R로 만드는 웹 애플리케이션

# R로 만드는 웹 애플리케이션
## 맞춤형 의학통계 웹
### 김진섭
### 2020-02-28

---

<div class="my-footer"><span><a href="https://www.zarathu.com">Zarathu Co.,Ltd</a>   
&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;
&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;
<a href="https://github.com/jinseob2kim">조선니체</a></span></div>

---
# Executive Summary

.large[
* [R](https://www.r-project.org/)로 통계분석 뿐 아니라 [논문](https://github.com/rstudio/rticles), [발표 슬라이드](https://github.com/yihui/xaringan), [홈페이지](https://github.com/rstudio/blogdown), [블로그](https://rstudio.github.io/distill/), [웹 어플리케이션](https://shiny.rstudio.com/)을 만들 수 있다. 
]

--
.large[

* 의학연구자들에게 [맞춤형 통계 웹](http://app.zarathu.com)을 제공.

* 범용으로 쓰일만한 것들을 [웹](http://app.zarathu.com)과 [R 패키지](https://github.com/jinseob2kim/jsmodule)로 배포.

]

--
.large[
모임 소개

* [<span><i class="fab  fa-github faa-float animated "></i>shinykorea</span>](https://github.com/shinykorea/Meetup) 밋업 후원: [R](https://www.r-project.org/) 웹만들기 지식 공유

* 카카오 오픈채팅: 프로그래밍 갤러리 R사용자 모임
]

---
# 주요 경험

* 수학 올림피아드

* 의과대학: **임상** 데이터

* 보건대학원: **유전체** 데이터

* 삼성전자 무선사업부: **모바일헬스** 데이터
]

--
.large[

의학연구지원법인 [차라투](https://www.zarathu.com) 설립

* **다양한 건강데이터를 다뤄본 경험**으로 맞춤형 의료데이터 분석 지원
]

---

# [R](https://www.r-project.org/)의 확장

---
# [R](https://www.r-project.org/)의 확장

[R](https://www.r-project.org/)은 이제 단순한 통계프로그램이 아님.

* [R Markdown](https://rmarkdown.rstudio.com/): 논문과 발표자료를 [R](https://www.r-project.org/) 에서 직접 만듦. [과거 정리 내용](https://blog.zarathu.com/posts/2019-01-03-rmarkdown/)

* [blogdown](https://github.com/rstudio/blogdown): 홈페이지도 만들 수 있음. 당사 홈페이지도 이것과 [distill](https://rstudio.github.io/distill/) 로 제작.

* [Shiny](https://shiny.rstudio.com/), [Shiny Server](https://www.rstudio.com/products/shiny/shiny-server/): 서버 구축하고 웹기반 앱을 만들 수 있음.

법인 설립 후 모든 작업에 [R](https://www.r-project.org/)을 이용함.

---
# 논문

[R](https://www.r-project.org/)에서 글, 그림, 테이블, 참고문헌까지 직접 작성. 
 
* [rticles](https://github.com/rstudio/rticles): 대부분 학술지의 템플릿을 포함.

[준비하던 박사논문](https://blog.zarathu.com/posts/2018-11-08-mdlm/)

---
# 발표 슬라이드

논문쓸 때 이용했던 R 코드 활용, 빠르게 발표 슬라이드 제작 가능.

* [기본 템플릿](https://rmarkdown.rstudio.com/lesson-11.html), [xaringan](https://github.com/yihui/xaringan) 패키지: 이 슬라이드도 [xaringan](https://github.com/yihui/xaringan)으로 제작.

---
# 홈페이지

[blogdown](https://github.com/rstudio/blogdown), [distill](https://rstudio.github.io/distill/): [깃허브](https://pages.github.com/) 통해 무료 웹호스팅 가능.

[홈페이지](https://github.com/zarathucorp/zarathu), [블로그](https://github.com/zarathucorp/blog)

---
# 웹 앱

[Shiny](https://shiny.rstudio.com/): [R](https://www.r-project.org/) 코드만으로 웹앱 제작

---
# 웹 대시보드

[shinydashboard](https://rstudio.github.io/shinydashboard/), [flexdashboard](https://rmarkdown.rstudio.com/flexdashboard/) 등

---
# 웹 서버

[Shiny Server](https://www.rstudio.com/products/shiny/shiny-server/): [Shiny](https://shiny.rstudio.com/)를 서버에서 구동.

[Zarathu app](http://app.zarathu.com)

---

# 맞춤형 서비스

---
# 전문적인 통계분석

* 외과
    + 신장이식 연구

* 내과 
    + 심혈관질환 위험 요인 생존분석
    
    + 심혈관 생리학 지표 계산 
    
    + 국민건강영양조사 신장 기능 연구

* 정신건강의학과
    + 외상후 스트레스 장애 네트워크 분석

---
# 신장이식

기술통계, 회귀/생존분석, 맞춤형 그림

[![](https://jinseob2kim.github.io/LectureRpackage/RUCK2019/ktsym.jpg)](http://app.zarathu.com)

---
# 심혈관질환 위험요인

반복측정, 한 사람이 2개 이상의 심혈관 시술 받음.

