Converted documentation links to Roxygen rmarkdown links and ensured …

…that all external links are anchored..

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: ergm.ego
-Version: 1.1-704
-Date: 2023-05-30
+Version: 1.1-729
+Date: 2024-10-09
 Title: Fit, Simulate and Diagnose Exponential-Family Random Graph Models to Egocentrically Sampled Network Data
 Authors@R: c(
             person(c("Pavel", "N."), "Krivitsky", role=c("aut","cre"), email="[email protected]", comment=c(ORCID="0000-0002-9101-3362")),
@@ -32,7 +32,7 @@ Description: Utilities for managing egocentrically sampled network data and a wr
 License: GPL-3 + file LICENSE
 URL: https://statnet.org
 BugReports: https://github.com/statnet/ergm.ego/issues
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2.9000
 Roxygen: list(markdown = TRUE)
 Encoding: UTF-8
 LazyData: true

R/EgoStat.R

@@ -153,17 +153,17 @@ split_aaties_by_ego <- function(x, egor){
   h
 }
 
-#' \code{\link[ergm]{ergm}} Terms Implemented for
-#' \code{\link{egor}}
+#' [ergm()] Terms Implemented for
+#' [`egor`]
 #' 
-#' This page describes the \code{\link[ergm]{ergm}} terms (and hence network
+#' This page describes the [ergm()] terms (and hence network
 #' statistics) for which inference based on egocentrically sampled data is
-#' implemented in \code{ergm.ego} package. Other packages may add their own
+#' implemented in \CRANpkg{ergm.ego} package. Other packages may add their own
 #' terms. These functions should not be called by the end-user.
 #' 
 #' The current recommendation for any package implementing additional
 #' egocentric calculator terms is to create a help file with a name or alias
-#' \code{ergm.ego-terms}, so that \code{help("ergm.ego-terms")} will
+#' \code{\link{ergm.ego-terms}}, so that \code{help("ergm.ego-terms")} will
 #' list egocentric ERGM terms available from all loaded packages.
 #' 
 #' 
@@ -178,9 +178,9 @@ split_aaties_by_ego <- function(x, egor){
 #' \describe{ \item{Special-purpose terms:}{ \describe{
 #' \item{netsize.adj(edges=+1, mutual=0, transitiveties=0,
 #' cyclicalties=0)}{A special-purpose term equivalent to a linear
-#' combination of \code{\link[ergm]{edges-ergmTerm}},
-#' \code{\link[ergm]{mutual-ergmTerm}}, \code{\link[ergm]{transitiveties-ergmTerm}}, and
-#' \code{\link[ergm]{cyclicalties-ergmTerm}}, to house the network-size
+#' combination of \code{\link[ergm:edges-ergmTerm]{edges}},
+#' \code{\link[ergm:mutual-ergmTerm]{mutual}}, \code{\link[ergm:transitiveties-ergmTerm]{transitiveties}}, and
+#' \code{\link[ergm:cyclicalties-ergmTerm]{cyclicalties}}, to house the network-size
 #' adjustment offset. This term is added to the model automatically
 #' and should not be used in the model formula directly.  } } }
 #' 
@@ -216,7 +216,7 @@ split_aaties_by_ego <- function(x, egor){
 #' evaluated, some inferential results and standard error calculation
 #' methods may not be applicable.
 #'
-#' @seealso \code{\link[ergm]{ergm-terms}}
+#' @seealso [`ergmTerm`]
 #' @keywords models
 NULL
 

R/control.ergm.ego.R

@@ -9,10 +9,10 @@
 ################################################################################
 
