Converted almost all documentation links to Rmarkdown; package links …

…are now almost all \CRANpkg{}; and a few documentation cleanups.

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: ergm
-Version: 4.7-7418
+Version: 4.7-7420
 Date: 2024-10-07
 Title: Fit, Simulate and Diagnose Exponential-Family Models for Networks
 Authors@R: c(

R/anova.ergm.R

@@ -47,19 +47,19 @@
 #' error, unless \code{eval.loglik=TRUE}.
 #' 
 #' @aliases anova.ergm anova.ergmlist
-#' @param object,... objects of class \code{\link{ergm}}, usually, a result of a
-#' call to \code{\link{ergm}}.
+#' @param object,... objects of [`ergm`], usually, a result of a
+#' call to [ergm()].
 #' @param eval.loglik a logical specifying whether the log-likelihood will be
 #' evaluated if missing.
 #' @return An object of class \code{"anova"} inheriting from class
 #' \code{"data.frame"}.
 #' @section Warning: The comparison between two or more models will only be
 #' valid if they are fitted to the same dataset. This may be a problem if there
 #' are missing values and 's default of \code{na.action = na.omit} is used, and
-#' \code{\link{anova.ergmlist}} will detect this with an error.
-#' @seealso The model fitting function \code{\link{ergm}}, \code{\link{anova}},
-#' \code{\link{logLik.ergm}} for adding the log-likelihood to an existing
-#' \code{\link[=ergm.object]{ergm}} object.
+#' [anova.ergmlist()] will detect this with an error.
+#' @seealso The model fitting function [ergm()], [anova()],
+#' [logLik.ergm()] for adding the log-likelihood to an existing
+#' [`ergm`] object.
 #' @keywords regression models
 #' @examples
 #' 

R/as.network.numeric.R

@@ -10,8 +10,8 @@
 
 #' Create a Simple Random network of a Given Size
 #' 
-#' \code{\link{as.network.numeric}} creates a random Bernoulli network of the
-#' given size as an object of class \code{\link[network]{network}}.
+#' [as.network.numeric()] creates a random Bernoulli network of the
+#' given size as an object of class [`network`].
 #' 
 #' The network will not have vertex, edge or network attributes.  These
 #' can be added with operators such as \code{\%v\%}, \code{\%n\%}, \code{\%e\%}.
@@ -40,8 +40,8 @@
 #' on this number of edges (rather than independently with the specified
 #' probability).
 #' @param ... additional arguments
-#' @return An object of class \code{\link[network]{network}}
-#' @seealso \code{\link[network]{network}}
+#' @return An object of class [`network`]
+#' @seealso [`network`]
 #' @references Butts, C.T.  2002.  ``Memory Structures for Relational Data in
 #' R: Classes and Interfaces'' Working Paper.
 #' @keywords classes graphs

R/check.ErgmTerm.R

@@ -13,10 +13,10 @@ ergm_Init_warn_once <- once(ergm_Init_warn)
 
 #' Ensures an Ergm Term and its Arguments Meet Appropriate Conditions
 #'
-#' Helper functions for implementing \code{\link[=ergm]{ergm()}}
+#' Helper functions for implementing [ergm()]
 #' terms, to check whether the term can be used with the specified
 #' network.  For information on ergm terms, see
-#' \link{ergmTerm}. \code{ergm.checkargs},
+#' [`ergmTerm`]. \code{ergm.checkargs},
 #' \code{ergm.checkbipartite}, and \code{ergm.checkderected} are
 #' helper functions for an old API and are deprecated. Use
 #' \code{check.ErgmTerm}.

