From c5309846822d2fc8b6559812ef43d5ff2991b65e Mon Sep 17 00:00:00 2001 From: "Pavel N. Krivitsky" Date: Sun, 4 Sep 2022 17:21:38 +1000 Subject: [PATCH] Removed man/ergm-terms-taper.Rd: example was moved to Taper-ergmTerm doc and references to a template. --- R/InitErgmTerm.Kpenalty.R | 1 + R/InitErgmTerm.M4.R | 1 + R/InitErgmTerm.Var.R | 1 + R/InitErgmTerm.stereo.R | 1 + R/InitErgmTerm.tapered.R | 6 ++ man-roxygen/ergmTerm-taper-references.R | 10 ++ man/Kpenalty-ergmTerm.Rd | 11 ++ man/M4-ergmTerm.Rd | 11 ++ man/Stereo-ergmTerm.Rd | 11 ++ man/Taper-ergmTerm.Rd | 17 +++ man/Var-ergmTerm.Rd | 11 ++ man/ergm-terms-taper.Rd | 135 ------------------------ 12 files changed, 81 insertions(+), 135 deletions(-) create mode 100644 man-roxygen/ergmTerm-taper-references.R delete mode 100644 man/ergm-terms-taper.Rd diff --git a/R/InitErgmTerm.Kpenalty.R b/R/InitErgmTerm.Kpenalty.R index ca5b5d9..c5f37bc 100644 --- a/R/InitErgmTerm.Kpenalty.R +++ b/R/InitErgmTerm.Kpenalty.R @@ -22,6 +22,7 @@ #' the LHS of \code{formula} if it is two-sided. #' #' @template ergmTerm-general +#' @template ergmTerm-taper-references #' #' @concept operator #' @concept tapered diff --git a/R/InitErgmTerm.M4.R b/R/InitErgmTerm.M4.R index e944b2d..1e46724 100755 --- a/R/InitErgmTerm.M4.R +++ b/R/InitErgmTerm.M4.R @@ -23,6 +23,7 @@ #' the LHS of \code{formula} if it is two-sided. #' #' @template ergmTerm-general +#' @template ergmTerm-taper-references #' #' @concept operator #' @concept tapered diff --git a/R/InitErgmTerm.Var.R b/R/InitErgmTerm.Var.R index e772350..b8cdf75 100755 --- a/R/InitErgmTerm.Var.R +++ b/R/InitErgmTerm.Var.R @@ -23,6 +23,7 @@ #' the LHS of \code{formula} if it is two-sided. #' #' @template ergmTerm-general +#' @template ergmTerm-taper-references #' #' @concept operator #' @concept tapered diff --git a/R/InitErgmTerm.stereo.R b/R/InitErgmTerm.stereo.R index 2201835..72213ac 100755 --- a/R/InitErgmTerm.stereo.R +++ b/R/InitErgmTerm.stereo.R @@ -25,6 +25,7 @@ #' the LHS of \code{formula} if it is two-sided. #' #' @template ergmTerm-general +#' @template ergmTerm-taper-references #' #' @concept operator #' @concept tapered diff --git a/R/InitErgmTerm.tapered.R b/R/InitErgmTerm.tapered.R index 9273114..b6c60d6 100644 --- a/R/InitErgmTerm.tapered.R +++ b/R/InitErgmTerm.tapered.R @@ -23,6 +23,12 @@ #' the LHS of \code{formula} if it is two-sided. #' #' @template ergmTerm-general +#' @template ergmTerm-taper-references +#' +#' @examples +#' data(florentine) +#' m <- summary(flomarriage~edges + triangles) +#' summary(ergm(flomarriage ~ Taper(~edges + triangles, coef=c(.1, .1),m=m))) #' #' @concept operator #' @concept tapered diff --git a/man-roxygen/ergmTerm-taper-references.R b/man-roxygen/ergmTerm-taper-references.R new file mode 100644 index 0000000..3b11e24 --- /dev/null +++ b/man-roxygen/ergmTerm-taper-references.R @@ -0,0 +1,10 @@ +#' @references +#' +#' * Fellows, I and Handcock, MS (2017). Removing Phase Transitions +#' from Gibbs Measures. \emph{Proceedings of Machine Learning +#' Research}, 54:289-297. +#' +#' * Blackburn, B and Handcock, MS (2022). Practical Network Modeling +#' via Tapered Exponential-family Random Graph Models. \emph{Journal +#' of Computational and Graphical Statistics} +#' \doi{10.1080/10618600.2022.2116444}. diff --git a/man/Kpenalty-ergmTerm.Rd b/man/Kpenalty-ergmTerm.Rd index 741b849..37fa4e3 100644 --- a/man/Kpenalty-ergmTerm.Rd +++ b/man/Kpenalty-ergmTerm.Rd @@ -27,6 +27,17 @@ the LHS of \code{formula} if it is two-sided.