From a38fe470a8aaa1ed9922e95e76e77c74f4a50b69 Mon Sep 17 00:00:00 2001
From: Saturnino Luz <luzs@acm.org>
Date: Thu, 10 Aug 2017 10:37:10 +0100
Subject: [PATCH] Fixed conditional dependency on igraph package
---
DESCRIPTION | 2 +-
R/markov.R | 66 ++++++++++++++++++++----------------
R/vocalgraphs.R | 3 +-
man/identifyVocalisations.Rd | 6 ++--
man/igraph.vocaldia.Rd | 4 ++-
man/plot.vocaldia.Rd | 9 ++---
man/toDotNotation.Rd | 5 +--
man/write.vocaldia.Rd | 7 ++--
8 files changed, 56 insertions(+), 46 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index 9ad4bda..3df33c3 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -3,7 +3,7 @@ LazyData: true
Package: vocaldia
Type: Package
Title: Create and Manipulate Vocalisation Diagrams
-Version: 0.8.1
+Version: 0.8.2
Date: 2017-04-03
Authors@R: person("Saturnino", "Luz", email = "luzs@acm.org", role = c("aut", "cre"))
Description: Create adjacency matrices of vocalisation graphs from
diff --git a/R/markov.R b/R/markov.R
index 7dc0e60..9948dc8 100644
--- a/R/markov.R
+++ b/R/markov.R
@@ -317,12 +317,12 @@ identifyPauses <- function(vocvector){
##'
##' E.g (speakers A, B, C):
##' \preformatted{
-##' AAAAAAAABBBBBBBCCCCCBBBBBPauseBBBBSwitchingPauseAAAAAGrpVocalisation
+##' AAAAAAAABBBBBBBCCCCCBBBBBPauseBBBBSwitchingPauseAAAAAGrp
##' ^ ^ ^ ^ ^ ^
##' | | | | | |
-##' | | | ---------------- Non-SwitchingVocalisation's
+##' | | | ----------- Non-SwitchingVocalisation
##' | | |
-##' ---------------------> SwitchingVocalisation's
+##' ---------------------> SwitchingVocalisation
##' }
##'
##' @title identifyVocalisations: replace appropriate vocalisation
@@ -417,23 +417,21 @@ getEntropy <- function (distribution){
##' Plot a vocalisation diagram
##' @title plot.vocaldia
##' @param x a vocalisation diagram
-##' @param package the package to be used for ploting (igraph
-##' (default) or Rgraphviz)
##' @param ... arguments for the layout algorithm
##' @return \code{NULL}
##' @examples
##' data(vocdia)
-##' require('igraph')
-##' plot(getSampledVocalMatrix(subset(atddia, id=='Abbott_Maddock_01'),
+##' if (require('igraph'))
+##' plot(getSampledVocalMatrix(subset(atddia, id=='Abbott_Maddock_01'),
##' individual=TRUE, nodecolumn='speaker'))
##' @export
-plot.vocaldia <- function(x, ..., package='igraph'){
- vd <- x
- if (requireNamespace("igraph", quietly = TRUE)){
- ## require('igraph')
- g <- igraph.vocaldia(vd)
- plot(g, layout=igraph::layout.fruchterman.reingold(g), ...)
- return(g)
+plot.vocaldia <- function(x, ...){
+ x
+ if (requireNamespace('igraph', quietly = TRUE)){
+ ## require('igraph')
+ g <- igraph.vocaldia(x)
+ plot(g, layout=igraph::layout.fruchterman.reingold(g), ...)
+ return(g)
}
##if (requireNamespace("Rgraphviz", quietly = TRUE)){
## cat('Rgraphviz support under construction. PLease use igraph instead')
@@ -449,7 +447,7 @@ plot.vocaldia <- function(x, ..., package='igraph'){
## plot(g, edgeAttrs=ea, attrs=at, ...)
## return(g)
##}
- warning(paste('Package ',package, ' not supported. Try igraph.'))
+ warning(paste('Package igraph not installed. Try installing igraph or "require(igraph)" if installed.'))
