Converted as many links as possible to Roxygen2 Markdown and roxygeni…

…zed to anchor external links.

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: tergm
-Version: 4.2-2562
+Version: 4.2-2563
 Date: 2024-10-08
 Title: Fit, Simulate and Diagnose Models for Network Evolution Based on Exponential-Family Random Graph Models
 Authors@R: c(
@@ -47,7 +47,7 @@ Description: An integrated set of extensions to the 'ergm' package to analyze an
 License: GPL-3 + file LICENSE
 URL: https://statnet.org
 VignetteBuilder: rmarkdown, knitr
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.2.9000
 Roxygen: list(markdown = TRUE)
 Config/testthat/parallel: true
 Config/testthat/edition: 3

R/InitErgmProposal.DynMoME.R

@@ -32,7 +32,7 @@ InitErgmProposal.discordTNT <- function(arguments, nw, ...) {
 #' @templateVar name discordBDStratTNT
 #' @aliases InitErgmProposal.discordBDStratTNT
 #' @title Temperal TNT proposal with degree bounds
-#' @description A temporal version of \code{\link[ergm:ergm-proposals]{BDStratTNT}}.  Within each
+#' @description A temporal version of \code{\link[ergm:BDStratTNT-ergmProposal]{BDStratTNT}}.  Within each
 #'   mixing type, approximately 50\% of proposed toggles are made on
 #'   dyads, and approximately 50\% of proposed toggles are
 #'   proposals from the network, all subject to the bounded degree

R/InitErgmTerm.netseries.R

@@ -47,7 +47,7 @@ join_nets <- function(nwl, blockID, blockName){
 #'
 #' @param NA.impute How missing dyads in transitioned-from networks
 #'   are be imputed when using conditional estimation. See argument
-#'   \code{imputers} of \code{\link{impute.network.list}} for details.
+#'   \code{imputers} of [impute.network.list()] for details.
 #'
 #' @return A network object with temporal metadata.
 #'
@@ -59,7 +59,7 @@ join_nets <- function(nwl, blockID, blockName){
 #'   It is almost always better to modify the original networks and
 #'   regenerate the series.
 #'
-#' @seealso [Help on model specification][ergm-terms] for specific terms.
+#' @seealso [`ergmTerm`] for specific terms.
 #' 
 #' @examples
 #'

R/control.simulate.stergm.R

@@ -76,17 +76,17 @@ control.simulate.network <- function(MCMC.burnin.min = 1000,
 #' 
 #' Auxiliary function as user interface for fine-tuning STERGM simulation.
 #' 
-#' This function is only used within a call to the \code{\link{simulate}}
-#' function.  See the \code{usage} section in \code{\link{simulate.stergm}} for
+#' This function is only used within a call to the [simulate()]
+#' function.  See the Usage section in [simulate.stergm()] for
 #' details.
 #'
 #' These functions are included for backwards compatibility, and users are  
 #' encouraged to use \code{control.simulate.tergm} or
-#' \code{control.simulate.formula.tergm} with the \code{\link{simulate.tergm}}
+#' \code{control.simulate.formula.tergm} with the [simulate.tergm()]
 #' family of functions instead.  When a
 #' \code{control.simulate.stergm} or \code{control.simulate.network} object 
-#' is passed to one of the \code{\link{simulate.stergm}} functions, 
-#' the corresponding \code{\link{simulate.tergm}} function is invoked,
+#' is passed to one of the [simulate.stergm()] functions, 
+#' the corresponding [simulate.tergm()] function is invoked,
 #' and uses the formation proposal control arguments, ignoring the 
 #' dissolution proposal control arguments.
 #' 
@@ -113,7 +113,7 @@ control.simulate.network <- function(MCMC.burnin.min = 1000,
 #' 
 #' @param MCMC.prop.weights.form Specifies the proposal weighting scheme to 
 #'   be used in the MCMC Metropolis-Hastings algorithm.  Possible
-#'   choices may be determined by calling \code{\link{ergm_proposal_table}}.
+#'   choices may be determined by calling [ergm_proposal_table()].
 #' 
 #' @param MCMC.prop.args.form An alternative,
 #'   direct way of specifying additional arguments to proposals.
@@ -135,9 +135,9 @@ control.simulate.network <- function(MCMC.burnin.min = 1000,
 #' 
 #' @return A list with arguments as components.
 #' 
-#' @seealso \code{\link{simulate.stergm}},
-#'   \code{\link{simulate.formula}}.  \code{\link{control.stergm}}
-#'   performs a similar function for \code{\link{stergm}}.
+#' @seealso [simulate.stergm()],
+#'   [simulate.formula()].  [control.stergm()]
+#'   performs a similar function for [stergm()].
 #'
 #' @keywords models
 #'

