ENH: R code follows consistant style guide

R/aaa_data.R

@@ -1,9 +1,8 @@
-
 #' DesikanKillianyTourville
-#' 
-#' A data frame label numbers and names for the neuroanatomical 
+#'
+#' A data frame label numbers and names for the neuroanatomical
 #' DesikanKillianyTourville labels.
-#' 
+#'
 #' @docType data
 #' @references  \url{http://www.ncbi.nlm.nih.gov/pubmed/23227001}
 #' @format A data frame listing the following variables.
@@ -16,26 +15,26 @@
 #'    \item{\code{hemisphere}}{ left or right hemisphere. }
 #' }
 #' @examples
-#' data(DesikanKillianyTourville) 
+#' data(DesikanKillianyTourville)
 "DesikanKillianyTourville"
 
 #' BOLD Correlation Matrix
-#' 
+#'
 #' A data frame with an example square BOLD correlation matrix.
-#' 
+#'
 #' @docType data
-#' 
-#' @format A data frame square correlation matrix listed by AAL 
+#'
+#' @format A data frame square correlation matrix listed by AAL
 #' anatomical column names.
 #' @references \url{http://en.wikipedia.org/wiki/Automated_Anatomical_Labeling}
-#' @examples 
+#' @examples
 #' data(bold_correlation_matrix)
 "bold_correlation_matrix"
 
 #' @title powers_areal_mni_itk
 #' @docType data
-#' @description A data frame providing coordinates for the nodes 
-#' identified by Powers at al. Coordinates have been modified from nifti 
+#' @description A data frame providing coordinates for the nodes
+#' identified by Powers at al. Coordinates have been modified from nifti
 #' space to ITK space
 #' @format A data frame listing the following variables.
 #' \describe{
@@ -49,43 +48,46 @@
 #'   \item{\code{r}}{ red value for system }
 #'   \item{\code{g}}{ green value for system }
 #'   \item{\code{b}}{ blue value for system }
-#'   \item{\code{Anatomy}}{ anatomical location as 
+#'   \item{\code{Anatomy}}{ anatomical location as
 #'   determined by OASIS labeling }
 #'   \item{\code{Lobe}}{ lobe location of node }
 #'   \item{\code{Brodmann}}{ Broadmann area number }
 #'   \item{\code{AAL}}{ AAL region label }
 #' }
 #' #' @references \url{http://www.nil.wustl.edu/labs/petersen/Resources.html}
-#' 
-#' @examples 
+#'
+#' @examples
 #' data(powers_areal_mni_itk)
 #' \dontrun{
-#'   fixed <- antsImageRead( getANTsRData("ch2") )
-#'   moving <- antsImageRead( getANTsRData("mni") )
-#'   mytx <- antsRegistration( fixed=fixed, moving=moving, 
-#'   typeofTransform = c("SyN") )
-#'   data( "powers_areal_mni_itk", package = "ANTsR", envir = environment() )
-#'   coords = powers_areal_mni_itk[,1:3]
-#'   ch2reg   = antsRegistration( fixed, moving, typeofTransform = "SyN" )
-#'   coordsw <- antsApplyTransformsToPoints( 
-#'   dim=3, points=coords,
-#'   transformlist=ch2reg$fwdtransforms,
-#'   whichtoinvert=c(FALSE,FALSE) )
-#'   ptrd = 3
-#'   powersLabels = makePointsImage( coordsw, moving, radius = pard )
-#'   plot( moving, powersLabels, axis=3, nslices=30 )
+#' fixed <- antsImageRead(getANTsRData("ch2"))
+#' moving <- antsImageRead(getANTsRData("mni"))
+#' mytx <- antsRegistration(
+#'   fixed = fixed, moving = moving,
+#'   typeofTransform = c("SyN")
+#' )
+#' data("powers_areal_mni_itk", package = "ANTsR", envir = environment())
+#' coords <- powers_areal_mni_itk[, 1:3]
+#' ch2reg <- antsRegistration(fixed, moving, typeofTransform = "SyN")
+#' coordsw <- antsApplyTransformsToPoints(
+#'   dim = 3, points = coords,
+#'   transformlist = ch2reg$fwdtransforms,
+#'   whichtoinvert = c(FALSE, FALSE)
+#' )
+#' ptrd <- 3
+#' powersLabels <- makePointsImage(coordsw, moving, radius = pard)
+#' plot(moving, powersLabels, axis = 3, nslices = 30)
 #' }
 #' @keywords datasets
 "powers_areal_mni_itk"
 
 
 #' @title tracts
 #' @docType data
-#' @description A data frame label numbers and names for 
+#' @description A data frame label numbers and names for
 #' the white matter tracts labels.
 #' @format A data frame listing the following variables.
 #' \describe{
-#' \item{\code{label_num}}{ Numerical label value. } 
+#' \item{\code{label_num}}{ Numerical label value. }
 #' \item{\code{label_name}}{ Shorthand anatomical value. }
 #' }
 #' @references \url{http://www.ncbi.nlm.nih.gov/pubmed/18407524}
@@ -96,7 +98,7 @@
 
 #' @title AAL Labels
 #' @docType data
-#' @description A data frame label numbers and names 
+#' @description A data frame label numbers and names
 #' for the neuroanatomical AAL labels.
 #' @format A data frame listing the following variables.
 #' \describe{
@@ -116,9 +118,9 @@
 #'   \item{\code{temporal}}{binary value}
 #'   \item{\code{unknown}}{binary value}
 #' }
-#' @references 
+#' @references
 #' \url{http://en.wikipedia.org/wiki/Automated_Anatomical_Labeling}
-#' @examples 
+#' @examples
 #' data(aal)
 #' @keywords datasets
 "aal"
@@ -127,15 +129,15 @@
 #' @name antsrVersions
 #' @title antsrVersions
 #' @docType data
-#' @description A data frame defining the git tag 
-#' for the current ANTsR version.  One can also see 
-#' antsrVersions from ANTsRCore to get the git tag for 
+#' @description A data frame defining the git tag
+#' for the current ANTsR version.  One can also see
+#' antsrVersions from ANTsRCore to get the git tag for
 #' those dependencies.
 #' @format   A data frame listing the following variables.
 #' \describe{
 #'   \item{\code{Dependency}}{ Name of software dependency. }
-#'   \item{\code{GitTag}}{ The git tag.  This can also be used to 
-#'   trace other dependencies, e.g. the ITK version used by the 
+#'   \item{\code{GitTag}}{ The git tag.  This can also be used to
+#'   trace other dependencies, e.g. the ITK version used by the
 #'   current ANTs version. }
 #' }
 #' @references \url{https://github.com/stnava/ANTs}