bcStressMin {stops} | R Documentation |
An MDS version for minimizing BoxCox Stress (Chen & Buja 2013)
bcStressMin(delta, init = NULL, verbose = 0, ndim = 2, mu = 1, lambda = 1, nu = 0, itmax = 5000, addD0 = 1e-04)
delta |
dissimilarity or distance matrix |
init |
initial configuration. If NULL a classical scaling solution is used. |
verbose |
prints progress if > 3. |
ndim |
the dimension of the configuration |
mu |
mu parameter. Should be 0 or larger for everything working ok. If mu<0 it works but the model is strange and normalized stress tends towards 0 regardless of fit. Use normalized stress at your own risk in that case. |
lambda |
lambda parameter. Must be larger than 0. |
nu |
the nu parameter. |
itmax |
number of optimizing iterations, defaults to 5000. |
addD0 |
a small number that's added for D(X)=0 for numerical evaluation of worst fit (numerical reasons, see details). If addD0=0 the normalized stress for mu!=0 and mu+lambda!=0 is correct, but will give useless normalized stress for mu=0 or mu+lambda!=0. |
For numerical reasons with certain parameter combinations, the normalized stress uses a configuration as worst result where every d(X) is 0+addD0. The same number is not added to the delta so there is a small inaccuracy of the normalized stress (but negligible of min(delta)>>addD0). Also, for mu<0 or mu+lambda<0 the normalization can not generally be trusted (in the worst case of D(X)=0 one would have an 0^(-a)).
Lisha Chen & Thomas Rusch
dis<-smacof::kinshipdelta res<-bcStressMin(as.matrix(dis),mu=2,lambda=1.5,nu=0) res summary(res) plot(res)