 
-#' Control parameters for \code{\link{ergm.ego}}.
+#' Control parameters for [ergm.ego()].
 #' 
 #' Constructs and checks the list of control parameters for estimation by
-#' \code{\link{ergm.ego}}.
+#' [ergm.ego()].
 #' 
 #' 
 #' @param ppopsize,ppopsize.mul Parameters to determine the size
@@ -78,12 +78,12 @@
 #'   number of nominations. Used to be `FALSE`, now `TRUE` in light of
 #'   the findings of Krivitsky et. al (2020).
 #' 
-#' @param ergm Control parameters for the \code{\link[ergm]{ergm}()} call
-#' to fit the model, constructed by \code{\link[ergm]{control.ergm}()}.
+#' @param ergm Control parameters for the [ergm()] call
+#' to fit the model, constructed by [control.ergm()].
 #' @param \dots Not used at this time.
 #' @return A list with arguments as components.
 #' @author Pavel N. Krivitsky
-#' @seealso \code{\link[ergm]{control.ergm}()}
+#' @seealso [control.ergm()]
 #' @references
 #' 
 #' Pavel N. Krivitsky and Martina Morris (2017). "Inference for social network models from egocentrically sampled data, with application to understanding persistent racial disparities in HIV prevalence in the US." *Annals of Applied Statistics*, 11(1): 427–455. \doi{10.1214/16-AOAS1010}

R/control.simulate.ergm.ego.R

@@ -9,10 +9,10 @@
 ################################################################################
 
 
-#' Control parameters for \code{\link{simulate.ergm.ego}}.
+#' Control parameters for [simulate.ergm.ego()].
 #' 
 #' Constructs and checks the list of control parameters for simulation by
-#' \code{\link{simulate.ergm.ego}}.
+#' [simulate.ergm.ego()].
 #' 
 #' 
 #' @param ppop.wt Because each ego must be represented in the pseuodopopulation
@@ -27,12 +27,12 @@
 #' the sum of these rounded freqencies.}
 #' \item{"sample"}{Resample in proportion to \eqn{w_i}.} }
 #' 
-#' @param SAN A list of control parameters for \code{\link[ergm]{san}}
-#' constructed by \code{\link[ergm]{control.ergm}}, called to construct a
+#' @param SAN A list of control parameters for [san()]
+#' constructed by [control.ergm()], called to construct a
 #' pseudopopulation network consistent with the data.
 #' @param simulate A list of control parameters for
-#' \code{\link[ergm]{simulate.formula}} constructed by
-#' \code{\link[ergm]{control.simulate}}, called to simulate from the model fit.
+#' [simulate.formula()] constructed by
+#' [control.simulate()], called to simulate from the model fit.
 #' @param \dots Not used at this time.
 #' @return A list with arguments as components.
 #' @author Pavel N. Krivitsky

R/degreedist.R

@@ -17,7 +17,7 @@
 #' graph.
 #' 
 #' @aliases degreedist
-#' @param object A \code{\link{egor}} object.
+#' @param object A [`egor`] object.
 #' @param freq,prob Whether to plot the raw frequencies or the conditional
 #' proportions of the degree values. Defaults to the latter.
 #' @param by A character vector giving the name of a vertex attribute; if
@@ -36,8 +36,7 @@
 #'   if `by=NULL` or a matrix with a row for each category if not. If
 #'   \code{plot==TRUE} returns invisibly.
 #' 
-#' @seealso \code{\link{degreedist}},
-#' \code{\link[ergm:summary_formula]{summary}}
+#' @seealso [degreedist()], \code{\link[ergm:summary_formula]{summary}} for formulas.
 #' @examples
 #' 
 #' data(faux.mesa.high)
@@ -151,12 +150,12 @@ degreedist.egor <- function(object, freq = FALSE, prob = !freq,
 #' Summarizing the mixing among groups in an egocentric dataset
 #' 
 #' A \code{\link[network]{mixingmatrix}} method for
-#' \code{\link{egor}} objects, to return counts of how often a ego
+#' [`egor`] objects, to return counts of how often a ego
 #' of each group nominates an alter of each group.
 #' 
 #' 
 #' @aliases mixingmatrix
-#' @param object A \code{\link{egor}} object.
+#' @param object A [`egor`] object.
 #' @param attrname A character vector containing the name of the network
 #' attribute whose mixing matrix is wanted.
 #' @param rowprob Whether the counts should be normalized by row sums. That is,
@@ -166,11 +165,11 @@ degreedist.egor <- function(object, freq = FALSE, prob = !freq,
 #' @param ... Additional arguments, currently unused.
 #' @return A matrix with a row and a column for each level of \code{attrname}.
 #' 
-#' Note that, unlike \code{\link[network]{mixingmatrix}}, what is counted are
+#' Note that, unlike [network::mixingmatrix()], what is counted are
 #' \emph{nominations}, not ties. This means that under an egocentric census,
 #' the diagonal of \code{mixingmatrix.egor} will be twice that returned by
-#' \code{\link[network]{mixingmatrix}} for the original undirected network.
-#' @seealso \code{\link[network]{mixingmatrix}}, \code{\link[ergm]{nodemix-ergmTerm}},
+#' [network::mixingmatrix()] for the original undirected network.
+#' @seealso [network::mixingmatrix()], \code{\link[ergm:nodemix-ergmTerm]{nodemix}} ERGM term,
 #' \code{\link[ergm.ego]{summary}} method for egocentric data
 #' @examples
 #' 

