Replaced a number of Rd links with Roxygen Markdown links so that ext…

…ernal links for those are anchored.

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: ergm
-Version: 4.7-7408
-Date: 2024-10-06
+Version: 4.7-7418
+Date: 2024-10-07
 Title: Fit, Simulate and Diagnose Exponential-Family Models for Networks
 Authors@R: c(
              person(c("Mark", "S."), "Handcock", role=c("aut"), email="[email protected]"),

R/data.R

@@ -489,7 +489,7 @@ NULL
 #' Longitudinal networks of positive affection within a monastery as a
 #' "network" object
 #' 
-#' Three \code{\link{network}} objects containing the "liking" nominations of
+#' Three [`network`] objects containing the "liking" nominations of
 #' Sampson's (1969) monks at the three time points.
 #' 
 #' Sampson (1969) recorded the social interactions among a group of monks while
@@ -585,7 +585,7 @@ NULL
 #' Cumulative network of positive affection within a monastery as a "network"
 #' object
 #' 
-#' A \code{\link{network}} object containing the cumulative "liking"
+#' A [`network`] object containing the cumulative "liking"
 #' nominations of Sampson's (1969) monks over the three time points.
 #' 
 #' Sampson (1969) recorded the social interactions among a group of monks while

R/ergm.R

@@ -26,7 +26,7 @@
 #' on a similar scheme.
 #' (For an overview of the package \insertCite{HuHa08e,KrHu23e}{ergm}, see \code{\link{ergm-package}}.)
 #' 
-#' @param formula An \R \code{\link{formula}} object, of the form
+#' @param formula An \R [`formula`], of the form
 #'   \code{y ~ <model terms>}, where \code{y} is a
 #'   \code{\link[network]{network}} object or a matrix that can be
 #'   coerced to a \code{\link[network]{network}} object.  For the
@@ -150,7 +150,7 @@
 #' \item{etamap}{The set of functions mapping the true parameter theta
 #' to the canonical parameter eta (irrelevant except in a curved exponential
 #' family model)}
-#' \item{formula}{The original \code{\link{formula}} entered into the \code{\link{ergm}} function.}
+#' \item{formula}{The original [`formula`] passed to [ergm()].}
 #' \item{target.stats}{The target.stats used during estimation (passed through from the Arguments)}
 #' \item{target.esteq}{Used for curved models to preserve the target mean values of the curved terms. It is identical to target.stats for non-curved models.}
 #' \item{constraints}{Constraints used during estimation (passed through from the Arguments)}

R/ergm.geodistn.R

@@ -21,13 +21,13 @@
 #' Calculate geodesic distance distribution for a network or edgelist
 #' 
 #' \code{ergm.geodistdist} calculates geodesic distance distribution for a
-#' given \code{\link{network}} and returns it as a vector.
+#' given [`network`] and returns it as a vector.
 #' 
 #' \code{ergm.geodistdist} is a network wrapper for \code{ergm.geodistn}, which
 #' calculates and returns the geodesic distance distribution for a given
 #' network via full_geodesic_distribution.C
 #' 
-#' @param nw \code{\link{network}} object over which distances should be
+#' @param nw [`network`] object over which distances should be
 #' calculated
 #' @param directed logical, should the network be treated as directed
 #' @param edgelist an edgelist representation of a network as an mx2 matrix
@@ -38,7 +38,7 @@
 #' geodesic length `i`
 #' \item `ans[n]` is the number of pairs of geodesic length
 #' infinity.  }
-#' @seealso See also the sna package \code{\link[sna]{geodist}} function
+#' @seealso See also the sna package [geodist()] function
 #' @examples
 #' 
 #' data(faux.mesa.high)

