Action: ARRANGE_POINTS

Module	dimred
Description	Usage
Arrange points in a low dimensional space so that the (transformed) distances between points in the low dimensional space match the dissimilarities provided in an input matrix.

Input

The arguments that serve as the input for this action are specified using one or more of the keywords in the following table.

Keyword	Type	Description
ARG	vector	the initial positions for the projections
TARGET	matrix	the matrix of target quantities that you would like to match
WEIGHTS	matrix	the matrix with the weights of the target quantities

Further details and examples

Text from manual goes here

Syntax

The following table describes the keywords and options that can be used with this action

Keyword	Type	Default	Description
ARG	input	none	the initial positions for the projections
TARGET	input	none	the matrix of target quantities that you would like to match
WEIGHTS	input	none	the matrix with the weights of the target quantities
MINTYPE	compulsory	conjgrad	the method to use for the minimisation
MAXITER	compulsory	1000	maximum number of optimization cycles for optimisation algorithms
CGTOL	compulsory	1E-6	the tolerance for the conjugate gradient minimization
NCYCLES	compulsory	5	the number of cycles of global optimization to attempt
BUFFER	compulsory	1.1	grid extent for search is (max projection - minimum projection) multiplied by this value
CGRID_SIZE	compulsory	10	number of points to use in each grid direction
FGRID_SIZE	compulsory	0	interpolate the grid onto this number of points -- only works in 2D
SMACTOL	compulsory	1E-4	the tolerance for the smacof algorithm
SMACREG	compulsory	0.001	this is used to ensure that we don't divide by zero when updating weights for SMACOF algorithm
NUMERICAL_DERIVATIVES	optional	false	calculate the derivatives for these quantities numerically
FUNC	optional	not used	a function that is applied on the distances between the points in the low dimensional space