augur frequencies¶
infer frequencies of mutations or clades
usage: augur frequencies [-h] --method {diffusion,kde} --metadata FILE
[--regions REGIONS [REGIONS ...]]
[--pivot-interval PIVOT_INTERVAL]
[--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, as CSV or TSV
- --regions
region to subsample to
Default: [‘global’]
- --pivot-interval
number of months between pivots
Default: 3
- --min-date
minimal pivot value
- --max-date
maximal pivot value
- --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