" /> class: center, middle, inverse, title-slide # From ShinyApps to CRAN ## RUCK 2019 ### <br><br>Jinseob Kim; <a href="https://github.com/jinseob2kim"><span><i class="fab fa-github faa-float animated "></i>jinseob2kim</span></a> ### Zarathu Co., Ltd ### <br><br>2019-10-25 --- class: bg-main1 # Executive Summary .large[ - 의학연구자들에게 맞춤형 **[ShinyApps](https://shiny.rstudio.com/)**를 제공하고, 범용으로 쓰일만한 것들을 **[Shiny module](https://shiny.rstudio.com/articles/modules.html)**로 만든 후, **[웹](http://app.zarathu.com)**을 통해 배포하였다. ] -- .large[ - 개인 PC에서 직접 이용할 수 있도록 **[Rstudio Addins](https://rstudio.github.io/rstudioaddins/)**을 포함한 패키지로 만들어 **github**에 배포하였다. ] -- .large[ - **[testthat](https://github.com/r-lib/testthat)**, **[covr](https://github.com/r-lib/covr)**로 코드 테스트를 수행하고 결과 리포트를 만들었으며, **[pkgdown](https://github.com/r-lib/pkgdown)**으로 패키지를 소개하는 웹사이트를 만들었다. ] -- .large[ - **[Travis CI](https://travis-ci.org/)**와 **[appveyor](https://www.appveyor.com/)**로 앞의 과정과 여러 운영체제에서의 테스트를 자동화하였다. ] -- .large[ - 최종적으로 **[CRAN](https://cran.r-project.org/)**에 패키지를 배포하고, .yellow[V1.0.1] 까지 업데이트 하였다. ] --- class: middle bg-main1 # 맞춤형 ShinyApps --- class: bg-main1 # 연구지원 분류 .large[ * 통계 분석 + 일반 데이터: Table 1, 회귀분석, 생존분석 + 반복측정: GEE(Generalized Estimating Equation) + 표본조사: [국민건강영양조사](https://knhanes.cdc.go.kr/knhanes/main.do) + Propensity score 분석: Matching, IPTW * [공통데이터모델(Common Data Model, CDM)](http://www.feedernet.org/html/) 결과 확인. * 심혈관 생리학 지표 계산: .yellow[드래그] * 정신질환 .yellow[네트워크 분석] ] --- class: bg-main1 # 일반데이터: 시야 ### 기술통계, 회귀/생존분석, 간단한 그림 <a href="http://app.zarathu.com"><img src="https://raw.githubusercontent.com/jinseob2kim/PresentationShinyMed/master/docs/VF.png" width=100%></a> --- class: bg-main1 # 신장이식 ### 기술통계, 회귀/생존분석, 맞춤형 그림 <img src="ktsym.jpg" width=100%> --- class: bg-main1 # Tip 1: 그림 편집 ### Shiny에서 모든 편집옵션 지원불가, .yellow[직접 편집] 가능해야 함. .large[ - `svg` 확장자: [Cairo](https://CRAN.R-project.org/package=Cairo) 패키지 이용, [Inkscape](https://inkscape.org/ko/)에서 편집. `ggsave()` 지원. - `emf` 확장자: [devEMF](https://cran.r-project.org/package=devEMF) 패키지 이용, **PPT**에서 편집, `ggsave()` 지원 안함. - 윈도우 환경에서는 `wmf` 확장자 이용, `ggsave()` 저장 후 **PPT** 편집 가능. ] --- class: bg-main1 # Example: `emf` ### **PPT** 정확한 그림인식 위해 .yellow[`emfPlus = F`] 옵션! ```r library(devEMF) *emf("plot.emf", width = 7, height = 7, emfPlus = F) ggplot(mtcars, aes(mpg, cyl)) + geom_point() dev.off() ``` <img src="https://raw.githubusercontent.com/jinseob2kim/PresentationShinyMed/master/docs/zzz.png" width="70%" style="display: block; margin: auto;" /> --- class: bg-main1 # Tip 2: 테이블 다운로드 .large[ [DT](https://rstudio.github.io/DT) 패키지의 `datatable` 함수 ] ```r datatable( * iris, extensions = 'Buttons', options = list( * dom = 'Bfrtip', # Button, filter, processing, table, information, pagination * buttons = c('copy', 'csv', 'excel', 'pdf', 'print'), scrollX = T # Scrolling X axis ) ) ``` 세부 `dom` 설정은 [여기](https://datatables.net/reference/option/dom) --- class: center <div 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class=\"display\">\n <thead>\n <tr>\n <th> <\/th>\n <th>Sepal.Length<\/th>\n <th>Sepal.Width<\/th>\n <th>Petal.Length<\/th>\n <th>Petal.Width<\/th>\n <th>Species<\/th>\n <\/tr>\n <\/thead>\n<\/table>","options":{"dom":"Bfrtip","buttons":["copy","csv","excel","pdf","print"],"scrollX":true,"columnDefs":[{"className":"dt-right","targets":[1,2,3,4]},{"orderable":false,"targets":0}],"order":[],"autoWidth":false,"orderClasses":false}},"evals":[],"jsHooks":[]}</script> --- class: bg-main1 # Tip 3: `dropdownButton` ### [shinyWidgets](https://github.com/dreamRs/shinyWidgets) Package <img src="https://github.com/dreamRs/shinyWidgets/raw/master/man/figures/dropdown_btn_off.png" width="50%" /><img src="https://github.com/dreamRs/shinyWidgets/raw/master/man/figures/dropdown_btn_on.png" width="50%" /> ```r shinyWidgets::dropdownButton( tags$h3("List of Input"), selectInput(inputId = 'xcol', label = 'X Variable', choices = names(iris)), selectInput(inputId = 'ycol', label = 'Y Variable', choices = names(iris), selected = names(iris)[[2]]), sliderInput(inputId = 'clusters', label = 'Cluster count', value = 3, min = 1, max = 9), circle = TRUE, status = "danger", icon = icon("gear"), width = "300px", tooltip = tooltipOptions(title = "Click to see inputs !")) ``` --- class: bg-main1 # Tip 4: [shinymanager](https://github.com/datastorm-open/shinymanager) - login module <a href="http://shinyapps.dreamrs.fr/shinymanager-demo/"><img src="https://github.com/datastorm-open/shinymanager/raw/master/man/figures/shinymanager-login.png" width=100%></a> example id & password: .yellow[shinymanager] ### 쉽게 로그인 모듈 추가 & 로그 수집 --- layout: true class: split-four white .split-four[ .row.bg-main1[.content[ `install.packages("shinymanager")` Demo: http://shinyapps.dreamrs.fr/shinymanager-demo/ (id & password: .yellow[shinymanager]) ]] .row.bg-main2[.content[ ### Make User info ``` credentials <- data.frame( user = c("shiny", "shinymanager"), password = c("azerty", "12345"), admin = c(T, F), stringsAsFactors = FALSE) ``` ]] .row.bg-main3[.content[ ### Apply to UI ``` ui <- secure_app(ui, enable_admin = T) ``` ]] .row.bg-main4[.content[ ### In server ``` res_auth <- secure_server( check_credentials = check_credentials(credentials) ) ``` ]] ] --- class: fade-row2 fade-row3 fade-row4 --- class: fade-row1 fade-row3 fade-row4 --- class: fade-row1 fade-row2 fade-row4 --- class: fade-row1 fade-row2 fade-row3 --- class: --- layout:false class: bg-main1 # `app.R` Example ```r credentials <- data.frame( user = c("shiny", "shinymanager"), password = c("shiny", "shinymanager"), stringsAsFactors = FALSE) library(shiny);library(shinymanager) ui <- fluidPage( tags$h2("My secure application"), verbatimTextOutput("auth_output")) ui <- secure_app(ui) server <- function(input, output, session) { res_auth <- secure_server(check_credentials = check_credentials(credentials)) output$auth_output <- renderPrint({ reactiveValuesToList(res_auth) }) } shinyApp(ui, server) ``` --- layout: false class:bg-main1 <img src="https://ryo-n7.github.io/assets/2019-07-21-user2019-reflections_files/shinymanager.PNG" style="display: block; margin: auto;" /> --- class: split-two white .row.bg-main1[.content[ # `dataframe` 은 .yellow[admin], .yellow[log] 기능 안됨. <br> ```r ui <- secure_app(ui, enable_admin = T) ``` ## Option doesn't run. ]] .row.bg-main2[.content.vmiddle.center[ # Need .yellow[DB]: for dynamic update. <br><br> # [shinymanager](https://github.com/datastorm-open/shinymanager) supports [RSQLite](https://db.rstudio.com/databases/sqlite/) <br> ### Simple .yellow[DB] with 1 file ]] --- layout: true class: split-two white .row.bg-main1[.content[ ### Make User info: no .yellow[DB] ``` credentials <- data.frame( user = c("shiny", "shinymanager"), password = c("azerty", "12345"), admin = c(T, F), stringsAsFactors = FALSE) ``` ### In server ``` res_auth <- secure_server( check_credentials = check_credentials(credentials)) ``` ]] .row.bg-main2[.content[ ### Make User info: .yellow[DB] ``` credentials <- data.frame( user = c("shiny", "shinymanager"), password = c("azerty", "12345"), admin = c(T, F), stringsAsFactors = FALSE) *create_db(credentials_data = credentials, sqlite_path = "database.sqlite") ``` ### In server ``` res_auth <- secure_server( * check_credentials = check_credentials("database.sqlite")) ``` ]] --- class: fade-row2 --- class: fade-row1 --- class: --- layout: false class: bg-main1 # .yellow[Caution]: Tip 4 end <br><br><br><br> ### [Shiny server](https://www.rstudio.com/products/shiny/shiny-server/) 통한 로그는 접근권한을 바꿔야. ```shell chmod 777 -R <App directory> ## write permission to all user ``` https://github.com/datastorm-open/shinymanager/issues/6 --- class: bg-main1 # 반복측정: 심혈관질환 위험요인 ### [geepack](https://cran.r-project.org/web/packages/geepack/index.html) 패키지 적용, 한 사람이 2개 이상의 심혈관 시술 받음. <a href="http://app.zarathu.com"><img src="https://raw.githubusercontent.com/jinseob2kim/PresentationShinyMed/master/docs/gee.png" width=100%></a> --- class: bg-main1 # 표본조사: 국민건강영양조사 ### [survey](http://r-survey.r-forge.r-project.org/survey/) 패키지 적용, 표본가중치 고려한 통계 <a href="http://app.zarathu.com"><img src="https://raw.githubusercontent.com/jinseob2kim/PresentationShinyMed/master/docs/cataract.png" width=100%></a> --- class: bg-main1 # Propensity score: 심혈관시술 효과 ### [MatchIt](https://CRAN.R-project.org/package=MatchIt) 패키지 적용, .yellow[matching & IPTW] <center><img src="ps.jpg" width=80%></center> --- class: bg-main1 # 공통데이터모델(CDM) 결과 확인. ### [zip](https://cran.r-project.org/package=zip) 패키지 이용, 결과 들어있는 .yellow[zip] 업로드하여 확인. <center><img src="cdm.jpg" width=80%></center> --- class: bg-main1 # Tip 5: Don't use `utils::zip` ### 기본함수인 `utils::zip` 은 .yellow[shiny] 와 궁합이 안좋음. `directory` 인식 문제 ```r userFile <- eventReactive(input$file, { input$file }) data <- eventReactive(input$file, { * tmp <- tempfile() * zip::unzip(userFile()$datapath, exdir = tmp) * ref <- readRDS(paste0(tmp, "/result/outcomeModelReference.rds")) return(list(dir = tmp, ref = ref)) }) ``` --- class: bg-main1 # 심혈관 생리지표 계산 ### 최대최소값 표시 & [brush](https://shiny.rstudio.com/articles/plot-interaction.html) 이용 [드래그](https://shiny.rstudio.com/gallery/plot-interaction-advanced.html)한 부분의 생리지표를 계산 <br> <center><a href="http://app.zarathu.com"><img src="https://raw.githubusercontent.com/jinseob2kim/PresentationShinyMed/master/docs/phys.png" width=100%></a></center> --- class: bg-main1 # Tip 6: [brush](https://shiny.rstudio.com/articles/plot-interaction.html) - interactive with Drag <br> <center><a href="https://shiny.rstudio.com/articles/plot-interaction.html"><img src="https://user-images.githubusercontent.com/1365941/46086339-7d256980-c16d-11e8-95a9-60c1cae9aa37.gif" width=100%></a></center> ### Other options: .yellow[click, dblclick], and .yellow[hover] --- class: bg-main1 # PTSD 네트워크 분석 ### [qgraph](https://CRAN.R-project.org/package=qgraph) 패키지 이용. [colourpicker](https://github.com/daattali/colourpicker), [shinyWidgets](https://github.com/dreamRs/shinyWidgets) 패키지로 색상 선택 UI. <center><a href="http://app.zarathu.com"><img src="https://raw.githubusercontent.com/jinseob2kim/PresentationShinyMed/master/docs/qgraph.png" width=100%></a></center> --- class: bg-main1 # Tip 7: [colourpicker](https://github.com/daattali/colourpicker) - color UI ```r library(shiny) shinyApp( ui = fluidPage( * colourInput("col", "Select colour", "purple", palette = "limited"), plotOutput("plot") ), server = function(input, output) { output$plot <- renderPlot({ set.seed(1) plot(rnorm(50), bg = input$col, col = input$col, pch = 21) }) } ) ``` --- class: middle bg-main1 # 범용 ShinyApps --- class: bg-main1 # 데이터 형태따라 분류 기술통계, 회귀분석/생존분석, ROC 분석을 포함. ### - [일반 데이터](http://app.zarathu.com/basic) ### - [반복측정 데이터](http://app.zarathu.com/repeated): [GEE](https://en.wikipedia.org/wiki/Generalized_estimating_equation) based ### - [표본조사(survey) 데이터](http://app.zarathu.com/survey): 샘플가중치(ex: 국건영) ### - [프로펜시티 점수 분석]((http://app.zarathu.com/ps)(experimental) --- class: bg-main1 # Problem: .yellow[File size limit] ### Shiny `fileInput`은 5메가 이하까지만 지원. -- 은 아니고, 용량 제한 바꿀 수 있음. ```r ## change to 30mb *options(shiny.maxRequestSize = 30*1024^2) ui <- navbarPage("Basic statistics", tabPanel("Data", ``` -- ### 서버 부담, 큰 데이터는 개인 컴퓨터에서 직접 하면 좋겠다. --- class: middle bg-main1 # [Rstudio Addins](https://rstudio.github.io/rstudioaddins) 만들기 --- class: bg-main1 # Rstudio Addins <div class="figure" style="text-align: center"> <img src="https://github.com/jinseob2kim/jsmodule/raw/master/vignettes/figures/addin.gif" alt="Rstudio Addins: jsmodule packages" width="100%" /> <p class="caption">Rstudio Addins: jsmodule packages</p> </div> --- class: bg-main1 # R packages ### [jsmodule](https://github.com/jinseob2kim/jsmodule): RStudio Addins와 Shiny Modules([CRAN](https://cran.r-project.org/package=jsmodule)) -- <br><br> ### Dependencies ### [jstable](https://github.com/jinseob2kim/jstable): 회귀분석 테이블([CRAN](https://cran.r-project.org/package=jstable)) ### [jskm](https://github.com/jinseob2kim/jskm): 카플란-마이어(Kaplan-meier) 그림([CRAN](https://cran.r-project.org/package=jskm)) --- class: bg-main1 ## CRAN download stats <center><a href="https://ipub.com/dev-corner/apps/r-package-downloads/"><img src="cranstats.png" width=100%></a></center> --- class: bg-main1 # Step 1: File upload -> Data read .large[ - ShinyApps의 `fileInput`을, **R**에서 데이터 읽는 것으로 바꿈. ] -- ```r ## app.R in ShinyApps server <- function(input, output, session) { output$import <- renderUI({ * csvFileInput("datafile") }) * data.info <- callModule(csvFile, "datafile") data <- reactive(data.info()$data) data.label <- reactive(data.info()$label) ... } * shinyApp(ui, server) ``` --- class: bg-main1 ```r ## Addin function jsBasicGadget <- function(data, nfactor.limit = 20) { * out <- data.table(data, check.names = T) ui <- navbarPage("Basic statistics", tabPanel("Data", ...) ) server <- function(input, output, session) { ... } * viewer <- browserViewer(browser = getOption("browser")) * runGadget(ui, server, viewer = viewer) ``` -- **Viewer options** - `paneViewer()`: Rstudio 우측 아래 **Viewer** - `dialogViewer()`: 따로 창을 실행 - `browserViewer()`: 따로 브라우저 실행 https://github.com/jinseob2kim/jsmodule/blob/master/R/jsBasicGadget.R --- class: bg-main1 # Step 2: UI choice ### [miniUI](https://github.com/rstudio/miniUI): Gadget용 간소화된 UI <div class="figure" style="text-align: center"> <img src="https://github.com/rstudio/miniUI/raw/master/tools/tabs.gif" alt="minuUI" width="80%" /> <p class="caption">minuUI</p> </div> --- class: bg-main1 ```r ui <- miniPage( gadgetTitleBar("Shiny gadget example"), miniTabstripPanel( miniTabPanel("Parameters", icon = icon("sliders"), miniContentPanel( sliderInput("year", "Year", 1978, 2010, c(2000, 2010), sep = "") ) ), miniTabPanel("Visualize", icon = icon("area-chart"), miniContentPanel( plotOutput("cars", height = "100%") ) ), miniTabPanel("Map", icon = icon("map-o"), miniContentPanel(padding = 0, leafletOutput("map", height = "100%") ), miniButtonBlock( actionButton("resetMap", "Reset") ) ), miniTabPanel("Data", icon = icon("table"), miniContentPanel( DT::dataTableOutput("table") ) ) ) ) ``` --- class: