From a9f1a7d1d3c10425c935a6fdb9abbd169e1ede3e Mon Sep 17 00:00:00 2001 From: "Pavel N. Krivitsky" Date: Mon, 7 Oct 2024 16:13:58 +1100 Subject: [PATCH] Replaced a number of Rd links with Roxygen Markdown links so that external links for those are anchored. --- DESCRIPTION | 4 ++-- R/data.R | 4 ++-- R/ergm.R | 4 ++-- R/ergm.geodistn.R | 6 +++--- R/ergm.utility.R | 12 ++++++------ R/ergm_proposal.R | 4 ++-- R/formula.utils.R | 8 ++++---- R/get.node.attr.R | 2 +- R/godfather.R | 8 ++++---- R/gof.ergm.R | 2 +- R/is.curved.R | 2 +- R/simulate.ergm.R | 6 +++--- man-roxygen/seed.R | 2 +- man/control.ergm.Rd | 2 +- man/control.ergm.bridge.Rd | 2 +- man/control.gof.Rd | 2 +- man/control.san.Rd | 2 +- man/ergm-errors.Rd | 4 ++-- man/ergm.Rd | 4 ++-- man/ergm.geodistdist.Rd | 6 +++--- man/ergm.godfather.Rd | 8 ++++---- man/get.node.attr.Rd | 2 +- man/nvattr.copy.network.Rd | 12 ++++++------ man/samplk.Rd | 2 +- man/sampson.Rd | 2 +- man/simulate.ergm.Rd | 2 +- 26 files changed, 57 insertions(+), 57 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 294ae2b76..dab28b88a 100644 --- a/DESCRIPTION +++ b/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="handcock@stat.ucla.edu"), diff --git a/R/data.R b/R/data.R index ca3cc74ae..98fe5db9a 100644 --- a/R/data.R +++ b/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 diff --git a/R/ergm.R b/R/ergm.R index 4ea78b5dc..4b61b54b3 100644 --- a/R/ergm.R +++ b/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 ~ }, 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)} diff --git a/R/ergm.geodistn.R b/R/ergm.geodistn.R index 9b2149dd6..6c7d42d1d 100644 --- a/R/ergm.geodistn.R +++ b/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) diff --git a/R/ergm.utility.R b/R/ergm.utility.R index 074345fcc..cbf16b115 100644 --- a/R/ergm.utility.R +++ b/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")){ diff --git a/R/ergm_proposal.R b/R/ergm_proposal.R index 78a6d9307..832565da3 100644 --- a/R/ergm_proposal.R +++ b/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: diff --git a/R/formula.utils.R b/R/formula.utils.R index affd70648..077a641e5 100644 --- a/R/formula.utils.R +++ b/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. diff --git a/R/get.node.attr.R b/R/get.node.attr.R index ce7585c3b..9a0731eb8 100644 --- a/R/get.node.attr.R +++ b/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 diff --git a/R/godfather.R b/R/godfather.R index d7ff3e781..58f764566 100644 --- a/R/godfather.R +++ b/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"}. diff --git a/R/gof.ergm.R b/R/gof.ergm.R index c842be890..9e1f8381b 100644 --- a/R/gof.ergm.R +++ b/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, diff --git a/R/is.curved.R b/R/is.curved.R index 6bec933dd..2b3ccbf84 100644 --- a/R/is.curved.R +++ b/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. diff --git a/R/simulate.ergm.R b/R/simulate.ergm.R index 44a95a661..cca305977 100644 --- a/R/simulate.ergm.R +++ b/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 ~ }, 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{}, 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.} diff --git a/man-roxygen/seed.R b/man-roxygen/seed.R index f674af791..5f17d683a 100644 --- a/man-roxygen/seed.R +++ b/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()]. diff --git a/man/control.ergm.Rd b/man/control.ergm.Rd index db9178883..46d3f8166 100644 --- a/man/control.ergm.Rd +++ b/man/control.ergm.Rd @@ -687,7 +687,7 @@ observed network, using a higher default number of steps.} \item{term.options}{A list of additional arguments to be passed to term initializers. See \code{\link[=term.options]{? term.options}}.} \item{seed}{Seed value (integer) for the random number generator. See -\code{\link[base]{set.seed}}.} +\code{\link[=set.seed]{set.seed()}}.} \item{parallel}{Number of threads in which to run the sampling. Defaults to 0 (no parallelism). See the entry on \link[=ergm-parallel]{parallel processing} diff --git a/man/control.ergm.bridge.Rd b/man/control.ergm.bridge.Rd index 19265ffc1..daa9d98c4 100644 --- a/man/control.ergm.bridge.Rd +++ b/man/control.ergm.bridge.Rd @@ -120,7 +120,7 @@ not be needed outside of very strange setups.