Multidimensional Unfolding
Multidimensional Unfolding with some adaptations for vegetation analysis
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)
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 |
|
omega |
|
plot |
ological data
An object of class "Unfolding"
Jose Luis Vicente Villardon
Ver Articulos
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)
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