R/ergm.utility.R

@@ -110,20 +110,20 @@ degreedist.network <- function(object, print=TRUE, ...)
 #' Copy network- and vertex-level attributes between two network objects
 #' 
 #' An internal ergm utility function to copy the network-level attributes and
-#' vertex-level attributes from one \code{\link{network}} object to another,
+#' vertex-level attributes from one [`network`] object to another,
 #' ignoring some standard properties by default.
 #' 
 #' 
-#' @param to the \code{\link{network}} that attributes should be copied to
-#' @param from the \code{\link{network}} that attributes should be copied to
+#' @param to the [`network`] that attributes should be copied to
+#' @param from the [`network`] that attributes should be copied to
 #' @param ignore vector of charcter names of network attributes that should not
 #' be copied. Default is the standard list of network properties created by
-#' \code{\link{network.initialize}}
+#' [network.initialize()]
 #' @return returns the \code{to} network, with attributes copied from
 #' \code{from}
 #' @note does not check that networks are of the same size, etc
-#' @seealso \code{\link{set.vertex.attribute}},
-#' \code{\link{set.network.attribute}}
+#' @seealso [set.vertex.attribute()],
+#' [set.network.attribute()]
 #' @keywords internal
 #' @export nvattr.copy.network
 nvattr.copy.network <- function(to, from, ignore=c("bipartite","directed","hyper","loops","mnext","multiple","n")){

R/ergm_proposal.R

@@ -151,8 +151,8 @@ prune.ergm_conlist <- function(conlist){
 #' 
 #' 
 #' @aliases ergm_proposal.NULL ergm_proposal.ergm_proposal
-#' @param object Either a character, a \code{\link{formula}} or an
-#' \code{\link{ergm}} object.  The \code{\link{formula}} should be of the format documented in the `constraints` argument of [ergm()] and in the [ERGM constraints][ergmConstraint] documentation.
+#' @param object Either a character, a [`formula`] or an
+#' [`ergm`] object.  The [`formula`] should be of the format documented in the `constraints` argument of [ergm()] and in the [ERGM constraints][ergmConstraint] documentation.
 #' @param \dots Further arguments passed to other functions.
 #' @return Returns an ergm_proposal object: a list with class `ergm_proposal`
 #' containing the following named elements:

R/formula.utils.R

@@ -138,7 +138,7 @@ model.transform.formula <- function(object, theta, recipes, ...){
 
 #' Convert a curved ERGM into a corresponding "fixed" ERGM.
 #' 
-#' The generic \code{fix.curved} converts an \code{\link{ergm}} object or
+#' The generic \code{fix.curved} converts an [`ergm`] object or
 #' formula of a model with curved terms to the variant in which the curved
 #' parameters are fixed. Note that each term has to be treated as a special
 #' case.
@@ -157,7 +157,7 @@ model.transform.formula <- function(object, theta, recipes, ...){
 #' curved ERGM terms included with the \code{\link[=ergm-package]{ergm}}
 #' package. It does not work with curved terms not included in ergm.
 #' 
-#' @param object An \code{\link{ergm}} object or an ERGM formula. The curved
+#' @param object An [`ergm`] object or an ERGM formula. The curved
 #' terms of the given formula (or the formula used in the fit) must have all of
 #' their arguments passed by name.
 #' @param \dots Unused at this time.
@@ -213,7 +213,7 @@ fix.curved.formula <- function(object, theta, ...){
 #' Convert a curved ERGM into a form suitable as initial values for the same
 #' ergm. Deprecated in 4.0.0.
 #' 
-#' The generic \code{enformulate.curved} converts an \code{\link{ergm}} object
+#' The generic \code{enformulate.curved} converts an [`ergm`] object
 #' or formula of a model with curved terms to the variant in which the curved
 #' parameters embedded into the formula and are removed from the parameter
 #' vector. This is the form that used to be required by \code{\link{ergm}} calls.
@@ -228,7 +228,7 @@ fix.curved.formula <- function(object, theta, ...){
 #' \code{\link[=ergm-package]{ergm}} package. It does not work with curved
 #' terms not included in ergm.
 #' 
-#' @param object An \code{\link{ergm}} object or an ERGM formula. The curved
+#' @param object An [`ergm`] object or an ERGM formula. The curved
 #' terms of the given formula (or the formula used in the fit) must have all of
 #' their arguments passed by name.
 #' @param \dots Unused at this time.