R/egor.R

@@ -9,15 +9,14 @@
 ################################################################################
 
 
-#' Convert (deprecated) \code{\link{egodata}} Objects to
-#' \code{\link{egor}} Objects
+#' Convert (deprecated) [`egodata`] Objects to [`egor`] Objects
 #'
 #' @aliases egodata
 #' 
-#' @param x a \code{\link{egodata}} object
+#' @param x an [`egodata`] object
 #' @param ... additional arguments, currently unused.
 #'
-#' @return An \code{\link{egor}} object.
+#' @return An [`egor`] object.
 #' 
 #' @author Pavel N. Krivitsky
 #' @keywords manip methods
@@ -34,21 +33,21 @@ as.egor.egodata <- function(x, ...){
 #' @export
 as_egor.egodata <- as.egor.egodata
 
-#' Construct an Egocentric View of a \code{\link{network}} Object
+#' Construct an Egocentric View of a [`network`] Object
 #' 
-#' Given a \code{\link[network]{network}} object, construct an
-#' \code{\link{egor}} object representing a census of all the actors in the
+#' Given a [`network`] object, construct an
+#' [`egor`] object representing a census of all the actors in the
 #' network. Used mainly for testing.
 #' 
 #' 
-#' @param x A \code{\link[network]{network}} object.
+#' @param x A [`network`] object.
 #' @param special.cols Vertex attributes that should not be copied to the
 #' \code{egos} and \code{alters} tables. Defaults to attributes special to the
-#' \code{\link[network]{network}} objects.
+#' [`network`] objects.
 #' @param ... Additional arguments, currently unused.
-#' @return An \code{\link{egor}} object.
+#' @return An [`egor`] object.
 #' @author Pavel N. Krivitsky
-#' @seealso \code{\link{template_network}}, which performs the inverse
+#' @seealso [template_network()], which performs the inverse
 #' operation (though drops the ties).
 #' @keywords datagen manip
 #' @examples
@@ -92,14 +91,14 @@ as.egor.network<-function(x,special.cols=c("na"),...){
 #' Construct an Empty ``Template'' Network Consistent with an Egocentric Sample
 #' 
 #' Taking an object with ego information, constructs a
-#' \code{\link[network]{network}} object with no edges whose vertices have the
+#' [`network`] object with no edges whose vertices have the
 #' attributes of the egos in the dataset, replicating the egos as needed, and
 #' taking into accounts their sampling weights.
 #' 
 #' 
-#' @param x A \code{\link{egor}} object.
+#' @param x A [`egor`] object.
 #' @param N The target number of vertices the output network should have.
-#' @param scaling If \code{\link{egor}} contains weights or \code{N} is not
+#' @param scaling If [`egor`] contains weights or \code{N} is not
 #' a multiple of number of egos in the sample, it may not be possible, for a
 #' finite \code{N} to represent each ego exactly according to its relative
 #' weight, and \code{scaling} controls how the fractional egos are allocated:
@@ -109,9 +108,9 @@ as.egor.network<-function(x,special.cols=c("na"),...){
 #' these rounded freqencies.} \item{"sample"}{Resample in
 #' proportion to \eqn{w_i}.} }
 #' @param ... Additional arguments, currently unused.
-#' @return A \code{\link[network]{network}} object.
+#' @return A [`network`] object.
 #' @author Pavel N. Krivitsky
-#' @seealso \code{\link{as.egor.network}}, which performs the inverse
+#' @seealso [as.egor.network()], which performs the inverse
 #' operation.
 #' @keywords manip
 #' @examples

