ade4: dudi – R documentation

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dudi

Duality Diagram

Description

as.dudi is called by many functions (dudi.pca, dudi.coa, dudi.acm, ...) and not directly by the user. It creates duality diagrams.

t.dudi returns an object of class 'dudi' where the rows are the columns and the columns are the rows of the initial dudi.

is.dudi returns TRUE if the object is of class dudi

redo.dudi computes again an analysis, eventually changing the number of kept axes. Used by other functions.

Usage

as.dudi(df, col.w, row.w, scannf, nf, call, type, tol = 1e-07, 
    full = FALSE) 
## S3 method for class 'dudi'
print(x, ...) 
is.dudi(x) 
redo.dudi(dudi, newnf = 2) 
## S3 method for class 'dudi'
t(x)
## S3 method for class 'dudi'
summary(object, ...) 
## S3 method for class 'dudi'
x[i,j]

Arguments

`df`	a data frame with n rows and p columns
`col.w`	a numeric vector containing the row weights
`row.w`	a numeric vector containing the column weights
`scannf`	a logical value indicating whether the eigenvalues bar plot should be displayed
`nf`	if scannf FALSE, an integer indicating the number of kept axes
`call`	generally `match.call()`
`type`	a string of characters : the returned list will be of class `c(type, "dudi")`
`tol`	a tolerance threshold for null eigenvalues (a value less than tol times the first one is considered as null)
`full`	a logical value indicating whether all non null eigenvalues should be kept
`x, dudi, object`	objects of class `dudi`
`...`	further arguments passed to or from other methods
`newnf`	an integer indicating the number of kept axes
`i,j`	elements to extract (integer or empty): index of rows (i) and columns (j)

Value

as.dudi and all the functions that use it return a list with the following components :

`tab`	a data frame with n rows and p columns
`cw`	column weights, a vector with n components
`lw`	row (lines) weights, a vector with p components
`eig`	eigenvalues, a vector with min(n,p) components
`nf`	integer, number of kept axes
`c1`	principal axes, data frame with p rows and nf columns
`l1`	principal components, data frame with n rows and nf columns
`co`	column coordinates, data frame with p rows and nf columns
`li`	row coordinates, data frame with n rows and nf columns
`call`	original call

Author(s)

Daniel Chessel
Anne-Béatrice Dufour anne-beatrice.dufour@univ-lyon1.fr
Stéphane Dray stephane.dray@univ-lyon1.fr

References

Escoufier, Y. (1987) The duality diagram : a means of better practical applications In Development in numerical ecology, Legendre, P. & Legendre, L. (Eds.) NATO advanced Institute, Serie G. Springer Verlag, Berlin, 139–156.

Examples

data(deug)
dd1 <- dudi.pca(deug$tab, scannf = FALSE)
dd1
t(dd1)
is.dudi(dd1)
redo.dudi(dd1,3)
summary(dd1)

ade4

Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences

v1.7-16

GPL (>= 2)

Authors

Stéphane Dray <stephane.dray@univ-lyon1.fr>, Anne-Béatrice Dufour <anne-beatrice.dufour@univ-lyon1.fr>, and Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>, with contributions from Thibaut Jombart, Sandrine Pavoine, Jean R. Lobry, Sébastien Ollier, Daniel Borcard, Pierre Legendre, Stéphanie Bougeard and Aurélie Siberchicot. Based on earlier work by Daniel Chessel.

Initial release