 0.36286485 0.40846960 0.42242500
+#> [61] 0.44659576 0.33423624 0.24901017 0.41034979 0.36124906 0.39231020
+#> [67] 0.41096158 0.42674551 0.48435443 0.31120524 0.32305950 0.36725477
+#> [73] 0.30924739 0.33125310 0.39539379 0.39829453 0.40970151 0.41107961
+#> [79] 0.42370217 0.31762357 0.38694777 0.36968894 0.39763671 0.39844608
+#> [85] 0.50102428 0.28071630 0.33078079 0.34003132 0.50716741 0.40352400
+#> [91] 0.33323799 0.25051276 0.26055080 0.29948805 0.35018835 0.42852656
+#> [97] 0.43497272 0.50877358 0.51241053 0.54958140 0.44753845 0.53863964
+#> [103] 0.47625068 0.49223108 0.52022847 0.50391708 0.46257094 0.47884416
+#> [109] 0.48334119 0.49467052 0.51565381 0.55738897 0.59729200 0.43646887
+#> [115] 0.47202024 0.49849169 0.53245736 0.63165033 0.40101988 0.53627556
+#> [121] 0.54651011 0.59900846 0.62514017 0.62785039 0.62809161 0.56899250
+#> [127] 0.34879111 0.49610845 0.53550912 0.64851795 0.69197726 0.58273174
+#> [133] 0.62612550 0.65420404 0.66121748 0.51888687 0.57701521 0.71418501
+#> [139] 0.63388453 0.67637200 0.67682660 0.67761179 0.70508272 0.66086221
+#> [145] 0.69638828 0.71441953 0.78502651 0.61879345 0.64244303 0.73517579
+#> [151] 0.85773794 0.61825303 0.65591536 0.79345781 0.68731515 0.72736504
+#> [157] 0.76607032 0.79623819 0.83435441 0.60600017 0.66545397 0.77922287
+#> [163] 0.81234479 0.86227284 0.78913366 0.80857239 0.82980688 0.78404922
+#> [169] 0.84828123 0.86389639 0.72628889 1.09442024 0.94109318 0.66055990
+#> [175] 0.75224271 0.83614323 0.92273188 0.92313200 1.00000000 1.10047553
+#>
+#> $dhat
+#> [1] 0.02506922 0.04888431 0.04888431 0.04888431 0.04888431 0.12553697
+#> [7] 0.12553697 0.12553697 0.13546072 0.13546072 0.13546072 0.14108018
+#> [13] 0.14108018 0.14108018 0.16362410 0.23955510 0.23955510 0.23955510
+#> [19] 0.23955510 0.23955510 0.23955510 0.23955510 0.23955510 0.27723494
+#> [25] 0.27723494 0.27723494 0.27723494 0.27723494 0.27723494 0.28551185
+#> [31] 0.30250179 0.30250179 0.30250179 0.30250179 0.30250179 0.30250179
+#> [37] 0.30250179 0.30250179 0.30250179 0.30250179 0.30250179 0.30250179
+#> [43] 0.30250179 0.30250179 0.30250179 0.30250179 0.30250179 0.30250179
+#> [49] 0.30250179 0.30250179 0.30250179 0.30250179 0.30250179 0.30250179
+#> [55] 0.30250179 0.30250179 0.30250179 0.36286485 0.37174227 0.37174227
+#> [61] 0.37174227 0.37174227 0.37174227 0.37174227 0.37174227 0.37174227
+#> [67] 0.37174227 0.37174227 0.37174227 0.37174227 0.37174227 0.37174227
+#> [73] 0.37174227 0.37174227 0.37174227 0.37174227 0.37174227 0.37174227
+#> [79] 0.37174227 0.37174227 0.37174227 0.37174227 0.37174227 0.37174227
+#> [85] 0.37174227 0.37174227 0.37174227 0.37174227 0.37174227 0.37174227
+#> [91] 0.37174227 0.37174227 0.37174227 0.37174227 0.37174227 0.42852656
+#> [97] 0.43497272 0.49761521 0.49761521 0.49761521 0.49761521 0.49761521
+#> [103] 0.49761521 0.49761521 0.49761521 0.49761521 0.49761521 0.49761521
+#> [109] 0.49761521 0.49761521 0.51288593 0.51288593 0.51288593 0.51288593
+#> [115] 0.51288593 0.51288593 0.52170919 0.52170919 0.52170919 0.53627556
+#> [121] 0.54651011 0.55368647 0.55368647 0.55368647 0.55368647 0.55368647
+#> [127] 0.55368647 0.55368647 0.55368647 0.62008451 0.62008451 0.62008451
+#> [133] 0.62008451 0.62008451 0.62008451 0.62008451 0.62008451 0.67403477
+#> [139] 0.67403477 0.67637200 0.67682660 0.67761179 0.68297246 0.68297246
+#> [145] 0.69141416 0.69141416 0.69141416 0.69141416 0.69141416 0.71677053
+#> [151] 0.71677053 0.71677053 0.71677053 0.73453188 0.73453188 0.73453188
+#> [157] 0.73453188 0.73453188 0.73453188 0.73453188 0.73453188 0.77922287
+#> [163] 0.81234479 0.81403769 0.81403769 0.81403769 0.81403769 0.81403769
+#> [169] 0.81403769 0.81403769 0.81403769 0.85689185 0.85689185 0.85689185
+#> [175] 0.85689185 0.85689185 0.92273188 0.92313200 1.00000000 1.10047553
+#>
+#> $points
+#> [,1] [,2]
+#> [1,] -0.43137950 -0.236404729
+#> [2,] -0.17295910 -0.168632467
+#> [3,] -0.04033661 -0.112016592
+#> [4,] -0.01782149 -0.124133678
+#> [5,] -0.25344757 0.077985334
+#> [6,] -0.20520233 0.121879257
+#> [7,] -0.21868100 0.143016694
+#> [8,] 0.14397378 0.008071928
+#> [9,] 0.05290771 0.023413697
+#> [10,] -0.26370540 0.048729150
+#> [11,] -0.01715761 0.298290799
+#> [12,] 0.18977726 0.139972520
+#> [13,] 0.22528010 -0.161993480
+#> [14,] 0.55839334 -0.093752241
+#> [15,] 0.45035844 0.035573808
+#> [16,] 0.42963663 -0.306890168
+#> [17,] -0.41224632 0.411830915
+#> [18,] -0.11359942 0.312070815
+#> [19,] 0.14219218 0.486912773
+#> [20,] 0.58925375 0.175121891
+#>
+#> $stress
+#> [1] 0.11879
+#>
+#> $strs
+#> [1] 0.11879
+#>
+#> $iters
+#> [1] 33
+#>
+#> $cause
+#> [1] 4
+#>
+#> $newpoints
+#> [,1] [,2]
+#> [1,] 0.4296366 -0.3068902
+#> [2,] -0.4122463 0.4118309
+#> [3,] -0.1135994 0.3120708
+#> [4,] 0.1421922 0.4869128
+#> [5,] 0.5892538 0.1751219
+#>
+#> $seeds
+#> [,1] [,2]
+#> [1,] 0.2832566 0.019571976
+#> [2,] -0.1920994 0.137270818
+#> [3,] -0.1529998 0.094374124
+#> [4,] -0.0244597 0.137988191
+#> [5,] 0.3212258 0.009941098
+#>
+#> attr(,"class")
+#> [1] "nmds"
+