Merge branch 'main' into unexport-funcs

.github/dependabot.yml

@@ -12,4 +12,4 @@ updates:
       day: "monday"
       time: "06:00"
     labels:
-      - "package_infrastructure"
+      - "pkg_infrastructure"

R/borel.r

@@ -27,8 +27,12 @@ dborel <- function(x, mu, log = FALSE) {
 ##' Random numbers are generated by simulating from a Poisson branching process
 ##' @param n Number of random variates to generate.
 ##' @inheritParams dborel
-##' @param infinite Any number to treat as infinite; simulations will be
-##' stopped if this number is reached
+##' @param infinite A threshold above which the random number is set to
+##'  `Inf` as a form of truncation. This is important because `rborel()` uses
+##'  `simulate_summary()` internally with `offspring_dist = rpois`, so
+##'  when `mu >= 1`, the simulation could grow out of proportion and chain
+##'  summaries (the random numbers generated here) need to be truncated using
+##'  `infinite`.
 ##' @return Vector of random numbers
 ##' @author Sebastian Funk
 ##' @export

R/likelihood.R

@@ -3,9 +3,14 @@
 #' @inheritParams .offspring_ll
 #' @inheritParams simulate_summary
 #' @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 nsim_obs Number of simulations to be used to approximate the
+#' log-likelihood/likelihood if `obs_prob < 1` (imperfect observation). If
+#' `obs_prob == 1`, this argument is ignored.
+#' @param obs_prob Observation probability. A number (probability) between 0
+#' and 1. A value greater than 0 but less 1 implies imperfect observation and
+#' simulations will be used to approximate the (log)likelihood. This will
+#' also require specifying `nsim_obs`. In the simulation, the observation
+#' process is assumed to be constant.
 #' @param log Logical; Should the log-likelihoods be transformed to
 #' likelihoods? (Defaults to TRUE).
 #' @param exclude A vector of indices of the sizes/lengths to exclude from the