From f827997d266d11b558fd9e3a50d8d60f6e1447d4 Mon Sep 17 00:00:00 2001 From: jamesaazam Date: Mon, 4 Sep 2023 22:18:38 +0100 Subject: [PATCH] Add details about which offspring distributions are supported --- R/simulate.r | 5 ++++- man/simulate_tree_from_pop.Rd | 6 +++++- 2 files changed, 9 insertions(+), 2 deletions(-) diff --git a/R/simulate.r b/R/simulate.r index 21a3c555..6f7105b6 100644 --- a/R/simulate.r +++ b/R/simulate.r @@ -308,7 +308,10 @@ simulate_summary <- function(nchains, statistic = c("size", "length"), #' of each element), and `generation`. #' @details #' -#' # Offspring models +#' # Offspring distributions +#' Currently only "pois" & "nbinom" are supported. Internally truncated +#' distributions are used to avoid infecting more people than susceptibles +#' available. #' #' The poisson model is parametrised so that: #' diff --git a/man/simulate_tree_from_pop.Rd b/man/simulate_tree_from_pop.Rd index c7cecd3b..17b5ad2f 100644 --- a/man/simulate_tree_from_pop.Rd +++ b/man/simulate_tree_from_pop.Rd @@ -51,7 +51,11 @@ of each element), and \code{generation}. Simulate a tree of infections from an initial susceptible population with initial immunity } -\section{Offspring models}{ +\section{Offspring distributions}{ +Currently only "pois" & "nbinom" are supported. Internally truncated +distributions are used to avoid infecting more people than susceptibles +available. + The poisson model is parametrised so that: lamda = offspring_mean * pop - initial_immune / pop