Initial commit

.Rbuildignore

+^.*\.Rproj$
+^\.Rproj\.user$
+^data-raw$
+dev_history.R
+^dev$
+$run_dev.*
+^LICENSE\.md$
+^README\.Rmd$
+^CODE_OF_CONDUCT\.md$

.gitignore

+.Rhistory
+.RData
+.Rproj.user

CODE_OF_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 
+(https://www.contributor-covenant.org), version 1.0.0, available at 
+https://contributor-covenant.org/version/1/0/0/.

DESCRIPTION

+Package: affiliationExplorer
+Title: Resolve multiaffilations from FROGS
+Version: 0.0.0.9000
+Authors@R: person('Sandra', 'Derozier', email = 'sandra.derozier@inrae.fr', role = c('cre', 'aut'))
+Description: Shiny app to help user choose one affilation among equally good ones.
+License: MIT + file LICENSE
+Encoding: UTF-8
+LazyData: true
+Imports: 
+    shiny, 
+    golem
+RoxygenNote: 6.1.0

LICENSE

+YEAR: 2020
+COPYRIGHT HOLDER: Sandra Derozier

LICENSE.md

+# MIT License
+
+Copyright (c) 2020 Sandra Derozier
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

NAMESPACE

+# Generated by roxygen2: do not edit by hand
+
+export(run_app)
+import(shiny)
+importFrom(golem,with_golem_options)
+importFrom(shiny,shinyApp)

NEWS.md

+# affiliationExplorer 0.0.0.9000
+
+* Added a `NEWS.md` file to track changes to the package.

R/app_server.R

+#' @import shiny
+app_server <- function(input, output,session) {
+  # List the first level callModules here
+}

R/app_ui.R

+#' @import shiny
+app_ui <- function() {
+  tagList(
+    # Leave this function for adding external resources
+    golem_add_external_resources(),
+    # List the first level UI elements here 
+    fluidPage(
+      h1("affiliationExplorer")
+    )
+  )
+}
+
+#' @import shiny
+golem_add_external_resources <- function(){
+  
+  addResourcePath(
+    'www', system.file('app/www', package = 'affiliationExplorer')
+  )
+ 
+  tags$head(
+    golem::activate_js(),
+    golem::favicon()
+    # Add here all the external resources
+    # If you have a custom.css in the inst/app/www
+    # Or for example, you can add shinyalert::useShinyalert() here
+    #tags$link(rel="stylesheet", type="text/css", href="www/custom.css")
+  )
+}

R/run_app.R

+#' Run the Shiny Application
+#'
+#' @export
+#' @importFrom shiny shinyApp
+#' @importFrom golem with_golem_options
+run_app <- function(...) {
+  with_golem_options(
+    app = shinyApp(ui = app_ui, server = app_server), 
+    golem_opts = list(...)
+  )
+}

README.Rmd

+---
+output: github_document
+---
+
+<!-- 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%"
+)
+```
+
+# affiliationExplorer
+
+<!-- badges: start -->
+[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://www.tidyverse.org/lifecycle/#experimental)
+<!-- badges: end -->
+
+The goal of affiliationExplorer is to ...
+
+## Installation
+
+You can install the released version of affiliationExplorer from [CRAN](https://CRAN.R-project.org) with:
+
+``` r
+install.packages("affiliationExplorer")
+```
+
+## Example
+
+This is a basic example which shows you how to solve a common problem:
+
+```{r example}
+library(affiliationExplorer)
+## basic example code
+```
+
+What is special about using `README.Rmd` instead of just `README.md`? You can include R chunks like so:
+
+```{r cars}
+summary(cars)
+```
+
+You'll still need to render `README.Rmd` regularly, to keep `README.md` up-to-date.
+
+You can also embed plots, for example:
+
+```{r pressure, echo = FALSE}
+plot(pressure)
+```
+
+In that case, don't forget to commit and push the resulting figure files, so they display on GitHub!

