linCombDist {RFLPtools} | R Documentation |
Linear Combination of Distances
Description
This function computes linear combinations of distances.
Usage
linCombDist(x, distfun1, w1, distfun2, w2, diag = FALSE, upper = FALSE)
Arguments
x |
object which is passed to |
distfun1 |
function used to compute an object of class |
w1 |
weight for result of |
distfun2 |
function used to compute an object of class |
w2 |
weight for result of |
diag |
see |
upper |
see |
Details
This function computes and returns the distance matrix computed by a linear combination of two distance matrices.
Value
linCombDist
returns an object of class "dist"
; cf. dist
.
Author(s)
Matthias Kohl Matthias.Kohl@stamats.de
References
Flessa, F., Kehl, A., Kohl, M. Analysing diversity and community structures using PCR-RFLP: a new software application. Molecular Ecology Resources 2013 Jul; 13(4):726-33.
Examples
## assume a shift in the measured bands
M <- rbind(c(550, 500, 300, 250), c(510, 460, 260, 210),
c(700, 650, 450, 400), c(550, 490, 310, 250))
dist(M)
diffDist(M)
## convex combination of dist and diffDist
linCombDist(M, distfun1 = dist, w1 = 0.5, distfun2 = diffDist, w2 = 0.5)
## linear combination
linCombDist(M, distfun1 = dist, w1 = 2, distfun2 = diffDist, w2 = 5)
## maximum distance
linCombDist(M, distfun1 = function(x) dist(x, method = "maximum"), w1 = 0.5,
distfun2 = function(x) diffDist(x, method = "maximum"), w2 = 0.5)
data(RFLPdata)
distfun <- function(x) linCombDist(x, distfun1 = dist, w1 = 0.1, distfun2 = diffDist, w2 = 0.9)
par(mfrow = c(2, 2))
plot(hclust(RFLPdist(RFLPdata, nrBands = 3, distfun = distfun)), cex = 0.7, cex.lab = 0.7)
RFLPplot(RFLPdata, nrBands = 3, distfun = distfun, mar.bottom = 6, cex.axis = 0.8)
plot(hclust(RFLPdist(RFLPdata, nrBands = 3)), cex = 0.7, cex.lab = 0.7)
RFLPplot(RFLPdata, nrBands = 3, mar.bottom = 6, cex.axis = 0.8)
[Package RFLPtools version 2.0 Index]