bg-main1, middle # 그러나 난.. <br> ### 미리 만든 ShinyApps와 동일한 환경을 원함. ### [miniUI](https://github.com/rstudio/miniUI) 안함 : ShinyApps 의 UI 코드 그대로 이용. ### `browserViewer()` 사용 : 웹브라우저에서 실행. --- class: bg-main1 # Step 3: .yellow[Addin] 함수 만들기 ### 드래그된 데이터이름을 인식하여 Gadget 실행 ```r jsBasicAddin <- function(){ * context <- rstudioapi::getActiveDocumentContext() # Set the default data to use based on the selection. dataString <- context$selection[[1]]$text * data <- get(dataString, envir = .GlobalEnv) jsBasicGadget(data) } ``` | | | |---|---| | `getActiveDocumentContext()` | Returns information about the currently active RStudio document. | | `insertText(location, text, id = NULL)` | Insert text at a specific location within a document. | | `setDocumentContext(text, id = NULL)` | Set the contents of a document open in RStudio. | --- class: bg-main1 # **addins.dcf** 파일 만들기. ### R 패키지 `inst/rstudio/addins.dcf` 에 만들기. ```sh Name: Basic statistics Description: Gadget including Data, Label info, Table 1, Regression(liear, logistic), Basic plot. Binding: jsBasicAddin Interactive: true ``` https://github.com/jinseob2kim/jsmodule/blob/master/inst/rstudio/addins.dcf --- class: bg-main1 <div class="figure" style="text-align: center"> <img src="addin.png" alt="Addin tab" width="80%" /> <p class="caption">Addin tab</p> </div> --- class: bg-main1 # 개발 & 배포환경 .large[ 개발, 맞춤형 앱 * 대학원 서버에 [Docker 이미지](https://cloud.docker.com/u/jinseob2kim/repository/docker/jinseob2kim/docker-rshiny) 설치하여 기생. + [R](https://www.r-project.org/), [RStudio server](https://www.rstudio.com/products/rstudio/download-server/), [shiny server](https://www.rstudio.com/products/shiny/download-server/)와 자주 쓰는 패키지를 미리 설치. ] -- .large[ 범용 앱 * AWS에 [Docker swarm](https://github.com/jinseob2kim/swarm-setting) 환경 구축. + 부하정도에 따라 자동 인스턴스 추가/삭제. 1대면 충분..? ] -- .large[ 코드: [깃허브](https://github.com/jinseob2kim) * R 패키지, Docker 이미지, 홈페이지/블로그는 public repository * 맞춤형 앱은 private repository ] [RUCK2018 발표자료](https://blog.zarathu.com/posts/2018-11-08-ruck2018/) --- class: middle, bg-main1 # R package 관리 --- class: bg-main1 # 함수 문서: [sinew](https://github.com/metrumresearchgroup/sinew) addin with [roxygen2](https://CRAN.R-project.org/package=roxygen2) .large[ .yellow[함수 읽은 후] 실행 ] <br> <center><a href="https://github.com/metrumresearchgroup/sinew"><img src="sinew.gif" width=100%></a></center> --- class: bg-main1 # 패키지 상태 표현: Badge [](https://travis-ci.org/jinseob2kim/jstable) [](https://ci.appveyor.com/project/jinseob2kim/jstable) [](https://cran.r-project.org/package=jstable) [](https://CRAN.R-project.org/package=jstable) [](https://codecov.io/github/jinseob2kim/jstable) [](https://github.com/jinseob2kim/jstable/issues) [](https://github.com/jinseob2kim/jstable/stargazers) [](https://github.com/jinseob2kim/jstable/blob/master/LICENSE) ```md [](https://travis-ci.org/jinseob2kim/jstable) [](https://ci.appveyor.com/project/jinseob2kim/jstable) [](https://cran.r-project.org/package=jstable) [](https://CRAN.R-project.org/package=jstable) [](https://codecov.io/github/jinseob2kim/jstable) [](https://github.com/jinseob2kim/jstable/issues) [](https://github.com/jinseob2kim/jstable/stargazers) [](https://github.com/jinseob2kim/jstable/blob/master/LICENSE) ``` ### https://shields.io/ 에서 내 상태에 해당하는 뱃지 get. -- ### .yellow[오류는 없고, 인기는 많은] 패키지임을 과시? --- class: bg-main1 # 패키지 설명: 홈페이지 <img src="pkgdown.png" width="80%" style="display: block; margin: auto;" /> https://jinseob2kim.github.io/jskm/, https://jinseob2kim.github.io/jstable/, https://jinseob2kim.github.io/jsmodule/ --- class: bg-main1 # [pkgdown](https://pkgdown.r-lib.org/) .large[ 패키지 설치 후 **_pkgdown.yml** 파일에서 셋팅. `usethis::use_pkgdown()`으로 기본 설정 생성. ] ```yaml URL: https://jinseob2kim.github.io/jstable, https://github.com/jinseob2kim/jstable development: mode: auto authors: Jinseob Kim: href: https://github.com/jinseob2kim Zarathu: href: https://www.zarathu.com html: <img src="https://raw.githubusercontent.com/zarathucorp/Zarathu/master/horizontal_zarathu_transparent.png" height="24" /> template: params: docsearch: api_key: f6ab1678f68371b7775614662cffcb9d index_name: jstable ``` --- class: bg-main1 # 홈페이지 만들기 .large[ `build_site()` 실행하면 **/docs** 폴더에 홈페이지 만들어짐. ] <div class="figure" style="text-align: center"> <img src="https://github.blog/wp-content/uploads/2016/08/d516076e-640c-11e6-8086-ce1d246a87d2.png?fit=1460%2C860" alt="Setting webpage in github" width="60%" /> <p class="caption">Setting webpage in github</p> </div> ### 나중엔 [travis-ci](https://travis-ci.org/)를 이용, .yellow[gh-pages] 브랜치에 자동 배포. --- class: bg-main1 # Test code 넣기: [testthat](http://testthat.r-lib.org/) .large[ 함수의 테스트 코드를 작성하고 평가. ] - `usethis::use_testthat(), use_test()`로 기본 테스트 생성. `devtools::test()`로 테스트. ```r context("Show regression table") test_that("Run glmshow.display", { expect_is(glmshow.display(glm(mpg ~ cyl, data = mtcars)), "display") expect_is(glmshow.display(glm(am ~ cyl, data = mtcars, family = "binomial")), "display") }) test_that("Run cox2.display", { library(survival);data(lung) fit0 <- coxph(Surv(time, status) ~ ph.ecog + age, data = lung, model = TRUE) fit1 <- coxph(Surv(time, status) ~ ph.ecog + age + cluster(inst), data = lung, model = TRUE) expect_is(cox2.display(fit0), "list") expect_is(cox2.display(fit1), "list") }) ``` --- class: bg-main1 # [covr](https://covr.r-lib.org/) .large[ 코드 테스트 리포트를 제공하는 [Codecov](https://codecov.io/)나 [Coveralls](https://coveralls.io/)를 위한 R 패키지. - `covr::codecov(), coverall()` 로 실행. - [testthat](http://testthat.r-lib.org/) 결과 기반 리포트. https://codecov.io/gh/jinseob2kim/jstable/tree/master/R ] <img src="codecov.png" width="75%" style="display: block; margin: auto;" /> --- class: bg-main1 # Tip 8: Insert test code in [roxygen2](https://cran.r-project.org/package=roxygen2) ### [roxytest](https://github.com/mikldk/roxytest) package ```r #' A function to do y #' #' @param x Character vector #' @param y Character vector #' *#' @tests *#' expect_equal(bar("A", "B"), paste("A", "B", sep = "/")) #' #' @export bar <- function(x, y) { paste0(x, "/", y) } ``` --- class: bg-main1 # 귀찮다 .large[ 업데이트 때마다 **홈페이지**와 **코드리포트** 만들기 싫다. ] -- .large[ 사실, 패키지 **빌드(build) 체크**도 하기 싫지만 필요하긴 하다. 게다가.. - 내 컴퓨터에서 체크해봤자 리눅스환경만 확인한 것임. - 맥이나 윈도우에서 실행이 보장안됨. ] --- class: bg-main1 # 홈페이지, test coverage 자동화. ### 홈페이지: [pkgdown](https://pkgdown.r-lib.org/) ### test coverage: [testthat](http://testthat.r-lib.org/), [covr](https://covr.r-lib.org/) ### 자동 배포: [travis-ci](https://travis-ci.org/), [appveyor](https://www.appveyor.com/) --- class: bg-main1 <img src="https://nesoy.github.io/assets/posts/20170105/travis-ci.jpg" width="75%" style="display: block; margin: auto;" /> [](https://travis-ci.org/jinseob2kim/jstable) .large[ [travis-ci](https://travis-ci.org/): 가장 유명한 **CI**(Continuous Integration) tool, github와 연동. - github commit 때마다 프로그램 **테스트, 빌드, 배포**가 자동 실행. - .travis.yml 에 설정 저장. ] https://travis-ci.org/jinseob2kim/jsmodule/jobs/495263115 --- class: bg-main1 ```yaml language: r cache: packages: true directories: - travis_phantomjs ## for shinytest matrix: allow_failures: - r: devel include: - r: devel - r: release r_packages: - covr after_success: - Rscript -e 'covr::codecov()' before_deploy: Rscript -e 'remotes::install_cran("pkgdown")' deploy: provider: script script: Rscript -e 'pkgdown::deploy_site_github()' skip-cleanup: true - r: release os: osx ## for Mac OS - r: oldrel ``` --- class: bg-main1 # [travis-ci](https://travis-ci.org/) with R package .large[ - `usethis::use_travis()` 로 **.travis.yml** 기본 설정파일 생성. ] ```yaml # R for travis: see documentation at https://docs.travis-ci.com/user/languages/r language: R sudo: false cache: packages ``` --- class: bg-main1 # Codecov .large[ `usethis::use_coverage("codecov")` 로 **.travis.yml** 에 `covr::codecov()` 실행 추가. ] ```yaml language: R sudo: false cache: packages r_packages: - covr after_success: - Rscript -e 'covr::codecov()' ``` --- class: bg-main1 # 홈페이지 빌드, 배포 .large[ [travis-ci](https://travis-ci.org/) 가 직접 github에 배포하기 위해 .yellow[gh-pages 브랜치와 key]가 필요. ] <img src="gh-pages.png" width="75%" style="display: block; margin: auto;" /> --- class: bg-main1 1. github에서 .yellow[gh-pages] 브랜치 만들기. 2. .yellow[key] 생성: `travis::use_travis_deploy()` 를 .yellow[로컬 환경]에서 실행. <img src="key-travis.png" width="100%" style="display: block; margin: auto;" /> -- .yellow[.travis.yml] 에 추가 ```yaml before_deploy: Rscript -e 'remotes::install_cran("pkgdown")' deploy: provider: script script: Rscript -e 'pkgdown::deploy_site_github()' skip-cleanup: true ``` https://pkgdown.r-lib.org/reference/deploy_site_github.html --- class: bg-main1 # [appveyor](https://travis-ci.org/) .large[ [travis-ci](https://travis-ci.org/)는 리눅스와 맥만 지원 - **윈도우** 환경에서 테스트 못함. ] -- [](https://ci.appveyor.com/project/jinseob2kim/jstable) .large[ [appveyor](https://travis-ci.org/)는 리눅스와 **윈도우** 지원 - `usethis::use_appveyor()` 로 기본 **appveyor.yml** 파일 생성. ] --- class: bg-main1 ```yaml # DO NOT CHANGE the "init" and "install" sections below # 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 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 ``` --- class: bg-main1, middle # Tip 9: [tic](https://github.com/ropenscilabs/tic) - CI setting ### [pkgdown](https://pkgdown.r-lib.org/), [Codecov](https://codecov.io/), [travis-ci](https://travis-ci.org/), [appveyor](https://travis-ci.org/) 를 한번에 처리 https://ropenscilabs.github.io/tic/articles/tic.html --- class: middle, bg-main1 # CRAN 배포 --- class: bg-main1 # 평소에 잘 관리하자! .large[ - .yellow[Build check]: WARNING 뿐 아니라 .yellow[NOTE]도 없어야됨. - 오타, 대소문자: 특히 .yellow[DESCRIPTION] 파일 - .yellow[README, NEWS, cran-comments] 작성. - 최소 하나의 .yellow[vignette] - 함수 설명: 충실하진 않더라도 .yellow[빠진건 없어야]. - 함수 example: 가급적 다 넣자. 한줄에 100글자 넘으면 안됨(.yellow[NOTE]). ] http://r-pkgs.had.co.nz/release.html --- class: bg-main1 # 오타, 대소문자 .blockquote.font_large[ Thanks, please write package names, software names and API names in .yellow[single quotes (e.g. 'RStudio', 'shiny')] in Title and Description] ```yaml Package: jsmodule Title: RStudio addins and Shiny modules for medical research Description: RStudio addins and Shiny modules for descriptive statistics, regression and survival analysis. Version: 0.7.10 Date: 2019-02-19 ``` -- ```yaml Package: jsmodule Title: 'RStudio' Addins and 'Shiny' Modules for Medical Research Description: 'RStudio' addins and 'Shiny' modules for descriptive statistics, regression and survival analysis. Version: 0.7.10 Date: 2019-02-19 ``` --- class: bg-main1 # 필수 markdown https://CRAN.R-project.org/package=jskm ### .yellow[README.md]: CRAN의 REAMDE ### .yellow[News.md]: CRAN의 NEWS ### .yellow[cran-comments.md]: 패키지 자체 테스트 결과를 적는다. --- class: bg-main1 # cran-comments.md 예시 ```md ## Resubmission This is a resubmission. In this version I have: ** Add examples and tests for the non-UI functionality. ** Add examples to all Rd files. ## Test environments ** local Ubuntu 18.10 install, R 3.5.2 ** Ubuntu 14.04.5 LTS (on travis-ci), R 3.5.1 ** win-builder (stable and oldrelease) ## R CMD check results There were no ERRORs, WARNINGs or NOTEs. ## Downstream dependencies There are currently no downstream dependencies for this package ``` --- class: bg-main1 # Vignette ### `usethis::use_vignette("jsmodule")` 로 기본 파일 생성. .large[ - 귀찮으면 .yellow[README] 복붙하자. - 홈페이지에도 추가됨. ] --- class: bg-main1 # 함수 설명, example .blockquote.font_large[ Please omit .yellow[example code] that looks like this one:] ```r \dontrun{ if(interactive()){ #EXAMPLE1 } } ``` -- .blockquote.font_large[ We see many Rd files with lines such as] ```r \details{ DETAILS } \examples{ #EXAMPLE1 } ``` .blockquote.font_large[ These should alyways be deleted unless you have ral examples to insert.] --- class: bg-main1 # interactive() examples .blockquote.font_large[Thanks, unfortunately, your ceode is never tested at runtime, as you only have interactive() examples,if at all, and your test cases do not cover much code.] .blockquote.font_large[Can you perhaps add examples and tests for the non-UI functionality?] -- ### 코멘트들을 반영하여 [jsmodule](https://github.com/jinseob2kim/jsmodule) 다시 .yellow[CRAN] 업로드. https://cransays.itsalocke.com/articles/dashboard.html --- class: bg-main1 # CRAN release 신청 ### `devtools::release()` 실행 .large[ - 확인 질문들이 나옴: 문제 없다고 답하면 됨. - 확인 메일 보고 몇 가지 클릭하면 완료. - **CRAN-RELEASE** 파일 생성됨: release 때 필요한 정보. - 진행과정 메일이 온다. 결정까지 10일 이내 ] --- class: bg-main1 # CRAN-RELEASE ```sh This package was submitted to CRAN on 2019-02-22. Once it is accepted, delete this file and tag the release (commit ec7a36c1d8). ``` -- .large[ .yellow[CRAN] 배포 확정되면 해당 commit 번호로 release ] <center><a href="https://github.com/jinseob2kim/jstable/releases"><img src="release.png" width=60%></a></center> --- class: bg-main1 # Update ### .yellow[CRAN] 등록보다는 수월함. 잦은 업데이트 자제. .yellow[CRAN] .blockquote.font_large[ Thanks, we see: Days since last update: 5 Number of updates in past 6 months: 10 .yellow[Why is such a quick update needed? Please explain]. Please also re-read the CRAN policies about submission frequency.] -- .yellow[Me] .blockquote.font_large[ .yellow[I`m sorry]. I update many feature & fix bugs recently. please cancel my submit. I will follow CRAN policies. ] --- class: bg-main1 # Executive Summary .large[ - 의학연구자들에게 맞춤형 **[ShinyApps](https://shiny.rstudio.com/)**를 제공하고, 범용으로 쓰일만한 것들을 **[Shiny module](https://shiny.rstudio.com/articles/modules.html)**로 만든 후, **[웹](http://app.zarathu.com)**을 통해 배포하였다. - 개인 PC에서 직접 이용할 수 있도록 **[Rstudio Addins](https://rstudio.github.io/rstudioaddins/)**을 포함한 패키지로 만들어 **github**에 배포하였다. - **[testthat](https://github.com/r-lib/testthat)**, **[covr](https://github.com/r-lib/covr)**로 코드 테스트를 수행하고 결과 리포트를 만들었으며, **[pkgdown](https://github.com/r-lib/pkgdown)**으로 패키지를 소개하는 웹사이트를 만들었다. - **[Travis CI](https://travis-ci.org/)**와 **[appveyor](https://www.appveyor.com/)**로 앞의 과정과 여러 운영체제에서의 테스트를 자동화하였다. - 최종적으로 **[CRAN](https://cran.r-project.org/)**에 패키지를 배포하고, .yellow[V1.0.1] 까지 업데이트 하였다. ] --- class: bg-main1 middle #Thanks! ### Shiny 스터디 [<span><i class="fab fa-github faa-float animated "></i>shinykorea</span>](https://github.com/shinykorea)