From 5c346d8b56b18cd3420417be6675b784e1e90cf8 Mon Sep 17 00:00:00 2001
From: Gregory Jefferis <jefferis@gmail.com>
Date: Fri, 29 May 2020 20:51:04 +0100
Subject: [PATCH] Small doc tweaks

---
 R/nat-package.R    | 18 +++++++++---------
 R/neuron.R         |  3 +--
 man/nat-package.Rd | 18 +++++++++---------
 3 files changed, 19 insertions(+), 20 deletions(-)

diff --git a/R/nat-package.R b/R/nat-package.R
index 723e5be0..c560e731 100644
--- a/R/nat-package.R
+++ b/R/nat-package.R
@@ -53,16 +53,16 @@
 #'   streamline arithmetic (e.g. scaling all the points in all neurons see
 #'   \code{\link{*.neuronlist}}) and transformations (see \bold{Transformations}
 #'   section below and \code{\link{xform}}). Arbitrary functions can be applied
-#'   to each individual neuron can be applied using the \code{\link{nlapply}}
-#'   function, which also provides options for progress bars and simple
-#'   parallelisation.
+#'   to each individual neuron using the \code{\link{nlapply}} function, which
+#'   also provides options for progress bars and simple parallelisation.
 #'
 #' @section Transformations: \code{\link{neuron}} or \code{\link{dotprops}}
 #'   objects can be transformed from e.g. sample to template brain space using
-#'   affine or non-rigid registrations, typically calculated with the open
-#'   source CMTK package available at \url{www.nitrc.org/projects/cmtk/}, see
-#'   ?\link{cmtk} for installation details. The function \code{\link{xform}} has
-#'   methods to deal with a variety of types of interest.
+#'   affine or non-rigid registrations. \bold{nat} has built in support for
+#'   registrations calculated with the open source CMTK package available at
+#'   \url{www.nitrc.org/projects/cmtk}. See ?\link{cmtk} for installation
+#'   details. The function \code{\link{xform}} has methods to deal with a
+#'   variety of types of interest.
 #'
 #' @section 3D Image Data: In addition to data types defined by unstructured
 #'   collections of 3D vertices such as \code{\link{neuron}},
@@ -115,8 +115,8 @@
 #'
 #' @section plotly Package: Since \bold{nat} v1.9.2 there is support for
 #'   \code{\link[plotly:plot_ly]{plotly}} as an alternative 3D visualisation
-#'   engine. You can set \code{option(nat.plotengine='plotly')} to make this
-#'   the default. See the 3D graphics vignette for further details.
+#'   engine. You can set \code{option(nat.plotengine='plotly')} to make this the
+#'   default. See the 3D graphics vignette for further details.
 #'
 #' @section File Formats: \bold{nat} supports multiple input and output data
 #'   formats for the object classes. There is a registry-based mechanism which
diff --git a/R/neuron.R b/R/neuron.R
index 0156cbcc..75796f2d 100644
--- a/R/neuron.R
+++ b/R/neuron.R
@@ -918,8 +918,7 @@ simplify_neuron <- function(x, n=1, invert=FALSE, ...) {
   # The approach is to find the longest tree (lets call it spine) from the root to the 
   # farthest leaf node first..
   # Then additional branches are added to the spine such that they are longest that can be
-  # added..
-  
+  # added.
   for (i in 0:n) {
     if (i == 0) {
       # Step 4a: Compute the spine, so for that compute the farthest leaf node 
diff --git a/man/nat-package.Rd b/man/nat-package.Rd
index 7604ea97..a691dd3a 100644
--- a/man/nat-package.Rd
+++ b/man/nat-package.Rd
@@ -63,18 +63,18 @@ neuroanatomical data, especially representations of neurons.
   streamline arithmetic (e.g. scaling all the points in all neurons see
   \code{\link{*.neuronlist}}) and transformations (see \bold{Transformations}
   section below and \code{\link{xform}}). Arbitrary functions can be applied
-  to each individual neuron can be applied using the \code{\link{nlapply}}
-  function, which also provides options for progress bars and simple
-  parallelisation.
+  to each individual neuron using the \code{\link{nlapply}} function, which
+  also provides options for progress bars and simple parallelisation.
 }
 
 \section{Transformations}{
  \code{\link{neuron}} or \code{\link{dotprops}}
   objects can be transformed from e.g. sample to template brain space using
-  affine or non-rigid registrations, typically calculated with the open
-  source CMTK package available at \url{www.nitrc.org/projects/cmtk/}, see
-  ?\link{cmtk} for installation details. The function \code{\link{xform}} has
-  methods to deal with a variety of types of interest.
+  affine or non-rigid registrations. \bold{nat} has built in support for
+  registrations calculated with the open source CMTK package available at
+  \url{www.nitrc.org/projects/cmtk}. See ?\link{cmtk} for installation
+  details. The function \code{\link{xform}} has methods to deal with a
+  variety of types of interest.
 }
 
 \section{3D Image Data}{
@@ -135,8 +135,8 @@ neuroanatomical data, especially representations of neurons.
 \section{plotly Package}{
  Since \bold{nat} v1.9.2 there is support for
   \code{\link[plotly:plot_ly]{plotly}} as an alternative 3D visualisation
-  engine. You can set \code{option(nat.plotengine='plotly')} to make this
-  the default. See the 3D graphics vignette for further details.
+  engine. You can set \code{option(nat.plotengine='plotly')} to make this the
+  default. See the 3D graphics vignette for further details.
 }
 
 \section{File Formats}{