From 8188b6380d3e955f9c7f151003c7c07ff4f21f2c Mon Sep 17 00:00:00 2001 From: James Azam Date: Thu, 31 Aug 2023 17:09:25 +0100 Subject: [PATCH] Cleaned up the changelog --- NEWS.md | 43 ++++++++++++++++++++++++------------------- 1 file changed, 24 insertions(+), 19 deletions(-) diff --git a/NEWS.md b/NEWS.md index e83021b4..228aab65 100644 --- a/NEWS.md +++ b/NEWS.md @@ -3,32 +3,37 @@ ## Package name change * `epichains` is a re-implementation of `bpmodels` with a focus on providing -a dedicated class of data structures for easy manipulation and interoperability -with other new tools in the pipeline. + a dedicated class of data structures for easy manipulation and interoperability + with other new tools in the pipeline. -### Features +### Functions * `simulate_tree()`: simulate transmission trees from a given number of chains. -* `simulate_tree_from_pop()`: simulate transmission trees from a given number +* `simulate_tree_from_pop()`: simulate transmission trees from a given population size and initial immunity. -* `simulate_vect()`: simulate a vector of observed transmission chains +* `simulate_summary()`: simulate a vector of observed transmission chains sizes/lengths from a given number of chains. -* `estimate_likelihood()`: estimate the likelihood/loglikelihood of observing +* `likelihood()`: estimate the likelihood/loglikelihood of observing chains of given sizes/lengths. -#### Classes - -* An `epichains` class: - * superclass of `data.frame` with attributes for tracking `chain_type` as: - * `chains_tree`, if returned from `simulate_tree()` or - `simulate_tree_from_pop()` - * `chains_vec`, if returned from `simulate_vect()`. -* An `epichains_aggregate_df` class: - * superclass of `data.frame` with attributes for tracking if aggregation is - done over "time", "generation" or "both". Useful for `plot` method dispatch - (see methods section below). - -#### Methods +### Classes + +* An `epichains` class, which inherits from `data.frame` with attributes for + tracking: + - `chains`: number of chains simulated + - `chain_type`: + - `chains_tree`, if returned from `simulate_tree()` or + `simulate_tree_from_pop()` + - `chains_summary`, if returned from `simulate_summary()`. + - `track_pop`: whether the susceptible population is tracked or not. +* An `epichains_aggregate_df` class, which inherits from `data.frame` with + attributes for tracking: + - `chain_type`: as defined above, and + - `aggregated_over`: the variable(s) over which aggregation was done: "time", + "generation" or "both". Useful for easy plotting with the `plot` method (see + methods section below). + +### Methods * `print()` * `summary()`