affiliationExplorer.Rproj

+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: knitr
+LaTeX: pdfLaTeX
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source

dev/01_start.R

+# Building a Prod-Ready, Robust Shiny Application.
+# 
+# Each step is optional. 
+# 
+# 1 - On init
+# 
+## 1.1 - Fill the descripion & set options
+## 
+## Add information about the package that will contain your app
+
+golem::fill_desc(
+  pkg_name = "affiliationExplorer", # The Name of the package containing the App 
+  pkg_title = "Resolve multiaffilations from FROGS", # The Title of the package containing the App 
+  pkg_description = "Shiny app to help user choose one affilation among equally good ones.", # The Description of the package containing the App 
+  author_first_name = "Sandra", # Your First Name
+  author_last_name = "Derozier",  # Your Last Name
+  author_email = "sandra.derozier@inrae.fr",      # Your Email
+  repo_url = NULL # The (optional) URL of the GitHub Repo
+)     
+
+## Use this desc to set {golem} options
+
+golem::set_golem_options()
+
+## 1.2 - Set common Files 
+## 
+## If you want to use the MIT licence, README, code of conduct, lifecycle badge, and news
+
+usethis::use_mit_license( name = "Sandra Derozier" )  # You can set another licence here
+usethis::use_readme_rmd( open = FALSE )
+usethis::use_code_of_conduct()
+usethis::use_lifecycle_badge( "Experimental" )
+
+usethis::use_news_md( open = FALSE )
+usethis::use_git()
+
+## 1.3 - Add a data-raw folder
+## 
+## If you have data in your package
+usethis::use_data_raw( name = "my_dataset", open = FALSE ) # Change "my_dataset"
+
+## 1.4 - Init Tests
+## 
+## Create a template for tests
+
+golem::use_recommended_tests()
+
+## 1.5 : Use Recommended Package
+
+golem::use_recommended_deps()
+
+## 1.6 Add various tools
+
+# If you want to change the favicon (default is golem's one)
+golem::remove_favicon()
+golem::use_favicon() # path = "path/to/ico". Can be an online file. 
+
+# Add helper functions 
+golem::use_utils_ui()
+golem::use_utils_server()
+
+# You're now set! 
+# go to dev/02_dev.R
+rstudioapi::navigateToFile( "dev/02_dev.R" )
+

dev/02_dev.R

+# Building a Prod-Ready, Robust Shiny Application.
+# 
+# Each step is optional. 
+# 
+
+# 2. All along your project
+
+## 2.1 Add modules
+## 
+golem::add_module( name = "my_first_module" ) # Name of the module
+golem::add_module( name = "my_other_module" ) # Name of the module
+
+## 2.2 Add dependencies
+
+usethis::use_package( "thinkr" ) # To call each time you need a new package
+
+## 2.3 Add tests
+
+usethis::use_test( "app" )
+
+## 2.4 Add a browser button
+
+golem::browser_button()
+
+## 2.5 Add external files
+
+golem::add_js_file( "script" )
+golem::add_js_handler( "handlers" )
+golem::add_css_file( "custom" )
+
+# 3. Documentation
+
+## 3.1 Vignette
+usethis::use_vignette("affiliationExplorer")
+devtools::build_vignettes()
+
+## 3.2 Code coverage
+## You'll need GitHub there
+usethis::use_github()
+usethis::use_travis()
+usethis::use_appveyor()
+
+# You're now set! 
+# go to dev/03_deploy.R
+rstudioapi::navigateToFile("dev/03_deploy.R")

dev/03_deploy.R

+# Deploy a Prod-Ready, Robust Shiny Application.
+# 
+# 4. Test my package
+
+devtools::test()
+rhub::check_for_cran()
+
+# 5. Deployment elements
+
+## 5.1 If you want to deploy on RStudio related platforms
+golem::add_rstudioconnect_file()
+golem::add_shinyappsio_file()
+golem::add_shinyserver_file()
+
+## 5.2 If you want to deploy via a generic Dockerfile
+golem::add_dockerfile()
+
+## 5.2 If you want to deploy to ShinyProxy
+golem::add_dockerfile_shinyproxy()
+
+## 5.2 If you want to deploy to Heroku
+golem::add_dockerfile_heroku()

dev/run_dev.R

+# Set options here
+options(golem.app.prod = FALSE) # TRUE = production mode, FALSE = development mode
+
+# Detach all loaded packages and clean your environment
+golem::detach_all_attached()
+# rm(list=ls(all.names = TRUE))
+
+# Document and reload your package
+golem::document_and_reload()
+
+# Run the application
+affiliationExplorer::run_app()

man/run_app.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/run_app.R
+\name{run_app}
+\alias{run_app}
+\title{run the Shiny Application}
+\usage{
+run_app()
+}
+\description{
+run the Shiny Application
+}