updating cran and graphviz links to resolve check NOTEs ref #35

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(){

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}
 }
 }
 

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. 
 

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/}  
 }