} \item{term.options}{A list of additional arguments to be passed to term initializers. See \code{\link[=term.options]{? term.options}}.} \item{seed}{Seed value (integer) for the random number generator. See -\code{\link[base]{set.seed}}.} +\code{\link[=set.seed]{set.seed()}}.} \item{parallel}{Number of threads in which to run the sampling. Defaults to 0 (no parallelism). See the entry on \link[=ergm-parallel]{parallel processing} diff --git a/man/control.gof.Rd b/man/control.gof.Rd index 8be397c6c..2b6b1f9de 100644 --- a/man/control.gof.Rd +++ b/man/control.gof.Rd @@ -94,7 +94,7 @@ sample.} supports networks without vertex attributes)} \item{seed}{Seed value (integer) for the random number generator. See -\code{\link[base]{set.seed}}.} +\code{\link[=set.seed]{set.seed()}}.} \item{parallel}{Number of threads in which to run the sampling. Defaults to 0 (no parallelism). See the entry on \link[=ergm-parallel]{parallel processing} diff --git a/man/control.san.Rd b/man/control.san.Rd index 3f8f2fdb5..cefeb4f77 100644 --- a/man/control.san.Rd +++ b/man/control.san.Rd @@ -81,7 +81,7 @@ not be needed outside of very strange setups.} \item{term.options}{A list of additional arguments to be passed to term initializers. See \code{\link[=term.options]{? term.options}}.} \item{seed}{Seed value (integer) for the random number generator. See -\code{\link[base]{set.seed}}.} +\code{\link[=set.seed]{set.seed()}}.} \item{parallel}{Number of threads in which to run the sampling. Defaults to 0 (no parallelism). See the entry on \link[=ergm-parallel]{parallel processing} diff --git a/man/ergm-errors.Rd b/man/ergm-errors.Rd index 9c40a0648..9fde9d8ce 100644 --- a/man/ergm-errors.Rd +++ b/man/ergm-errors.Rd @@ -48,12 +48,12 @@ end-users, but may be useful to developers. \itemize{ \item \code{ergm_Init_try()}: A helper function that evaluates the specified expression in the caller's environment, passing any -errors to \code{\link[=ergm_Init_abort]{ergm_Init_abort()}}. +errors to \code{\link[=ergm_Init_stop]{ergm_Init_stop()}}. }} \note{ At this time, the \CRANpkg{rlang} analogues -\code{ergm_Init_abort()}, \code{ergm_Init_warn()}, and \code{ergm_Init_inform()} +\code{ergm_Init_stop()}, \code{ergm_Init_warning()}, and \code{ergm_Init_message()} all concatenate their arguments like their base \R counterparts. This may change in the future, and if you wish to retain their old behavior, please switch to their base \R diff --git a/man/ergm.Rd b/man/ergm.Rd index dbf6c1038..43bac240e 100644 --- a/man/ergm.Rd +++ b/man/ergm.Rd @@ -42,7 +42,7 @@ is.ergm(object) \method{vcov}{ergm}(object, sources = c("all", "model", "estimation"), ...) } \arguments{ -\item{formula}{An \R \code{\link{formula}} object, of the form +\item{formula}{An \R \code{\link{formula}}, of the form \code{y ~ }, 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 @@ -222,7 +222,7 @@ For the MCMLE method, the history of coefficients, Hummel step lengths, and aver \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 \code{\link{formula}} passed to \code{\link[=ergm]{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)} diff --git a/man/ergm.geodistdist.Rd b/man/ergm.geodistdist.Rd index cae465381..5a1a7c077 100644 --- a/man/ergm.geodistdist.Rd +++ b/man/ergm.geodistdist.Rd @@ -10,7 +10,7 @@ ergm.geodistdist(nw, directed = is.directed(nw)) ergm.geodistn(edgelist, n = max(edgelist), directed = FALSE) } \arguments{ -\item{nw}{\code{\link{network}} object over which distances should be +\item{nw}{\code{\link[network:network]{network}} object over which distances should be calculated} \item{directed}{logical, should the network be treated as directed} @@ -29,7 +29,7 @@ infinity. } } \description{ \code{ergm.geodistdist} calculates geodesic distance distribution for a -given \code{\link{network}} and returns it as a vector. +given \code{\link[network:network]{network}} and returns it as a vector. \code{ergm.geodistn} calculates geodesic deistance distribution based on an input edgelist, and has very little @@ -48,6 +48,6 @@ ergm.geodistdist(faux.mesa.high) } \seealso{ -See also the sna package \code{\link[sna]{geodist}} function +See also the sna package \code{\link[sna:geodist]{geodist()}} function } \keyword{internal} diff --git a/man/ergm.godfather.Rd b/man/ergm.godfather.Rd index ca4db4396..0e0c962d7 100644 --- a/man/ergm.godfather.Rd +++ b/man/ergm.godfather.Rd @@ -17,7 +17,7 @@ ergm.godfather( } \arguments{ \item{formula}{An \code{\link{ergm}}-style formula, with a -\code{\link{network}} on its LHS.