diff --git a/DESCRIPTION b/DESCRIPTION index 119bb80..a77ae5b 100644 --- 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 -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 index 7361bb8..4358901 100644 --- 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 index 2496d2d..4085f27 100644 --- 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 index a419c8e..d7da412 100644 --- 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 index 2a7c818..fc7e398 100644 --- 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 index 99b6fe5..08a5ff9 100644 --- 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 index b10345a..0565bdb 100644 --- a/man/casino.Rd +++ b/man/casino.Rd @@ -4,7 +4,7 @@ \name{casino} \alias{casino} \title{Dishonest casino.} -\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/man/whichmax.Rd b/man/whichmax.Rd index 0949626..b1c7e4f 100644 --- a/man/whichmax.Rd +++ b/man/whichmax.Rd @@ -23,8 +23,8 @@ Returns the position (index) of the maximum value in a numeric or integer vector with ties broken at random. } \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 +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{ diff --git a/src/ViterbiC.cpp b/src/ViterbiC.cpp index 8fee6c3..9f174f6 100644 --- 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 //'