Code for reproducing analyses in the manuscript:
Takashi Okada, Giulio Isacchini, QinQin Yu, and Oskar Hallatschek
In this study, we developed a method for inferring the importation rates, i.e., the proportion of infections that a community imports from other communities, based on how rapidly the allele frequencies in the focal community converge to those in the donor communities.
The HMM-EM method is demonstrated using simulated data.
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INPUT
- Spatio-temporal data of allele (or lineage) counts.
- Spatio-temporal data of the total number of sampled sequences.
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OUTPUT
- Record of log likelihood across EM cycles.
- Inferred importation-rate matrix
${\mathbf A}_{ij}$ . - Inferred effective population size.
- Least squares estimation of
${\mathbf A}_{ij}$ .(noise ignored). - Inferred measurement noise overdispersion.
Miscellaneous tools used for analysis.
Data from England and the USA used in the analysis.
Data from England and USA used in analysis.