setup barebones package

.Rbuildignore

+^.*\.Rproj$
+^\.Rproj\.user$
+^README\.Rmd$
+^README\.md
+^README-.*\.png$
+^\.travis\.yml$
+^\.lintr$
+^appveyor\.yml$
+^codecov\.yml$
+^cran-comments\.md$
+^docs/
+
+^CONDUCT\.md$

.gitignore

+^\.Rproj.user
+^\.Rhistory
+^\.RData
+^\.Ruserdata
+^\.httr-oauth
+*~$
+^inst/doc
+.Rproj.user
+riskanalyser.Rproj

.lintr

+linters: with_defaults()

.travis.yml

+language: r
+cache: packages
+
+matrix:
+  include:
+    - os: linux
+      r: release
+      env:
+        - R_CODECOV=true
+    - os: linux
+      r: devel
+    - os: linux
+      r: oldrel
+    - os: osx
+      osx_image: xcode8.3
+
+
+r_github_packages:
+  - jimhester/covr
+
+warnings_are_errors: true
+
+notifications:
+  email:
+    on_success: change
+    on_failure: change
+
+after_success:
+  - if [[ "${R_CODECOV}" ]]; then Rscript -e 'covr::codecov()'; fi

CONDUCT.md

+# Contributor Code of Conduct
+
+As contributors and maintainers of this project, we pledge to respect all people who 
+contribute through reporting issues, posting feature requests, updating documentation,
+submitting pull requests or patches, and other activities.
+
+We are committed to making participation in this project a harassment-free experience for
+everyone, regardless of level of experience, gender, gender identity and expression,
+sexual orientation, disability, personal appearance, body size, race, ethnicity, age, or religion.
+
+Examples of unacceptable behavior by participants include the use of sexual language or
+imagery, derogatory comments or personal attacks, trolling, public or private harassment,
+insults, or other unprofessional conduct.
+
+Project maintainers have the right and responsibility to remove, edit, or reject comments,
+commits, code, wiki edits, issues, and other contributions that are not aligned to this 
+Code of Conduct. Project maintainers who do not follow the Code of Conduct may be removed 
+from the project team.
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by 
+opening an issue or contacting one or more of the project maintainers.
+
+This Code of Conduct is adapted from the Contributor Covenant 
+(http:contributor-covenant.org), version 1.0.0, available at 
+http://contributor-covenant.org/version/1/0/0/

DESCRIPTION

+Package: riskanalyser
+Title: Produce an epidemiological risk map by weighting multiple risk factors
+Version: 0.0.1.9000
+Authors@R: c(
+  person("Elena", "Arsevska", email = "elena.arsevska@cirad.fr", role = c("ctb"),
+  person("Sylvain", "Falala", email = "sylvain.falala@cirad.fr", role = c("aut", "cre"),
+  person("Renaud", "Lancelot", email = "renaud.lancelot@cirad.fr", role = c("ctb"),
+  person("Raphaëlle", "Metras", email = "raphaelle.metras@cirad.fr", role = c("ctb"),
+  person("Facundo", "Muñoz", email = "facundo.munoz@cirad.fr", role = c("aut", "cre")
+  )
+Description: Use a Shiny interface to help users import multiple layers of risk
+  factors, scale them and combine them using a Multi-Criteria Decision Analysis
+  approach to produce a risk map as an outcome.
+Depends: R (>= 3.2)
+License: GPL-3 + file LICENSE
+Encoding: UTF-8
+LazyData: true
+Imports: 
+  classInt,
+  geojsonio,
+  geojsonlint,
+  ggplot2
+  maptools,
+  maps,
+  plyr,
+  raster,
+  rgdal,
+  rgeos,
+  RColorBrewer,
+  sp
+Suggests: testthat, roxygen2
+RoxygenNote: 6.0.1
+URL: https://github.com/reconhub/riskanalyser
+BugReports: https://github.com/reconhub/riskanalyser/issues
+VignetteBuilder: knitr

NAMESPACE

+# Generated by roxygen2: do not edit by hand
+
+export(hello_recon)

NEWS.md

+# riskanalyser 0.0.1.9000
+
+* Added a `NEWS.md` file to track changes to the package.
+
+
+

R/please-change.R

+#' Hello World
+#'
+#' This is an example of how to create and document exported functions.
+#'
+#' @param input you should always document the paramters.
+#'              Including the expected data type.
+#'
+#' @export
+hello_recon <- function(input) {
+  "Hello RECON"
+}
+
+#' You can also document internal package function with roxygen
+#'
+#' Just make sure you add 'noRd' so no latex help files are being created.
+#' @noRd
+some_internal_function <- function() {
+  NA
+}
+