[![](gee.png)](http://app.zarathu.com)

---
# PPT에서 편집: `emf` 확장자

**PPT** 정확한 그림인식 위해 **emfPlus = F** 옵션 필수!

```r
library(devEMF)
emf("plot.emf", width = 7, height = 7, emfPlus = F)
ggplot(mtcars, aes(mpg, cyl)) + geom_point()
dev.off()
```

---
# 테이블 다운로드 예

[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)

---

<div id="htmlwidget-e198132044b2eb5dfc5d" style="width:100%;height:auto;" class="datatables html-widget"></div>
<script type="application/json" data-for="htmlwidget-e198132044b2eb5dfc5d">{"x":{"filter":"none","extensions":["Buttons"],"data":[["1","2","3","4","5","6","7","8","9","10","11","12","13","14","15","16","17","18","19","20","21","22","23","24","25","26","27","28","29","30","31","32","33","34","35","36","37","38","39","40","41","42","43","44","45","46","47","48","49","50","51","52","53","54","55","56","57","58","59","60","61","62","63","64","65","66","67","68","69","70","71","72","73","74","75","76","77","78","79","80","81","82","83","84","85","86","87","88","89","90","91","92","93","94","95","96","97","98","99","100","101","102","103","104","105","106","107","108","109","110","111","112","113","114","115","116","117","118","119","120","121","122","123","124","125","126","127","128","129","130","131","132","133","134","135","136","137","138","139","140","141","142","143","144","145","146","147","148","149","150"],[5.1,4.9,4.7,4.6,5,5.4,4.6,5,4.4,4.9,5.4,4.8,4.8,4.3,5.8,5.7,5.4,5.1,5.7,5.1,5.4,5.1,4.6,5.1,4.8,5,5,5.2,5.2,4.7,4.8,5.4,5.2,5.5,4.9,5,5.5,4.9,4.4,5.1,5,4.5,4.4,5,5.1,4.8,5.1,4.6,5.3,5,7,6.4,6.9,5.5,6.5,5.7,6.3,4.9,6.6,5.2,5,5.9,6,6.1,5.6,6.7,5.6,5.8,6.2,5.6,5.9,6.1,6.3,6.1,6.4,6.6,6.8,6.7,6,5.7,5.5,5.5,5.8,6,5.4,6,6.7,6.3,5.6,5.5,5.5,6.1,5.8,5,5.6,5.7,5.7,6.2,5.1,5.7,6.3,5.8,7.1,6.3,6.5,7.6,4.9,7.3,6.7,7.2,6.5,6.4,6.8,5.7,5.8,6.4,6.5,7.7,7.7,6,6.9,5.6,7.7,6.3,6.7,7.2,6.2,6.1,6.4,7.2,7.4,7.9,6.4,6.3,6.1,7.7,6.3,6.4,6,6.9,6.7,6.9,5.8,6.8,6.7,6.7,6.3,6.5,6.2,5.9],[3.5,3,3.2,3.1,3.6,3.9,3.4,3.4,2.9,3.1,3.7,3.4,3,3,4,4.4,3.9,3.5,3.8,3.8,3.4,3.7,3.6,3.3,3.4,3,3.4,3.5,3.4,3.2,3.1,3.4,4.1,4.2,3.1,3.2,3.5,3.6,3,3.4,3.5,2.3,3.2,3.5,3.8,3,3.8,3.2,3.7,3.3,3.2,3.2,3.1,2.3,2.8,2.8,3.3,2.4,2.9,2.7,2,3,2.2,2.9,2.9,3.1,3,2.7,2.2,2.5,3.2,2.8,2.5,2.8,2.9,3,2.8,3,2.9,2.6,2.4,2.4,2.7,2.7,3,3.4,3.1,2.3,3,2.5,2.6,3,2.6,2.3,2.7,3,2.9,2.9,2.5,2.8,3.3,2.7,3,2.9,3,3,2.5,2.9,2.5,3.6,3.2,2.7,3,2.5,2.8,3.2,3,3.8,2.6,2.2,3.2,2.8,2.8,2.7,3.3,3.2,2.8,3,2.8,3,2.8,3.8,2.8,2.8,2.6,3,3.4,3.1,3,3.1,3.1,3.1,2.7,3.2,3.3,3,2.5,3,3.4,3],[1.4,1.4,1.3,1.5,1.4,1.7,1.4,1.5,1.4,1.5,1.5,1.6,1.4,1.1,1.2,1.5,1.3,1.4,1.7,1.5,1.7,1.5,1,1.7,1.9,1.6,1.6,1.5,1.4,1.6,1.6,1.5,1.5,1.4,1.5,1.2,1.3,1.4,1.3,1.5,1.3,1.3,1.3,1.6,1.9,1.4,1.6,1.4,1.5,1.4,4.7,4.5,4.9,4,4.6,4.5,4.7,3.3,4.6,3.9,3.5,4.2,4,4.7,3.6,4.4,4.5,4.1,4.5,3.9,4.8,4,4.9,4.7,4.3,4.4,4.8,5,4.5,3.5,3.8,3.7,3.9,5.1,4.5,4.5,4.7,4.4,4.1,4,4.4,4.6,4,3.3,4.2,4.2,4.2,4.3,3,4.1,6,5.1,5.9,5.6,5.8