A trait set represent a collection of properties of taxons, for the use of initializing a tree. The traits are represented as text content in taxon=value form, for example, for a date trait, wecould have a content of chimp=1950,human=1991,neander=-10000. All white space is ignored, so they canbe put on multiple tabbed lines in the XML. The type of node in the tree determines what happes with this information. The default Node only recognizes 'date', 'date-forward' and 'date-backward' as a trait, but by creating custom Node classes other traits can be supported as well.
Initialize a trait set from a CSV/TSV file.
fileName, sep, taxonNameCol, traitValueCol, skipFirstRow, traitname, units, value, taxa, dateFormat
| type: java.lang.String |
| Name of CSV/TSV file to extract values from. |
| Required input |
| type: java.lang.String |
| Separator for CSV/TSV file. Default is TAB. |
| Optional input. Default: |
| type: java.lang.Integer |
| Index of column containing taxon names (Default 0). |
| Optional input. Default: 0 |
| type: java.lang.Integer |
| Index of column containing trait names (Default 1). |
| Optional input. Default: 1 |
| type: java.lang.Boolean |
| If true, skip first row. (Default false.) |
| Optional input. Default: false |
| type: java.lang.String |
| name of the trait, used as meta data name for the tree. Special traitnames that are recognized are 'age','date','date-forward' and 'date-backward'. |
| Required input |
| type: beast.base.evolution.tree.TraitSet$Units |
| name of the units in which values are posed, used for conversion to a real value. This can be [year, month, day] (default 'year') |
| Optional input |
| type: java.lang.String |
| traits encoded as taxon=value pairs separated by commas |
| Optional input |
| type: beast.base.evolution.alignment.TaxonSet |
| contains list of taxa to map traits to |
| Required input |
| type: java.lang.String |
| the date/time format to be parsed, (e.g., 'dd/M/yyyy') |
| Optional input |