From 7172ffd0df64fe5839cf8e787d4fa383fb2648c3 Mon Sep 17 00:00:00 2001
From: jamesaazam <james.azam@lshtm.ac.uk>
Date: Fri, 8 Mar 2024 10:37:34 +0000
Subject: [PATCH] Move obs_prob next to nsim_obs for logical flow

---
 R/likelihood.R    | 4 ++--
 man/likelihood.Rd | 6 +++---
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/R/likelihood.R b/R/likelihood.R
index 2d1668a4..ad768b0e 100644
--- a/R/likelihood.R
+++ b/R/likelihood.R
@@ -5,9 +5,9 @@
 #' @param chains Vector of chain summaries (sizes/lengths)
 #' @param nsim_obs Number of simulations if the log-likelihood/likelihood is to
 #' be approximated for imperfect observations.
+#' @param obs_prob Observation probability (assumed constant)
 #' @param log Logical; Should the log-likelihoods be transformed to
 #' likelihoods? (Defaults to TRUE).
-#' @param obs_prob Observation probability (assumed constant)
 #' @param exclude A vector of indices of the sizes/lengths to exclude from the
 #' log-likelihood calculation.
 #' @param individual If TRUE, a vector of individual log-likelihood/likelihood
@@ -42,7 +42,7 @@
 #' )
 #' @export
 likelihood <- function(chains, statistic = c("size", "length"), offspring_dist,
-                       nsim_obs, log = TRUE, obs_prob = 1, stat_max = Inf,
+                       nsim_obs, obs_prob = 1, log = TRUE, stat_max = Inf,
                        exclude = NULL, individual = FALSE, ...) {
   statistic <- match.arg(statistic)
 
diff --git a/man/likelihood.Rd b/man/likelihood.Rd
index 989880db..ecf4ce49 100644
--- a/man/likelihood.Rd
+++ b/man/likelihood.Rd
@@ -9,8 +9,8 @@ likelihood(
   statistic = c("size", "length"),
   offspring_dist,
   nsim_obs,
-  log = TRUE,
   obs_prob = 1,
+  log = TRUE,
   stat_max = Inf,
   exclude = NULL,
   individual = FALSE,
@@ -42,11 +42,11 @@ binomial offspring, or custom functions.}
 \item{nsim_obs}{Number of simulations if the log-likelihood/likelihood is to
 be approximated for imperfect observations.}
 
+\item{obs_prob}{Observation probability (assumed constant)}
+
 \item{log}{Logical; Should the log-likelihoods be transformed to
 likelihoods? (Defaults to TRUE).}
 
-\item{obs_prob}{Observation probability (assumed constant)}
-
 \item{stat_max}{A cut off for the chain statistic (size/length) being
 computed. Results above the specified value, are set to \code{Inf}.}