JSS Journal of Statistical Software

April 2022, Volume 102, Issue 10. doi: 10.18637/jss.v102.i10

More on Multidimensional Scaling and Unfolding

in R: smacof Version 2

Patrick Mair Patrick J. F. Groenen Jan de Leeuw

Harvard University Erasmus University University of California,
Rotterdam Los Angeles

Abstract
The smacof package offers a comprehensive implementation of multidimensional scal-
ing (MDS) techniques in R. Since its first publication (De Leeuw and Mair 2009b) the
functionality of the package has been enhanced, and several additional methods, features
and utilities were added. Major updates include a complete re-implementation of mul-
tidimensional unfolding allowing for monotone dissimilarity transformations, including
row-conditional, circular, and external unfolding. Additionally, the constrained MDS im-
plementation was extended in terms of optimal scaling of the external variables. Further
package additions include various tools and functions for goodness-of-fit assessment, uni-
dimensional scaling, gravity MDS, asymmetric MDS, Procrustes, and MDS biplots. All
these new package functionalities are illustrated using a variety of real-life applications.

Keywords: multidimensional scaling, constrained multidimensional scaling, multidimensional

unfolding, SMACOF, R.

1. Introduction
Multidimensional scaling (MDS; Torgerson 1952; Kruskal 1964; Borg and Groenen 2005)
is a technique that represents proximities among objects as distances among points in a
low-dimensional space. Multidimensional unfolding (Coombs 1964; Busing, Groenen, and
Heiser 2005; Borg and Groenen 2005) is a related technique that represents input preference
data as distances (among individuals and objects) in a low-dimensional space. Nowadays,
MDS as well as unfolding problems are typically solved through numeric optimization. The
state-of-the-art approach is called SMACOF (Stress Majorization of a Complicated Function;
De Leeuw 1977)1 and provides the user with a great amount of flexibility for specifying

1
Originally, the “C” in SMACOF stood for “convex” which was later changed to “complicated” as the stress
function is not convex.
2 smacof Version 2: Multidimensional Scaling and Unfolding in R

Purpose Function names

Goodness-of-fit icExplore, randomstress, permtest
Stability jackmds, bootmds, confEllipse
Constrained MDS smacofConstraint (arguments type, constraint.type)
Unfolding unfolding (arguments type, conditionality, circle,
fixed, fixed.coord), vmu
MDS variants uniscale, gravity, driftVectors, Procrustes
Plots biplotmds
Utilities sim2diss, stress0

Table 1: Overview of newly implemented smacof functions (and key arguments), grouped by
their purpose.

MDS and unfolding variants. Since the first publication of the smacof package in R by De
Leeuw and Mair (2009b), several additional MDS and unfolding approaches as well as various
extensions and utility functions have been implemented, as presented in this article. We keep
our elaborations fairly applied since the core technical details were already provided in the
original publication.
The first part of this paper gives the reader the key ingredients of MDS, with a special focus
on newly implemented dissimilarity transformation functions. This is followed by a section
on MDS goodness-of-fit assessment, including various ways of assessing the stability of a
solution, and a section on MDS biplots. The incorporation of optimal scaling on the external
variables, as presented in a subsequent section, makes MDS an attractive tool for confirmatory
research. What follows next is a detailed presentation of the recently implemented unfolding
function, which adds great amounts of flexibility in model specification as compared to the
original implementation. Finally, several smaller additions such as Procrustes transformation,
asymmetric MDS, gravity MDS, and unidimensional scaling are presented. Table 1 gives an
overview of these developments. Related R packages are mentioned in the respective sections.

2. SMACOF in a nutshell
MDS takes a symmetric dissimilarity matrix ∆ of dimension n×n with non-negative elements
δij as input. These dissimilarities can be either directly observed (e.g., in an experimental
setting a participant has to rate similarities between pairs of stimuli) or derived (e.g., by ap-
plying a proximity measure on a multivariate data frame). If the data are collected or derived
as similarities sij , the sim2diss function supports users to convert them into dissimilarities
δij . Corresponding conversion formulas are given in Table 2. Additional technical details on
various conversions can be found in Shepard (1957), Gower and Legendre (1986), Ramsay
(1997), Esposito, Malerba, Tamma, and Bock (2000), Fleiss, Levin, and Paik (2003), Heiser
and Busing (2004), and Keshavarzi, Dehghan, and Mashinchi (2009). The resulting matrix
∆ can then be passed to the respective MDS functions.
SMACOF uses majorization (see De Leeuw and Mair 2009b, for details) to solve Kruskal’s
stress target function (Kruskal 1964)

σ 2 (D̂, X) = wij (dˆij − dij (X))2 → min! (1)

X

i<j
 Journal of Statistical Software 3

Method (argument) Conversion formula

Correlation ("corr") δij = 1 − rij
p

Reverse ("reverse") δij = min(sij ) + max(sij ) − sij

Reciprocal ("reciprocal") δij = 1/sij
Membership ("membership") δij = 1 − sij
Rank orders ("ranks") δij = rank(−sij )
Exponential ("exp") δij = q
− log(sij / max(sij ))
Gaussian ("Gaussian") δij = − log(sij / max(sij ))
Transition frequencies ("transition") δij = 1/ fij
p
 P −1
fij f
i,j ij
Co-occurrences ("cooccurrence") δij = 1 + P
f
P
f
sP i ij j ij
P
fij f
j ij
Gravity ("gravity") δij = i P
fij fij
i,j

Confusion proportions ("confusion") δij = 1 −qpij

Probabilities ("probability") δij = 1/ arcsin(pij )
Integer value z δij = z − sij

Table 2: Conversions of similarities into dissimilarities: similarities sij , correlations rij , fre-
quencies fij , proportions/probabilities pij .

with i<j wij dˆ2ij = n(n − 1)/2 as constraint. Let us explain the components involved in this
P

expression (i.e., wij , dˆij , dij (X)) in more detail.

We begin with wij which denotes a non-negative a priori weight for δij . By default, wij = 1.
If a δij is missing, all functions in smacof set the corresponding wij = 0 such that these entries
are blanked out from optimization. Solving the stress function results in an n × p matrix X of
point coordinates located in a p-dimensional space (p fixed a priori) with Euclidean distances
v
u p
dij (X) = t (xis − xjs )2 .
uX

s=1

The dˆij ’s are the disparities (also called d-hats), collected in the n × n matrix D̂. Disparities
are optimally scaled dissimilarities. That is, a transformation admissible on the assumed scale
level (“measurement levels as functions”; see, e.g., Jacoby 1999) is applied. The first smacof
package incarnation offered only two specification options: metric or non-metric. The new
package version implements the following bundle of transformation functions (ordered from
most restrictive to least restrictive):

• Ratio MDS: dˆij = bδij .

• Interval MDS: dˆij = a + bδij .

• Monotone spline MDS: dˆij = f (δij ) where f is an I-spline (integrated spline) transfor-
mation (Ramsay 1988) with fixed number of knots and spline degree.

• Ordinal MDS: dˆij = f (δij ) where f is a monotone step function. Approaches for tie
handling (i.e., in case of δij = δi′ j ′ ) are the following:
4 smacof Version 2: Multidimensional Scaling and Unfolding in R

– Primary approach (“break ties”): does not require that dˆij = dˆi′ j ′ .
– Secondary approach (“keep ties tied”): requires that dˆij = dˆi′ j ′ .
– Tertiary approach: requires that the means of the tie blocks are in the correct
order.

Since dissimilarities are non-negative, these monotone transformations impose non-negativity

on the disparities as well.
In order to make stress scale-free, it needs to be normalized either implicitly or explicitly.
SMACOF uses an explicit normalization using the constraint i<j wij dˆ2ij = n(n − 1)/2. This
P

results in the normalized stress expression

wij (dˆij − dij (X))2

P
i<j
σn (D̂, X) =
wij dˆ2
P
i<j ij
wij (dˆij − dij (X))2
P
i<j
= . (2)
n(n − 1)/2

Kruskal (1964) proposed an implicit stress normalization called “stress-1”:

v
u i<j wij (dˆij − dij (X))2
uP
σ1 (D̂, X) = t . (3)
2 wij dij (X)
P
i<j

In the MDS literature, many experiments and other MDS software in mainstream statistical
packages have been using stress-1. Fortunately, there exists a simple relation between σn and
σ1 , as shown in detail in Borg and Groenen (2005, Chapter 11). They prove that at a local
minimum X∗ q
σ1 (D̂, X∗ ) = σn (D̂, X∗ ). (4)
Therefore, without loss of generality, we report stress-1 in all MDS functions implemented in
smacof2 .
To illustrate MDS with different types of transformation functions we use a simple dataset
from Guttman (1965). The data consist of an 8 × 8 matrix containing correlations of eight
items in an intelligence test. First, we need to convert these similarities into dissimilarities, as
all smacof functions operate on dissimilarities. Second, we fit four MDS versions and report
the corresponding stress values.

R> library("smacof")
R> idiss <- sim2diss(intelligence[,paste0("T", 1:8)])
R> fitrat <- mds(idiss)
R> fitint <- mds(idiss, type = "interval")
R> fitord <- mds(idiss, type = "ordinal")
R> fitspl <- mds(idiss, type = "mspline")
R> round(c(fitrat$stress, fitint$stress, fitord$stress, fitspl$stress), 3)

[1] 0.227 0.080 0.015 0.070

2
From now on, whenever we say “stress”, we refer to “stress-1”.
 Journal of Statistical Software 5

Ratio MDS Interval MDS

0.0 0.2 0.4 0.6 0.8 1.0 1.2 1.4

0.0 0.2 0.4 0.6 0.8 1.0 1.2 1.4

Configuration Distances

Configuration Distances
0.6 0.7 0.8 0.9 0.6 0.7 0.8 0.9

Dissimilarities Dissimilarities

Ordinal MDS Spline MDS

1.5
1.5
Configuration Distances

Configuration Distances

1.0
1.0

0.5
0.5
0.0

0.0

0.6 0.7 0.8 0.9 0.6 0.7 0.8 0.9

Dissimilarities Dissimilarities

Figure 1: Shepard diagrams for four different dissimilarity transformations.

The variability in the stress values across the different transformations is due to the differing
amounts of flexibility provided by each of the transformations. Figure 1 shows the Shepard
diagrams involving four different transformation functions. These diagrams plot the observed
dissimilarities δij against the fitted distances dij (X), and map the disparities dˆij into the
point cloud (De Leeuw and Mair 2015).

The option to apply various dissimilarity transformations is one of the advantages of the
SMACOF framework compared to classical scaling (Torgerson 1952) as implemented in stats’
cmdscale. In smacof, these transformation functions are now also available for all kinds of
three-way MDS models (indscal and idioscal functions), as well as for confirmatory MDS
and unfolding, as described further below.
6 smacof Version 2: Multidimensional Scaling and Unfolding in R

3. Tools for goodness-of-fit assessment

Mair, Borg, and Rusch (2016) give an extensive treatment of how to assess goodness-of-fit in
MDS. Here we present some recently implemented utility functions that support users with
this task.

3.1. Configuration starting values

Optimizing the stress function in Equation 1 through majorization leads to local minima
problems since the stress surface is generally bumpy. By default, smacof uses a classical
scaling solution to support the algorithm with a reasonable starting configuration. This is
not necessarily the best choice because it does not always lead to the lowest stress value. A
common heuristic strategy is to try out several random starting configurations, and pick the
fit with the lowest stress value.
To illustrate this approach, we use one of the classical MDS textbook datasets from Wish
(1971), containing similarity ratings for 12 countries, for which we fit a ratio MDS. The first
line converts the input similarities into dissimilarities by subtracting each sij from 7 (cf. last
row in Table 2).