README.Rmd

+---
+output: github_document
+---
+
+[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/riskanalyser)](https://cran.r-project.org/package=riskanalyser)
+
+# Welcome to the *riskanalyser* package!
+
+This is just a template. Please remove, add or edit parts as you see fit.
+
+## Installing the package
+
+To install the current stable, CRAN version of the package, type:
+```{r install, eval = FALSE}
+install.packages("riskanalyser")
+```
+
+To benefit from the latest features and bug fixes, install the development, *github* version of the package using:
+```{r install2, eval = FALSE}
+devtools::install_github("reconhub/riskanalyser")
+```
+
+Note that this requires the package *devtools* installed.
+
+
+# What does it do?
+
+The main features of the package include:
+
+
+
+# Resources
+
+## Vignettes
+
+An overview and examples of *riskanalyser* are provided in the vignettes:
+
+...
+
+## Websites
+
+The following websites are available:
+
+...
+
+## Getting help online
+
+Bug reports and feature requests should be posted on *github* using the [*issue*](http://github.com/reconhub/riskanalyser/issues) system. All other questions should be posted on the **RECON forum**: <br>
+[http://www.repidemicsconsortium.org/forum/](http://www.repidemicsconsortium.org/forum/)
+
+Contributions are welcome via **pull requests**.
+
+Please note that this project is released with a [Contributor Code of Conduct](CONDUCT.md). By participating in this project you agree to abide by its terms.
+

README.md

+---
+output: github_document
+---
+
+[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/riskanalyser)](https://cran.r-project.org/package=riskanalyser)
+
+# Welcome to the *riskanalyser* package!
+
+This is just a template. Please remove, add or edit parts as you see fit.
+
+## Installing the package
+
+To install the current stable, CRAN version of the package, type:
+
+```r
+install.packages("riskanalyser")
+```
+
+To benefit from the latest features and bug fixes, install the development, *github* version of the package using:
+
+```r
+devtools::install_github("reconhub/riskanalyser")
+```
+
+Note that this requires the package *devtools* installed.
+
+
+# What does it do?
+
+The main features of the package include:
+
+
+
+# Resources
+
+## Vignettes
+
+An overview and examples of *riskanalyser* are provided in the vignettes:
+
+...
+
+## Websites
+
+The following websites are available:
+
+...
+
+## Getting help online
+
+Bug reports and feature requests should be posted on *github* using the [*issue*](http://github.com/reconhub/riskanalyser/issues) system. All other questions should be posted on the **RECON forum**: <br>
+[http://www.repidemicsconsortium.org/forum/](http://www.repidemicsconsortium.org/forum/)
+
+Contributions are welcome via **pull requests**.
+
+Please note that this project is released with a [Contributor Code of Conduct](CONDUCT.md). By participating in this project you agree to abide by its terms.
+

appveyor.yml

+# DO NOT CHANGE the "init" and "install" sections below
+# based on the devtools appveyor config
+
+# Download script file from GitHub
+init:
+  ps: |
+        $ErrorActionPreference = "Stop"
+        Invoke-WebRequest http://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
+
+# Adapt as necessary starting from here
+
+environment:
+  global:
+    USE_RTOOLS: true
+
+  matrix:
+  - R_VERSION: stable
+
+  - R_VERSION: oldrel
+
+  - R_VERSION: devel
+
+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

man/hello_recon.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/please-change.R
+\name{hello_recon}
+\alias{hello_recon}
+\title{Hello World}
+\usage{
+hello_recon(input)
+}
+\arguments{
+\item{input}{you should always document the paramters.
+Including the expected data type.}
+}
+\description{
+This is an example of how to create and document exported functions.
+}

tests/testthat.R

+library(testthat)
+library(riskanalyser)
+
+test_check("riskanalyser")

tests/testthat/test-example.R

+context("example tests")
+test_that("1 + 1 = 2", {
+  expect_equal(2, 1 + 1)
+})
+

vignettes/riskanalyser.Rmd

+---
+title: "riskanalyser: package overview"
+date: "`r Sys.Date()`"
+output:
+   rmarkdown::html_vignette:
+     toc: true
+     toc_depth: 2
+vignette: >
+  %\VignetteIndexEntry{Overview}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+*riskanalyser* provides ...
+
+# Installing the package
+
+To install the current stable, CRAN version of the package, type:
+```{r install, eval=FALSE}
+install.packages("riskanalyser")
+```
+
+To benefit from the latest features and bug fixes, install the development, *github* version of the package using:
+```{r install2, eval=FALSE}
+devtools::install_github("reconhub/riskanalyser")
+```
+
+Note that this requires the package *devtools* installed.
+
+# Main visible functions of the package
+
+The main functions of the package include:
+
+...
+
+Also consider adding some examples.
+
+# Main internal functions
+
+In case you want to describe internal function as well.
+... 
+
+