R/ergm.ego.R

@@ -12,18 +12,18 @@
 #' Inference for Exponential-Family Random Graph Models based on Egocentrically
 #' Sampled Data
 #' 
-#' A wrapper around the \code{\link[ergm]{ergm}} to fit an ERGM to an
-#' \code{\link{egor}}.
+#' A wrapper around the [ergm()] to fit an ERGM to an
+#' [`egor`].
 #' 
 #' 
-#' @param formula An \code{\link{formula}} object, of the form \code{e
-#'   ~ <model terms>}, where \code{e} is a \code{\link{egor}}
-#'   object. See \code{\link[ergm]{ergm}} for details and examples.
+#' @param formula A [`formula`] object, of the form \code{e
+#'   ~ <model terms>}, where \code{e} is a [`egor`]
+#'   object. See [ergm()] for details and examples.
 #' 
 #' For a list of currently implemented egocentric terms for the RHS, see
-#' \code{\link{ergm.ego-terms}}.
-#' @param constraints A one-sided formula \code{\link{formula}} giving
-#'   the sample space constraints. See \code{\link[ergm]{ergm}} for
+#' [`ergm.ego-terms`].
+#' @param constraints A one-sided formula [`formula`] giving
+#'   the sample space constraints. See [ergm()] for
 #'   details and examples.
 #'
 #' @param popsize The size \eqn{|N|} of the finite population network
@@ -43,19 +43,19 @@
 #' when the terms need them for  models that scale.
 #' @param na.rm How to handle missing actor attributes in egos or alters,
 #' when the terms need them for models that do not scale.
-#' @param \dots Additional arguments passed to \code{\link[ergm]{ergm}}.
-#' @param control A \code{\link{control.ergm.ego}} control list.
-#' @param do.fit Whether to actually call \code{\link[ergm]{ergm}}
-#' @return An object of class \code{ergm.ego} inheriting from
-#' \code{\link[ergm]{ergm}}, with the following additional or overridden
+#' @param \dots Additional arguments passed to [ergm()].
+#' @param control A [control.ergm.ego()] control list.
+#' @param do.fit Whether to actually call [ergm()]
+#' @return An object of class [`ergm.ego`] inheriting from
+#' [`ergm`], with the following additional or overridden
 #' elements:
 #' \item{"v"}{Variance-covariance matrix of the estimate of the
 #' sufficient statistics}
 #' \item{"m"}{Estimate of the sufficient
 #' statistics}
 #' \item{"egor"}{The [`egor`] object passed}
 #' \item{"popsize"}{Population network size used}
-#' \item{"ppopsize"}{Pseudopopulation size used, see \code{\link{control.ergm.ego}}}
+#' \item{"ppopsize"}{Pseudopopulation size used, see [control.ergm.ego()]}
 #' \item{"coef"}{The
 #' coefficients, along with the network size adjustment \code{netsize.adj}
 #' coefficient.}
@@ -82,7 +82,7 @@
 #' Models." \emph{Statistical Methodology}, 8(4): 319–339. \doi{10.1016/j.stamet.2011.01.005}
 #'
 #' @keywords models
-#' @seealso \code{\link[ergm]{ergm}()}
+#' @seealso [ergm()]
 #' @examples
 #' \donttest{
 #' data(faux.mesa.high)

