seqalign: Computation details about a pairwise alignment

In TraMineR: Trajectory Miner: a Sequence Analysis Toolkit

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.axis = 1, cex.plot, ...)

## 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.axis	Axis annotation magnification. See par.
digits	number of digits for printed output
cex.plot	Deprecated. Use cex.axis instead.
...	additional arguments passed to other functions

Details

There are print and plot methods for seqalign objects.

Value

Object of class seqalign

Author(s)

Alexis Gabadinho (plot.seqalign) and Matthias Studer (seqalign) (with Gilbert Ritschard for the help page)

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)

TraMineR documentation built on June 29, 2025, 3:01 p.m.