setup general package framework and CI

.Rbuildignore

@@ -2,3 +2,11 @@
 ^\.Rproj\.user$
 ^README\.Rmd$
 ^R/TEMP_original_fxns\.R$
+^doc$
+^Meta$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+^\.travis\.yml$
+^appveyor\.yml$
+^codecov\.yml$

.gitignore

@@ -39,3 +39,5 @@ inst/doc
 data-raw/*.rds
 .Rhistory
 .Rproj.user
+doc
+Meta

.travis.yml

@@ -0,0 +1,7 @@
+# R for travis: see documentation at https://docs.travis-ci.com/user/languages/r
+
+language: R
+cache: packages
+
+after_success:
+ - Rscript -e 'covr::codecov()'

DESCRIPTION

@@ -4,17 +4,17 @@ Title: Read HotNet2 Results and Convert to Graph object
 Version: 0.0.0.9000
 Author: person(c("Joshua", "H"), "Cook", email = "[email protected]",
  role = c("aut", "cre"))
+Maintainer: Joshua Cook <[email protected]>
 Description: This package reads the results from HotNet2 for further analysis.
  It can return the results as a list of list of genes or transform them into
  `igraph` or `tidygraph` objects.
 License: file LICENSE
 Encoding: UTF-8
 LazyData: true
 Depends: R (>= 3.5.0)
-Imports:
- dplyr (>= 0.8.0),
- ggplot2 (>= 3.1.0),
- magrittr (>= 1.5.0),
- purrr (>= 0.3.0),
- rlang (>= 0.3.0),
- tibble(>= 2.0.0)
+Suggests: 
+ knitr,
+ rmarkdown,
+ covr
+VignetteBuilder: knitr
+RoxygenNote: 6.1.1

HotNetvieweR.Rproj

@@ -18,3 +18,4 @@ StripTrailingWhitespace: Yes
 BuildType: Package
 PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace

NAMESPACE

@@ -1 +1,2 @@
-exportPattern("^[[:alpha:]]+")
+# Generated by roxygen2: do not edit by hand
+

R/TEMP_original_fxns.R

@@ -2,17 +2,6 @@
 ## Extracting Results from a HotNet2 Run ##
 ###########################################
 
-library(igraph)
-library(tidygraph)
-library(RColorBrewer)
-library(scales)
-library(reshape)
-library(pryr)
-library(data.table)
-library(plyr)
-library(magrittr)
-library(tidyverse)
-
 #### ---- Subroutines ---- ####
 
 # gets the k for a given delta

README.Rmd

@@ -1,23 +1,49 @@
 ---
-title: "README.Rmd"
-author: "Joshua H. Cook"
-date: "2/22/2019"
-output:
- md_document:
- variant: markdown_github
+output: github_document
 ---
 
