augur frequencies

infer frequencies of mutations or clades

usage: augur frequencies [-h] --method {diffusion,kde} --metadata FILE
                         [--metadata-delimiters METADATA_DELIMITERS [METADATA_DELIMITERS ...]]
                         [--metadata-id-columns METADATA_ID_COLUMNS [METADATA_ID_COLUMNS ...]]
                         [--regions REGIONS [REGIONS ...]]
                         [--pivot-interval PIVOT_INTERVAL]
                         [--pivot-interval-units {months,weeks}]
                         [--min-date MIN_DATE] [--max-date MAX_DATE]
                         [--tree TREE] [--include-internal-nodes]
                         [--alignments ALIGNMENTS [ALIGNMENTS ...]]
                         [--gene-names GENE_NAMES [GENE_NAMES ...]]
                         [--ignore-char IGNORE_CHAR]
                         [--minimal-frequency MINIMAL_FREQUENCY]
                         [--narrow-bandwidth NARROW_BANDWIDTH]
                         [--wide-bandwidth WIDE_BANDWIDTH]
                         [--proportion-wide PROPORTION_WIDE]
                         [--weights WEIGHTS]
                         [--weights-attribute WEIGHTS_ATTRIBUTE] [--censored]
                         [--minimal-clade-size MINIMAL_CLADE_SIZE]
                         [--minimal-clade-size-to-estimate MINIMAL_CLADE_SIZE_TO_ESTIMATE]
                         [--stiffness STIFFNESS] [--inertia INERTIA]
                         [--output-format {auspice,nextflu}] [--output OUTPUT]

Named Arguments

--method

Possible choices: diffusion, kde

method by which frequencies should be estimated

--metadata

metadata including dates for given samples

--metadata-delimiters

delimiters to accept when reading a metadata file. Only one delimiter will be inferred.

Default: (',', '\t')

--metadata-id-columns

names of possible metadata columns containing identifier information, ordered by priority. Only one ID column will be inferred.

Default: ('strain', 'name')

--regions

region to filter to. Regions should match values in the ‘region’ column of the metadata file if specifying values other than the default ‘global’ region.

Default: ['global']

--pivot-interval

number of units between pivots

Default: 3

--pivot-interval-units

Possible choices: months, weeks

space pivots by months (default) or by weeks

Default: 'months'

--min-date

date to begin frequencies calculations; may be specified as: 1. an Augur-style numeric date with the year as the integer part (e.g. 2020.42) or 2. a date in ISO 8601 date format (i.e. YYYY-MM-DD) (e.g. ‘2020-06-04’) or 3. a backwards-looking relative date in ISO 8601 duration format with optional P prefix (e.g. ‘1W’, ‘P1W’)

--max-date

date to end frequencies calculations; may be specified as: 1. an Augur-style numeric date with the year as the integer part (e.g. 2020.42) or 2. a date in ISO 8601 date format (i.e. YYYY-MM-DD) (e.g. ‘2020-06-04’) or 3. a backwards-looking relative date in ISO 8601 duration format with optional P prefix (e.g. ‘1W’, ‘P1W’)

--tree, -t

tree to estimate clade frequencies for

--include-internal-nodes

calculate frequencies for internal nodes as well as tips

Default: False

--alignments

alignments to estimate mutations frequencies for

--gene-names

names of the sequences in the alignment, same order assumed

--ignore-char

character to be ignored in frequency calculations

Default: ''

--minimal-frequency

minimal all-time frequencies for a trajectory to be estimates

Default: 0.05

--narrow-bandwidth

the bandwidth for the narrow KDE

Default: 0.08333333333333333

--wide-bandwidth

the bandwidth for the wide KDE

Default: 0.25

--proportion-wide

the proportion of the wide bandwidth to use in the KDE mixture model

Default: 0.2

--weights

a dictionary of key/value mappings in JSON format used to weight KDE tip frequencies

--weights-attribute

name of the attribute on each tip whose values map to the given weights dictionary

--censored

calculate censored frequencies at each pivot

Default: False

--minimal-clade-size

minimal number of tips a clade must have for its diffusion frequencies to be reported

Default: 0

--minimal-clade-size-to-estimate

minimal number of tips a clade must have for its diffusion frequencies to be estimated

by the diffusion likelihood; all smaller clades will inherit frequencies from their parents

Default: 10

--stiffness

parameter penalizing curvature of the frequency trajectory

Default: 10.0

--inertia

determines how frequencies continue in absense of data (inertia=0 -> go flat, inertia=1.0 -> continue current trend)

Default: 0.0

--output-format

Possible choices: auspice, nextflu

format to export frequencies JSON depending on the viewing interface

Default: 'auspice'

--output, -o

JSON file to save estimated frequencies to