Unfolding: Multidimensional Unfolding

In MultBiplotR: Multivariate Analysis Using Biplots in R

Multidimensional Unfolding

Description

Multidimensional Unfolding with some adaptations for vegetation analysis

Usage

Unfolding(A, ENV = NULL, TransAbund = "Gaussian Columns", offset = 0.5, 
weight = "All_1", Constrained = FALSE, 
TransEnv = "Standardize columns", 
InitConfig = "SVD", model = "Ratio", 
condition = "Columns", Algorithm = "SMACOF", 
OptimMethod = "CG", r = 2, maxiter = 100, 
tolerance = 1e-05, lambda = 1, omega = 0, plot = FALSE)

Arguments

A	The original proximities matrix
ENV	The matrix of environmental variables
TransAbund	Initial transformation of the abundances : "None", "Gaussian", "Column Percent", "Gaussian Columns", "Inverse Square Root", "Divide by Column Maximum")
offset	offset is the quantity added to the zeros of the table
weight	A matrix of weights for each cell of the table
Constrained	Should fit a constrained analysis
TransEnv	Transformation of the environmental variables
InitConfig	Init configuration for the algorithm
model	Type of model to be fitted: "Identity", "Ratio", "Interval" or "Ordinal".
condition	"Matrix", "Columns" to condition to the whole matrix or to each column
Algorithm	Algorithm to fit the model: "SMACOF", "GD", "Genefold"
OptimMethod	Optimization method for gradient descent
r	Dimension of the solution
maxiter	Maximum number of iterations in the algorithm
tolerance	Tolerace for the algorithm
lambda	First penalization parameter
omega	Second penalization parameter
plot	Should the results be plotted?

Details

ological data

Value

An object of class "Unfolding"

Author(s)

Jose Luis Vicente Villardon

References

Ver Articulos

Examples

unf=Unfolding(SpidersSp, ENV=SpidersEnv, model="Ratio", Constrained = FALSE, condition="Matrix")
plot(unf, PlotTol=TRUE, PlotEnv = FALSE)
plot(unf, PlotTol=TRUE, PlotEnv = TRUE)
cbind(unf$QualityVars, unf$Var_Fit)
unf2=Unfolding(SpidersSp, ENV=SpidersEnv, model="Ratio", Constrained = TRUE, condition="Matrix")
plot(unf2, PlotTol=FALSE, PlotEnv = TRUE, mode="s")
cbind(unf2$QualityVars, unf2$Var_Fit)

MultBiplotR documentation built on Nov. 21, 2023, 5:08 p.m.