Function reference • provoc

Fitting a Model

provoc(): Proportions of Variants of Concern (provoc) Analysis

coverage_by_lineage_defs(): Summarise coverage by lineage/mutation combo

get_convergence(): Check if provoc converged

get_res(): Extract just the results of lineage estimation

Model diagnostics

autoplot(<provoc>): Plot a provoc object using ggplot2

plot(<provoc>): Plot the results of model fitting

residuals(<provoc>): Calculate the residuals of a provoc object

resid(<provoc>): Calculate the residuals of a provoc object

plot_resids(): Plot the residuals, by lineage

plot_lineages(): plot the similarities of lineage

lineage_similarity(): Finds and prints all similarities among lineage

predict(<provoc>): Predict using Proportions of Lineages

print(<provoc>): Print the results of lineage abundance estimation

summary(<provoc>): Summarise results of model fitting

print(<summary.provoc>): Print the summary of a provoc object

summarise_lineages(): Summarise the similarities in lineage matrices

Making and managing lineage definitions

astronomize(): Extract mutation list from a directory of constellation files.

constellation_lists: Lists of mutations per lineage, as per Constellations

usher_barcodes(): Obtain and clean barcodes file from usher_barcores in Freyja (or from disk)

covariants(): Gather CoVariants defintions

lineage_defs_from_list(): Create a lineage definition matrix from a list of lineages with their mutations

filter_lineages(): Filter lineage_defs for specific lineages, keeping mutations that are present in at least one lineage

extant_lineages(): Filter lineages active on a given date.

get_actual_defs(): Extract the actual lineage defitions used when fitting the models.

get_lineage_defs(): Extract the lineage definitions used as input for the model

get_lineage_info(): Gather information about lineages

lineage_facts: Facts about the lineages

Example data

Baaijens: Data from bioproject PRJNA741211 (Baaijens et al. (2022))

Helper functions

parse_ivar(): Parse Mutations from the ivar pipeline

parse_mutations(): Parse output of the Gromstole pipeline, from SNVs to AAs

pos_from_aa(): Find position from amino acid string.

add_coverage(): Add coverage of missing mutations to a data set

coverage_at_aa(): Get coverage at mutation positions.

Viewing lineage definitions

plot_lineage_defs(): Plot a lineage definition matrix

plot_lineage_defs2(): Compare two lineage definition matrices

plot_actual_defs(): Visualize how lineage definitions were used in analysis

Simulating data (deprecated for now)

simulate_coco(): Simulate counts and coverage from a lineage definition matrix

simulate_lineage_defs(): Simulate a small lineage matrix for testing