}
@@ -462,16 +460,22 @@ plot.vocaldia <- function(x, ..., package='igraph'){
##' @return an igraph
##' @examples
##' data(vocdia)
-##' igraph.vocaldia(getSampledVocalMatrix(subset(atddia, id=='Abbott_Maddock_01'),
+##' if (require('igraph'))
+##' igraph.vocaldia(getSampledVocalMatrix(subset(atddia,
+##' id=='Abbott_Maddock_01'),
##' individual=TRUE, nodecolumn='speaker'))
##' @export
igraph.vocaldia <- function(vd, ...){
- g <- igraph::graph.adjacency(vd$ttarray, weighted=T)
- igraph::V(g)$label <- names(vd$ttarray[1,])
- igraph::E(g)$label <- round(igraph::E(g)$weight,digits=3)
- igraph::V(g)$size <- 25*exp(vd$tdarray)
- g$layout <- igraph::layout.kamada.kawai(g)
- g
+ if (requireNamespace('igraph', quietly = TRUE)){
+ g <- igraph::graph.adjacency(vd$ttarray, weighted=T)
+ igraph::V(g)$label <- names(vd$ttarray[1,])
+ igraph::E(g)$label <- round(igraph::E(g)$weight,digits=3)
+ igraph::V(g)$size <- 25*exp(vd$tdarray)
+ g$layout <- igraph::layout.kamada.kawai(g)
+ return(g)
+ }
+ else
+ warning(paste('Package igraph not supported. Try installing igraph or "require(igraph)" if installed.'))
}
## ##' Create a graphNEL vocalisation diagram
@@ -501,9 +505,10 @@ igraph.vocaldia <- function(vd, ...){
##' @return \code{NULL}
##' @examples
##' data(vocdia)
-##' write.vocaldia(getSampledVocalMatrix(subset(atddia, id=='Abbott_Maddock_01'),
-##' individual=TRUE, nodecolumn='speaker'),
-##' file=tempfile(pattern='vocaldia-', fileext='.dot') )
+##' write.vocaldia(getSampledVocalMatrix(subset(atddia,
+##' id=='Abbott_Maddock_01'),
+##' individual=TRUE, nodecolumn='speaker'),
+##' file=tempfile(pattern='vocaldia-', fileext='.dot'))
##' @export
write.vocaldia <- function(vd, file="", ...){
o <- toDotNotation(vd, ...)
@@ -528,12 +533,15 @@ write.vocaldia <- function(vd, file="", ...){
##' @return character data containing the diagram in dot format.
##' @examples
##' data(vocdia)
-##' toDotNotation(getSampledVocalMatrix(subset(atddia, id=='Abbott_Maddock_01'),
-##' individual=TRUE, nodecolumn='speaker'))
+##' toDotNotation(getSampledVocalMatrix(subset(atddia,
+##' id=='Abbott_Maddock_01'),
+##' individual=TRUE, nodecolumn='speaker'))
##' @seealso graphviz manual
##' @export
-toDotNotation <- function(vd, individual=T, varsizenode=T, shape='circle',
- fontsize=16, rankdir='LR', nodeattribs='fixedsize=true;',
+toDotNotation <- function(vd, individual=T, varsizenode=T,
+ shape='circle',
+ fontsize=16, rankdir='LR',
+ nodeattribs='fixedsize=true;',
comment="")
{
head <- paste("## diagram generated by vocalgraphs.r\n## ", comment,
diff --git a/R/vocalgraphs.R b/R/vocalgraphs.R
index a8f294a..3e7a633 100644
--- a/R/vocalgraphs.R
+++ b/R/vocalgraphs.R
@@ -421,7 +421,8 @@ getTurnTakingProbMatrix <- function(df, individual=FALSE, ...)
##' getTurnTakingMatrix(x)
##' getTurnTakingMatrix(x, individual=TRUE)
##' @export
-getTurnTakingMatrix <- function(df, begin='begin', end='end', nodecolumn='role',
+getTurnTakingMatrix <- function(df, begin='begin', end='end',
+ nodecolumn='role',
individual=FALSE, noPauseTypes=FALSE)
{
##df <- subset(df, df$id %in% ids)
diff --git a/man/identifyVocalisations.Rd b/man/identifyVocalisations.Rd
index 87e3038..e60a836 100644
--- a/man/identifyVocalisations.Rd
+++ b/man/identifyVocalisations.Rd
@@ -28,12 +28,12 @@ speaker (as opposed to speaker to Grp or speaker to Pause).
