Merge pull request #42 from drammock/1.0-7

version 1.0-7

.Rbuildignore

@@ -2,8 +2,11 @@
 .Rproj.user
 extras
 old-versions
+cache
+gists
 
 index.html
+index_utf8.html
 footer.html
 knit_phonR.bash
 phonR.pdf

DESCRIPTION

@@ -1,15 +1,15 @@
 Package: phonR
 Type: Package
 Title: Tools for Phoneticians and Phonologists
-Version: 1.0-6
-Date: 2015-06-22
+Version: 1.0-7
+Date: 2016-08-22
 Author: Daniel R. McCloy
 Maintainer: Daniel R. McCloy <[email protected]>
 Depends: R (>= 2.10)
-Imports: splancs, deldir, plotrix
+Imports: splancs, deldir, plotrix, stats, grDevices, graphics
 Description: Tools for phoneticians and phonologists, including functions for normalization and plotting of vowels.
 License: GPL-3
 URL: http://drammock.github.io/phonR/
-BugReports: https://github.com/drammock/phonR/issues 
+BugReports: https://github.com/drammock/phonR/issues
 LazyLoad: yes
 LazyData: yes

NAMESPACE

@@ -17,3 +17,6 @@ export(repulsiveForce)
 export(repulsiveForceHeatmap)
 export(repulsiveForceHeatmapLegend)
 export(vowelMeansPolygonArea)
+import(graphics)
+import(grDevices)
+import(stats)

inst/CITATION

@@ -1,16 +1,15 @@
 citHeader("To cite package 'phonR' in publications use:")
 
-     year <- sub(".*(2[[:digit:]]{3})-.*", "\\1", meta$Date, perl = TRUE)
+     year <- sub(".*(2[[:digit:]]{3})-.*", "\\1", meta$Date, perl=TRUE)
      vers <- paste("R package version", meta$Version)
 
      citEntry(entry="Manual",
               title = "phonR: tools for phoneticians and phonologists",
-              author = personList(as.person("Daniel McCloy")),
+              author = personList(as.person("Daniel R. McCloy")),
               year = year,
               note = vers,
 
               textVersion =
-              paste("Daniel McCloy (",
-                    year,
+              paste0("Daniel R. McCloy (", year,
                     "). phonR: tools for phoneticians and phonologists. ",
-                    vers, ".", sep=""))
+                    vers, "."))

man/normVowels.Rd

@@ -27,7 +27,7 @@
     normNearey2(f, group=NULL, exp=FALSE, ...)
     normSharedLogmean(f, group=NULL, exp=FALSE, ...)
     normWattFabricius(f, vowel, group=NULL)
-    normVowels(method, f0=NULL, f1=NULL, f2=NULL, f3=NULL, 
+    normVowels(method, f0=NULL, f1=NULL, f2=NULL, f3=NULL,
                vowel=NULL, group=NULL, ...)
 }
 \arguments{
@@ -106,7 +106,7 @@ Glasberg, B. R., & Moore, B. C. J. 1990 \dQuote{Derivation of auditory filter sh
 
 Lobanov, B. M. 1971 \dQuote{Classification of Russian vowels spoken by different speakers.} \emph{The Journal of the Acoustical Society of America}, 49(2), 606-608. \url{http://dx.doi.org/10.1121/1.1912396}
 
-McCloy, D. R. 2012 \dQuote{Normalizing and plotting vowels with the phonR package.} \emph{Technical Reports of the UW Linguistic Phonetics Laboratory}. \url{http://depts.washington.edu/phonlab/pubs/McCloy2012_phonR.pdf}
+McCloy, D. R. 2012 \dQuote{Normalizing and plotting vowels with the phonR package.} \emph{Technical Reports of the UW Linguistic Phonetics Laboratory}. \url{http://dan.mccloy.info/pubs/McCloy2012_phonR.pdf}
 