R/gof.ergm.ego.R

@@ -84,24 +84,24 @@
 #' Conduct Goodness-of-Fit Diagnostics on a Exponential Family Random Graph
 #' Model fit to Egocentrically Sampled Data
 #' 
-#' \code{\link{gof.ergm.ego}} implements the \code{\link[ergm]{gof}} method for
-#' \code{\link{ergm.ego}} fit objects.
+#' [gof.ergm.ego()] implements the [gof()] method for
+#' [`ergm.ego`] fit objects.
 #' 
 #' 
-#' @param object An \code{\link{ergm.ego}} fit.
+#' @param object An [`ergm.ego`] fit.
 #' @param ... Additional arguments. Unused by [gof.ergm.ego()], passed to
 #'   [ergm::plot.gof()] by [plot.gof.ergm.ego()]
 #' @param GOF A string specifying the statistics whose goodness of fit is to be
 #' evaluated. Currently, only \dQuote{degree}, \dQuote{espartners} and \dQuote{model} are
-#' implemented; see \code{\link[ergm]{gof}} documentation for details.
+#' implemented; see [gof()] documentation for details.
 #' @param control A list to control parameters, constructed using
-#' \code{\link{control.gof.formula}} or \code{\link{control.gof.ergm}} (which
+#' [control.gof.formula()] or [control.gof.ergm()] (which
 #' have different defaults).
 #' @param verbose Provide verbose information on the progress of the
 #' simulation.
-#' @return An object of class [`gof.ergm.ego`], inheriting from \code{\link[ergm:gof.ergm]{gof.ergm}}.
+#' @return An object of class [`gof.ergm.ego`], inheriting from [gof.ergm()].
 #' @author Pavel N. Krivitsky
-#' @seealso For examples, see \code{\link{ergm.ego}}.
+#' @seealso For examples, see [ergm.ego()].
 #' @keywords models
 #' @examples
 #' \donttest{

R/simulate.ergm.ego.R

@@ -9,13 +9,13 @@
 ################################################################################
 
 
-#' Simulate from a \code{\link{ergm.ego}} fit.
+#' Simulate from a [ergm.ego()] fit.
 #' 
-#' A wrapper around \code{\link[ergm]{simulate.formula}} to simulate networks
-#' from an ERGM fit using \code{\link{ergm.ego}}.
-#' 
-#' 
-#' @param object An \code{\link{ergm.ego}} fit.
+#' A wrapper around [simulate.formula()] to simulate networks
+#' from an ERGM fit using [ergm.ego()].
+#'
+#'
+#' @param object An [`ergm.ego`] fit.
 #' @param nsim Number of realizations to simulate.
 #' @template seed
 #' @param popsize,basis A network size to which to scale the model for
@@ -24,23 +24,22 @@
 #'   actors; or a [`network`] object to use as is. `basis` is provided
 #'   for consistency with [ergm()], [ergm.ego()], [simulate.ergm()],
 #'   and others. If both are specified, `popsize` overrules.
-#' @param control A \code{\link{control.simulate.ergm.ego}} control list.
+#' @param control A [control.simulate.ergm.ego()] control list.
 #' @param output one of `"network"`, `"stats"`, `"edgelist"`,
 #'   `"pending_update_network"`, or, for future compatibility,
 #'   `"ergm_state"`. See help for [simulate.ergm()] for explanation.
 #' 
-#' @param constraints,\dots Additional arguments passed to \code{\link[ergm]{san}} and
-#' \code{\link[ergm]{simulate.formula}}.
+#' @param constraints,\dots Additional arguments passed to [san()] and
+#' [simulate.formula()].
 #' @template verbose
 #' @return The ouput has the same format (with the same options) as
-#' \code{\link[ergm]{simulate.formula}}. If \code{output="stats"} is passed, an
+#' [simulate.formula()]. If \code{output="stats"} is passed, an
 #' additional attribute, \code{"ppopsize"} is set, giving the actual size of
 #' the network reconstructed, when the \code{pop.wt} control parameter is set
 #' to \code{"round"} and \code{"popsize"} is not a multiple of the egocentric
 #' sample size or the sampling weights.
 #' @author Pavel N. Krivitsky
-#' @seealso \code{\link[ergm]{simulate.formula}},
-#' \code{\link[ergm]{simulate.ergm}}
+#' @seealso [simulate.formula()], [simulate.ergm()]
 #' @references
 #'
 #' * Pavel N. Krivitsky and Martina Morris (2017). "Inference for social network models from egocentrically sampled data, with application to understanding persistent racial disparities in HIV prevalence in the US." *Annals of Applied Statistics*, 11(1): 427–455. \doi{10.1214/16-AOAS1010}