From 99539007407585f55c433e13959b2c780d651ae1 Mon Sep 17 00:00:00 2001 From: Sebastian Funk Date: Tue, 6 Feb 2024 13:23:44 +0000 Subject: [PATCH] update vignette text --- vignettes/epichains.Rmd | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/vignettes/epichains.Rmd b/vignettes/epichains.Rmd index ad56553b..89602da4 100644 --- a/vignettes/epichains.Rmd +++ b/vignettes/epichains.Rmd @@ -48,11 +48,12 @@ This function calculates the likelihood/loglikelihood of observing a vector of o `likelihood()` requires a vector of chain summaries (sizes or lengths), `chains`, the corresponding statistic to calculate, `statistic`, the offspring distribution, `offspring_dist` and its associated parameters. `offspring_dist` -is specified as the "base name" of the inbuilt distributions in R, for example, -"pois", "nbinom", etc. `likelihood()` also requires `nsim_offspring`, which is the -number of simulations to run if the likelihoods do not have a closed-form -solution and must be simulated. This argument will be explained further in -the next section. +is specified as the function that is used to generate random numbers, i.e. +`rpois` for Poisson, `rnbinom` for negative binomial, or a custom function. If no +the closed-form solution is available then simulated replicates are used to +estimate the likelihoods. In that case `likelihood()` also requires +`nsim_offspring`, which is the number of simulations to run . This argument will +be explained further in the next section. By default, the result is a log-likelihood but if `log = FALSE`, then likelihoods are returned.