R/control.simulate.tergm.R

@@ -12,8 +12,8 @@
 #' 
 #' Auxiliary function as user interface for fine-tuning TERGM simulation.
 #' 
-#' This function is only used within a call to the \code{\link{simulate}}
-#' function.  See the \code{usage} section in \code{\link{simulate.tergm}} for
+#' This function is only used within a call to the [simulate()]
+#' function.  See the Usage section in [simulate.tergm()] for
 #' details.
 #' 
 #' @param
@@ -36,7 +36,7 @@
 #'
 #' @param MCMC.prop.weights Specifies the proposal weighting scheme to 
 #'   be used in the MCMC Metropolis-Hastings algorithm.  Possible
-#'   choices may be determined by calling \code{\link{ergm_proposal_table}}.
+#'   choices may be determined by calling [ergm_proposal_table()].
 #'
 #' @param MCMC.prop.args An alternative, direct way of specifying 
 #'   additional arguments to the proposal.
@@ -54,9 +54,9 @@
 #'
 #' @return A list with arguments as components.
 #'
-#' @seealso \code{\link{simulate.tergm}},
-#'   \code{\link{simulate.formula}}.  \code{\link{control.tergm}}
-#'   performs a similar function for \code{\link{tergm}}.
+#' @seealso [simulate.tergm()],
+#'   [simulate.formula()].  [control.tergm()]
+#'   performs a similar function for [tergm()].
 #'
 #' @keywords models
 #'

R/control.stergm.R

@@ -18,8 +18,8 @@
 #' 
 #' Auxiliary function as user interface for fine-tuning 'stergm' fitting.
 #' 
-#' This function is only used within a call to the \code{\link{stergm}}
-#' function.  See the \code{usage} section in \code{\link{stergm}} for details.
+#' This function is only used within a call to the [stergm()]
+#' function.  See the Usage section in [stergm()] for details.
 #' Generally speaking, \code{control.stergm} is remapped to \code{control.tergm},
 #' with dissolution controls ignored and formation controls used as controls
 #' for the overall \code{tergm} process.  An exception to this rule is the
@@ -49,14 +49,14 @@
 #' 
 #'   \item Initial values for the elements that are \code{NA} are fit
 #'   using the method specified by
-#'   \code{\link[=control.ergm]{control$init.method}}.
+#'   \code{\link[ergm:control.ergm]{control$init.method}}.
 #' 
 #'   } Passing coefficients from a previous run can be used to
-#'   "resume" an uncoverged \code{\link{stergm}} run.
+#'   "resume" an uncoverged [stergm()] run.
 #' @param init.method Estimation method used to acquire initial values
 #'   for estimation. If \code{NULL} (the default), the initial values
 #'   are computed using the edges dissolution approximation (Carnegie
-#'   et al.) when appropriate; note that this relies on \code{\link{.extract.fd.formulae}}
+#'   et al.) when appropriate; note that this relies on [.extract.fd.formulae()]
 #'   to identify the formation and dissolution parts of the formula; the user should
 #'   be aware of its behavior and limitations.
 #'   If \code{init.method} is set to "zeros", the initial values are set to zeros.
@@ -77,9 +77,9 @@
 #'   between successive draws when running MCMC MLE.
 #' @param CMLE.ergm A convenience argument for specifying both
 #'   \code{CMLE.form.ergm} and \code{CMLE.diss.ergm} at once.
-#'   See \code{\link{control.ergm}}.
+#'   See [control.ergm()].
 #' @param CMLE.form.ergm Control parameters used to fit the CMLE.  See
-#'   \code{\link{control.ergm}}.
+#'   [control.ergm()].
 #' @param CMLE.diss.ergm
 #'   Ignored, with the exception of initial parameter values.
 #' @param CMLE.NA.impute In STERGM CMLE, missing dyads in
@@ -89,13 +89,13 @@
 #'   that are not, currently, implemented.  \code{CMLE.NA.impute}
 #'   controls how missing dyads in transitioned-from networks are be
 #'   imputed. See argument \code{imputers} of
-#'   \code{\link{impute.network.list}} for details.
+#'   [impute.network.list()] for details.
 #' 
 #'   By default, no imputation is performed, and the fitting stops
 #'   with an error if any transitioned-from networks have missing
 #'   dyads.
 #' @param CMLE.term.check.override The method
-#'   \code{\link{stergm}{stergm}} uses at this time to fit a series of
+#'   [stergm()] uses at this time to fit a series of
 #'   more than two networks requires certain assumptions to be made
 #'   about the ERGM terms being used, which are tested before a fit is
 #'   attempted. This test sometimes fails despite the model being
@@ -141,14 +141,14 @@
 #'   \code{EGMME.MCMC.burnin.min} and \code{EGMME.MCMC.burnin.max} to
 #'   the same value.
 #' @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 SAN control parameters.  See
-#'   \code{\link{control.san}}
+#'   [control.san()]
 #' @param SA.restarts Maximum number of times to restart a failed
 #'   optimization process.
 #' @param SA.burnin Number of time steps to advance the starting
@@ -161,7 +161,7 @@
 #'   heatmap representing the estimated gradient.
 #' 
 #'   Do NOT use these with non-interactive plotting devices like
-#'   \code{\link{pdf}}. (In fact, it will refuse to do that with a
+#'   [pdf()]. (In fact, it will refuse to do that with a
 #'   warning.)
 #' @param SA.max.plot.points If \code{SA.plot.progress==TRUE}, the
 #'   maximum number of time points to be plotted. Defaults to 400. If
@@ -299,9 +299,9 @@
 #' deprecated; a warning message is printed in case of deprecated arguments.
 #'
 #' @return A list with arguments as components.
-#' @seealso \code{\link{stergm}},\code{\link{tergm}},\code{\link{control.tergm}}. The
-#'   \code{\link{control.simulate.stergm}} function performs a similar
-#'   function for \code{\link{simulate.tergm}}.
+#' @seealso [stergm()], [tergm()], [control.tergm()]. The
+#'   [control.simulate.stergm()] function performs a similar
+#'   function for [simulate.tergm()].
 #' @references Boer, P., Huisman, M., Snijders,
 #'   T.A.B., and Zeggelink, E.P.H. (2003), StOCNET User\'s
 #'   Manual. Version 1.4.