} +\code{\link[network:network]{network}} on its LHS.} \item{changes}{Either a matrix with three columns: tail, head, and new value, describing the changes to be made; or a list of such @@ -64,15 +64,15 @@ functions and limited argument name checking.} } \value{ If \code{end.network==FALSE} (the default), an -\code{\link{mcmc}} object with the requested network statistics +\code{\link[coda:mcmc]{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 \code{\link[coda:mcmc]{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 \code{\link[network:network]{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"}. diff --git a/man/get.node.attr.Rd b/man/get.node.attr.Rd index 5624bfa4b..d600ea03a 100644 --- a/man/get.node.attr.Rd +++ b/man/get.node.attr.Rd @@ -8,7 +8,7 @@ a network} get.node.attr(nw, attrname, functionname = NULL, numeric = FALSE) } \arguments{ -\item{nw}{a \code{\link{network}} object} +\item{nw}{a \code{\link[network:network]{network}} object} \item{attrname}{the name of a nodal attribute, as a character string} diff --git a/man/nvattr.copy.network.Rd b/man/nvattr.copy.network.Rd index d286d6447..caa283721 100644 --- a/man/nvattr.copy.network.Rd +++ b/man/nvattr.copy.network.Rd @@ -11,13 +11,13 @@ nvattr.copy.network( ) } \arguments{ -\item{to}{the \code{\link{network}} that attributes should be copied to} +\item{to}{the \code{\link[network:network]{network}} that attributes should be copied to} -\item{from}{the \code{\link{network}} that attributes should be copied to} +\item{from}{the \code{\link[network:network]{network}} that attributes should be copied to} \item{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}}} +\code{\link[network:network.initialize]{network.initialize()}}} } \value{ returns the \code{to} network, with attributes copied from @@ -25,14 +25,14 @@ returns the \code{to} network, with attributes copied from } \description{ 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 \code{\link[network:network]{network}} object to another, ignoring some standard properties by default. } \note{ does not check that networks are of the same size, etc } \seealso{ -\code{\link{set.vertex.attribute}}, -\code{\link{set.network.attribute}} +\code{\link[network:attribute.methods]{set.vertex.attribute()}}, +\code{\link[network:attribute.methods]{set.network.attribute()}} } \keyword{internal} diff --git a/man/samplk.Rd b/man/samplk.Rd index 32ce070eb..95d87ba73 100644 --- a/man/samplk.Rd +++ b/man/samplk.Rd @@ -19,7 +19,7 @@ dissertation, Department of Sociology, Cornell University. data(samplk) } \description{ -Three \code{\link{network}} objects containing the "liking" nominations of +Three \code{\link[network:network]{network}} objects containing the "liking" nominations of Sampson's (1969) monks at the three time points. } \details{ diff --git a/man/sampson.Rd b/man/sampson.Rd index 437b22d5a..f6aafd4c4 100644 --- a/man/sampson.Rd +++ b/man/sampson.Rd @@ -17,7 +17,7 @@ dissertation, Department of Sociology, Cornell University. data(sampson) } \description{ -A \code{\link{network}} object containing the cumulative "liking" +A \code{\link[network:network]{network}} object containing the cumulative "liking" nominations of Sampson's (1969) monks over the three time points. } \details{ diff --git a/man/simulate.ergm.Rd b/man/simulate.ergm.Rd index 6b39e7ead..8ea606099 100644 --- a/man/simulate.ergm.Rd +++ b/man/simulate.ergm.Rd @@ -136,7 +136,7 @@ distribution on the set of all networks, returned by the Metropolis-Hastings algorithm.} \item{seed}{Seed value (integer) for the random number generator. See -\code{\link[base]{set.seed}}.} +\code{\link[=set.seed]{set.seed()}}.} \item{\dots}{Further arguments passed to or used by methods.}