Description Usage Arguments Details Value Author(s) Examples

View source: R/workflowPsiHP.R

Ideal for large analyses with hundreds to thousands of sequences. Several options available in `workflowPsi`

have been removed from this function in order to simplify the code as much as possible. Psi is computed with the options `diagonal = TRUE`

, `ignore.blocks = TRUE`

, and `method = "euclidean"`

.

1 2 3 4 5 6 7 |

`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 |

`parallel.execution` |
boolean, if |

Due to limitations of the function `permutations`

, the maximum number of groups (according to `grouping.column`

) is around 30000. Besides, a combinations table of this size takes, roughlyl, 7GB of memory.

A dataframe with sequence names and psi values.

Blas Benito <blasbenito@gmail.com>

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | ```
data("sequencesMIS")
#prepare sequences
MIS.sequences <- prepareSequences(
sequences = sequencesMIS[sequencesMIS$MIS %in% c("MIS-1", "MIS-2"), ],
grouping.column = "MIS",
if.empty.cases = "zero",
transformation = "hellinger"
)
#execute workflow to compute psi
MIS.psi <- workflowPsiHP(
sequences = MIS.sequences,
grouping.column = "MIS",
parallel.execution = FALSE
)
MIS.psi
``` |

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