 Nearey, T. M. 1978 \dQuote{Phonetic feature systems for vowels} (Doctoral dissertation, University of Alberta). Reprinted by the Indiana University Linguistics Club. \url{http://www.ualberta.ca/~tnearey/Nearey1978_compressed.pdf}
 

man/plotVowels.Rd

@@ -22,7 +22,7 @@
                diph.mean.timept=1, diph.smooth=FALSE,
                heatmap=FALSE, heatmap.args=NULL,
                heatmap.legend=FALSE, heatmap.legend.args=NULL,
-               var.col.by=NULL, var.style.by=NULL,
+               var.col.by=NULL, var.sty.by=NULL,
                fill.opacity=0.3, label.las=NULL,
                legend.kwd=NULL, legend.args=NULL,
                pretty=FALSE, output='screen', ...)
@@ -59,8 +59,8 @@
     \item{hull.args,poly.args,ellipse.args}{Named list of arguments to be passed
                                             to \code{\link[graphics]{polygon}}.
                                             Useful for controlling line width,
-                                            etc. See "Details" for notes about
-                                            color handling.}
+                                            etc. See \dQuote{Details} for notes
+                                            about color handling.}
     \item{poly.line}{Logical; should a line be drawn tracing the polygon
                      connecting the mean values for each vowel (separately for
                      each level of \code{group})?}
@@ -74,10 +74,12 @@
     \item{ellipse.line}{Logical; should vowel density ellipses be drawn with an
                         outer line?}
     \item{ellipse.fill}{Logical; should vowel density ellipses be filled?}
-    \item{ellipse.conf}{Size of the ellipse (0,1] expressed as a confidence level
-                        (i.e., 0.95 gives a 95\% confidence ellipse).  Defaults
-                        to a confidence level of 0.6827 (equivalent to
-                        plus-or-minus 1 sample standard deviation).}
+    \item{ellipse.conf}{Numeric in range (0,1]; the size of the ellipse
+                        expressed as a confidence level of the estimate of the
+                        true mean (i.e., 0.95 gives a 95\% confidence ellipse).
+                        The default value (0.6827) corresponds to plus-or-minus
+                        one sample standard deviation along the major and minor
+                        axes of the bivariate normal density contour.}
     \item{diph.arrows}{Logical; should the last timepoint of each vowel be
                        marked with an arrowhead?}
     \item{diph.args.tokens,diph.args.means}{List of named arguments to be passed
@@ -133,8 +135,8 @@
                                a more complete description of the available arguments.}
     \item{var.col.by}{Vector or factor indicating the dimension along which to vary
                       color.}
-    \item{var.style.by}{Vector or factor indicating the dimension along which to
-                        vary linetype and plotting symbol.}
+    \item{var.sty.by}{Vector or factor indicating the dimension along which to
+                      vary linetype and plotting symbol.}
     \item{fill.opacity}{Number in the range [0, 1] indicating the opacity of
                         color fills for ellipses, hulls, and polygons (if drawn).
                         Does not affect \code{force.heatmap} colors, which are
@@ -184,7 +186,7 @@ data(indoVowels)
 with(indo, plotVowels(f1, f2, vowel, group=gender, plot.means=TRUE,
                       pch.means=vowel, ellipse.line=TRUE, poly.line=TRUE,
                       poly.order=c('i','e','a','o','u'), var.col.by=vowel,
-                      var.style.by=gender, pretty=TRUE, alpha.tokens=0.3,
+                      var.sty.by=gender, pretty=TRUE, alpha.tokens=0.3,
                       cex.means=2))
 # simulate some diphthongs
 f1delta <- sample(c(-10:-5, 5:15), nrow(indo), replace=TRUE)
@@ -202,7 +204,7 @@ indo <- within(indo, {
 with(indo, plotVowels(cbind(f1, f1a, f1b), cbind(f2, f2a, f2b), vowel,
                       group=gender, plot.tokens=TRUE, pch.tokens=NA,
                       alpha.tokens=0.3, plot.means=TRUE, pch.means=vowel,
-                      var.col.by=vowel, var.style.by=gender, pretty=TRUE,
+                      var.col.by=vowel, var.sty.by=gender, pretty=TRUE,
                       diph.arrows=TRUE, diph.args.tokens=list(lwd=0.8),
                       diph.args.means=list(lwd=2)))
 }