Commit a02be556 authored by Facundo Muñoz's avatar Facundo Muñoz ®️
Browse files

setup barebones package

parents
^.*\.Rproj$
^\.Rproj\.user$
^README\.Rmd$
^README\.md
^README-.*\.png$
^\.travis\.yml$
^\.lintr$
^appveyor\.yml$
^codecov\.yml$
^cran-comments\.md$
^docs/
^CONDUCT\.md$
^\.Rproj.user
^\.Rhistory
^\.RData
^\.Ruserdata
^\.httr-oauth
*~$
^inst/doc
.Rproj.user
riskanalyser.Rproj
linters: with_defaults()
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
# 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/
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
This diff is collapsed.
# Generated by roxygen2: do not edit by hand
export(hello_recon)
# riskanalyser 0.0.1.9000
* Added a `NEWS.md` file to track changes to the package.
#' 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
}
---
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.
---
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.
# 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
% 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.
}
library(testthat)
library(riskanalyser)
test_check("riskanalyser")
context("example tests")
test_that("1 + 1 = 2", {
expect_equal(2, 1 + 1)
})
---
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.
...
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