R/get.node.attr.R

@@ -41,7 +41,7 @@
 #' attribute data into an ergm term.
 #' 
 #' 
-#' @param nw a \code{\link{network}} object
+#' @param nw a [`network`] object
 #' @param attrname the name of a nodal attribute, as a character string
 #' @param functionname the name of the calling function a character string;
 #' this is only used for the warning messages that accompany a halt

R/godfather.R

@@ -23,7 +23,7 @@
 #' 
 #' 
 #' @param formula An \code{\link{ergm}}-style formula, with a
-#'   \code{\link{network}} on its LHS.
+#'   [`network`] on its LHS.
 #' @param changes Either a matrix with three columns: tail, head, and
 #'   new value, describing the changes to be made; or a list of such
 #'   matrices to apply these changes in a sequence. For binary network
@@ -47,15 +47,15 @@
 #' @template verbose
 #'
 #' @return If \code{end.network==FALSE} (the default), an
-#'   \code{\link{mcmc}} object with the requested network statistics
+#'   [`mcmc`] object with the requested network statistics
 #'   associed with the network series produced by applying the
-#'   specified changes. Its \code{\link{mcmc}} attributes encode the
+#'   specified changes. Its [`mcmc`] attributes encode the
 #'   timing information: so \code{\link{start}(out)} gives the time
 #'   point associated with the first row returned, and
 #'   \code{\link{end}(out)} out the last. The "thinning interval" is
 #'   always 1.
 #' 
-#' If \code{end.network==TRUE}, return a \code{\link{network}} object,
+#' If \code{end.network==TRUE}, return a [`network`] object,
 #' representing the final network, with a matrix of statistics
 #' described in the previous paragraph attached to it as an
 #' \code{attr}-style attribute \code{"stats"}.

R/gof.ergm.R

@@ -29,7 +29,7 @@
 #' argument described above.
 #'
 #' @aliases gof.default
-#' @param object Either a formula or an \code{\link{ergm}} object.
+#' @param object Either a formula or an [`ergm`] object.
 #' See documentation for \code{\link{ergm}}.
 #' @param \dots Additional arguments, to be passed to lower-level functions.
 #' @param coef When given either a formula or an object of class ergm,

R/is.curved.R

@@ -21,7 +21,7 @@
 #' 
 #' Curvature is checked by testing if all model parameters are canonical.
 #' 
-#' @param object An \code{\link{ergm}} object or an ERGM formula.
+#' @param object An [`ergm`] object or an ERGM formula.
 #' @param \dots Arguments passed on to lower-level functions.
 #' @return \code{TRUE} if the object represents a
 #' curved exponential family; \code{FALSE} otherwise.

R/simulate.ergm.R

@@ -37,8 +37,8 @@
 #' More information can be found by looking at the documentation of
 #' \code{\link{ergm}}.
 #' 
-#' @param object Either a \code{\link{formula}} or an
-#' \code{\link{ergm}} object.  The \code{\link{formula}} should be of the form
+#' @param object Either a [`formula`] or an
+#' [`ergm`] object.  The [`formula`] should be of the form
 #' \code{y ~ <model terms>}, where \code{y} is a network object or a matrix
 #' that can be coerced to a \code{\link[network]{network}} object.  For the
 #' details on the possible \code{<model terms>}, see \code{\link{ergmTerm}}.
@@ -131,7 +131,7 @@
 #' representation or a list thereof, they have the following
 #' \code{\link{attr}}-style attributes: \describe{
 #'
-#' \item{`formula`}{The \code{\link{formula}} used to generate the
+#' \item{`formula`}{The [`formula`] used to generate the
 #' sample.}
 #'
 #' \item{`stats`}{An [`mcmc`] or [`mcmc.list`] object as above.}

man-roxygen/seed.R

@@ -8,4 +8,4 @@
 #  Copyright 2003-2024 Statnet Commons
 ################################################################################
 #' @param seed Seed value (integer) for the random number generator.  See
-#' \code{\link[base]{set.seed}}.
+#' [set.seed()].