R-universe - cygei (Cy Geismar)

pipetime - Tools to Time Pipe Operations

Enable users to measure and record the execution time of pipe operations (using |>) with optional logging to dataframes and output to the console.

Last updated

4.95 score 1 stars 6 scripts 157 downloads

linktree - Estimate Transmission Assortativity Coefficients

Estimates group transmission assortativity coefficients from transmission trees. Group transmission assortativity coefficients measure the tendency for individuals to transmit within their own group (e.g. age group, vaccination status, or location) compared to other groups. The package requires information on who infected whom, group membership for all individuals, and the relative sizes of each group in the population. For more details see Geismar et al. (2024) <doi:10.1371/journal.pone.0313037>.

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4.60 score 2 stars 4 scripts 185 downloads

mixtree - A Statistical Framework for Comparing Sets of Trees

Apply hypothesis testing methods to assess differences between sets of trees.

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4.30 score 1 stars 10 scripts 226 downloads

o2ools - Tools for 'outbreaker2'

Streamlines the post-processing, summarization, and visualization of 'outbreaker2' output via a suite of helper functions. Facilitates tidy manipulation of posterior samples, integration with case metadata, generation of diagnostic plots and summary statistics.

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3.48 score 10 scripts 562 downloads