R> WishD <- sim2diss(wish, method = 7)

R> fitWish <- mds(WishD)

This leads to a stress value of 0.2185. Now we fit 100 additional ratio MDS models based on
different random starts, and report the lowest stress value.

R> set.seed(123)
R> stressvec <- rep(NA, 100)
R> fitbest <- mds(WishD, init = "random")
R> stressvec[1] <- fitbest$stress
R> for(i in 2:100) {
+ fitran <- mds(WishD, init = "random")
+ stressvec[i] <- fitran$stress
+ if (fitran$stress < fitbest$stress) fitbest <- fitran
+ }
R> round(fitbest$stress, 4)

[1] 0.2178

This solution leads to a slightly lower stress value than the one obtained with a classical
scaling start. From a purely statistical point of view the user would normally decide to go
with this solution. However, from a more substantive perspective, interpretability plays an
important role. For instance, there might be a solution with a reasonably low stress value
(but not the lowest) which leads to better interpretability. This issue is studied in detail in
Borg and Mair (2017) who propose the following strategy (p. 21–22):

1. Run an MDS analysis with a set of different initial configurations (e.g., using many
random configurations).
 Journal of Statistical Software 7

2. Save all resulting MDS solutions and their stress values.

3. Use Procrustean fitting (see Section 7.4) to eliminate all meaningless differences (i.e.,
differences not driven by the data) among the MDS solutions.

4. Compute the similarity of each pair of MDS configurations.

5. Analyze the similarity structure of the MDS configurations with two-dimensional MDS
(to visualize the similarity structure) or cluster analysis (to identify types of MDS
configurations).

6. For each type of MDS configuration with a reasonably low stress value, plot one proto-
typical MDS solution and check its interpretability.

7. Pick the MDS solution that is acceptable in terms of stress value and gives the best
interpretation.

These steps to explore initial configurations are implemented in the icExplore function.
Again, we fit 100 ratio MDS models with random starts and save all fitted MDS objects
(returnfit argument).

R> set.seed(123)
R> icWish <- icExplore(WishD, nrep = 100, returnfit = TRUE)
R> plot(icWish, main = "IC Plot Wish")

Figure 2 shows the configuration plot of the 100 MDS solutions based on random starts
(cf. Step 5).3 The larger the size of the label, the larger the stress value and, therefore, the
worse the fit of the solution. Based on this plot the user can extract various solutions that fit
satisfactorily, plot the configurations, and interpret the solutions.

3.2. Stress norms and permutation tests

Regarding stress-1 values (on a percentage scale), Kruskal (1964, p. 3) says that “our expe-
rience with experimental and synthetic data suggests the following verbal evaluation: 20%
poor, 10% fair, 5% good, 2.5% excellent, 0% perfect”. In subsequent years, these rules of
thumb have been applied in a somewhat mechanical manner. This is problematic for various
reasons (see Mair et al. 2016; Borg, Groenen, and Mair 2018); one of which is that the stress
value depends on n, as is obvious in Equation 1: the larger n, the larger the stress value4 .
This issue was recognized in the early days of MDS. Throughout the 1970s various researchers
have studied this phenomenon by means of Monte Carlo simulations within the context of
ordinal MDS (see Spence and Young 1978, for an overview). These studies lead to the concept
of stress norms. The idea is to create random dissimilarities (e.g., by drawing from a uniform
U (0, 1) distribution) for a given n and p. For each random draw an MDS solution is fitted.
Subsequently, the average stress value and the standard deviation can be computed.
A corresponding implementation is provided by the function randomstress which allows
users to not only derive ordinal MDS norms, but also to obtain stress norms for other types
3
Despite setting random seeds some of the figures in this paper may have swapped labels or axis orientations
compared to results obtained on other systems.
4
In modern MDS applications researchers often have to scale a large number of objects.
8 smacof Version 2: Multidimensional Scaling and Unfolding in R

IC Plot Wish

22 27

1.5
46
1.0

80 91
12 8364
94 65 81
Dimension 2

0.5

66 60
77 39 18 58
9875 26
34 1659 535095
38 7 17 31 44 87
76 55 96 69 33 32 43 84
79
0.0

72 35 11 4071
70 47 24 28
89 61 25 23 455159
100
73 29 6 1021 57
86 48 52 74 36 1418 1954
56 4 41 97 90 63 42 3049 82
93 13 2 37 85 67 62 68
−0.5

92
78 20 315
8899
−1.5 −1.0 −0.5 0.0 0.5

Dimension 1

Figure 2: Similarity structure of 100 MDS solutions. Each label corresponds to an MDS
solution. The size of the labels (and their color shading) is proportional to the stress value.

of MDS from Section 2. As an example, we use a dataset from Lawler (1967) who studied
the performance of managers. There are three traits (T1 = quality of output, T2 = ability to
generate output, T3 = demonstrated effort to perform), and three methods (M1 = rating by
superior, M2 = peer rating, M3 = self-rating). We start the stress norm analysis by fitting a
2D ratio MDS model:

R> LawlerD <- sim2diss(Lawler, to.dist = TRUE)

R> fitLaw <- mds(LawlerD)

This leads to a stress value of 0.241. Let us explore the random stress values for this example
(n = 9, p = 2; 500 replications):

R> set.seed(123)
R> rstress <- randomstress(n = 9, ndim = 2, nrep = 500, type = "ratio")

This function call returns a vector of 500 stress values. Let x̄r denote the average random
stress value and σr the standard deviation. The default in the random stress literature (see,
e.g., Spence and Ogilvie 1973) is to use x̄r − 2σr as upper bound: if the observed stress value
is smaller than this cutoff, the stress can be considered as “significant”.

R> bound <- mean(rstress) - 2 * sd(rstress)

R> round(bound, 3)

[1] 0.22
 Journal of Statistical Software 9

In our example the stress value of 0.241 from the original MDS fit is above this cutoff. This
suggests a “non-significant” result which implies that the 2D ratio MDS solution does not fit
satisfactorily.
There are several issues associated with such random stress norms. First, as Spence and
Ogilvie (1973) point out, the dispersion of the random stress norms is in general very small.
In most practical applications the strategy applied above leads to “significant” results; our
example is somewhat of a rare exception. Second, apart from n and p, other circumstances
such as the error in the data, missing values, as well as ties affect the stress (Mair et al. 2016;
Borg and Groenen 2005). Third, the benchmark is based on completely random configura-
tions. Real-life data almost always have some sort of structure in it such that the random
stress strategy leads to “significant” results in most cases.
Instead of generating random dissimilarities, permutation tests can be used, as formalized in
Mair et al. (2016). They lead to “sharper” tests than random null configurations. There are
two scenarios for setting up a permutation scheme. First, in the case of directly observed
dissimilarities the elements in ∆ can be permuted. For each permutation sample an MDS
model of choice is fitted. By doing this many times it results in a null distribution of stress
values. Second, for derived dissimilarities, Mair et al. (2016) propose a strategy for systematic
column-wise permutations (one variable at a time). This permutation scheme gives a more
informative null distribution compared to full column-wise permutations. For each permuta-
tion sample a dissimilarity matrix is computed, and an MDS fitted. Again, this gives a stress
distribution under the H0 of little departure from complete exchangeability of dissimilarities
in the data-generating process.
Let us illustrate both permutation scenarios. For directly observed dissimilarities we continue
with the Lawler example from above (500 permutations):

R> set.seed(123)
R> permLaw <- permtest(fitLaw, nrep = 500, verbose = FALSE)
R> permLaw

Call: permtest.smacof(object = fitLaw, nrep = 500, verbose = FALSE)

SMACOF Permutation Test

Number of objects: 9
Number of replications (permutations): 500

Observed stress value: 0.241

p-value: 0.294

We cannot reject the H0 of “stress/configuration are obtained from a random permutation

of dissimilarities”. For the derived dissimilarity situation we use a dataset from McNally,
Robinaugh, Wu, Wang, Deserno, and Borsboom (2015) which is included in the MPsychoR
package (Mair 2020). It includes 17 posttraumatic stress disorder (PTSD) symptoms reported
by survivors of the Wenchuan earthquake in 2008, scaled on a 5-point rating scale. We use
the Euclidean distance as (derived) dissimilarity measure and compute an interval MDS. This
leads to the following stress value:
10 smacof Version 2: Multidimensional Scaling and Unfolding in R

ECDF SMACOF Permutation Test Wenchuan Permutation Histogram

1.0

Stress: 0.184

250
0.8

200
0.6

Frequency
Probability

150
0.4

100
0.2

50
p−value: <0.001
0.0

0
0.20 0.22 0.24 0.26 0.28 0.30 0.10 0.15 0.20 0.25 0.30 0.35 0.40

Stress Values Stress Values

Figure 3: Left panel: ECDF of the permuted stress values (dashed gray line at α = 0.05,
solid gray line at the p-value). Right panel: Permutation stress histogram (red dashed line at
critical value, solid black line at observed stress value).

R> library("MPsychoR")
R> data("Wenchuan", package = "MPsychoR")
R> Wdelta <- dist(t(Wenchuan))
R> fitWen <- mds(Wdelta, type = "interval")
R> round(fitWen$stress, 3)

[1] 0.184

In the subsequent permtest call we provide the raw input data through the data argument.
This way the function knows that the permutations should be performed on the raw data
rather than on ∆. We also need to tell the function which dissimilarity measure we used
above before fitting the MDS. We perform 1000 replications.

R> set.seed(123)
R> permWen <- permtest(fitWen, data = Wenchuan, method.dat = "euclidean",
+ nrep = 1000, verbose = FALSE)
R> permWen

Call: permtest.smacof(object = fitWen, data = Wenchuan,

method.dat = "euclidean", nrep = 1000, verbose = FALSE)

SMACOF Permutation Test

Number of objects: 17
Number of replications (permutations): 1000

Observed stress value: 0.184

p-value: <0.001
 Journal of Statistical Software 11

This time we reject H0 . Figure 3, obtained by calling plot(permWen), visualizes the results in
two ways: the left panel shows the empirical cumulative distribution function (ECDF) of the
permutation stress values, whereas the right panel shows the permutation stress histogram
including the critical value (lower 5% quantile) and the observed stress value.
Note that such permutation strategies can be applied to unfolding models (see Section 6) as
well (see Mair et al. 2016, for details).

3.3. Stability of a solution I: Jackknife

De Leeuw and Meulman (1986) developed a jackknife strategy for MDS in order to examine
the stability of a solution. Their approach, implemented in the jackknife function, computes
i = 1, . . . , n additional solutions with configurations X−i (object i being left out). Note that
each X−i has row i missing and has therefore n − 1 rows in total. To make the X−i ’s
comparable, the location of the missing point is estimated by minimizing a least squares
problem, and subsequently transformed using Procrustes (see Section 7.4) with X as target.
Let us denote the resulting configurations by X∗−i , each of them of dimension n × p. From
these configurations the average (centroid) jackknife solution X̄∗ can be computed. Thus, we
have n + 2 comparable configurations in total which can be represented in a single plot, as
shown below.
De Leeuw and Meulman (1986) also introduced various measures related to the jackknife
solution. The first one is a stability measure and is computed as follows:
Pn ∗ ∗ 2
i=1 ∥X−i − X̄ ∥
ST = 1 − Pn ∗ 2 . (5)
i=1 ∥X−i ∥

ST can be interpreted as the ratio of between and total variance. To measure the cross-
validity, that is, comparing the “predicted” configuration of object i as the i-th row in X̄∗
with the actual configuration (i-th row in X),

n∥X − X̄∗ ∥2
CV = 1 − Pn ∗ 2 (6)
i=1 ∥X−i ∥

can be used. Using these two normalized measures the dispersion around the original solution
X can be simply expressed as
DI = 2 − (ST + CV ). (7)

The dataset we use to illustrate the jackknife MDS is from McNally, Mair, Mugno, and
Riemann (2017), included in the MPsychoR package. Below we scale 16 depression symptoms
reported by patients using the Quick Inventory of Depressive Symptomatology (QIDS-SR).
We fit a 2D ordinal MDS on the Euclidean distance input matrix, subject to an MDS jackknife.

