orthobasis {ade4} | R Documentation |
These functions returns object of class 'orthobasis'
that
contains data frame defining an orthonormal basis.
orthobasic.neig
returns the eigen vectors of the matrix N-M where M is the symmetric n by n matrix of the between-sites neighbouring graph and N is the diagonal matrix of neighbour numbers.
orthobasis.line
returns the analytical solution for the linear neighbouring graph.
orthobasic.circ
returns the analytical solution for the circular neighbouring graph.
orthobsic.mat
returns the eigen vectors of the general link matrix M.
orthobasis.haar
returns wavelet haar basis.
orthobasis.neig(neig) orthobasis.line(n) orthobasis.circ(n) orthobasis.mat(mat, cnw=TRUE) orthobasis.haar(n) ## S3 method for class 'orthobasis' print(x,..., nr = 6, nc = 4) ## S3 method for class 'orthobasis' plot(x,...) ## S3 method for class 'orthobasis' summary(object,...) is.orthobasis(x)
neig |
is an object of class |
n |
is an integer that defines length of vectors |
mat |
is a n by n phylogenetic or spatial link matrix |
cnw |
if TRUE, the matrix of the neighbouring graph is modified to give Constant Neighbouring Weights |
x, object |
is an object of class |
nr, nc |
the number of rows and columns to be printed |
... |
: further arguments passed to or from other methods |
All the functions return an object of class orthobasis
containing a data frame.
This data frame defines an orthonormal basis with various attributes:
names |
names of the vectors |
row.names |
row names of the data frame |
class |
class |
values |
optional associated eigenvalues |
weights |
weights for the rows |
call |
: call |
the function orthobasis.haar
uses function wavelet.filter
from package waveslim.
Sébastien Ollier sebastien.ollier@u-psud.fr
Daniel Chessel
Misiti, M., Misiti, Y., Oppenheim, G. and Poggi, J.M. (1993) Analyse de signaux classiques par décomposition en ondelettes. Revue de Statistique Appliqu?e, 41, 5–32.
Cornillon, P.A. (1998) Prise en compte de proximit?s en analyse factorielle et comparative. Thèse, Ecole Nationale Supérieure Agronomique, Montpellier.
gridrowcol
that defines an orthobasis for square grid, phylog
that defines an orthobasis for phylogenetic tree, orthogram
and mld
# a 2D spatial orthobasis w <- gridrowcol(8, 8) if(adegraphicsLoaded()) { g1 <- s.value(w$xy, w$orthobasis[, 1:16], pleg.drawKey = F, pgri.text.cex = 0, ylim = c(0, 10), pori.inc = F, paxes.dr = F) g2 <- s1d.barchart(attr(w$orthobasis, "values"), p1d.hori = F, labels = names(attr(w$orthobasis, "values")), plabels.cex = 0.7) } else { par(mfrow = c(4, 4)) for(k in 1:16) s.value(w$xy, w$orthobasis[, k], cleg = 0, csi = 2, incl = FALSE, addax = FALSE, sub = k, csub = 4, ylim = c(0, 10), cgri = 0) par(mfrow = c(1, 1)) barplot(attr(w$orthobasis, "values")) } # Haar 1D orthobasis w <- orthobasis.haar(32) par(mfrow = c(8, 4)) par(mar = c(0.1, 0.1, 0.1, 0.1)) for (k in 1:31) { plot(w[, k], type = "S", xlab = "", ylab = "", xaxt = "n", yaxt = "n", xaxs = "i", yaxs = "i", ylim = c(-4.5, 4.5)) points(w[, k], type = "p", pch = 20, cex = 1.5) } # a 1D orthobasis w <- orthobasis.line(n = 33) par(mfrow = c(8, 4)) par(mar = c(0.1, 0.1, 0.1, 0.1)) for (k in 1:32) { plot(w[, k], type = "l", xlab = "", ylab = "", xaxt = "n", yaxt = "n", xaxs = "i", yaxs = "i", ylim = c(-1.5, 1.5)) points(w[, k], type = "p", pch = 20, cex = 1.5) } if(adegraphicsLoaded()) { s1d.barchart(attr(w, "values"), p1d.hori = F, labels = names(attr(w, "values")), plab.cex = 0.7) } else { par(mfrow = c(1, 1)) barplot(attr(w, "values")) } w <- orthobasis.circ(n = 26) #par(mfrow = c(5, 5)) #par(mar = c(0.1, 0.1, 0.1, 0.1)) # for (k in 1:25) # dotcircle(w[, k], xlim = c(-1.5, 1.5), cleg = 0) par(mfrow = c(1, 1)) #barplot(attr(w, "values")) ## Not run: # a spatial orthobasis data(mafragh) w <- orthobasis.neig(mafragh$neig) if(adegraphicsLoaded()) { s.value(mafragh$xy, w[, 1:8], pleg.drawKey = F) s1d.barchart(attr(w, "values"), p1d.hori = F) } else { par(mfrow = c(4, 2)) for(k in 1:8) s.value(mafragh$xy, w[, k], cleg = 0, sub = as.character(k), csub = 3) par(mfrow = c(1, 1)) barplot(attr(w, "values")) } # a phylogenetic orthobasis data(njplot) phy <- newick2phylog(njplot$tre) wA <- phy$Ascores wW <- phy$Wscores table.phylog(phylog = phy, wA, clabel.row = 0, clabel.col = 0.5) table.phylog(phylog = phy, wW, clabel.row = 0, clabel.col = 0.5) ## End(Not run)