Description Usage Arguments Value Examples
Metaparameter selection for MDS models baseed on the Profile COPS approach (COPS Variant 2). It uses copstress for hyperparameter selection. It is a special case of a STOPS model.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28  pcops(
dis,
loss = c("stress", "smacofSym", "smacofSphere", "strain", "sammon", "rstress",
"powermds", "sstress", "elastic", "powersammon", "powerelastic", "powerstress",
"sammon2", "powerstrain", "apstress", "rpowerstress"),
weightmat = NULL,
ndim = 2,
init = NULL,
theta = c(1, 1, 1),
stressweight = 1,
cordweight,
q = 2,
minpts = ndim + 1,
epsilon = 100,
rang,
optimmethod = c("ALJ", "pso", "SANN", "DIRECT", "DIRECTL", "stogo", "MADS", "hjk"),
lower = c(1, 1, 0.5),
upper = c(5, 5, 2),
verbose = 0,
scale = c("proc", "sd", "none", "std"),
normed = TRUE,
s = 4,
stresstype = "default",
acc = 1e07,
itmaxo = 200,
itmaxi = 10000,
...
)

dis 
numeric matrix or dist object of a matrix of proximities 
loss 
which loss function to be used for fitting, defaults to strain. Currently allows for the following models:

weightmat 
(optional) a matrix of nonnegative weights; defaults to 1 for all off diagonals 
ndim 
number of dimensions of the target space 
init 
(optional) initial configuration. If not supplied, the Torgerson scaling result of the dissimilarity matrix dis^theta[2]/enorm(dis^theta[2],weightmat) is used. 
theta 
the theta vector of powers; the first is kappa (for the fitted distances if it exists), the second lambda (for the observed proximities if it exist), the third is nu (for the weights if it exists). If a scalar is given as argument, it will take the role designated by the loss argument (typially recycled). Defaults to 1 1 1 
stressweight 
weight to be used for the fit measure; defaults to 1 
cordweight 
weight to be used for the cordillera; if missing gets estimated from the initial configuration so that copstress = 0 for theta=c(1,1) 
q 
the norm of the cordillera; defaults to 1 
minpts 
the minimum points to make up a cluster in OPTICS; defaults to ndim+1 
epsilon 
the epsilon parameter of OPTICS, the neighbourhood that is checked; defaults to 10 
rang 
range of the minimum reachabilities to be considered. If missing it is found from the initial configuration by taking 1.5 times the maximal minimum reachability of the model with theta=c(1,1). If NULL it will be normed to each configuration's minimum and maximum distance, so an absolute value of goodnessofclusteredness. Note that the latter is not necessarily desirable when comparing configurations for their relative clusteredness. See also 
optimmethod 
What general purpose optimizer to use? Defaults to our adaptive LJ version (ALJ). Also allows particle swarm optimization with s particles ("pso") and simulated annealing ("SANN"), "DIRECT" and "DIRECTL", HookeJeeves ("hjk"), StoGo ("stogo"), and "MADS". We recommend not using SANN and pso with the rstress, sstress and the power stress models. We amde good experiences with ALJ, stogo, DIRECT and DIRECTL and also MADS. 
lower 
The lower contraints of the search region 
upper 
The upper contraints of the search region 
verbose 
numeric value hat prints information on the fitting process; >2 is extremely verbose. Note that for models with some parameters fixed, the iteration progress of the optimizer shows different values also for the fixed parameters because due to the modular setup we always optimize over a three parameter vector. These values are inconsequential however as internally they will be fixed. 
scale 
should the configuration be scaled and/or centered for calculating the cordillera? "std" standardizes each column of the configurations to mean=0 and sd=1 (typically not a good idea), "sd" scales the configuration by the maximum standard devation of any column (default), "proc" adjusts the fitted configuration to the init configuration (or the Togerson scaling solution if init=NULL). This parameter only has an effect for calculating the cordillera, the fitted and returned configuration is NOT scaled. 
normed 
should the cordillera be normed; defaults to TRUE 
s 
number of particles if pso is used 
stresstype 
what stress to be used for comparisons between solutions. Currently not implemented and pcops uses explicitly normalized stress for copstress (not stress1). Stress1 is reported by the print function though. 
acc 
termination threshold difference of two successive outer minimization steps. 
itmaxo 
iterations of the outer step (optimization over the hyperparmeters; if solver allows it). Defaults to 200. 
itmaxi 
iterations of the inner step (optimization of the MDS). Defaults to 10000 (whichis huge). 
... 
additional arguments to be passed to the optimization procedure 
A list with the components
copstress: the weighted loss value
OC: the OPTICS cordillera for the scaled configuration (as defined by scale)
optim: the object returned from the optimization procedure
stress: the stress (square root of stress.m)
stress.m: default normalized stress
parameters: the parameters used for fitting (kappa, lambda)
fit: the returned object of the fitting procedure
cordillera: the cordillera object
1 2 3 4 5 6 7 
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.