} Adds \emph{only} the quadratic penalty of Fellows and Handcock (2017) for the terms specified in \code{formula} to the model. } +\references{ +\itemize{ +\item Fellows, I and Handcock, MS (2017). Removing Phase Transitions +from Gibbs Measures. \emph{Proceedings of Machine Learning +Research}, 54:289-297. +\item Blackburn, B and Handcock, MS (2022). Practical Network Modeling +via Tapered Exponential-family Random Graph Models. \emph{Journal +of Computational and Graphical Statistics} +\doi{10.1080/10618600.2022.2116444}. +} +} \seealso{ \code{\link{ergmTerm}} for index of model terms currently visible to the package. } diff --git a/man/M4-ergmTerm.Rd b/man/M4-ergmTerm.Rd index 8aa79c8..90a6baa 100644 --- a/man/M4-ergmTerm.Rd +++ b/man/M4-ergmTerm.Rd @@ -28,6 +28,17 @@ Adds the fourth moment of each statistics specified by the terms in \code{formul This is sometimes applied directly to control the fourth moment of the standard statistics, but more typically as part of a Tapered ERGM. } +\references{ +\itemize{ +\item Fellows, I and Handcock, MS (2017). Removing Phase Transitions +from Gibbs Measures. \emph{Proceedings of Machine Learning +Research}, 54:289-297. +\item Blackburn, B and Handcock, MS (2022). Practical Network Modeling +via Tapered Exponential-family Random Graph Models. \emph{Journal +of Computational and Graphical Statistics} +\doi{10.1080/10618600.2022.2116444}. +} +} \seealso{ \code{\link{ergmTerm}} for index of model terms currently visible to the package. } diff --git a/man/Stereo-ergmTerm.Rd b/man/Stereo-ergmTerm.Rd index 1e8d893..135b15f 100644 --- a/man/Stereo-ergmTerm.Rd +++ b/man/Stereo-ergmTerm.Rd @@ -30,6 +30,17 @@ stereographic projection onto a sphere. See Section 5.3 for a development. The stereo penalty is weaker than the variance tapering of Fellows and Handcock (2017). } +\references{ +\itemize{ +\item Fellows, I and Handcock, MS (2017). Removing Phase Transitions +from Gibbs Measures. \emph{Proceedings of Machine Learning +Research}, 54:289-297. +\item Blackburn, B and Handcock, MS (2022). Practical Network Modeling +via Tapered Exponential-family Random Graph Models. \emph{Journal +of Computational and Graphical Statistics} +\doi{10.1080/10618600.2022.2116444}. +} +} \seealso{ \code{\link{ergmTerm}} for index of model terms currently visible to the package. } diff --git a/man/Taper-ergmTerm.Rd b/man/Taper-ergmTerm.Rd index 3c6d55c..d4e2faf 100644 --- a/man/Taper-ergmTerm.Rd +++ b/man/Taper-ergmTerm.Rd @@ -28,6 +28,23 @@ Adds the terms specified in \code{formula} to the model \emph{and} imposes the quadratic penalty of Fellows and Handcock (2017). } +\examples{ +data(florentine) +m <- summary(flomarriage~edges + triangles) +summary(ergm(flomarriage ~ Taper(~edges + triangles, coef=c(.1, .1),m=m))) + +} +\references{ +\itemize{ +\item Fellows, I and Handcock, MS (2017). Removing Phase Transitions +from Gibbs Measures. \emph{Proceedings of Machine Learning +Research}, 54:289-297. +\item Blackburn, B and Handcock, MS (2022). Practical Network Modeling +via Tapered Exponential-family Random Graph Models. \emph{Journal +of Computational and Graphical Statistics} +\doi{10.1080/10618600.2022.2116444}. +} +} \seealso{ \code{\link{ergmTerm}} for index of model terms currently visible to the package. } diff --git a/man/Var-ergmTerm.Rd b/man/Var-ergmTerm.Rd index 050433a..481c6ca 100644 --- a/man/Var-ergmTerm.Rd +++ b/man/Var-ergmTerm.Rd @@ -28,6 +28,17 @@ Adds the variance of the terms specified in \code{formula} to the model. This is sometimes applied directly to control the variance of the standard statistics, but more typically as part of a Tapered ERGM. } +\references{ +\itemize{ +\item Fellows, I and Handcock, MS (2017). Removing Phase Transitions +from Gibbs Measures. \emph{Proceedings of Machine Learning +Research}, 54:289-297. +\item Blackburn, B and Handcock, MS (2022). Practical Network Modeling +via Tapered Exponential-family Random Graph Models. \emph{Journal +of Computational and