Skip to contents

Information about currently defined sequence data structures

Source: R/sequence.R
tda_seq_info.Rd

Runs TDA's seq; against the sequence structure(s) given – the same table TDA itself prints after defining them, listing each structure's number of state variables, its time axis, and the distinct states it actually contains.

Usage

tda_seq_info(
  sequences,
  data = NULL,
  options = list(),
  type = 1,
  dir = tempfile("tda"),
  ...
)

Arguments

sequences

a data frame or matrix, one row per case, one column per time point, in order – the same shape tda_seqm takes – or, given data too, a character vector naming those columns within it directly, rather than requiring a separately pre-subsetted data frame: real sequence data typically carries an ID column and covariates alongside the states in the same data frame (TDA's examples/exam/seq.d4, e.g.), not only the states on their own. For tda_seqev/tda_seqevd, also a list of several such specs, to define several independent sequence data structures at once – TDA's seqdef(sn=1), seqdef(sn=2), ... – the pattern TDA's own manual uses to build a second sequence structure from seq.d4's S0..S5 columns, entirely separate from the first (Y0..Y5), not a covariate of it. Use sn= to say which one a given call analyzes.

data

optional data frame sequences (and, for tda_seqmd, covariates) name columns within, instead of sequences/covariates being the actual data already.

options

a named list of further TDA options, passed through.

type

the sequence data type, TDA's seqdef m=: 1 (default) one column per time point, 2 columns read as state/time pairs, one pair per spell.

dir

working directory.

...

passed to tda_run.

Value

A data frame, one row per sequence structure: sn, type, variables (number of time points), tmin/tmax (the time axis), nstates, and states (a list column, the actual state values, since their count varies by structure).

See also

Other sequence analysis: tda_evalfi(), tda_fml(), tda_frml(), tda_seqgc(), tda_seqm(), tda_seqmd(), tda_seqpe(), tda_seqpm()

Examples

s <- data.frame(Y0 = c(1, 1, 2), Y1 = c(1, 2, 1), Y2 = c(2, 1, 1))
tda_seq_info(s)
#>   sn type variables tmin tmax nstates states
#> 1  1    1         3    0    2       2   1, 2

# several structures at once, the same way tda_seqev's sn= does
d <- data.frame(Y0 = c(1, 1, 2), Y1 = c(1, 2, 1), S0 = c(1, 3, 1),
                S1 = c(3, 1, 3))
tda_seq_info(list(c("Y0", "Y1"), c("S0", "S1")), data = d)
#>   sn type variables tmin tmax nstates states
#> 1  1    1         2    0    1       2   1, 2
#> 2  2    1         2    0    1       2   1, 3