R/control.tergm.R

@@ -18,8 +18,8 @@
 #' 
 #' Auxiliary function as user interface for fine-tuning 'tergm' fitting.
 #' 
-#' This function is only used within a call to the \code{\link{tergm}}
-#' function.  See the \code{usage} section in \code{\link{tergm}} for details.
+#' This function is only used within a call to the [tergm()]
+#' function.  See the Usage section in [tergm()] for details.
 #' 
 #' @param init numeric or \code{NA} vector equal in
 #'   length to the number of parameters in the
@@ -38,14 +38,14 @@
 #' 
 #'   \item Initial values for the elements that are \code{NA} are fit
 #'   using the method specified by
-#'   \code{\link[=control.ergm]{control$init.method}}.
+#'   \code{\link[ergm:control.ergm]{control$init.method}}.
 #' 
 #'   } Passing coefficients from a previous run can be used to
-#'   "resume" an uncoverged \code{\link{tergm}} run.
+#'   "resume" an uncoverged [tergm()] run.
 #' @param init.method Estimation method used to acquire initial values
 #'   for estimation. If \code{NULL} (the default), the initial values
 #'   are computed using the edges dissolution approximation (Carnegie
-#'   et al.) when appropriate; note that this relies on \code{\link{.extract.fd.formulae}}
+#'   et al.) when appropriate; note that this relies on [.extract.fd.formulae()]
 #'   to identify the formation and dissolution parts of the formula; the user should
 #'   be aware of its behavior and limitations.
 #'   If \code{init.method} is set to "zeros", the initial values are set to zeros.
@@ -62,21 +62,21 @@
 #' @param CMLE.MCMC.interval Number of Metropolis-Hastings steps
 #'   between successive draws when running MCMC MLE.
 #' @param CMLE.ergm Control parameters used
-#'   to fit the CMLE.  See \code{\link{control.ergm}}.
+#'   to fit the CMLE.  See [control.ergm()].
 #' @param CMLE.NA.impute In TERGM CMLE, missing dyads in
 #'   transitioned-to networks are accommodated using methods of
 #'   Handcock and Gile (2009), but a similar approach to
 #'   transitioned-from networks requires much more complex methods
 #'   that are not, currently, implemented.  \code{CMLE.NA.impute}
 #'   controls how missing dyads in transitioned-from networks are be
 #'   imputed. See argument \code{imputers} of
-#'   \code{\link{impute.network.list}} for details.
+#'   [impute.network.list()] for details.
 #' 
 #'   By default, no imputation is performed, and the fitting stops
 #'   with an error if any transitioned-from networks have missing
 #'   dyads.
 #' @param CMLE.term.check.override The method
-#'   \code{\link{tergm}{tergm}} uses at this time to fit a series of
+#'   [tergm()] uses at this time to fit a series of
 #'   more than two networks requires certain assumptions to be made
 #'   about the ERGM terms being used, which are tested before a fit is
 #'   attempted. This test sometimes fails despite the model being
@@ -124,14 +124,14 @@
 #'   \code{EGMME.MCMC.burnin.min} and \code{EGMME.MCMC.burnin.max} to
 #'   the same value.
 #' @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 SAN control parameters.  See
-#'   \code{\link{control.san}}
+#'   [control.san()]
 #' @param SA.restarts Maximum number of times to restart a failed
 #'   optimization process.
 #' @param SA.burnin Number of time steps to advance the starting
@@ -144,7 +144,7 @@
 #'   heatmap representing the estimated gradient.
 #' 
 #'   Do NOT use these with non-interactive plotting devices like
-#'   \code{\link{pdf}}. (In fact, it will refuse to do that with a
+#'   [pdf()]. (In fact, it will refuse to do that with a
 #'   warning.)
 #' @param SA.max.plot.points If \code{SA.plot.progress==TRUE}, the
 #'   maximum number of time points to be plotted. Defaults to 400. If
@@ -277,9 +277,9 @@
 #'   \code{EGMME.MCMC.burnin.add} and \code{CMLE.MCMC.burnin} and
 #'   \code{CMLE.MCMC.interval}.
 #' @return A list with arguments as components.
-#' @seealso \code{\link{tergm}}. The
-#'   \code{\link{control.simulate.tergm}} function performs a similar
-#'   function for \code{\link{simulate.tergm}}.
+#' @seealso [tergm()]. The
+#'   [control.simulate.tergm()] function performs a similar
+#'   function for [simulate.tergm()].
 #' @references Boer, P., Huisman, M., Snijders,
 #'   T.A.B., and Zeggelink, E.P.H. (2003), StOCNET User\'s
 #'   Manual. Version 1.4.

