augur traits

Contents

• augur traits

  • Named Arguments

  • What about missing data?

Infer ancestral traits based on a tree.

usage: augur traits [-h] --tree TREE --metadata METADATA --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

--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.