R> data("Rogers", package = "MPsychoR")

R> RogersSub <- Rogers[,1:16]
R> RogersD <- dist(t(RogersSub))
R> fitRogers <- mds(RogersD, type = "ordinal")
R> jackRogers <- jackmds(fitRogers)
R> jackRogers
12 smacof Version 2: Multidimensional Scaling and Unfolding in R

SMACOF Jackknife Plot

Objects
onset
middle
1.0 late
hypersom
sad
decappetite
incappetite
weightloss
0.5

weightgain
concen
guilt
suicide
Dimension 2

anhedonia
fatigue
retard
0.0

agitation
−0.5
−1.0

−0.5 0.0 0.5 1.0

Dimension 1

Figure 4: Jackknife MDS plot. The labels are positioned at the original point coordinates,
and the stars represent the resampled solutions with the jackknife centroid at the center.

Call: jackmds.smacofB(object = fitRogers)

SMACOF Jackknife
Number of objects: 16
Value loss function: 0.3444
Number of iterations: 12

Stability measure: 0.998

Cross validity: 1
Dispersion: 0.002

R> plot(jackRogers, legend = TRUE, cex.legend = 0.8, inset = c(-0.3, 0))

The print output shows the jackknife measures reported above. Figure 4 shows the jackknife
MDS plot. The points are placed at X (MDS configuration). The centers of the stars denote
the jackknife centroids, the rays the n − 1 jackknife solutions. This result suggests that the
solution is very stable.
Further options for using jackknife in MDS are presented in Vera (2017) where the distances
are subject to stability analysis.
 Journal of Statistical Software 13

3.4. Stability of a solution II: Bootstrap

Bootstrap approaches for stability assessment in MDS were proposed by Meulman and Heiser
(1983), Heiser and Meulman (1983), Weinberg, Carroll, and Cohen (1984), and further refined
by Jacoby and Armstrong (2014). The smacof implementation resamples the original data
and therefore works for derived dissimilarities only. The confidence ellipsoids are computed as
follows. Let xi denote the row coordinates of object i from the original configuration X. Let
Si be the p × p covariance matrix of the bootstrapped solutions of object i. The 100(1 − α)%
confidence ellipsoid for object i is determined by the points zj for which

(zj − xi )S−1 ⊤
i (zj − xi ) = χ (α; p),
2
(8)

where χ2 (α; p) is the α-quantile of the χ2 -distribution with df = p. In R, this computation

can be easily achieved using the ellipse package (Murdoch and Chow 2020). As a stability
measure, we can use a slight modification of Equation 5:
PN ∗ ∗ 2
l=1 ∥Xl − X̄ ∥
ST = 1 − PN ∗ 2
. (9)
l=1 ∥Xl ∥

N denotes the number of bootstrap replications, X∗l the configuration of the l-th replication,
X̄∗ the bootstrap centroid configuration. Again, ST reflects a between/total variance ratio
and can be used to compare various MDS solutions against each other (Heiser and Meulman
1983). For instance, one could compare an unrestricted solution with a restricted solution
(see Section 5). The larger ST , the more stable the solution.
Let us apply the corresponding bootmds function on the depression data from above. We use
N = 500 bootstrap replications.

R> set.seed(123)
R> bootRogers <- bootmds(fitRogers, RogersSub, method.dat = "euclidean",
+ nrep = 500)
R> bootRogers

Call: bootmds.smacofB(object = fitRogers, data = RogersSub,

method.dat = "euclidean", nrep = 500)

SMACOF Bootstrap:
Number of objects: 16
Number of replications: 500

Mean bootstrap stress: 0.1179

Stress percentile CI:
2.5% 97.5%
0.0974 0.1433

Stability coefficient: 0.9631

In addition to the stability coefficient, the function also reports the stress averaged across
bootstrap samples, including the 95% confidence interval (bootstrap percentile).
14 smacof Version 2: Multidimensional Scaling and Unfolding in R

MDS Bootstrap Plot

1.0
hypersom
weightgain
0.5

guilt
incappetite
anhedonia
fatigue
suicide
retard concen sad
0.0
Dimension 2

decappetite agitation

middle
weightloss
−0.5

late onset
−1.0
−1.5

−1.5 −1.0 −0.5 0.0 0.5 1.0 1.5

Dimension 1

Figure 5: Bootstrap MDS plot with 95% confidence ellipsoids.

R> plot(bootRogers)

Figure 5 shows the resulting bootstrap configuration with the confidence ellipsoids. There is
a fair amount of instability associated with the sleep-onset insomnia item (labeled “onset”).

3.5. Stability of a solution III: Pseudo-confidence ellipses

Ramsay (1977, 1982) incorporated MDS into a parametric (log-)normal framework with
maximum-likelihood estimation. This idea makes it easy to derive confidence ellipsoids around
the points in the configuration. De Leeuw (2019) achieved similar ellipsoids without any dis-
tributional assumptions, based on taking the second derivatives of the stress. This approach
works for symmetric MDS solutions as well as for individual difference models (INDSCAL,
IDIOSCAL) of arbitrary dimensions. In its current form, its implementation is limited to ra-
tio transformations. Expressions for the stress derivatives can be found in the corresponding
paper.
Let us use the same dataset as above and fit a ratio MDS. The confEllipse function computes
the stress derivatives and subsequently the confidence ellipsoids.

R> fitRogers2 <- mds(RogersD)

R> confRogers <- confEllipse(fitRogers2)
 Journal of Statistical Software 15

Pseudo−Confidence Ellipses

0.10
hypersom

weightgain

guilt

fatigue
0.05

incappetite suicide concen

Dimension 2

sad
0.00

retard
anhedonia

decappetite
agitation
−0.05

weightloss middle

late onset
−0.10

−0.10 −0.05 0.00 0.05 0.10

Dimension 1

Figure 6: Pseudo-confidence ellipses for ratio MDS solution.

The following plot function takes this object and produces the configuration plot with the
ellipsoids. Of importance is the eps argument which we set to 0.01 below. This value implies
that we look at a perturbation region where the stress value is at most 1% larger than the
local minimum we have found. Figure 6 shows the corresponding configuration plot.

R> plot(confRogers, eps = 0.01, ylim = c(-0.11, 0.11),

+ ell = list(lty = 1, col = "gray"))

Note that the scales along the axes differ from the ones in Figures 5 and 6 (apart from the
fact that ratio MDS is used). This is because the SMACOF engine for estimating pseudo-
confidence ellipsoids normalizes the coordinates differently (see De Leeuw 2019, for details).
Also, the shape differences in the confidence ellipsoids are due to different methods used to
construct the ellipsoids.

4. MDS biplots
Biplots were developed within the context of principal component analysis (PCA; Gabriel
1971). In a PCA biplot the loading vectors are mapped on top of the scatterplot of the prin-
cipal component scores. However, the concept of biplots can be applied to other multivariate
techniques as well, as elaborated in Greenacre (2010), Gower, Lubbe, and Le Roux (2011),
16 smacof Version 2: Multidimensional Scaling and Unfolding in R

and Mair (2018). In MDS, biplots are often used to map external variables onto the MDS
configuration. Such covariates allow users to explore meaningful directions in the MDS space
rather than trying to interpret the dimensions directly. Note that Rabinowitz (1975) was one
of the first to suggest embedding axes representing external variables into MDS solutions in
order to facilitate substantive interpretations.
Let Y be a n × q matrix with q external variables in the columns, each of them centered
and optionally standardized (the latter simply changes the length of the biplot vector, not its
direction). To produce an MDS biplot, the following multivariate regression problem needs
to be solved:
Y = XB + E, (10)
where B is a p × q containing p regression coefficients for each of the q variables, and E is
the n × q matrix of errors. The corresponding OLS estimates B̂ = (X⊤ X)−1 X⊤ Y give the
coordinates of the external variables in the MDS space. The smacof package provides the
biplotmds function which performs the regression fit. By default, the external variables are
standardized internally (default scale = TRUE; scale = FALSE does centering only).
Let us start with a simple example where we map a single metric variable onto a configuration.
We use a dataset taken from Engen, Levy, and Schlosberg (1958) on facial expressions (see
also Heiser and Meulman 1983). Participants had to rate proximities of 13 facial expressions,
resulting in the dissimilarity matrix ∆. Rating scale values were collected by Abelson and
Sermat (1962) for the dimensions “pleasant-unpleasant” (PU), “attention-rejection” (AR),
and “tension-sleep” (TS).
We fit an ordinal MDS solution, and map the pleasant-unpleasant (PU) variable on top of the
configuration. We present two biplot versions. First, we focus on the vector representation.

R> fitFace <- mds(FaceExp, type = "ordinal")

R> ext <- data.frame(PU = FaceScale[,1])
R> biFace <- biplotmds(fitFace, extvar = ext)
R> coef(biFace)

PU
D1 -1.6214189
D2 -0.6295513

These regression coefficients determine the direction and length of the biplot vector.
Second, we use the axis representation for which the calibrate package (Graffelman 2020)
turns out to be helpful. We start by computing the regression coefficients based on the
centered external variable. In order to make sure that the ticks on the biplot axis correspond
to the original scale, some additional preliminary lines are needed.

R> library("calibrate")
R> biFace2 <- biplotmds(fitFace, extvar = ext, scale = FALSE)
R> coef(biFace2)

PU
D1 -3.865508
D2 -1.500868
 Journal of Statistical Software 17

R> PUc <- scale(ext, scale = FALSE)

R> tm <- seq(floor(min(ext)), ceiling(max(ext)), by = 1)
R> tmc_PU <- tm - mean(tm)
R> X <- fitFace$conf

The plots from Figure 7 can be produced as follows:

R> plot(biFace, main = "Biplot Vector Representation", vecscale = 0.8,

+ xlim = c(-1.5, 1.5), vec.conf = list(col = "brown"), pch = 20, cex = 0.5)
R> plot(fitFace, main = "Biplot Axis Representation", xlim = c(-1.5, 1.5))
R> abline(h = 0, v = 0, lty = 2, col = "gray")
R> calPU <- calibrate(coef(biFace2), PUc, tm = tmc_PU, tmlab = tm, Fr = X,
+ dp = TRUE, axiscol = "brown", axislab = "PU", labpos = 3, verb = FALSE)

The top panel uses the vector representation as advocated in Greenacre (2010). Using the
vecscale argument the biplot vector can be scaled by its length. The bottom panel uses the
axis representation as preferred by Gower et al. (2011). For the axis representation we can
do an orthogonal projection of the points on the axis, which gives the fitted values.
Let us move on with a second, more complex example involving multiple external variables
which reproduces part of the analysis presented in Mair (2018). We use the mental states
dataset from Tamir, Thornton, Contreras, and Mitchell (2016) who, for each individual,
collected a dissimilarity matrix involving 60 mental states, derived from functional magnetic
resonance imaging (fMRI) scans. The data are included in the MPsychoR package. We
average across the individuals, which leads to a single 60 × 60 dissimilarity matrix, subject to
a 2D monotone spline MDS. After the biplot computations, we print out the R2 values from
the individual regression fits.

