Table 2.
Content of multiphyDat objects. The content of each slot can be accessed using ‘@[slot name]’, where ‘[slot name]’ is any of the values listed in the first column
| Slot name | Data stored | Description |
|---|---|---|
| seq a | list of phyDat objects | A list of phyDat objects, each storing sequences of a given locus/gene; names are optional, and if provided identify the genes; all matrices have the same individuals in rows, and nucleotide positions in columns |
| type | character vector | A character string indicating the type of sequences (e.g. DNA, protein) |
| labels | character vector | A vector of labels for the individuals |
| n.ind | integer | The number of individuals in the data set |
| n.seq | integer | The total number of sequences, pooling all genes, and including gap‐only sequences |
| n.seq.miss | integer | The total number of gap‐only sequences |
| ind.info a | data.frame | A data.frame containing information on the individuals, where individuals are in rows |
| gene.info a | data.frame | A data.frame containing information on the genes, where genes are in rows |
a
Slots whose content is NULL when empty.