seqalign {TraMineR} R Documentation

## 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)

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)


[Package TraMineR version 2.2-10 Index]