R> data("NeuralActivity")
R> data("NeuralScales")
R> NeuralD <- Reduce("+", NeuralActivity)/length(NeuralActivity)
R> fitNeural <- mds(NeuralD, type = "mspline")
R> biNeural <- biplotmds(fitNeural, NeuralScales[,1:8])
R> round(biNeural$R2vec, 3)

Agency Experience High.Arousal Low.Arousal Body

0.242 0.299 0.134 0.093 0.232
Mind Emotion Reason
0.085 0.441 0.357

The vector version of the MDS biplot is given in Figure 8. The longer a covariate vector, the
larger the corresponding R2 . That is, the more accurate the corresponding axis projections
are in relation to the raw data. The orientation of the vectors reflects the correlation patterns
among the external variables, assuming the plot gives an accurate representation of the data
(of course, we lose information here due to projecting into a low-dimensional space). Other
options such as nonlinear MDS biplots are presented in Gower et al. (2011, Chapter 5),
including corresponding R code.
18 smacof Version 2: Multidimensional Scaling and Unfolding in R

Biplot Vector Representation

1.0

Light sleep

Revulsion
Physical exhaustion
0.5

Grief at death of mother

Extreme pain
Dimension 2

Maternal love−baby in arms

0.0

Savoring a Coke Something wrong with plane

Unexpectedly meets old boyfriend Anger at seeing dog beaten

Pulling hard on seat of chair

−0.5

Very pleasant surprise

Knows plane will crash
PU
−1.0

−1.5 −1.0 −0.5 0.0 0.5 1.0 1.5

Dimension 1

Biplot Axis Representation

1.0

Light sleep

Revulsion
Physical exhaustion
0.5

Grief at death of mother

Extreme pain
Dimension 2

1
Maternal love−baby in arms 2
3
0.0

4
Savoring a Coke Something wrong with plane
5
Unexpectedly meets old boyfriend
6 Anger at seeing dog beaten
PU 7
8 hard on seat of chair
Pulling
−0.5

9
Very pleasant surprise
Knows plane will crash
−1.0

−1.5 −1.0 −0.5 0.0 0.5 1.0 1.5

Dimension 1

Figure 7: Top panel: Vector representation of external variable. Bottom panel: Axis
representation of external variable.
 Journal of Statistical Software 19

Neural Biplot

1.5
Body
relaxation
peacefulness

1.0
sleepiness
Experience
fatigue
awe
anticipation Low.Arousalweariness
Emotion exaltation planning
drunkenness
0.5

disgust exhaustion
agitation imagination
affection
playfulness decision
laziness ecstasy trance
Dimension 2

inspiration
desire
self−consciousness
craziness attention
lust
skepticism lethargy
0.0

uneasiness
embarrassment pity
friendliness
distrust belief judgment
self−pity alarm insanity
subordination opinion transcendence
dominance contemplation
worryseriousness
satisfactioncuriosity awareness
High.Arousal disarrayintrigue
earnestness
reason
−0.5

nervousness objectivity
consciousness
thought cognition
patience

stupor
Mind
pensiveness
−1.0

Agency Reason
−1.5

−1.5 −1.0 −0.5 0.0 0.5 1.0 1.5

Dimension 1

Figure 8: Biplot for mental state MDS configuration. External variables are represented as
vectors.

5. MDS with optimal scaling on external predictors

Another advantage of the SMACOF framework compared to classical MDS is the option to fit
restricted MDS variants. There are two basic strategies to constrain an MDS configuration.
The first option involves internal constraints where the points are forced to be located on a
geometric shape. For the particular case of a sphere this can be achieved using smacofSphere.
The corresponding theory was described in De Leeuw and Mair (2009b). The only spherical
update since the original publication has been the incorporation of various types of dissimi-
larity transformations in smacofSphere.
Here we focus on a second strategy, that is, imposing external constraints on the configuration
in the tradition of De Leeuw and Heiser (1980), Borg and Lingoes (1980), and Heiser and
Meulman (1983). The simplest form of such a restriction is a linear restriction

X = ZC, (11)

directly incorporated into the stress formula given in (1). Z is a known covariate matrix of
dimension n × q with number of covariates q ≥ p. C is a q × p matrix of regression weights
to be estimated, subject to potential additional restrictions, as outlined below.
For practical purposes, however, this basic implementation is of limited use. For instance,
specifying a 2 × 2 ANOVA design in Z collapses point coordinates to only four points in a 2D
configuration. What makes the external restriction concept attractive in practice is to apply
an additional optimal scaling step on the external scales within each majorization iteration.
20 smacof Version 2: Multidimensional Scaling and Unfolding in R

Equation 11 changes to
X = ẐC. (12)
Each predictor variable z1 , . . . , zq is subject to an optimal scaling transformation. A popular
option is to scale these vectors in an ordinal way (i.e., using monotone regression). Other
transformations such as interval or splines (with or without monotonicity constraints) are
implemented in smacof as well. Note that, from a specification point of view, these exter-
nal variable transformations are unrelated to the dissimilarity transformations introduced in
Section 2.
Let us illustrate such a constrained MDS using the face expression data from Section 4. We
include the two external variables “pleasant-unpleasant” (PU) and “tension-sleep” (TS). They
constitute the matrix Z. We restrict C to be diagonal, which performs dimensional weighting.
Note that for this diagonal restriction the number of dimensions is determined by the number
of covariates (i.e., q = p), since each covariate defines an axis (dimension). We also use the
configuration from an unrestricted ordinal fit as initial configuration. It is important that
the user provides a reasonable starting configuration for the constrained MDS computation;
using one from an unrestricted fit is in general a good option.
Let us start with the first constrained MDS model: ordinal dissimilarity transformation of ∆,
interval transformed external variables in Z, diagonal regression weights restriction in C.
R> fitFace <- mds(FaceExp, type = "ordinal")
R> Z <- FaceScale[, c(1,3)]
R> fitFaceC1 <- smacofConstraint(FaceExp, type = "ordinal",
+ constraint = "diagonal", external = Z, constraint.type = "interval",
+ init = fitFace$conf)
R> round(fitFaceC1$C, 3)

[,1] [,2]
[1,] 1.068 0.000
[2,] 0.000 1.211

The last line shows the implied diagonal restriction in C. We obtain a stress value of 0.183
which, of course, is larger than the one from the unconstrained fit (0.106).
The resulting MDS configuration is given in Figure 9. Using the calibrate package the axes
of the external variables (original scales) can be added (see supplemental code materials).
These axes are a simple form of biplot axes, resulting from the diagonal restriction in C. For
this interval transformed solution the observed values in Z can be directly read from the PU
and TS axes; the configuration coordinates reproduce these values exactly.
In a second fit we relax the interval transformation of Z in terms of an ordinal transformation.
C is still kept diagonal.
R> fitFaceC2 <- smacofConstraint(FaceExp, type = "ordinal",
+ constraint = "diagonal", external = Z, constraint.type = "ordinal",
+ init = fitFace$conf)
R> round(fitFaceC2$C, 3)

[,1] [,2]
[1,] -1.034 0.00
[2,] 0.000 -1.08
 Journal of Statistical Software 21

Constrained MDS (Interval)

PU
9 8 7 6 5 4 3 2 1

1.0 Light sleep

1
2
Physical exhaustion
0.5

3
Maternal love−baby in Grief
arms at death of mother

4
Dimension 2

Savoring a Coke
Revulsion

TS
5
0.0

Unexpectedly meets old boyfriend

Extreme pain

6
Pulling hard on seat Something
of chair wrong with plane
Very pleasant surprise

7
Anger at seeing dog beaten
−0.5

8
Knows plane will crash

9
−1.0

−1.5 −1.0 −0.5 0.0 0.5 1.0 1.5

Dimension 1

Figure 9: Constrained MDS configurations (C diagonal) of face expression data: interval

transformed external variables.

Pleasant−Unpleasant Transformation Tension−Sleep Transformation

0.6
0.4
0.5
Transformed Scale

Transformed Scale

0.2
0.0
0.0

−0.2
−0.5

−0.6

2 4 6 8 2 4 6 8

Original Scale Original Scale

Figure 10: Transformation plots for external variables (original scores from Z on the x-axis,
transformed scores from Ẑ on the y-axis).

Due to the less restrictive nature of this specification this solution has a lower stress value
(0.159) than the interval transformed solution from above. Figure 10 gives some insight into
the ordinal transformations performed internally on each column of Z.
Figure 11 shows the configuration with the transformed axes on top and to the right. Again,
the points can be projected onto these axes. The corresponding values match the ones in Ẑ.
22 smacof Version 2: Multidimensional Scaling and Unfolding in R

Constrained MDS (Ordinal)

PU transformed
0.8 0.6 0.4 0.2 0 −0.2 −0.4 −0.6 −0.8

1.0

−0.2 −0.4 −0.6 −0.8

Light sleep

Physical exhaustion
0.5

TS transformed
Maternal love−baby in arms
Savoring Grief at death
a Coke of mother
Revulsion
Dimension 2

Unexpectedly meets old boyfriend Extreme pain

0.0

0
0.2
Pulling hard on Something
seat of chair
wrong with plane
Very pleasant surprise Anger at seeing dog beaten

0.4
−0.5

Knows plane will crash

0.6
0.8
−1.0

−1.5 −1.0 −0.5 0.0 0.5 1.0 1.5

Dimension 1

Figure 11: Constrained MDS configuration (C diagonal) of face expression data: ordinal
transformed external variables.

For the next constrained MDS variant we use all three external variables in the dataset (i.e.,
PU, AR, and TS). As q > p we need to relax the diagonal restriction in C: we keep C
unrestricted and use once more an interval transformation of Z.

R> Z <- FaceScale

R> fitFaceC3 <- smacofConstraint(FaceExp, type = "ordinal",
+ constraint = "unrestricted", external = Z, constraint.type = "interval",
+ init = fitFace$conf)
R> round(fitFaceC3$C, 3)

D1 D2
[1,] -0.887 -0.231
[2,] 0.087 -0.413
[3,] -2.571 4.344

Again, the three biplot axes can be mapped onto the configuration using the calibrate package,
after computing the regressions Z = XB with Z column-centered (see supplemental materials
for the entire code chunk).
Figure 12 displays the corresponding constrained MDS configuration with the biplot axes
on top. Each point can be projected on each axis. The projections are stored in each of
the calibrate objects (value: yt). Generally, the projected values do not correspond to the
observed values in Z as these calibrated biplot axes do not reproduce Z perfectly. As far as
 Journal of Statistical Software 23

Constraint MDS Biplot

1.0 Light sleep

1
2
Physical exhaustion
0.5

2
3
Revulsion

3
Extreme pain
Grief at death of mother

4
1
Dimension 2

4
2
Savoring a Coke 3

5
0.0

Maternal love−baby in arms

5
4
Something wrong with plane
Pulling hard on seat of chair
5

6 6
6
Unexpectedly meets old boyfriend Anger at seeing dog beaten
7
PU

7
Knows plane will crash

7
8
−0.5

8
Very pleasant surprise
8

TS
AR
9
9
−1.0

−1.0 −0.5 0.0 0.5 1.0

Dimension 1

Figure 12: Constraint MDS configuration with C unrestricted. Three external covariates
are added as biplot axes.

the axes are concerned, the biplot suggests that PS and TU are almost orthogonal, whereas
the predictions TS and AR are highly correlated in this 2D space. Dimension 2 lines up with
the AR axis which is useful for the interpretation of the configuration.
A general dimensional interpretation on the basis of the external variables no longer holds
since C is not diagonal: the solution is rotated/reflected followed by dimensional stretching.
By applying an SVD on C the user can get the rotation matrices and the dimension stretching
values (see Borg and Groenen 2005, p. 232, for details).

