Refactor patient flow function to separate out getting flow and finding number of closely related pairs - Githubissues

Snitkin-Lab-Umich / regentrans

regentrans: R package for investigating regional pathogen transmission using genomic data

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Refactor patient flow function to separate out getting flow and finding number of closely related pairs #31

Closed zenalapp closed 3 years ago

zenalapp commented 3 years ago

Allows to only find patient flow once, and then can find number of closely related pairs for different thresholds more quickly & efficiently.

Replacement functions:

[x] get_patient_flow(edge_df, paths = FALSE)
[x] summarize_inter_pairs(snv_dists, summary_fns = c('min'), threshs = seq(5,20,5))
[x] merge_inter_summaries(patient_flow = NULL, inter_pair_summary = NULL, fsp = NULL)

Other to dos:

[x] Add input checks
[x] Add unit tests (for checks and main functions)
[x] Update vignette