Class representing Multi Dimensional Scaling (MDS) projection.
returns the value of the stress criterion, minimized by the SMACOF algorithm.
returns a vector of nPoints dimension, containing the stress
indicator per point. The stress
minimization criterion can indeed be
allocated per represented point. The more the stress of a particular point,
the less accurate its distances w.r.t. the other points.
# S4 method for class 'MDS'
show(object)
nDim(x)
nPoints(x)
pwDist(x)
projections(x)
projDist(x)
stress(x)
spp(x)
eigenVals(x)
pctvar(x)
RSq(x)
RSqVec(x)
GoF(x)
smacofRes(x)
nothing
nDim
numeric
, nb of dimensions of the projection
pwDist
An object of class dist
storing
the triangular relevant part of the symmetric, zero diagonal
pairwise distance matrix (nPoints * nPoints), BEFORE projection.
proj
The projection matrix, resulting from MDS
projDist
An object of class dist
storing
the triangular relevant part of the symmetric, zero diagonal
pairwise distance matrix (nPoints * nPoints), AFTER projection.
eigen
numeric
, vector of nDim
length, containing the eigen
values of the PCA that is applied after the Smacof algorithm.
pctvar
numeric
, vector of nDim
length, containing the percentage
of explained variance per axis.
RSq
numeric
, vector of pseudo R square indicators,
as a function of number of dimensions.
RSq[nDim]
is the global pseudo R square, as displayed on plots.
GoF
numeric
, vector of goodness of fit indicators,
as a function of number of dimensions.
GoF[nDim]
is the global goodness of fit.
smacofRes
an object of class 'smacofB' containing the algorithmic
optimization results, for example stress and stress per point,
as returned by smacof::smacofSym()
method.
nHD <- 10
nLD <- 2
nPoints <- 20
# generate uniformly distributed points in 10 dimensions
points <- matrix(
data = runif(n = nPoints * nHD),
nrow = nPoints)
# calculate euclidian distances
pwDist <- dist(points)
# compute Metric MDS object by reaching a target pseudo RSquare
mdsObj <- computeMetricMDS(pwDist, targetPseudoRSq = 0.95)
#> Warning: RGL: unable to open X11 display
#> Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
show(mdsObj)
#> MDS object containing MDS projection (using Smacof algorithm) data:
#> Nb of dimensions: 7
#> Nb of points: 20
#> Stress: 0.035678
#> Pseudo RSquare: 0.964146
#> Goodness of fit: 0.998727