6. Unfolding
As mentioned in the introduction, one of the major updates since the first publication of the
package was a complete re-implementation of the unfolding function. This update gives the
user the possibility to apply the usual transformations on the dissimilarities, to incorporate
circular restrictions, and to fit row-conditional and external unfolding models.

6.1. Unfolding theory

Unfolding takes a rectangular dissimilarity matrix ∆ of dimension n × m with elements δij
(i = 1, . . . , n and j = 1, . . . , m) as input. Such data are most often rankings or ratings. The
24 smacof Version 2: Multidimensional Scaling and Unfolding in R

stress function from Equation 1 changes to

n X
m
σ 2 (D̂, X1 , X2 ) = wij (dˆij − dij (X1 , X2 ))2 , (13)
X

i=1 j=1

with the fitted Euclidean distances (p-dimensional space) expressed as

v
u p
dij (X1 , X2 ) = t (x1is − x2js )2 . (14)
uX

s=1

X1 is an n × p matrix (row configuration), X2 an m × p matrix (column configuration), and

D̂ the n × m matrix of disparities. Again, the weights wij and the dissimilarities δij must be
non-negative.
In terms of stress normalization, Borg and Groenen (2005, Section 11.1) argue that one could
find an optimal dilation factor that multiplies both the row and column coordinates by the
same constant, leading to

ˆ
v
i,j (wij dij dij (X1 , X2 ))
2
u P
σ1 (D̂, X1 , X2 ) = 1 − P (15)
u
.
ˆ2
t
2 wij dij (X1 , X2 )
P
i,j wij dij i,j

This expression provides a short cut to compute the stress-1 value, given that we allow for
an optimal dilation constant. At the same time it is a trick for interpretation in terms of
the well known stress-1 value after all the majorization computations are done. Details on
the majorization approach in the case of ratio transformations are given in (De Leeuw and
Mair 2009b). Below we elaborate on a modification that is able to handle general monotone
dissimilarity transformations from Section 2.

6.2. Transformation functions

Early versions of non-metric multidimensional unfolding (i.e., ordinal transformation) are
described in Coombs (1964). Busing et al. (2005) elaborate in detail on the challenges of
including transformation functions in unfolding with respect to optimization. One major
problem is degeneracy of the solution due to equal disparities. They suggest to penalize the
stress function by the coefficient of variation, which moves the algorithm away from solutions
with small variation in the fitted distances. The corresponding badness-of-fit target is called
p-stress:
σp2 (D̂, X1 , X2 ) = σ 2λ (D̂, X1 , X2 )µ(D̂). (16)
The coefficient of variation ν(D̂) is calculated on the basis of the disparities and enters the
penalty term as follows:
ω
µ(D̂) = 1 + . (17)
ν (D̂)
2

Obviously this penalty term acts as a multiplicative factor in Equation 16. As ν(D̂) decreases,
the p-stress penalization increases. There are two tuning parameters involved in this p-stress
setup:

• λ ∈ (0; 1] is a lack-of-penalty parameter that controls the influence of penalty term: the
larger λ, the smaller the penalty influence.
 Journal of Statistical Software 25

• ω acts as range parameter in the penalty term: for a small ω the penalty is especially
effective if ν(D̂) is small.

Busing et al. (2005) did an extensive simulation study in order to provide suggestions on how
to fix the tuning parameters. For conditional unfolding, it is suggested to set λ = 0.5, and
ω = 1 (default settings in unfolding)5 . For unconditional unfolding, they suggest that one
uses λ = 0.5 and ω > 0.1. Further details can be found in the corresponding publication.
The p-stress target can be minimized using majorization, for which the details are again given
in Busing et al. (2005). From a practical point of view, after obtaining a p-stress optimized
solution, users can consider the stress-1 from Equation 15 as goodness-of-fit index6 . Note that
all the dissimilarity transformation functions from MDS (i.e., ratio, interval, ordinal, spline;
cf. Section 2) are implemented for unfolding as well.
Let us illustrate an example of an ordinal unfolding solution. We use a dataset from Dabic
and Hatzinger (2009), available in the prefmod package (Hatzinger and Dittrich 2012), where
individuals were asked to configure a car according to their preferences. They could choose
freely from several modules such as exterior and interior design, technical equipment, brand,
price, and producing country. We use only the first 100 individuals in this analysis.

R> library("prefmod")
R> carconf1 <- carconf[1:100, 1:6]
R> head(carconf1)

price exterior brand tech.equip country interior

1 3 2 5 6 4 1
2 4 1 5 2 6 3
3 6 3 2 5 4 1
4 1 4 2 3 6 5
5 NA 2 4 NA 3 1
6 NA 2 4 3 NA 1

Since not all individuals ranked all objects, we have the situation of “partial rankings”. The
unfolding function specifies a proper weight matrix W automatically: wij = 0 if δij is
missing; wij = 1 otherwise. This way, the corresponding missing dissimilarities are blanked
out from the optimization. For the ordinal unfolding model we are going to fit, this weight
matrix can be extracted using unf_ord$weightmat.

R> unf_ord <- unfolding(carconf1, type = "ordinal")

R> unf_ord

Call: unfolding(delta = carconf1, type = "ordinal")

Model: Rectangular smacof

Number of subjects: 100
Number of objects: 6
5
Personal communication with Frank Busing.
6
For details on how to assess the goodness-of-fit of an unfolding solution see Mair et al. (2016).
26 smacof Version 2: Multidimensional Scaling and Unfolding in R

Unfolding Configuration Car Preferences Shepard Diagram Car Preferences

1.0

country
33
tech.equip 26

1.5
20
94 85 13
21

Configuration Distances/d−hats
38
37
0.5

18 43 17
80 99
3177 15 92
89 27
price 3986 71 100
6547 1162 14 52 57
Dimension 2

72 68 56 91
90
58 22 2
51 32 61 41 74 49

1.0
66 46 60 6
959 88 7955 73
0.0

7075
97 10
4 98 28 4434
83 82
35 24 54
87
16 exterior 85
48
3625 63
76 96
84 50 93 1
19 67 29
69 8153
7 64 59
42 23
40

0.5
−0.5

78 12
30 interior3
45

brand
−1.0

0.0
−1.0 −0.5 0.0 0.5 1.0 1 2 3 4 5 6

Dimension 1 Dissimilarities

Figure 13: Left panel: Unfolding configuration of car preference data. Right panel: Shepard
diagram car preference data (ordinal transformation).

Transformation: ordinalp
Conditionality: matrix

Stress-1 value: 0.297371

Penalized Stress: 2.330348
Number of iterations: 135

This call prints out the stress-1 value as well as the final p-stress value. The configuration
plot and Shepard diagram shown in Figure 13 can be produced as follows:

R> plot(unf_ord, main = "Unfolding Configuration Car Preferences",

+ ylim = c(-1, 1))
R> plot(unf_ord, plot.type = "Shepard",
+ main = "Shepard Diagram Car Preferences")

The Shepard diagram shows the ordinal transformation of the input dissimilarities, whereas
the configuration plot maps the row and column coordinates into a joint space, which makes
distances between any pair of points interpretable.

6.3. Row-conditional unfolding

The solution above is an unconditional (also called matrix-conditional) unfolding solution
since a single transformation function is estimated that applies to all individuals. The ranks
are compared unconditionally which, in some situations, is a fairly restrictive assumption.
For instance, in our example it might be the case that individual i is quite indifferent to all
car characteristics, but still ranks them. Individual i′ , however, could have strong preferences
but might end up with the same ranking as individual i. Treating these ranks as equal is a
strong assumption. Similarly, for rating data in ∆, individual i’s rating of, for instance, 2 is
assumed to be equal to any other individual’s rating of 2.
 Journal of Statistical Software 27

Row-conditional unfolding relaxes this single transformation assumption by estimating sepa-

rate transformation functions for each individual (i.e., for each row in ∆). Technically, what
changes with respect to the p-stress expression in Equation 16 is the penalty term. Bus-
ing et al. (2005) suggest using the harmonic mean for row-wise aggregation of the penalty
components which modifies Equation 17 to
ω
µc (D̂) = 1 +  P −1 . (18)
1 n −2 (d̂ )
n i=1 ν i

The d̂i ’s are the row vectors in D̂. The raw stress term in Equation 16 remains unadjusted
since it is additive over the rows.
Let us fit a row-conditional version of the ordinal unfolding on the car characteristics data.
We use the final configuration obtained above as starting configuration. Note that for running
time purposes we set a slightly more generous convergence boundary ε than the default7 . In
general, we recommend to increase the number of iterations using the itmax argument, if
needed. For a reasonably large sample size it can take a while for the algorithm to converge.
A parallelized fit can be evoked through the parallelize argument.

R> startconf <- list(unf_ord$conf.row, unf_ord$conf.col)

R> unf_cond <- unfolding(carconf1, type = "ordinal", conditionality = "row",
+ eps = 6e-5, init = startconf)
R> unf_cond

Call: unfolding(delta = carconf1, type = "ordinal", conditionality = "row",

init = startconf, eps = 6e-05)

Model: Rectangular smacof

Number of subjects: 100
Number of objects: 6
Transformation: ordinalp
Conditionality: row

Stress-1 value: 0.202789

Penalized Stress: 29.40951
Number of iterations: 744

Compared to the unconditional fit, the row-conditional version clearly reduced the stress-1.
Figure 14 shows the resulting configuration plot in the left panel. The Shepard diagram in
the right panel nicely illustrates the difference between unconditional and row-conditional
unfolding. While in unconditional unfolding we fitted only a single transformation function
(see right panel of Figure 13), in row-conditional unfolding each individual gets its own trans-
formation function. Since we have missing values in our data, not all individuals have the full
six-ranking monotone trajectories.
7
In the t-th iteration the convergence criterion used in unfolding is
2(σp (X1 , X2 )(t−1) − σp (X1 , X2 )(t) ) ≤ ε(σp (X1 , X2 )(t−1) + σp (X1 , X2 )(t) + 10−15 ) .
28 smacof Version 2: Multidimensional Scaling and Unfolding in R

Conditional Unfolding Configuration Car Preferences Shepard Diagram Car Preferences

11

23
1.0

2.5
54 55
33 56 country
15 9962 52 44
26 34
100
46 17 20
14 16
23
60 9485 38 13
21
18 54380
0.5

Configuration Distances/d−hats
31 tech.equip
77 37 7
11
34
44
55
60
96
97
54

2.0
27
92
3986 71 84
76
36
25
67
65
47 89 5
14
50
52
56
62
6
88 78
price
7268 57 90
91 4
98
9 66
51 58
32 2 53
83
46
63
99
100 35
51
95
41 49 75 15 72
32
73exterior 30
0.0

498 70 58
68
65
26
Dimension 2

9535 22
74 82 6 24
61
39
90
91
70
79
87
13
21
82
20
3
37

1.5
6179
87
24 28 10 83 85
86
94
8
93 1 8 43
49
10
57
47
18
22
74
80
25 8159 9 45
19
66
29
69
36
76
84
48 19 1264
42 41
93
71
42
64
27
28
92
73
33
81
77
38
12
29 interior 75
48
31
17
−0.5

67 69 633 53 2
59
40
16
23 1
89
88 78 30
4045 50
brand

1.0
−1.0

97 11
34
44
54
55
60
96
97
7

0.5
96 37
61
7 27
52
56
62
5
6
14
50
88
92
79
24
87
25
36
−1.5

22
74
15
100
46
63
99
83
19
33
38
89
76
84
48
12
41
35
53
45
8
16 77
86
95
26
59
42
64
81
1
67
20
82
30
31
90
91
93
98
29
69
4
13
21
18
40
71
75
73
9

0.0
10
2
58
68
17
70
39
28
32
47
57
65
3
94
51
78
72
43
66
80
85
49

−2.0 −1.5 −1.0 −0.5 0.0 0.5 1.0 1.5 1 2 3 4 5 6

Dimension 1 Dissimilarities

Figure 14: Left panel: Row-conditional unfolding configuration of car preference data. Right
panel: Shepard diagram (ordinal transformation) row-conditional unfolding.

