TraMineR (version 1.8-9)

seqalign: Computation details about a pairwise alignment

Description

The function provides details about a pairwise alignment.

Usage

seqalign(seqdata, indices, indel=1, sm, with.missing = FALSE)

## S3 method for class 'seqalign':
plot(x, cpal=NULL, missing.color=NULL,
    ylab=NULL, yaxis=TRUE, xaxis=TRUE, ytlab=NULL, ylas=0,
    xtlab=NULL, cex.plot=1, ...)

## S3 method for class 'seqalign':
print(x, digits=3, ...)

Arguments

seqdata

a state sequence object defined with the seqdef function.

indices

a vector of length 2 giving the indexes of the two sequences

indel

indel cost (see seqdist)

sm

matrix of substitution costs or a method for computing the costs (see seqdist)

with.missing

logical: Should the missing state be considered as an element of the alphabet?

x

an object of class seqalign

cpal

color palette

missing.color

color for missing elements

ylab

y label

yaxis

yaxis

xaxis

xaxis

ytlab

ytlab

ylas

ylas

xtlab

xtlab

cex.plot

plot font size

digits

number of digits for printed output

...

additional arguments passed to other functions

Value

• Object of class seqalign

encoding

latin1

Details

There are print and plot methods for seqalign objects.

See Also

seqdist

Examples

data(biofam)
biofam.seq <- seqdef(biofam, 10:25)
costs <- seqsubm(biofam.seq, method="TRATE")
sa <- seqalign(biofam.seq, 1:2, indel=1, sm=costs)
print(sa)
plot(sa)
sa <- seqalign(biofam.seq, c(1,5), indel=0.5, sm=costs)
print(sa)
plot(sa)