E.g (speakers A, B, C):
\preformatted{
-AAAAAAAABBBBBBBCCCCCBBBBBPauseBBBBSwitchingPauseAAAAAGrpVocalisation
+AAAAAAAABBBBBBBCCCCCBBBBBPauseBBBBSwitchingPauseAAAAAGrp
^ ^ ^ ^ ^ ^
| | | | | |
- | | | ---------------- Non-SwitchingVocalisation's
+ | | | ----------- Non-SwitchingVocalisation
| | |
- ---------------------> SwitchingVocalisation's
+ ---------------------> SwitchingVocalisation
}
}
\examples{
diff --git a/man/igraph.vocaldia.Rd b/man/igraph.vocaldia.Rd
index 0f31590..e0e0af1 100644
--- a/man/igraph.vocaldia.Rd
+++ b/man/igraph.vocaldia.Rd
@@ -22,6 +22,8 @@ Create a vocalisation diagram
}
\examples{
data(vocdia)
-igraph.vocaldia(getSampledVocalMatrix(subset(atddia, id=='Abbott_Maddock_01'),
+if (require('igraph'))
+ igraph.vocaldia(getSampledVocalMatrix(subset(atddia,
+ id=='Abbott_Maddock_01'),
individual=TRUE, nodecolumn='speaker'))
}
diff --git a/man/plot.vocaldia.Rd b/man/plot.vocaldia.Rd
index ad47186..d3b7ba0 100644
--- a/man/plot.vocaldia.Rd
+++ b/man/plot.vocaldia.Rd
@@ -4,15 +4,12 @@
\alias{plot.vocaldia}
\title{plot.vocaldia}
\usage{
-\method{plot}{vocaldia}(x, ..., package = "igraph")
+\method{plot}{vocaldia}(x, ...)
}
\arguments{
\item{x}{a vocalisation diagram}
\item{...}{arguments for the layout algorithm}
-
-\item{package}{the package to be used for ploting (igraph
-(default) or Rgraphviz)}
}
\value{
\code{NULL}
@@ -25,7 +22,7 @@ Plot a vocalisation diagram
}
\examples{
data(vocdia)
-require('igraph')
-plot(getSampledVocalMatrix(subset(atddia, id=='Abbott_Maddock_01'),
+if (require('igraph'))
+ plot(getSampledVocalMatrix(subset(atddia, id=='Abbott_Maddock_01'),
individual=TRUE, nodecolumn='speaker'))
}
diff --git a/man/toDotNotation.Rd b/man/toDotNotation.Rd
index c21731e..f44d87c 100644
--- a/man/toDotNotation.Rd
+++ b/man/toDotNotation.Rd
@@ -36,8 +36,9 @@ Create a vocalisation diagram in dot notation
}
\examples{
data(vocdia)
-toDotNotation(getSampledVocalMatrix(subset(atddia, id=='Abbott_Maddock_01'),
- individual=TRUE, nodecolumn='speaker'))
+toDotNotation(getSampledVocalMatrix(subset(atddia,
+ id=='Abbott_Maddock_01'),
+ individual=TRUE, nodecolumn='speaker'))
}
\seealso{
graphviz manual
diff --git a/man/write.vocaldia.Rd b/man/write.vocaldia.Rd
index 4f0c059..f548b6e 100644
--- a/man/write.vocaldia.Rd
+++ b/man/write.vocaldia.Rd
@@ -24,7 +24,8 @@ Write a vocalisation diagram
}
\examples{
data(vocdia)
-write.vocaldia(getSampledVocalMatrix(subset(atddia, id=='Abbott_Maddock_01'),
- individual=TRUE, nodecolumn='speaker'),
- file=tempfile(pattern='vocaldia-', fileext='.dot') )
+write.vocaldia(getSampledVocalMatrix(subset(atddia,
+ id=='Abbott_Maddock_01'),
+ individual=TRUE, nodecolumn='speaker'),
+ file=tempfile(pattern='vocaldia-', fileext='.dot'))
}
--
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