R: Tree structured analysis of a state sequence object.

seqtree {TraMineR} | R Documentation

## Tree structured analysis of a state sequence object.

### Description

Facility for growing a regression tree for a state sequence object.

### Usage

    seqtree(formula, data = NULL, weighted = TRUE, min.size = 0.05,
      max.depth = 5, R = 1000, pval = 0.01, weight.permutation = "replicate",
      seqdist.args = list(method = "LCS", norm = "auto"), diss = NULL,
      squared = FALSE, first = NULL, minSize, maxdepth, seqdist_arg)

### Arguments

`formula` | a formula where the left hand side is a state sequence object (see `seqdef`) and the right hand specifies the candidate variables for partitioning the set of sequences.
`weighted` | Logical. If `TRUE`, use the weights of the state sequence object.
`data` | a data frame where variables in the formula will be searched
`min.size` | minimum number of cases in a node, in percentage if less than 1.
`max.depth` | maximum depth of the tree.
`R` | Number of permutations used to assess the significance of the split.
`pval` | Maximum p-value, in percent.
`weight.permutation` | Weights permutation method: "diss" (attach weights to the dissimilarity matrix), "replicate" (replicate case according to the `weights` arguments), "rounded-replicate" (replicate case according to the rounded `weights` arguments), "random-sampling" (random assignment of covariate profiles to the objects using distributions defined by the weights.)
`seqdist.args` | list of arguments directly passed to `seqdist`, only used if `diss=NULL`
`diss` | An optional dissimilarity matrix. If not provided, a dissimilarity matrix is computed using `seqdist` and `seqdist.args`
`squared` | Logical. If `TRUE`, the dissimilarity matrix is squared
`first` | Character. An optional variable name to force the first split.
`minSize` | Deprecated. Use `min.size` instead.
`maxdepth` | Deprecated. Use `max.depth` instead.
`seqdist_arg` | Deprecated. Use `seqdist.args` instead.

### Details

The function provides a simplified interface for applying `disstree` on state sequence objects.

The `seqtree` objects can be "plotted" with `seqtreedisplay`. A print method is also available which prints the medoid sequence for each terminal node.

### Value

A `seqtree` object with same attributes as `disstree` objects.

The leaf membership is in the first column of the fitted attribute. For example, the leaf memberships for a tree `dt` are in `dt$fitted[,1]`.

### Author(s)

Matthias Studer (with Gilbert Ritschard for the help page)

### References

Studer, M., G. Ritschard, A. Gabadinho and N. S. Müller (2011). Discrepancy analysis of state sequences, Sociological Methods and Research, Vol. 40(3), 471-510, doi: 10.1177/0049124111415372.

### See Also

`seqtreedisplay`, `disstree`

### Examples

    data(mvad)

    ## Defining a state sequence object
    mvad.seq <- seqdef(mvad[, 17:86])

    ## Growing a seqtree from Hamming distances:
    ##   Warning: The R=10 used here to save computation time is
    ##   much too small and will generate strongly unstable results.
    ##   We recommend to set R at least as R=1000.
    ##   To comply with this small R value, we set pval = 0.1.
    seqt <- seqtree(mvad.seq~ male + Grammar + funemp + gcse5eq + fmpr + livboth,
        data=mvad, R=10, pval=0.1, seqdist.arg=list(method="HAM", norm="auto"))
    print(seqt)

    ## Growing a seqtree from an existing distance matrix
    mvad.dhd <- seqdist(mvad.seq, method="DHD")
    seqt <- seqtree(mvad.seq~ male + Grammar + funemp + gcse5eq + fmpr + livboth,
        data=mvad, R=10, pval=0.1, diss=mvad.dhd)
    print(seqt)

    ### Following commands only work if GraphViz is properly installed
    ## Not run:
    seqtreedisplay(seqt, type="d", border=NA)
    seqtreedisplay(seqt, type="I", sortv=cmdscale(mvad.dhd, k=1))

    ## End(Not run)

[Package TraMineR version 2.2-2 Index]