R/control.ergm.R

@@ -10,7 +10,7 @@
 #' Auxiliary function for fine-tuning ERGM fitting.
 #' 
 #' This function is only used within a call to the [ergm()] function.
-#' See the \code{usage} section in [ergm()] for details. Also see the
+#' See the Usage section in [ergm()] for details. Also see the
 #' Details section about some of the interactions between its
 #' arguments.
 #'
@@ -125,7 +125,7 @@
 #'
 #' @param MPLE.type One of `"glm"`, `"penalized"`, or
 #' `"logitreg"`.  Chooses method of calculating MPLE.  `"glm"` is the
-#' usual formal logistic regression called via \code{\link{glm}}, whereas
+#' usual formal logistic regression called via [glm()], whereas
 #' `"penalized"` uses the bias-reduced method of Firth (1993) as
 #' originally implemented by Meinhard Ploner, Daniela Dunkler, Harry
 #' Southworth, and Georg Heinze in the "logistf" package. `"logitreg"` is
@@ -215,14 +215,14 @@
 #' @param MCMC.addto.se Whether to add the standard errors induced by the MCMC
 #' algorithm to the estimates' standard errors.
 #' @param SAN.maxit When \code{target.stats} argument is passed to
-#' [ergm()], the maximum number of attempts to use \code{\link{san}}
+#' [ergm()], the maximum number of attempts to use [san()]
 #' to obtain a network with statistics close to those specified.
 #' @param SAN.nsteps.times Multiplier for \code{SAN.nsteps} relative to
 #' \code{MCMC.burnin}. This lets one control the amount of SAN burn-in
 #' (arguably, the most important of SAN parameters) without overriding the
 #' other `SAN` defaults.
-#' @param SAN Control arguments to \code{\link{san}}.  See
-#' \code{\link{control.san}} for details.
+#' @param SAN Control arguments to [san()].  See
+#' [control.san()] for details.
 #' @param MCMLE.termination The criterion used for terminating MCMLE
 #' estimation:  
 #' * `"Hummel"` Terminate when the Hummel step length is
@@ -480,17 +480,17 @@
 #'   Note that only the Hotelling's stopping criterion is implemented
 #'   for CD.
 #' 
-#' @param loglik See \code{\link{control.ergm.bridge}}
+#' @param loglik See [control.ergm.bridge()]
 #' @template term_options
 #' @template control_MCMC_parallel
 #' @template seed
 #' @template control_MCMC_packagenames
 #' @template control_dots
 #'
 #' @return A list with arguments as components.
-#' @seealso [ergm()]. The \code{\link{control.simulate}} function
-#' performs a similar function for \code{\link{simulate.ergm}};
-#' \code{\link{control.gof}} performs a similar function for \code{\link{gof}}.
+#' @seealso [ergm()]. The [control.simulate()] function
+#' performs a similar function for [simulate.ergm()];
+#' [control.gof()] performs a similar function for [gof()].
 #' @references \insertAllCited{}
 #'
 #' * Firth (1993), Bias Reduction in Maximum Likelihood Estimates.

R/control.gof.R

@@ -51,8 +51,8 @@
 #' Auxiliary function as user interface for fine-tuning ERGM Goodness-of-Fit
 #' Evaluation.
 #' 
-#' This function is only used within a call to the \code{\link{gof}} function.
-#' See the \code{usage} section in \code{\link{gof}} for details.
+#' This function is only used within a call to the [gof()] function.
+#' See the Usage section in [gof()] for details.
 #' 
 #' @aliases control.gof control.gof.formula control.gof.ergm
 #'
@@ -76,10 +76,10 @@
 #' @template seed
 #' @template control_MCMC_packagenames
 #' @return A list with arguments as components.
-#' @seealso \code{\link{gof}}. The \code{\link{control.simulate}} function
-#' performs a similar function for \code{\link{simulate.ergm}};
-#' \code{\link{control.ergm}} performs a similar function for
-#' \code{\link{ergm}}.
+#' @seealso [gof()]. The [control.simulate()] function
+#' performs a similar function for [simulate.ergm()];
+#' [control.ergm()] performs a similar function for
+#' [ergm()].
 #' @name control.gof
 #' @export control.gof.ergm
 control.gof.formula<-function(nsim=100,

R/control.logLik.ergm.R

@@ -18,7 +18,7 @@
 #' @details `control.logLik.ergm()` is only used within a call to the
 #'   [logLik.ergm()].
 #'
-#' @seealso \code{\link{logLik.ergm}}
+#' @seealso [logLik.ergm()]
 #' @export control.logLik.ergm
 control.logLik.ergm<-function(bridge.nsteps=16,
                               bridge.target.se=NULL,

R/control.san.R

@@ -14,8 +14,8 @@
 #' Auxiliary function as user interface for fine-tuning simulated annealing
 #' algorithm.
 #' 
-#' This function is only used within a call to the \code{\link{san}} function.
-#' See the \code{usage} section in \code{\link{san}} for details.
+#' This function is only used within a call to the [san()] function.
+#' See the Usage section in [san()] for details.
 #'
 #' @templateVar MCMCType SAN
 #'
@@ -51,7 +51,7 @@
 #' @template control_MCMC_parallel
 #' @template seed
 #' @return A list with arguments as components.
-#' @seealso \code{\link{san}}
+#' @seealso [san()]
 #' @keywords models
 #' @export control.san
 control.san<-function(SAN.maxit=4,

R/control.simulate.R

@@ -15,8 +15,8 @@
 #' `control.simulate.formula.ergm` are all aliases for the same
 #' function.
 #' 
-#' This function is only used within a call to the \code{\link{simulate}}
-#' function.  See the \code{usage} section in \code{\link{simulate.ergm}} for
+#' This function is only used within a call to the ERGM [simulate()]
+#' function.  See the Usage section in [simulate.ergm()] for
 #' details.
 #'
 #' @templateVar MCMCType MCMC
@@ -49,10 +49,10 @@
 #' @template control_MCMC_packagenames
 #' @template control_dots
 #' @return A list with arguments as components.
-#' @seealso \code{\link{simulate.ergm}}, \code{\link{simulate.formula}}.
-#' \code{\link{control.ergm}} performs a similar function for
-#' \code{\link{ergm}}; \code{\link{control.gof}} performs a similar function
-#' for \code{\link{gof}}.
+#' @seealso [simulate.ergm()], [simulate.formula()].
+#' [control.ergm()] performs a similar function for
+#' [ergm()]; [control.gof()] performs a similar function
+#' for [gof()].
 #'
 #' @name control.simulate.ergm
 #' @keywords models