Kurt's edits for CRAN release

shaunpwilkinson · Jun 24, 2017 · 23acfd5 · 23acfd5
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -6,16 +6,16 @@ Authors@R: person("Shaun", "Wilkinson", email = "shaunpwilkinson@gmail.com",
     role = c("aut", "cre"))
 Author: Shaun Wilkinson [aut, cre]
 Maintainer: Shaun Wilkinson <shaunpwilkinson@gmail.com>
-Description: The aphid package is designed for the development and application of
+Description: Designed for the development and application of
     hidden Markov models and profile HMMs for biological sequence analysis. 
-    It contains functions for multiple and pairwise sequence alignment, 
+    Contains functions for multiple and pairwise sequence alignment, 
     model construction and parameter optimization, file import/export,
     implementation of the forward, backward and Viterbi algorithms for 
     conditional sequence probabilities, tree-based sequence weighting, 
     and sequence simulation. 
-    The package has a wide variety of uses including database searching, 
-    gene-finding and annotation, phylogenetic analysis and sequence 
-    classification.
+    Features a wide variety of potential applications including 
+    database searching, gene-finding and annotation, phylogenetic 
+    analysis and sequence classification.
 License: GPL-3
 URL: http://github.com/shaunpwilkinson/aphid
 BugReports: http://github.com/shaunpwilkinson/aphid/issues

diff --git a/NEWS.md b/NEWS.md
@@ -1,2 +1,2 @@
 # aphid 1.0.0
-Submitted to CRAN 2017-06-22.
+Released on CRAN 2017-06-24.
diff --git a/R/RcppExports.R b/R/RcppExports.R
@@ -53,8 +53,8 @@ logsum <- function(x) {
 #'   an index of 0).
 #' @return returns an integer representing the position (index) of the maximum
 #'   value in the input vector.
-#' @details This is a simple compiled function similar to which.max{base} but
-#'   with random breaking of ties. Unlike which.max{base}, logical vectors are
+#' @details This is a simple function similar to which.max (base R) but
+#'   with random breaking of ties. Unlike which.max, logical vectors are
 #'   not accepted.
 #' @author Shaun Wilkinson
 #'

diff --git a/R/data.R b/R/data.R
@@ -20,7 +20,7 @@
 #'
 #' The 'dishonest casino' example from Durbin et al (1998) chapter 3.2.
 #'
-#' @format A named character vector showing the result of 300 rolls of a die
+#' @format A named character vector showing the result of 300 rolls of a dice
 #'   that switches from "Fair" to "Loaded" with a probability
 #'   of 0.05 and back to "Fair" with a probability of 0.1. In the Fair
 #'   state each outcome from 1 to 6 has an equal probability of occurring,

diff --git a/README.md b/README.md
@@ -2,6 +2,14 @@
 
 Analysis with profile hidden Markov models
 
+[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/aphid)](https://cran.r-project.org/package=aphid)
+[![](http://cranlogs.r-pkg.org/badges/grand-total/aphid)](https://cran.r-project.org/package=aphid)
+[![Build Status](https://travis-ci.org/shaunpwilkinson/aphid.svg?branch=master)](https://travis-ci.org/shaunpwilkinson/aphid)
+[![codecov](https://codecov.io/github/shaunpwilkinson/aphid/branch/master/graphs/badge.svg)](https://codecov.io/github/shaunpwilkinson/aphid)
+[![ORCiD](https://img.shields.io/badge/ORCiD-0000--0002--7332--7931-brightgreen.svg)](http://orcid.org/0000-0002-7332-7931)
+[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
+[![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](http://www.gnu.org/licenses/gpl-3.0)
+
 --------------------------------------------------------------------------------
 
 `aphid` is an R package for the development and application of

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,9 +1,19 @@
-Initial submission to CRAN 2017-06-23.
+This is a resubmission addressing Kurt's request to edit on syntax in 
+Description:
+
+> PLs write
+> 
+>   Designed for ...
+> 
+> 
+>   Contains ...
+  
+These have been changed as requested.  
 
 ## Test environments
  * local ubuntu 16.04 x86_64-pc-linux-gnu; R version 3.4.0 
  * travis-ci ubuntu 12.04.5 x86_64-pc-linux-gnu; R 3.4.0
- * winbuilder devel (2017-06-12 r72786)
+ * winbuilder devel (2017-06-21 r72825)
 
 ## R CMD check results
 There were no ERRORs or WARNINGs. there was one NOTE.
@@ -13,7 +23,7 @@ Possibly mis-spelled words in DESCRIPTION:
   Viterbi (13:49)
   phylogenetic (17:34)
 
-These have been checked and are spelled correctly
+These have been checked and are spelled correctly.
 
 ## Downstream dependencies
 There were no issues.
diff --git a/man/casino.Rd b/man/casino.Rd
diff --git a/man/whichmax.Rd b/man/whichmax.Rd
diff --git a/src/ViterbiC.cpp b/src/ViterbiC.cpp
@@ -40,8 +40,8 @@ double logsum(NumericVector x){
 //'   an index of 0).
 //' @return returns an integer representing the position (index) of the maximum
 //'   value in the input vector.
-//' @details This is a simple compiled function similar to which.max{base} but
-//'   with random breaking of ties. Unlike which.max{base}, logical vectors are
+//' @details This is a simple function similar to which.max (base R) but
+//'   with random breaking of ties. Unlike which.max, logical vectors are
 //'   not accepted.
 //' @author Shaun Wilkinson
 //'