R> plot(unf_cond,
+ main = "Conditional Unfolding Configuration Car Preferences")
R> plot(unf_cond, plot.type = "Shepard",
+ main = "Shepard Diagram Car Preferences", col.dhat = "gray",
+ xlim = c(0.9, 6.1))

Some practical suggestions on when to use row-conditional unfolding as opposed to uncondi-

tional unfolding are given in Borg et al. (2018, p. 100).

6.4. External unfolding

External unfolding uses fixed coordinates for either the rows or the columns. Such fixed
coordinates might come from a previous analysis, or might be based on an underlying the-
ory. Early external unfolding references are Carroll (1972), Srinivasan and Shocker (1973),
Rodgers and Young (1981), and DeSarbo and Rao (1984). Within each iteration either the
row coordinates in X1 (in case of fixed coordinates denoted as F1 ), or the column coordinates
in X2 (in case of fixed coordinates denoted as F2 ) need to be constrained and scaled. The
scaling factors for fixed rows and fixed columns, respectively, are

trace(F⊤
1 X1 )
s1 = ,
∥F1 ∥
trace(F⊤
2 X2 )
s2 = .
∥F2 ∥

Based on these scaling factors the updated coordinates are X1 := s1 F1 in the case of row
restrictions, or X2 := s2 F2 in the case of column restrictions. Using this adjustment the new
coordinates are properly scaled with respect to the unconstrained column/row coordinates,
while maintaining the specified shape constraints.
 Journal of Statistical Software 29

PVQ Unrestricted PVQ Fixed Value Circle

1.0

1.0
BE TR
137
20
125
66
141 SE 150
95
147118 AC 81
13319 10
9611
90 65 UN CO
73 100
37 TR
0.5

0.5
25
1 76 4061
72 PO
88 64
CO 105 59
101 3
110 126
70 127 122
124 109107 8 23 38 116 91 138
104 98 44 85
36
114
42 56
129 144 136 45 93
47
71 113
104
11121 113 83 69 75 111
Dimension 2

Dimension 2
85 54 63 119
805852143 151 57143 134
136
21
48 41 78134 49 121146 9479140974133 52
30
74103
78
51 130 135
112
6827132
74
133946 SD 99 15
128
149
139 27589135
2 16 151 SE
115 57 108 50
117 768 4
0.0

0.0
139148
3155 81 53 108
3587658 132 64
HE 89 75 120 80 39
678
7131 33
10614 6 91
140 30
16 25 62 24 28
22 51 112
861382
ST 142123
4329
115
131
26
31 60109 107
6936
586 82 138 145
77 55 17 130
14 144
43 28
117
26
59 128
47
84
12392
71
150 102 34
8492
483212 106 148
37 18 4665 88
22 34 120 4 67 70 12772 73
1 110 124
40
56 9 126
90 3122141
95
146 60918
12 97 114
103 421961 10
129 100
773829 99 76101 20
6232 14515 3511644
17 147 11
−0.5

−0.5
102 24121 23 50
8753
149
11979 2 ST 9666 PO
98 142
94 83 137 125
SD 5463 45 105 133118
BE
UN 49
93
HE AC
−1.0

−1.0
−1.0 −0.5 0.0 0.5 1.0 −1.0 −0.5 0.0 0.5 1.0

Dimension 1 Dimension 1

Figure 15: Left panel: Unrestricted unfolding solution. Right panel: Externally restricted
unfolding solution (fixed circular coordinates for personal values).

To illustrate, we use a dataset from Borg, Bardi, and Schwartz (2017). We focus on the
Portrait Value Questionnaire (PVQ) portion of the data which result from a questionnaire of
40 items assessing how persons rate the personal importance of ten basic values: power (PO),
achievement (AC), hedonism (HE), stimulation (ST), self-direction (SD), universalism (UN),
benevolence (BE), tradition (TR), conformity (CO), security (SE) on a scale from 0 to 6. We
use an aggregated version where the item scores belonging to the same psychological value
are averaged. As fixed coordinates we use the following value circle coordinates:

R> tuv <- matrix(NA, nrow = ncol(PVQ40agg), ncol = 2)

R> alpha <- -360/10
R> for (i in 1:10){
+ alpha <- alpha+360/10
+ tuv[i,1] <- cos(alpha*pi/180)
+ tuv[i,2] <- sin(alpha*pi/180)
+ }

This specification is different from spherical unfolding introduced below, as we fix the value
coordinates on the circle (equidistant) instead of just forcing them to be aligned on a circle.
Of course, in external unfolding we can specify any arbitrarily fixed configuration; it does not
have to be a circle.
Below we fit two solutions: an unconstrained ordinal unfolding solution, and a constrained
ordinal unfolding solution with fixed circular column coordinates. Since smaller responses in
the PVQ data reflect larger dissimilarities, we reverse the category scores.

R> delta <- (max(PVQ40agg) + 1) - PVQ40agg

R> unf_pvq <- unfolding(delta, type = "ordinal")
R> unf_pvqext <- unfolding(delta, type = "ordinal", fixed = "column",
+ fixed.coord = tuv)
30 smacof Version 2: Multidimensional Scaling and Unfolding in R

The stress value of the unconstrained solution is 0.208, whereas that of the external solution is
0.274, which is clearly larger. The plots given in Figure 15 reflect the corresponding differences
in the configurations. The unrestricted solution clearly deviates from the theoretical circle.

6.5. Spherical unfolding

Sometimes it is of interest to restrict either row coordinates or column coordinates to be on a
geometric shape such as a sphere. Technically, this implies that within each iteration the row
(or column) coordinates have to be spherically restricted. Let us elaborate on this restriction
for the row coordinates in X := X1 for p = 2 (for the column coordinates in X2 it works in
an analogous fashion). Each row vector xi can be expressed in polar coordinates (see Cox
and Cox 1991):
xi = (ri cos(θi ), ri sin(θi ))⊤ ,
with θi as the corresponding angle and ri as the radius. We aim to find a circular restricted
configuration Xc for which the row vectors have polar coordinates

xc,i = (r cos(θc,i ), r sin(θc,i ))⊤ .

We have a single radius r and the corresponding angle θc,i . To compute Xc , we want to
minimize the quadratic part of the majorizing function:

∥X − Xc ∥2 = ∥X∥2 + ∥Xc ∥2 − 2 × trace(X⊤

c X)
= ∥X∥2 + nr2 − 2 × trace(X⊤
c X)
n
= ∥X∥ + nr − 2 r × ri (cos(θc,i ) cos(θi ) + sin(θc,i ) sin(θi )).
X
2 2

i=1

In the last term, the best θci that can be chosen is the one that maximizes the following
expression: cos(θc,i ) cos(θi ) + sin(θc,i ) sin(θi ). This implies choosing θc,i = θi so that

cos(θc,i ) cos(θi ) + sin(θc,i ) sin(θi ) = cos2 (θc,i ) + sin2 (θi ) = 1.

Substituting the optimal θc,i = θi gives

n
∥X − Xc ∥ = ∥X∥ + nr − 2r
X
2 2 2
ri .
i=1

Setting the first derivative equal to zero yields the update

n
1X
r= ri .
n i=1

This simple expression gives us the optimal circular projection of the row coordinates in X.
As mentioned above, the same steps can be carried out for the column coordinates (X := X2 ;
replace i by j, and n by m in these equations).
To illustrate an unfolding solution where we restrict the column coordinates to be on a circle,
we use once more a dataset from Borg et al. (2017) which builds on the Schwartz (1992)
value circle theory. The data are derived from the Schwartz Value Survey (SVS). They were
centered (row-wise) and converted from preferences into dissimilarities, hence representing a
 Journal of Statistical Software 31

Values Unfolding Configuration (Unrestricted) Values Unfolding Configuration (Circular Restriction)

stimulation
achievement
1.0

1.0
stimulation hedonism
self−direction
achievement
hedonism
self−direction
98 88 16 66
49
0.5

0.5
8898 16 66 271
313143 292 248
20 97
316142
327 189
103
109
197242 132 81
101
203
118 202
300
18
220
327313 49 176 1 52
139
104
17 167
50 102
125
296 26
10 130
198
214
41
283276
152
205 259
316 142
176 271
103
189
109 143 24897 202 324
299
133187
44
37
162 113
206
234
177
9
126
264
165
115 160
129
164
6382
57
151 43
60
188
212
46
156
250 8
320
210
48
7268
116131
237
298
321
299139
1 197
10417
50
167 292 20
101
203 83275
124 14181
146
260291
12
78
253
19
317
282 42
278
240
186
137
45
243
322166
3188785
263
252169
235
27
158 56
231 72
128
145
120
7325100
324
133187
126
44
83 242
102296
177
942
2681
206
132
234
125 63
41
10129
264 118
198
283
13018
165
214
300
152
250 225
286
58 28207
136
108
183
279
323
171
105
277
306
217
34 157
199
222 5
194
228
185 80
4
40
69
6
285
326
22
319
174
135
154
89
159
192 110
119
148
127
213
224
153
168 93
215
84 321
258
229
184
61 211
216
111
149
59
218
121
175
293
227
209 182
power 275
28115
124
136
207 37
162
14
113
146
253
19 82
52
306
181
137 164
151
205
291
277 60
57
278
235
186 160
276 259
848
7
156
220 30
141 54
15
273
76
29 107
254
302
281
5568
150
196
246
190
179
92
255 155
13
267
272
288
140
307
232 117
67
261
265
23294
64
36 9953
58 286
225
279
78
323
192171
105 34
183
108
217
222
15
185 322
806
159
199
228
157
194 45
260
274 12
166
87
243
317
326
282
46 43
212
252
240
40263
285
148 188320
158
85
56169
72
128145
131120 universalism power 269
47
71
86208
312
315
28031 233
287
325
241
147
94
35
303
251
29791
295
3833 77
51
239
221
204 305
122
178
274
74
79
289 226
311 262
266
138
310
30 154
141 4754
273
76
92
55
269
25558922
69
213
135
319
29
68
272 318
127
174
184 231
258
119
153
168
110
150 61
21 298
73
59
321 3210
116 249
134 195
65
11
230
304
96 95
2284
301
245
270
70
161114
144
191
112
180 75123
173
200 24
Dimension 2

Dimension 2
302
208
280
315
241
312
71
249232 107
246
2 265
325
13
303
297 93
229
288
254
196
81 224
155
14067
215
84
216
117
307
94 149
211
64
268 100
25
293 121 314
32
163170 219
0.0

