Commit 29c4015b authored by Chris Jewell's avatar Chris Jewell
Browse files

Updated roxygen2 generated manpages.

parent 167118c7
......@@ -42,6 +42,7 @@ to use the correct update algorithm for the appropriate nodes.
\item{\code{node}}{the node to which the updater is attached}
}}
\section{Methods}{
\describe{
......@@ -52,7 +53,7 @@ to use the correct update algorithm for the appropriate nodes.
\item{\code{acceptance()}}{return the acceptance rate}
}
}
\keyword{DAG}
\keyword{MCMC}
\keyword{node}
......@@ -43,6 +43,7 @@ to use the correct update algorithm for the appropriate nodes.
\item{\code{node}}{the node to which the updater is attached}
}}
\section{Methods}{
\describe{
......@@ -53,7 +54,7 @@ to use the correct update algorithm for the appropriate nodes.
\item{\code{acceptance()}}{return the acceptance rate}
}
}
\keyword{DAG}
\keyword{MCMC}
\keyword{node}
......@@ -40,6 +40,7 @@ to use the correct update algorithm for the appropriate nodes.
\item{\code{node}}{the node to which the updater is attached}
}}
\section{Methods}{
\describe{
......@@ -49,7 +50,7 @@ to use the correct update algorithm for the appropriate nodes.
\item{\code{acceptance()}}{return the acceptance rate}
}
}
\keyword{DAG}
\keyword{MCMC}
\keyword{node}
......@@ -54,5 +54,5 @@ Developers only here!
\item{\code{alpha}}{3D array of [source, time, location] giving initial values for the alpha
parameters}
}}
\keyword{datasets}
\keyword{datasets}
......@@ -22,12 +22,13 @@ Derived from \link{Node}, please see base class documentation.
\describe{
\item{\code{data}}{the data}
}}
\section{Methods}{
\describe{
\item{\code{getData()}}{returns the node's data.}
}
}
\keyword{DAG}
\keyword{node}
......@@ -24,6 +24,6 @@ Derived from \link{StochasticNode}, please see base class documentation.
\code{alpha}}.
}
}
\keyword{DAG}
\keyword{node}
......@@ -3,7 +3,7 @@
\docType{class}
\name{DirichletProcessNode}
\alias{DirichletProcessNode}
\title{Transformed Dirichlet node}
\title{DirichletProcessNode}
\format{Object of \code{\link{R6Class}} with methods for constructing a DAG.}
\usage{
DirichletProcessNode
......@@ -12,15 +12,9 @@ DirichletProcessNode
Object of \code{\link{DirichletProcessNode}}
}
\description{
Uses transformation due to Betancourt 2013
https://arxiv.org/pdf/1010.3436v4.pdf
Represents a Dirichlet process as a single node in a DAG.
}
\details{
Experimental -- do not use.
DirichletProcessNode
Represents a Dirichlet process as a single node in a DAG.
Derived from \link{StochasticNode}, please see base class documentation.
}
\section{Methods}{
......@@ -32,6 +26,6 @@ Derived from \link{StochasticNode}, please see base class documentation.
are specified in \code{...}.}
}
}
\keyword{DAG}
\keyword{node}
......@@ -25,6 +25,6 @@ Derived from \link{Node}, please see base class documentation.
\item{\code{getData()}}{returns the node's transformed data.}
}
}
\keyword{DAG}
\keyword{node}
......@@ -25,6 +25,6 @@ Derived from \link{StochasticNode}, please see base class documentation.
\code{shape} and \code{rate} as specified in \link{dgamma}.}
}
}
\keyword{DAG}
\keyword{node}
......@@ -221,6 +221,7 @@ divided by the number of negative samples) \eqn{j}
\deqn{q\sim DP(a_q, Gamma(a_{theta},b_{theta}))}
}
}
\examples{
data(campy)
zero_rows <- which(apply(campy[,c(2:7)], 1, sum) == 0)
......@@ -252,9 +253,6 @@ posteriors <- res$extract(params = c("alpha", "r", "q", "lambda_j"),
types = c("474", "52"),
iters = 50:100, drop = FALSE, flatten = FALSE)
}
\author{
Chris Jewell and Poppy Miller \email{p.miller at lancaster.ac.uk}
}
\references{
Chen, M.-H. and Shao, Q.-M. (1998). Monte Carlo estimation of Bayesian
credible and HPD intervals, \emph{Journal of Computational and Graphical Statistics}, 7.
......@@ -262,5 +260,7 @@ credible and HPD intervals, \emph{Journal of Computational and Graphical Statist
Liu Y, Gelman A, Zheng T (2015). "Simulation-efficient shortest probability
intervals." Statistics and Computing.
}
\author{
Chris Jewell and Poppy Miller \email{p.miller at lancaster.ac.uk}
}
\keyword{datasets}
......@@ -23,6 +23,7 @@ This is a base class representing a node in a DAG. Is not intended to be used by
\item{\code{name}}{a tag name applied to the node}
}}
\section{Methods}{
\describe{
......@@ -34,6 +35,6 @@ This is a base class representing a node in a DAG. Is not intended to be used by
\item{\code{removeChild(name)}}{remove the child node named \code{name}. Returns \code{node}.}
}
}
\keyword{DAG}
\keyword{node}
......@@ -31,7 +31,7 @@ to use the correct update algorithm for the appropriate nodes.
\item{\code{update()}}{when called, updates \code{node}}
}
}
\keyword{DAG}
\keyword{Dirichlet-process}
\keyword{node}
......@@ -23,6 +23,6 @@ Derived from \link{StochasticNode}, please see base class documentation.
\item{\code{new(data, lambda, offset)}}{create a PoissonNode, with mean \link{Node} \code{lambda}, and offset \link{Node} \code{offset}.}
}
}
\keyword{DAG}
\keyword{node}
......@@ -22,6 +22,7 @@ Derived from \link{Node}, please see base class documentation.
\describe{
\item{\code{data}}{contains the node's data}
}}
\section{Methods}{
\describe{
......@@ -29,6 +30,6 @@ Derived from \link{Node}, please see base class documentation.
\item{\code{getData()}}{returns the node's data.}
}
}
\keyword{DAG}
\keyword{node}
......@@ -26,4 +26,3 @@ A dataset containing the number of human cases of campylobacteriosis and numbers
positive for \emph{Campylobacter} for each bacterial subtype.
}
\keyword{datasets}
......@@ -25,4 +25,3 @@ A simulated dataset containing the number of human cases of campylobacteriosis a
positive for \emph{Campylobacter} for each bacterial subtype.
}
\keyword{datasets}
......@@ -17,4 +17,3 @@ sim_SA_prev
Source prevalences for the simulated data (sim_SA_data).
}
\keyword{datasets}
......@@ -24,4 +24,3 @@ sim_SA_true
A list containing the true values of the parameters used to simulate the sim_SA_data dataset.
}
\keyword{datasets}
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