From 332aca1e0968d07d0b71e0b3dda8c0dbf68d1faa Mon Sep 17 00:00:00 2001 From: Skye Bender-deMoll Date: Wed, 2 May 2018 22:27:48 -0700 Subject: [PATCH] updating cran and graphviz links to resolve check NOTEs ref #35 --- ndtv/R/installers.R | 4 ++-- ndtv/man/install.graphviz.Rd | 7 ++++--- ndtv/man/network.layout.animate.Rd | 4 ++-- ndtv/man/toy_epi_sim.Rd | 2 +- 4 files changed, 9 insertions(+), 8 deletions(-) diff --git a/ndtv/R/installers.R b/ndtv/R/installers.R index 061d135..2bc2eb2 100644 --- a/ndtv/R/installers.R +++ b/ndtv/R/installers.R @@ -97,8 +97,8 @@ check.graphviz <-function(){ } install.graphviz <-function(){ - message("Please visit the Graphviz website and install the libraries on your machine: http://www.graphviz.org/Download.php See ?install.graphviz for more information") - browseURL("http://www.graphviz.org/Download.php") + message("Please visit the Graphviz website and install the libraries on your machine: https://www.graphviz.org/download See ?install.graphviz for more information") + browseURL("https://www.graphviz.org/download") } check.ffmpeg <- function(){ diff --git a/ndtv/man/install.graphviz.Rd b/ndtv/man/install.graphviz.Rd index 15927cc..424e3bf 100644 --- a/ndtv/man/install.graphviz.Rd +++ b/ndtv/man/install.graphviz.Rd @@ -25,16 +25,17 @@ This function doesn't actually install Graphviz, it just points to these docs wh \subsection{Installing on Windows}{ \itemize{ - \item download the "current stable release" installer from \url{http://www.graphviz.org/Download_windows.php} + \item download the "current stable release" installer from \url{https://graphviz.gitlab.io/_pages/Download/Download_windows.html} \item run the installer \item Edit your system path variable to include the path to the directory containing the graphviz .exe files. } } \subsection{Installing on a Mac}{ +It seems that there is no longer a .pkg for the mac, but it can be installed easily via homebrew \itemize{ -\item download the most recent "current stable release" .pkg file for your system from \url{http://www.graphviz.org/Download_macos.php} -\item double click the package to run the installer or, if you are working from the OSX command line, run something like \code{sudo installer -pkg graphviz-2.34.0.pkg -target /} +\item install the brew package manager from \url{https://brew.sh/} +\item from the Terminal, run \code{brew install graphviz} } } diff --git a/ndtv/man/network.layout.animate.Rd b/ndtv/man/network.layout.animate.Rd index a09b155..daa82de 100644 --- a/ndtv/man/network.layout.animate.Rd +++ b/ndtv/man/network.layout.animate.Rd @@ -74,9 +74,9 @@ The \code{useAttribute} layout makes it possible to define vertex positions usin The \code{Graphviz} layout is a wrapper for the Graphviz \url{http://www.graphviz.org} software library. If the library is installed on your system (see \code{\link{install.graphviz}}), it provides a number of additional high-quality layouts. When layout is called it checks for a working Graphviz installation (falling back to KamadaKawai if Graphviz cannot be found) and writes the network to a temp file using \code{\link{export.dot}}. Then the appropriate Graphviz layout engine (default is \code{neato}) is executed via a \code{system} call, and the coordinates of the vertices are parsed from the output. -Currently, the arguments to \code{layout.par} can be used to specify the Graphviz layout engine to use (i.e. \code{gv.engine='neato'} for stress-minimized, \code{gv.engine='dot'} for hierarchal, \code{gv.engine='fdp'} for force-directed, etc) and additional command-line control parameters can be passed in via \code{gv.args}. For example, to use the 'dot' layout, but change layout rank direction to Left-Right: \code{layout.par=list(gv.engine='dot',gv.args='-Grankdir=LR')}. See \url{http://www.graphviz.org/content/command-line-invocation}. Note that Graphviz's graphic rendering parameters are not used to control network plot rendering (but they may impact layout positions). +Currently, the arguments to \code{layout.par} can be used to specify the Graphviz layout engine to use (i.e. \code{gv.engine='neato'} for stress-minimized, \code{gv.engine='dot'} for hierarchal, \code{gv.engine='fdp'} for force-directed, etc) and additional command-line control parameters can be passed in via \code{gv.args}. For example, to use the 'dot' layout, but change layout rank direction to Left-Right: \code{layout.par=list(gv.engine='dot',gv.args='-Grankdir=LR')}. See \url{https://graphviz.gitlab.io/_pages/doc/info/command.html}. Note that Graphviz's graphic rendering parameters are not used to control network plot rendering (but they may impact layout positions). -It is also possible to pass edge attributes of the network directly through to the Graphviz .dot file by passing in the names of the attributes using \code{gv.edge.attrs} argument to \code{layout.par}. For example, \code{layout.par=list(gv.edge.attrs='len')} will write the value of the edge attribute 'len' to a gv attribute 'len', which would control the edge lengths when using neato or fdp \url{http://www.graphviz.org/content/attrs#dlen}. +It is also possible to pass edge attributes of the network directly through to the Graphviz .dot file by passing in the names of the attributes using \code{gv.edge.attrs} argument to \code{layout.par}. For example, \code{layout.par=list(gv.edge.attrs='len')} will write the value of the edge attribute 'len' to a gv attribute 'len', which would control the edge lengths when using neato or fdp \url{https://graphviz.gitlab.io/_pages/doc/info/attrs.html#d:len}. The Graphviz layout normally ignores the values in \code{dist.mat}, but for compatibility with other layouts, it is possible to use the values in \code{dist.mat} to influence Graphviz's edge length by setting \code{layout.par} \code{gv.len.mode='ndtv.distance.matrix'} instead of its default \code{'gv.edge.len'}. This writes out all of the possible edges to the file and will overide any other edge attributes. diff --git a/ndtv/man/toy_epi_sim.Rd b/ndtv/man/toy_epi_sim.Rd index 65a0e4e..40230f3 100644 --- a/ndtv/man/toy_epi_sim.Rd +++ b/ndtv/man/toy_epi_sim.Rd @@ -58,7 +58,7 @@ toy_epi_sim <- color_tea(toy_epi_sim) } \references{ Samuel Jenness, Steven M. Goodreau and Martina Morris (2015). EpiModel: Mathematical Modeling of Infectious - Disease. R package version 1.1.4. \url{http://CRAN.R-project.org/package=EpiModel} + Disease. R package version 1.1.4. \url{https://CRAN.R-project.org/package=EpiModel} Statnet EpiModel Tutorial \url{http://www.epimodel.org/} }