295

0.0
134 179
74
96233
91
33
6535261
251
190
287
267 218
147
77237
23 172236244 256309 193 39
172 86163
195
1138
245
230
304
236
274
32 31
239
7951
221
305
284178
31470
204
144
191
294
95
3012
270
161
122
36
289111
99
226
114
112
266
311
175
53
227
262 182 257 223
201
247
180 170
244 138
219
256257
209
173
309 123
200
310
308
290
238 62 90benevolence
75
2473924
223
201 106
308 106 238
62 193
290
90benevolence universalism
−0.5

−0.5
conformity
security
security
conformity
−1.0

−1.0
tradition

tradition
−1.5

−1.5
−1.5 −1.0 −0.5 0.0 0.5 1.0 −1.5 −1.0 −0.5 0.0 0.5 1.0 1.5

Dimension 1 Dimension 1

Figure 16: Left panel: Unrestricted unfolding configuration of personal values. Right panel:
Circular unfolding solution personal values (circle superimposed).

rectangular dissimilarity matrix ∆ with 327 persons and 10 variables referring to Schwartz’
psychological values: power, achievement, hedonism, stimulation, self-direction, universalism,
benevolence, tradition, conformity, and security. We fit two (ratio) unfolding solutions: an
unrestricted one as well as one with circular restrictions on the column coordinates (values):

R> unf_vals <- unfolding(indvalues)

R> unf_valsc <- unfolding(indvalues, circle = "column")

Comparing the stress-1 values we get 0.171 for the unrestricted solution, and 0.179 for the
restricted solution. This suggests that the circular solution is basically as good as the unre-
stricted one.
The reason for this becomes obvious when looking at the configuration plots in Figure 16.
The unrestricted solution in the left panel suggests that the personal values approximate a
circle, as suggested by Schwartz’ value theory. The configuration in the right panel results
from forcing the psychological values to be arranged on a circle.

6.6. Vector model of unfolding

Tucker (1960) propsed the vector model of unfolding (VMU) which Carroll (1972) later called
MDPREF. It is basically a principal component analysis (PCA) on the transposed input sim-
ilarity matrix P. After a singular value decomposition
√ P⊤ ≈ UΣV⊤ for given dimensionality
p, the row coordinates are obtained by X1 = m − 1UΣ, and the column coordinates by
X2 = (m − 1)−1/2 V.
We apply the VMU on the unreversed PVQ data from above, since the inputs have to be
similarities. Note that, by default, the vmu function does an internal row-wise centering of
the data.

R> fit_vmu <- vmu(PVQ40agg)

R> fit_vmu
32 smacof Version 2: Multidimensional Scaling and Unfolding in R

−2.0 −1.5 −1.0 −0.5 0.0 0.5 1.0 1.5

1.5
133
ST
HE

1.0
118
42 70

1.0
129
96 1 48
AC
101 76 127
102
125 147 72
66 19 32

0.5
PO 106 77 62 SD

0.5
61 56 22
110 55
40 43
12 24
124 1073 34
137 115
11 390 20 31 142
37
9148
17 84 145
14 51
92 60
131
100
126 122 2618 28
123 29
130 49 45 63 54
141 121
117 94
0.0

0.0
87
144 112
86
35 50
120
146 UN
109 7 149
2
65 5 128 99
15 97 79
88 10746 82 13 58 806867 4 53 13993119
D2

95 89 6 98
10838
14039
103 27
132 71
83 23 BE
57 135
33 105

−0.5
8 41 44 47
−0.5

74
30
78 16
52 114
69
143
64 36 116
13475 59
21 136151 138 91
SE

−1.0
111
−1.0

85
104 113
150

−1.5
25
TR
−1.5

81

−2.0
CO

−1.5 −1.0 −0.5 0.0 0.5 1.0

D1

Figure 17: VMU biplot for PVQ data.

Call: vmu(delta = PVQ40agg)

Number of subjects: 151

Number of objects: 10
Number of dimensions: 2
Variance accounted for: 66.21%

The results can be visualized using a biplot, where the row scores are represented as preference
vectors (see Figure 17).

R> plot(fit_vmu, col = c("black", "coral3"), cex = c(1, 0.7))

Note that ordinal versions of VMU amount to fitting an ordinal PCA (Princals; Gifi 1990; De
Leeuw and Mair 2009a).

7. Other MDS variants and utilities

7.1. Unidimensional scaling

Unidimensional scaling can be applied in situations where one has a strong reason to believe
that there is only one underlying dimension, such as time, ability, or preference. Even though
unidimensional scaling can be considered as a special case of MDS, it is generally discussed
separately (Mair and De Leeuw 2015) since the local minimum problem becomes serious if
 Journal of Statistical Software 33

mds is used with ndim = 1. The smacof package provides a simple implementation where
all possible n! dissimilarity permutations are considered for scaling, and the one which leads
to a minimal stress value is returned. Obviously, this strategy is applicable only to a small
number of objects, say less than 10 objects8 .
In the following example we examine seven works by Plato, map them on a single dimension,
and explore to which degree the mapping reflects the chronological order by which they are
written. The input dissimilarities are derived according to the following strategy: Cox and
Brandwood (1959) extracted the last five syllables of each sentence; each syllable is classified
as long or short which gives 32 types; and based on this classification a percentage distribution
across the 32 scenarios for each of the seven works can be computed, subject to a Euclidean
distance computation.

R> PlatoD <- dist(t(Plato7))

R> fitPlato <- uniscale(PlatoD, verbose = FALSE)
R> round(sort(fitPlato$conf), 3)

Critias Republic Timaeus Sophist Politicus Philebus Laws

-0.903 -0.599 -0.335 -0.060 0.373 0.656 0.869

The last line prints the 1D “time” configuration of Plato’s works that lead to the lowest stress
value. Note that the exact chronological order of Plato’s works is unknown; scholars only know
that “Republic” was the first work, and “Laws” his last one. Copleston (1949, p. 140) suggests
the following temporal order of these selected seven works: Republic, Sophist, Politicus,
Philebus, Timaeus, Critias, Laws. Obviously, our unidimensional scaling model advocates a
different chronological order.

7.2. Gravity model

The idea of the gravity model goes back to Newton’s law of universal gravitation where he
states that force is proportional to the product of the two masses, and inversely proportional
to the square of the distance between them. Haynes and Fotheringham (1984) present a
wide range of statistical applications of this gravity concept with special emphasis on spatial
interactions. Within an MDS context, the gravity model turns out to be especially useful for
text co-occurrence data (Mair, Rusch, and Hornik 2014; Borg et al. 2018) in order to avoid
that words with high co-occurrences dominate the solution. Note that the sim2diss function
already includes a basic gravity computation (see Table 2). Here we present the gravity
function, which does a very similar transformation, but is designed to take a document-term
matrix (DTM) as input.
The first step is to binarize the DTM: if a word (columns) is mentioned at least once in a
particular document (rows), the corresponding cell entry is 1, and 0 otherwise. Let Y denote
this binarized DTM. From this simplified structure the word co-occurrence matrix C can be
computed by C = Y⊤ Y. Thus, only the information on whether words occur together or not
is considered. C is a symmetric matrix (with elements cij ) with co-occurrence frequencies
in the off-diagonals. Let ci+ = j̸=i cij and c+j = i̸=j cij be the respective margins of C
P P

8
Approximate timings: 1s for n = 7; 8s for n = 8; 75s for n = 9; for n = 10 the running time is already
exceedingly long.
34 smacof Version 2: Multidimensional Scaling and Unfolding in R

Bubble Plot

1.0
principles
liberty

freedom
americaamerican

great
will
0.5

individual
party
work
hardconstitution
country
founding
limited
life
god
best
Dimension 2

right
defense
0.0

fiscal
nation people personal
national
market
conservative

responsibility
strong
−0.5

family
values
military
free
government

taxes
−1.0

low

small

−1.0 −0.5 0.0 0.5 1.0

Dimension 1

Figure 18: Bubble plot for gravity MDS solution on GOP data. The larger the bubbles, the
larger the SPP.

(diagonal blanked out). The gravity model defines the following dissimilarities (for i ̸= j):
s
ci+ c+j
δij = . (19)
cij

To illustrate a gravity application on text data we use a DTM similar to the one presented
in Mair et al. (2014). This DTM was created on the basis of statements of 254 Republican
voters who had to complete the sentence “I am a Republican because...”. First, let us create
the gravity dissimilarities according to the strategy outlined above.

R> gopD <- gravity(GOPdtm)$gravdiss

Note that using text data, C is typically sparse (i.e., many elements cij = 0). For these
elements we cannot compute Equation (19) since we divide by 0. The function sets the
corresponding entries to NA. In the subsequent MDS call, these elements are automatically
blanked out by setting the corresponding weight wij to 0 in the basic stress equation.

R> fitGOP <- mds(gopD, type = "ordinal")

R> plot(fitGOP, plot.type = "bubbleplot", bubscale = 20)

Figure 18 shows the bubble plot which incorporates the stress-per-point (SPP) information.
The larger a bubble, the larger the contribution of a particular object (here, word) to the
 Journal of Statistical Software 35

total stress. Objects with large SPP values are responsible for misfit. The closer two words
are in the configuration, the more frequently they have been mentioned together in a single
statement.
An extension of this model is presented in Mair et al. (2014), who introduce the exponent λ
in order to emphasize larger dissimilarities. The reason for this is that in text data we often
end up with little variance in the input dissimilarities which leads to a concentric, circular
representation of the configuration. Equation 19 changes to
!λ
2
ci+ c+j
δij = . (20)
cij
This extension is called power gravity model. The parameter λ needs to be chosen ad hoc
and can take values from [−∞, ∞]. For λ < 1 we shrink large dissimilarities, for λ = 1 we
end up with the ordinary gravity model, and for λ > 1 we stretch large dissimilarities. Note
that there is a trade-off between the choice of λ and the stress value: the more structure we
create, the higher the stress value. This extension is relevant for metric MDS strategies such
as ratio, interval, or spline MDS. The λ parameter can be specified in the gravity function.
A recent work by Rusch, Mair, and Hornik (2021) embeds the gravity formulation into a more
general loss function which, among other things, finds an optimal λ during the optimization
process.

7.3. Asymmetric MDS

So far, except in unfolding, ∆ has been a symmetric matrix of input dissimilarities. In this
section we aim to scale square asymmetric dissimilarity matrices. Young (1975), Collins
(1987), Zielman and Heiser (1996), Borg and Groenen (2005, Chapter 23), and Bove and
Okada (2018) present various asymmetric MDS variants of which smacof implements the
drift vector model (Borg 1979). The starting point of this approach is to decompose the
asymmetric dissimilarity matrix ∆ into a symmetric part M, and a skew-symmetric part N:
∆ = M + N, (21)
with M = (∆ + ∆⊤ )/2, and N = (∆ − ∆⊤ )/2. In smacof, the symdecomp function can be
used for this decomposition. Drift vector models display simultaneously the symmetric and
the skew-symmetric part of ∆. They first fit an MDS (of any type) on the symmetric matrix
M, resulting in the configuration X. The asymmetric information is then incorporated as
follows (Borg and Groenen 2005, p. 503):

• For each object pair i, j compute aij = xi − xj which results in a vector of length p.
q
• Norm aij to unit length, resulting in bij = aij / aij
⊤a .
ij

• Incorporate the skew-symmetric part: cij = nij bij with nij as the corresponding element
in N (drift vectors).
• For a given point i, average the elements in cij : di = n−1 cij (average drift vectors).
P
j

• For plotting, compute the vector lengths of di (root mean square of its elements, scaled
√
by a factor of n/mean(M)),
q and the direction angle (relative to the y-axis) of
αi = arccos(d⊤
i u/ di di ) with u = (0, 1).
⊤ ⊤
36 smacof Version 2: Multidimensional Scaling and Unfolding in R

Drift Vectors Morse Codes

− .