R/impute.network.list.R

@@ -16,8 +16,8 @@
 #' directives.
 #' 
 #' 
-#' @param nwl A list of \code{\link{network}} objects or a
-#'   \code{\link{network.list}} object.
+#' @param nwl A list of [`network`] objects or a
+#'   [`network.list`] object.
 #' @param imputers A character vector giving one or more methods to
 #'   impute missing dyads. Currenly implemented methods are as
 #'   follows: \describe{ \item{`next`}{Impute the state of the same
@@ -53,7 +53,7 @@
 #'   returned, but they can be useful for imputing dyads in the last
 #'   network in \code{nwl}, when using \code{"next"} imputer.
 #' @return A list of networks with missing dyads imputed.
-#' @seealso \code{\link{network}}, \code{\link{is.na}}
+#' @seealso [`network`], [is.na()]
 #' @keywords manip
 #' @export impute.network.list
 impute.network.list <- function(nwl, imputers=c(), nwl.prepend=list(), nwl.append=list()){

R/is.durational.R

@@ -19,8 +19,8 @@
 #' 
 #' These functions test whether an ERGM is duration dependent or not.
 #' 
-#' @param object An ERGM formula, \code{\link{ergm_model}} object, or
-#'                 \code{\link{ergm_state}} object.
+#' @param object An ERGM formula, [`ergm_model`] object, or
+#'                 [`ergm_state`] object.
 #' @param \dots Unused at this time.
 #' @return \code{TRUE} if the ERGM terms in the model are duration dependent; 
 #'           \code{FALSE} otherwise.
@@ -34,14 +34,14 @@ is.durational<-function(object,...) UseMethod("is.durational")
 #' @export
 is.durational.NULL <- function(object, ...) FALSE # By convention.
 
-#' @describeIn is.durational Test if the \code{\link{ergm_model}} has duration-dependent terms, which call for \code{\link{lasttoggle}} data structures.
+#' @describeIn is.durational Test if the [`ergm_model`] has duration-dependent terms, which call for [`lasttoggle`] data structures.
 #' @export
 is.durational.ergm_model <- function(object, ...){
 #' @import purrr
   map(object$terms, "duration") %>% unlist %>% NVL(FALSE) %>% max %>% as.logical
 }
 
-#' @describeIn is.durational Test if the \code{\link{ergm_state}} has duration-dependent terms, which call for \code{\link{lasttoggle}} data structures.
+#' @describeIn is.durational Test if the [`ergm_state`] has duration-dependent terms, which call for [`lasttoggle`] data structures.
 #' @export
 is.durational.ergm_state <- function(object, ...){
   is.durational(object$model)

R/is.lasttoggle.R

@@ -20,7 +20,7 @@
 #'                about dyad edge histories.
 #' 
 #' @details The \code{tergm} package handles durational information attached to
-#'            \code{\link{network}} objects by way of the \code{time} and 
+#'            [`network`] objects by way of the \code{time} and 
 #'            \code{lasttoggle} network attributes.  The \code{lasttoggle} data
 #'            structure is a 3-column matrix; the first two columns are tails 
 #'            and heads (respectively) of dyads, and the third column is the last