Graphical Statistics} +\doi{10.1080/10618600.2022.2116444}. +} +} \seealso{ \code{\link{ergmTerm}} for index of model terms currently visible to the package. } diff --git a/man/ergm-terms-taper.Rd b/man/ergm-terms-taper.Rd deleted file mode 100644 index 36bf480..0000000 --- a/man/ergm-terms-taper.Rd +++ /dev/null @@ -1,135 +0,0 @@ -\name{ergm-terms-taper} -\alias{ergm-terms-taper} -\alias{Taper} -\alias{Stereo} -\alias{Kpenalty} -\alias{Var} -\alias{M4} -\docType{methods} -\title{Terms Implemented in the \code{ergm.tapered} Package} -\description{ - This page describes the possible terms (and hence network statistics) - included in the \code{ergm.tapered} package. - - See the \code{\link[ergm]{ergm-terms}} documentation in the - \code{ergm} package for a complete description of what ERGM terms are - and how they are used. - - These terms are usually accessed via the \code{ergm.tapered} function call to mimic \code{ergm}. - -} - -\section{Terms}{ - \describe{ - \item{\code{Taper(formula, coef, m)} (binary) (operator)}{\emph{Tapered ERGM terms}: - - Adds the terms specified in \code{formula} to the model \emph{and} - imposes the quadratic penalty of Fellows and Handcock - (2017). \code{coef} is a numeric vector of coefficients giving the penalty coefficients \eqn{\beta} for the tapering of the terms. - If \code{NULL} is passed, the tapering coefficients are set to \code{1/(4*summary(formula))}, the default - in Fellows and Handcock (2017). - If a numeric vector is given, there are interpreted as the tapering coefficients of the terms in the - model, including the terms enclosed in \code{offset()}. - If a numeric scalar is given, it is interpreted as a multiplier of the default tapering coefficients , that is, \code{1/(4*summary(formula))} - \code{m}, if given, is - the value of the network statistic relative to which the model is - tapered. If omitted, it defaults to that of the model's LHS - network if \code{formula} is one-sided and that of the network on - the LHS of \code{formula} if it is two-sided. - - } - \item{\code{Stereo(formula, coef, m)} (binary) (operator)}{\emph{Stero Tapered ERGM terms}: - - Adds the terms specified in \code{formula} to the model \emph{and} - imposes the Stereo penalty of Blackburn (2021). This is akin to using an inverse - stereographic projection onto a sphere. See Section 5.3 for a development. - The stereo penalty is weaker than the variance tapering of Fellows and Handcock - (2017). - - \code{coef} is a numeric vector of coefficients giving the penalty coefficients \eqn{\beta} for the tapering of the terms. - If \code{NULL} is passed, the tapering coefficients are set to \code{1/(4*summary(formula))}, the default - in Fellows and Handcock (2017). - If a numeric vector is given, there are interpreted as the tapering coefficients of the terms in the - model, including the terms enclosed in \code{offset()}. - If a numeric scalar is given, it is interpreted as a multiplier of the default tapering coefficients , that is, \code{1/(4*summary(formula))} - \code{m}, if given, is - the value of the network statistic relative to which the model is - tapered. If omitted, it defaults to that of the model's LHS - network if \code{formula} is one-sided and that of the network on - the LHS of \code{formula} if it is two-sided. - - } - \item{\code{Kpenalty(formula, coef, m)} (binary) (operator)}{\emph{Stereo Tapered ERGM terms}: - - Adds \emph{only} the quadratic penalty of Fellows and Handcock - (2017) for the terms specified in \code{formula} to the model. - - \code{coef} is a numeric vector of coefficients giving the penalty coefficients \eqn{\beta} for the tapering of the terms. - If \code{NULL} is passed, the tapering coefficients are set to \code{1/(4*summary(formula))}, the default - in Fellows and Handcock (2017). - If a numeric vector is given, there are interpreted as the tapering coefficients of the terms in the - model, including the terms enclosed in \code{offset()}. - If a numeric scalar is given, it is interpreted as a multiplier of the default tapering coefficients , that is, \code{1/(4*summary(formula))} - \code{m}, if given, is - the value of the network statistic relative to which the model is - tapered. If omitted, it defaults to that of the model's LHS - network if \code{formula} is one-sided and that of the network on - the LHS of \code{formula} if it is two-sided. - - } - \item{\code{Var(formula, coef, m)} (binary) (operator)}{\emph{Var ERGM terms}: - - Adds the variance of the terms specified in \code{formula} to the model. - This is sometimes applied directly to control the variance of the standard - statistics, but more typically as part of a Tapered ERGM. - \code{coef} is a numeric vector of coefficients giving the penalty coefficients \eqn{\beta} for the tapering of the terms. - If \code{NULL} is passed, the tapering coefficients are set to \code{1/(4*summary(formula))}, the default - in Fellows and Handcock (2017). - If a numeric vector is given, there are interpreted as the tapering coefficients of the terms in the - model, including the terms enclosed in \code{offset()}. - If a numeric scalar is given, it is interpreted as a multiplier of the default tapering coefficients , that is, \code{1/(4*summary(formula))} - \code{m}, if given, is - the value of the network statistic relative to which the model is - tapered. If omitted, it defaults to that of the model's LHS - network if \code{formula} is one-sided and that of the network on - the LHS of \code{formula} if it is two-sided. - - } - \item{\code{M4(formula, coef, m)} (binary) (operator)}{\emph{M4 Tapered ERGM terms}: - - Adds the fourth moment of each statistics specified by the terms in \code{formula} to the model. - This is sometimes applied directly to control the fourth moment of the standard - statistics, but more typically as part of a Tapered ERGM. - - \code{coef} is a numeric vector of coefficients giving the penalty coefficients \eqn{\beta} for the tapering of the terms. - If \code{NULL} is passed, the tapering coefficients are set to \code{1/(4*summary(formula))}, the default - in Fellows and Handcock (2017). - If a numeric vector is given, there are interpreted as the tapering coefficients of the terms in the - model, including the terms enclosed in \code{offset()}. - If a numeric scalar is given, it is interpreted as a multiplier of the default tapering coefficients , that is, \code{1/(4*summary(formula))} - \code{m}, if given, is - the value of the network statistic relative to which the model is - tapered. If omitted, it defaults to that of the model's LHS - network if \code{formula} is one-sided and that of the network on - the LHS of \code{formula} if it is two-sided. - - } - } -} -\references{ - \itemize{ - \item{Fellows, I and Handcock, MS (2017). Removing Phase Transitions from - Gibbs Measures. \emph{Proceedings of Machine Learning Research}, 54:289-297.} - \item{Blackburn, B and Handcock, MS (2022). Practical Network Modeling via Tapered - Exponential-family Random Graph Models. \emph{Journal of Computational and Graphical Statistics} - \doi{10.1080/10618600.2022.2116444}.} - } -} -\seealso{\code{\link[=ergm-package]{ergm}} package, \code{\link{search.ergmTerms}}, \code{\link{ergm}}, \code{\link{network}}, \code{\link{\%v\%}}, \code{\link{\%n\%}}} -\examples{ -data(florentine) -m <- summary(flomarriage~edges + triangles) -summary(ergm(flomarriage ~ Taper(~edges + triangles, coef=c(.1, .1),m=m))) -} -\keyword{models} -\concept{tapered}