workflowPsi {distantia} | R Documentation |

If the sequences are not aligned (`paired.samples = FALSE`

), the function executes these steps.

Computes the autosum of the sequences with

`autoSum`

.Computes the distance matrix with

`distanceMatrix`

.Uses the distance matrix to compute the least cost matrix with

`leastCostMatrix`

.Extracts the cost of the least cost path with

`leastCost`

.Computes the dissimilarity measure

*psi*with the function`psi`

.Delivers an output of type "list" (default), "data.frame" or "matrix", depending on the user input, through

`formatPsi`

.

If the sequences are aligned (`paired.samples = TRUE`

), these steps are executed:

Computes the autosum of the sequences with

`autoSum`

.Sums the distances between paired samples with

`distancePairedSamples`

.Computes the dissimilarity measure

*psi*with the function`psi`

.Delivers an output of type "list" (default), "data.frame" or "matrix", depending on the user input, through

`formatPsi`

.

```
workflowPsi(
sequences = NULL,
grouping.column = NULL,
time.column = NULL,
exclude.columns = NULL,
method = "manhattan",
diagonal = FALSE,
format = "dataframe",
paired.samples = FALSE,
same.time = FALSE,
ignore.blocks = FALSE,
parallel.execution = TRUE
)
```

`sequences` |
dataframe with multiple sequences identified by a grouping column generated by |

`grouping.column` |
character string, name of the column in |

`time.column` |
character string, name of the column with time/depth/rank data. |

`exclude.columns` |
character string or character vector with column names in |

`method` |
character string naming a distance metric. Valid entries are: "manhattan", "euclidean", "chi", and "hellinger". Invalid entries will throw an error. |

`diagonal` |
boolean, if |

`format` |
string, type of output. One of: "data.frame", "matrix". If |

`paired.samples` |
boolean, if |

`same.time` |
boolean. If |

`ignore.blocks` |
boolean. If |

`parallel.execution` |
boolean, if |

A list, matrix, or dataframe, with sequence names and psi values.

Blas Benito <blasbenito@gmail.com>

```
data("sequencesMIS")
#prepare sequences
MIS.sequences <- prepareSequences(
sequences = sequencesMIS,
grouping.column = "MIS",
if.empty.cases = "zero",
transformation = "hellinger"
)
#execute workflow to compute psi
MIS.psi <- workflowPsi(
sequences = MIS.sequences[MIS.sequences$MIS %in% c("MIS-1", "MIS-2"), ],
grouping.column = "MIS",
time.column = NULL,
exclude.columns = NULL,
method = "manhattan",
diagonal = FALSE,
parallel.execution = FALSE
)
MIS.psi
```

[Package *distantia* version 1.0.2 Index]