-```{r setup, include=FALSE}
-knitr::opts_chunk$set(echo = TRUE)
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+ collapse = TRUE,
+ comment = "#>",
+ fig.path = "man/figures/README-",
+ out.width = "100%"
+)
 ```
 
 # HotNetvieweR
 
-**author: Joshua H. Cook**
+<!-- badges: start -->
+![CRAN_Release_Badge](https://www.r-pkg.org/badges/version/HotNetvieweR)
+[![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0) 
+[![Travis build status](https://travis-ci.org/jhrcook/HotNetvieweR.svg?branch=master)](https://travis-ci.org/jhrcook/HotNetvieweR)
+[![AppVeyor build status](https://ci.appveyor.com/api/projects/status/github/jhrcook/HotNetvieweR?branch=master&svg=true)](https://ci.appveyor.com/project/jhrcook/HotNetvieweR)
+[![Codecov test coverage](https://codecov.io/gh/jhrcook/HotNetvieweR/branch/master/graph/badge.svg)](https://codecov.io/gh/jhrcook/HotNetvieweR?branch=master)
+<!-- badges: end -->
 
-**date: 2019-02-22**
+The goal of HotNetvieweR is to ...
 
-[![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
-![CRAN_Release_Badge](https://www.r-pkg.org/badges/version/HotNetvieweR)
+## Installation
+
+You can install the released version of HotNetvieweR from [CRAN](https://CRAN.R-project.org) with:
+
+``` r
+install.packages("HotNetvieweR")
+```
 
-Just started this package, but I have most of the pieces from my personal use. Should be able to get this up soon.
+And the development version from [GitHub](https://github.com/) with:
+
+``` r
+# install.packages("devtools")
+devtools::install_github("jhrcook/HotNetvieweR")
+```
+## Example
+
+This is a basic example which shows you how to solve a common problem:
+
+```{r example, eval=FALSE}
+library(HotNetvieweR)
+## basic example code
+```

README.md

@@ -1,10 +1,44 @@
-HotNetvieweR
-============
 
-**author: Joshua H. Cook**
+<!-- README.md is generated from README.Rmd. Please edit that file -->
 
-**date: 2019-02-22**
+# HotNetvieweR
 
-[![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0) ![CRAN\_Release\_Badge](https://www.r-pkg.org/badges/version/HotNetvieweR)
+<!-- badges: start -->
 
-Just started this package, but I have most of the pieces from my personal use. Should be able to get this up soon.
+![CRAN\_Release\_Badge](https://www.r-pkg.org/badges/version/HotNetvieweR)
+[![License: GPL
+v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0) 
+[![Travis build
+status](https://travis-ci.org/jhrcook/HotNetvieweR.svg?branch=master)](https://travis-ci.org/jhrcook/HotNetvieweR)
+[![AppVeyor build
+status](https://ci.appveyor.com/api/projects/status/github/jhrcook/HotNetvieweR?branch=master&svg=true)](https://ci.appveyor.com/project/jhrcook/HotNetvieweR)
+[![Codecov test
+coverage](https://codecov.io/gh/jhrcook/HotNetvieweR/branch/master/graph/badge.svg)](https://codecov.io/gh/jhrcook/HotNetvieweR?branch=master)
+<!-- badges: end -->
+
+The goal of HotNetvieweR is to …
+
+## Installation
+
+You can install the released version of HotNetvieweR from
+[CRAN](https://CRAN.R-project.org) with:
+
+``` r
+install.packages("HotNetvieweR")
+```
+
+And the development version from [GitHub](https://github.com/) with:
+
+``` r
+# install.packages("devtools")
+devtools::install_github("jhrcook/HotNetvieweR")
+```
+
+## Example
+
+This is a basic example which shows you how to solve a common problem:
+
+``` r
+library(HotNetvieweR)
+## basic example code
+```

_pkgdown.yml

@@ -0,0 +1,39 @@
+destination: docs
+
+template:
+ params:
+ bootswatch: flatly
+
+navbar:
+ structure:
+ left:
+ - home
+ - intro
+ - reference
+ - articles
+ - tutorials
+ right:
+ - news
+ - github
+ - twitter
+ components:
+ home:
+ icon: fas fa-home fa-lg
+ href: index.html
+ reference:
+ text: Reference
+ href: reference/index.html
+ articles:
+ text: Articles
+ menu:
+ - text: HotNet2 Setup and Example
+ href: articles/HotNet2-setup-and-example.html
+ news:
+ text: Versions
+ href: news/index.html
+ github:
+ icon: fa-github fa-lg
+ href: https://github.com/jhrcook/ggasym
+ twitter:
+ icon: fab fa-twitter fa-lg
+ href: https://twitter.com/JoshDoesa

appveyor.yml

@@ -0,0 +1,52 @@
+# DO NOT CHANGE the "init" and "install" sections below
+
+# Download script file from GitHub
+init:
+ ps: |
+ $ErrorActionPreference = "Stop"
+ Invoke-WebRequest https://raw.github.com/krlmlr/r-appveyor/master/scripts/appveyor-tool.ps1 -OutFile "..\appveyor-tool.ps1"
+ Import-Module '..\appveyor-tool.ps1'
+
+install:
+ ps: Bootstrap
+
+cache:
+ - C:\RLibrary
+
+environment:
+ NOT_CRAN: true
+ # env vars that may need to be set, at least temporarily, from time to time
+ # see https://github.com/krlmlr/r-appveyor#readme for details
+ # USE_RTOOLS: true
+ # R_REMOTES_STANDALONE: true
+
+# Adapt as necessary starting from here
+
+build_script:
+ - travis-tool.sh install_deps
+
+test_script:
+ - travis-tool.sh run_tests
+
+on_failure:
+ - 7z a failure.zip *.Rcheck\*
+ - appveyor PushArtifact failure.zip
+
+artifacts:
+ - path: '*.Rcheck\**\*.log'
+ name: Logs
+
+ - path: '*.Rcheck\**\*.out'
+ name: Logs
+
+ - path: '*.Rcheck\**\*.fail'
+ name: Logs
+
+ - path: '*.Rcheck\**\*.Rout'
+ name: Logs
+
+ - path: '\*_*.tar.gz'
+ name: Bits
+
+ - path: '\*_*.zip'
+ name: Bits

codecov.yml

@@ -0,0 +1,12 @@
+comment: false
+
+coverage:
+ status:
+ project:
+ default:
+ target: auto
+ threshold: 1%
+ patch:
+ default:
+ target: auto
+ threshold: 1%