augur traits¶
Infer ancestral traits based on a tree.
usage: augur traits [-h] --tree TREE --metadata METADATA [--weights WEIGHTS]
--columns COLUMNS [COLUMNS ...] [--confidence]
[--sampling-bias-correction SAMPLING_BIAS_CORRECTION]
[--output-node-data OUTPUT_NODE_DATA] [--output OUTPUT]
Named Arguments¶
- --tree, -t
tree to perform trait reconstruction on
- --metadata
tsv/csv table with meta data
- --weights
tsv/csv table with equilibrium probabilities of discrete states
- --columns
metadata fields to perform discrete reconstruction on
- --confidence
record the distribution of subleading mugration states
Default: False
- --sampling-bias-correction
a rough estimate of how many more events would have been observed if sequences represented an even sample. This should be roughly the (1-sum_i p_i^2)/(1-sum_i t_i^2), where p_i are the equilibrium frequencies and t_i are apparent ones.(or rather the time spent in a particular state on the tree)
- --output-node-data
name of JSON file to save trait inferences to
- --output, -o
DEPRECATED. Same as –output-node-data
Note that missing data must be represented by a ? character. Missing data will currently be inferred.
What about missing data?¶
If you have strains with missing data then you must give them the value ?
.
For example, if you are running a reconstruction of country
and you don’t know the country for a particular strain, you must set country to ?
in the metadata file for that strain.
Note that anything else – empty strings, NA
, unknown
– will be interpretted as a valid value!
Currently there is no way to not infer the value of these missing data, but we are working on making this option available in the future.