1.0

−− −.
0.5

−−− .− ..
−−.
Dimension 2

−−−−.
−−−−− .−−
−.− .−.
.−−−− .−−−
.−−. −..
0.0

−−.− −−..
−.−. ..−
−−−.. −.−− ...
..−−− .−..
−..− −... ..−.
−−...
....
−0.5

−.... ...−
...−−
....−
.....
−1.0

−1.0 −0.5 0.0 0.5 1.0

Dimension 1

Figure 19: MDS solution for asymmetric Morse code data including drift vectors.

To illustrate the drift vector model, we use the classical Morse code data by Rothkopf (1957).
Rothkopf asked 598 subjects to judge whether two signals, presented acoustically one after
another, were the same or not. The values are the average percentages for which the answer
“Same!” was given in each combination of row stimulus i and column stimulus j, where
either i or j was the first signal presented. The responses were aggregated to confusion
rates and subsequently subtracted from 1, such that the values represent dissimilarities. The
driftVector function performs the decomposition from Equation 21, fits an MDS of choice on
M, and applies the drift vector computation steps outlined above. For the Morse code data,
the resulting drift configuration plot based on a 2D ordinal MDS fit, is given in Figure 19.

R> morseDrift <- driftVectors(morse2, type = "ordinal")

R> plot(morseDrift, main = "Drift Vectors Morse Codes",
+ col.drift = "darkgray")

We see that the vectors tend to point in the bottom left direction; they are certainly not
random. In the bottom left quadrant we mostly have longer signals suggesting that shorter
signals are more often confused with longer ones than vice versa. Note that the plot function
has a vecscale argument by which the user can modify the length of the drift vectors by a
scaling factor.
Other approaches to scale asymmetric data implemented in R are the following. Vera and
Rivera (2014) embed MDS into a structural equation modeling framework. Their approach
is implemented in the semds package (Vera and Mair 2019). Zielman and Heiser (1993)
 Journal of Statistical Software 37

developed a slide-vector approach which is implemented in asymmetry (Zielman 2021). Un-

folding strategies from Section 6 can also be used for asymmetric dissimilarity matrices. An
application can be found in Sagarra, Busing, Mar-Molinero, and Rialp (2018).

7.4. Procrustes
Sometimes it is of interest to compare multiple MDS configurations based on, for instance,
different experimental conditions (the objects need to be the same within each condition).
The idea of Procrustes (Hurley and Cattell 1962) is to remove “meaningless” configuration
differences such as rotation, translation, and dilation (see Commandeur 1991, for an overview
of Procrustean models). Note that Procrustes transformations do not change the fit (stress
value) of an MDS.
In brief, Procrustes works as follows. Let X and Y be two MDS configuration matrices.
X is the target configuration, and Y the configuration subject to Procrustes transformation
leading to the transformed configuration matrix Ŷ. Further, let Z be a centering matrix
(Z = I − n−1 11⊤ ). Procrustes involves the following steps:

1. Compute C = X⊤ ZY.

2. Perform an SVD on C, i.e., C = PΦQ⊤ . Compute:

• rotation matrix: T = QP⊤ ,

• dilation factor: s = tr(X⊤ ZYT)/tr(Y⊤ ZY),
• translation vector t = n−1 (X − sYT⊤ )1.

3. Final solution: Ŷ = sYT + 1t⊤ .

The matrix Ŷ contains the Procrustes transformed configuration and replaces Y. The target
configuration X and Ŷ can be plotted jointly and allows researchers to explore potential
differences between the configurations.
The dataset we use to illustrate Procrustes is taken from Vaziri-Pashkam and Xu (2019). In
their fMRI experiment on visual object representations they used both natural and artificial
shape categories to study the activation of various brain regions (each object represents a
particular brain region). We start with fitting two ordinal MDS solutions, one for each
condition

R> artD <- sim2diss(VaziriXu$artificialR)

R> fitart <- mds(artD, type = "ordinal")
R> realD <- sim2diss(VaziriXu$realR)
R> fitnat <- mds(realD, type = "ordinal")

By plotting the two configurations, Figure 20 suggests that these configurations are different.
Let us apply a Procrustes transformation with the artificial condition as target configura-
tion X, and the natural condition solution as testee configuration Y, subject to Procrustes
transformation.

R> fitproc <- Procrustes(fitart$conf, fitnat$conf)

R> fitproc
38 smacof Version 2: Multidimensional Scaling and Unfolding in R

Configuration Artificial Configuration Natural

V4
IPS4 IPS1
VOT
1.0

0.5
IPS0 LO
Superior IPS
IPS2 V3B
IPS3
0.5

IPS2
Dimension 2

Dimension 2
Inferior IPS
V3A

0.0
V2
V1 Superior IPS V3

V3 IPS3
0.0

V3A IPS1

−0.5
IPS0
IPS4
V4 VOT V1
Inferior IPS V2
−0.5

LO V3B

−1.0 −0.5 0.0 0.5 1.0 −1.0 −0.5 0.0 0.5

Dimension 1 Dimension 1

Figure 20: Left panel: MDS configuration natural condition. Right panel: MDS configura-
tion artificial condition.

Call: Procrustes(X = fitart$conf, Y = fitnat$conf)

Congruence coefficient: 0.971

Alienation coefficient: 0.241

Rotation matrix:
D1 D2
D1 -0.826 -0.564
D2 0.564 -0.826

Translation vector: 0 0
Dilation factor: 0.906

The print output shows the rotation matrix, the dilation factor, and the translation vector
(which is always 0 if two MDS configurations are involved, due to normalization constraints).
In addition, it reports Tucker’s congruence coefficient for judging the similarity of two con-
figurations. This coefficient is derived from factor analysis and can be computed as follows:
dij (X)dij (Y)
P
i<j
c(X, Y) = qP qP (22)
i<j dij (X) i<j dij (Y)
2 2

A few remarks regarding the congruence coefficient. First, it is generally recommended that
one uses the congruence coefficient to judge configurational similarity and not the correlation
coefficient, since correlating distances does not properly assess the similarity of configurations
(see Borg and Groenen 2005, p. 439–440 for details). Second, there is actually no Procrustes
transformation needed to compute the congruence coefficient, since c(X, Y) = c(X, Ŷ).
Third, when applying (22) within an MDS context, the resulting value of c(X, Y) is gen-
erally high. In factor analysis, values in the range of 0.85–0.94 are considered to be “fairly
 Journal of Statistical Software 39

Procrustes Configuration Plot

IPS4
IPS4

1.0
IPS3

IPS3
0.5

IPS2
V2
V2 V1
Dimension 2

V1 IPS2
Superior IPS

V3 Superior IPS
Inferior IPS
0.0

V3A V3A IPS1

V3
IPS0 IPS1
V3B
IPS0

V4 VOT
LO Inferior IPS
−0.5

LO V3B
VOT V4

artificial
natural

−1.0 −0.5 0.0 0.5 1.0

Dimension 1

Figure 21: Procrustes on two MDS configurations: the configuration from the artificial
condition acts as target; the one from the natural condition is Procrustes transformed.

similar”, and values higher than 0.95 suggest that the two factors are considered equal (see
Lorenzo-Seva and Ten Berge 2006, for details).
As an alternative we can consider Guttman’s alienation coefficient, which is simply
q
K(X, Y) = 1 − c(X, Y)2 . (23)

This measure differentiates better between two solutions than the congruence coefficient.
Figure 21 shows the Procrustes transformed solution (i.e., plotting X and Ŷ jointly) and
suggests that the two configurations are actually very similar, apart from a few points. The
user can request the (sorted) distances between each pair of testee and target points via
fitproc$pairdist. V4, inferior IPS, IPS3, and V3B show the biggest differences across the
two conditions.

R> plot(fitproc, legend = list(labels = c("artificial", "natural")))

Another option to apply Procrustes is to use a theoretical configuration as target. For in-
stance, Borg and Leutner (1983) constructed rectangles on the basis of a grid design (as
contained in rect_constr) which we use as target configuration. Participants had to rate
similarity among rectangles within this grid. Based on these ratings a dissimilarity matrix
was constructed, here subject to a 2D ordinal MDS solution. Within the context of theoretical
solutions it is sometimes interesting to determine the stress value based on the dissimilarity
matrix and an initial configuration (with 0 iterations). The stress0 function does the job.

R> stress0(rectangles, init = rect_constr)

40 smacof Version 2: Multidimensional Scaling and Unfolding in R

Procrustes Configuration Plot

4 12
8
16

3
4 8 12 16

3
7
11
15
3 7 11 15
2

2
Dimension 2

2 6 10 14
6 14
1

1 5 9 13

9
1 5
0

13
−1

theoretical
observed

2 3 4 5 6 7

Dimension 1

Figure 22: Procrustes with theoretical grid as target configuration (blue dots).

Call:
stress0(delta = rectangles, init = rect_constr)

Model: Symmetric SMACOF

Number of objects: 16
Stress-1 value: 0.323
Number of iterations: 0

Now we fit an ordinal MDS model, using the theoretical rectangle alignment as starting value.
The resulting MDS configuration is used as testee configuration Y, subject to Procrustes.

R> fitrect <- mds(rectangles, type = "ordinal", init = rect_constr)

R> procRect <- Procrustes(rect_constr, fitrect$conf)
R> plot(procRect, legend = list(labels = c("theoretical", "observed")),
+ xlim = c(2, 7))

Figure 22 plots the rectangle grid and the Procrustes transformed configuration jointly. We
see clear differences, especially in the right end of the rectangle grid. These differences are
also reflect in the considerably high alienation coefficient of 0.35.
Note that Procrustes is not limited to MDS applications. It can be applied to any configu-
ration matrices X and Y as long as the objects involved are the same and the matrices have
the same dimensions. Other forms of generalized Procustes analysis are given in Borg and
Groenen (2005, Section 20.9).
 Journal of Statistical Software 41

8. Conclusion
In this follow-up paper to De Leeuw and Mair (2009b), who introduced the smacof package,
we presented numerous updates that have been implemented over the years. It is safe to
say that these developments establish smacof as the most comprehensive implementation of
MDS and unfolding techniques in R. Still, there are several tasks on our to-do list. First,
we plan to implement a fastMDS routine entirely written in C to speed up computations for
large data settings. Second, we will work on an implementation of inverse MDS (De Leeuw
and Groenen 1997). Third, we aim to extend spherical MDS and unfolding to more general
geometric shapes such as a pre-specified polygon mesh.

Acknowledgments
We would like to thank Ingwer Borg for his contributions to the smacof package and his
critical applied remarks which enhanced the usability of the package, and Frank Busing for
his contributions to the unfolding implementation and the sim2diss function. In addition,
we would like to thank three anonymous reviewers and the associate editor for their helpful
comments.

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 Journal of Statistical Software 47

Affiliation:
Patrick Mair
Department of Psychology
Harvard University
33 Kirkland Street
Cambridge, MA 02138, United States of America
E-mail: [email protected]
URL: http://scholar.harvard.edu/mair

Journal of Statistical Software https://www.jstatsoft.org/

published by the Foundation for Open Access Statistics https://www.foastat.org/
April 2022, Volume 102, Issue 10 Submitted: 2019-06-06
doi:10.18637/jss.v102.i10 Accepted: 2021-09-27