diff --git a/DESCRIPTION b/DESCRIPTION index 0cf0c8ea7..5272d06fd 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: ergm -Version: 4.7-7420 +Version: 4.7-7421 Date: 2024-10-07 Title: Fit, Simulate and Diagnose Exponential-Family Models for Networks Authors@R: c( diff --git a/R/mcmc.diagnostics.ergm.R b/R/mcmc.diagnostics.ergm.R index 526f15612..73c5ff839 100644 --- a/R/mcmc.diagnostics.ergm.R +++ b/R/mcmc.diagnostics.ergm.R @@ -85,20 +85,19 @@ mcmc.diagnostics.default <- function(object, ...) { #' observed network statistics. For that functionality, please use #' the GOF command: \code{gof(object, GOF=~model)}. #' -#' In fact, an ergm output \code{object} contains the matrix of -#' statistics from the MCMC run as component \code{$sample}. This -#' matrix is actually an object of class \code{mcmc} and can be used -#' directly in the \code{coda} package to assess MCMC -#' convergence. \emph{Hence all MCMC diagnostic methods available in -#' \code{coda} are available directly.} See the examples and -#' \url{https://www.mrc-bsu.cam.ac.uk/software/bugs/the-bugs-project-winbugs/coda-readme/}. +#' In fact, an [ergm()] output object contains the sample of +#' statistics from the last MCMC run as element `$sample`. If +#' missing data MLE is fit, the corresponding element is named +#' `$sample.obs`. These are objects of [`mcmc`] and can be used +#' directly in the \CRANpkg{coda} package to assess MCMC +#' convergence. #' #' More information can be found by looking at the documentation of #' [ergm()]. #' -#' @param center Logical: If TRUE, center the samples on the observed +#' @param center Logical: If `TRUE`, center the samples on the observed #' statistics. -#' @param esteq Logical: If TRUE, for statistics corresponding to +#' @param esteq Logical: If `TRUE`, for statistics corresponding to #' curved ERGM terms, summarize the curved statistics by their #' negated estimating function values (evaluated at the MLE of any curved #' parameters) (i.e., \eqn{\eta'_{I}(\hat{\theta})\cdot (g_{I}(Y)-g_{I}(y))} diff --git a/man/mcmc.diagnostics.Rd b/man/mcmc.diagnostics.Rd index 69fa0b235..f5cb109b5 100644 --- a/man/mcmc.diagnostics.Rd +++ b/man/mcmc.diagnostics.Rd @@ -23,10 +23,10 @@ mcmc.diagnostics(object, ...) \item{\dots}{Additional arguments, to be passed to plotting functions.} -\item{center}{Logical: If TRUE, center the samples on the observed +\item{center}{Logical: If \code{TRUE}, center the samples on the observed statistics.} -\item{esteq}{Logical: If TRUE, for statistics corresponding to +\item{esteq}{Logical: If \code{TRUE}, for statistics corresponding to curved ERGM terms, summarize the curved statistics by their negated estimating function values (evaluated at the MLE of any curved parameters) (i.e., \eqn{\eta'_{I}(\hat{\theta})\cdot (g_{I}(Y)-g_{I}(y))} @@ -79,13 +79,12 @@ to ensure that the mean statistics from the model match the observed network statistics. For that functionality, please use the GOF command: \code{gof(object, GOF=~model)}. -In fact, an ergm output \code{object} contains the matrix of -statistics from the MCMC run as component \code{$sample}. This -matrix is actually an object of class \code{mcmc} and can be used -directly in the \code{coda} package to assess MCMC -convergence. \emph{Hence all MCMC diagnostic methods available in -\code{coda} are available directly.} See the examples and -\url{https://www.mrc-bsu.cam.ac.uk/software/bugs/the-bugs-project-winbugs/coda-readme/}. +In fact, an \code{\link[=ergm]{ergm()}} output object contains the sample of +statistics from the last MCMC run as element \verb{$sample}. If +missing data MLE is fit, the corresponding element is named +\verb{$sample.obs}. These are objects of \code{\link[coda:mcmc]{mcmc}} and can be used +directly in the \CRANpkg{coda} package to assess MCMC +convergence. More information can be found by looking at the documentation of \code{\link[=ergm]{ergm()}}.