,6.6,4.5,6.3,5.8,6.1,5.1,5.3,5.5,5,5.1,5.3,5.5,6.7,6.9,5,5.7,4.9,6.7,4.9,5.7,6,4.8,4.9,5.6,5.8,6.1,6.4,5.6,5.1,5.6,6.1,5.6,5.5,4.8,5.4,5.6,5.1,5.1,5.9,5.7,5.2,5,5.2,5.4,5.1],[0.2,0.2,0.2,0.2,0.2,0.4,0.3,0.2,0.2,0.1,0.2,0.2,0.1,0.1,0.2,0.4,0.4,0.3,0.3,0.3,0.2,0.4,0.2,0.5,0.2,0.2,0.4,0.2,0.2,0.2,0.2,0.4,0.1,0.2,0.2,0.2,0.2,0.1,0.2,0.2,0.3,0.3,0.2,0.6,0.4,0.3,0.2,0.2,0.2,0.2,1.4,1.5,1.5,1.3,1.5,1.3,1.6,1,1.3,1.4,1,1.5,1,1.4,1.3,1.4,1.5,1,1.5,1.1,1.8,1.3,1.5,1.2,1.3,1.4,1.4,1.7,1.5,1,1.1,1,1.2,1.6,1.5,1.6,1.5,1.3,1.3,1.3,1.2,1.4,1.2,1,1.3,1.2,1.3,1.3,1.1,1.3,2.5,1.9,2.1,1.8,2.2,2.1,1.7,1.8,1.8,2.5,2,1.9,2.1,2,2.4,2.3,1.8,2.2,2.3,1.5,2.3,2,2,1.8,2.1,1.8,1.8,1.8,2.1,1.6,1.9,2,2.2,1.5,1.4,2.3,2.4,1.8,1.8,2.1,2.4,2.3,1.9,2.3,2.5,2.3,1.9,2,2.3,1.8],["setosa","setosa","setosa","setosa","setosa","setosa","setosa","setosa","setosa","setosa","setosa","setosa","setosa","setosa","setosa","setosa","setosa","setosa","setosa","setosa","setosa","setosa","setosa","setosa","setosa","setosa","setosa","setosa","setosa","setosa","setosa","setosa","setosa","setosa","setosa","setosa","setosa","setosa","setosa","setosa","setosa","setosa","setosa","setosa","setosa","setosa","setosa","setosa","setosa","setosa","versicolor","versicolor","versicolor","versicolor","versicolor","versicolor","versicolor","versicolor","versicolor","versicolor","versicolor","versicolor","versicolor","versicolor","versicolor","versicolor","versicolor","versicolor","versicolor","versicolor","versicolor","versicolor","versicolor","versicolor","versicolor","versicolor","versicolor","versicolor","versicolor","versicolor","versicolor","versicolor","versicolor","versicolor","versicolor","versicolor","versicolor","versicolor","versicolor","versicolor","versicolor","versicolor","versicolor","versicolor","versicolor","versicolor","versicolor","versicolor","versicolor","versicolor","virginica","virginica","virginica","virginica","virginica","virginica","virginica","virginica","virginica","virginica","virginica","virginica","virginica","virginica","virginica","virginica","virginica","virginica","virginica","virginica","virginica","virginica","virginica","virginica","virginica","virginica","virginica","virginica","virginica","virginica","virginica","virginica","virginica","virginica","virginica","virginica","virginica","virginica","virginica","virginica","virginica","virginica","virginica","virginica","virginica","virginica","virginica","virginica","virginica","virginica"]],"container":"<table 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>
---
# 심혈관 생리지표 계산

최대최소값 표시 & [드래그](https://shiny.rstudio.com/gallery/plot-interaction-advanced.html)한 부분의 생리지표를 계산

[![](phys.png)](http://app.zarathu.com)

---
# 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.

[![](qgraph.png)](http://app.zarathu.com)

---
# 대시보드

* 미세먼지 데이터 [웹 크롤링](https://jinseob2kim.github.io/LectureRpackage/RSelenium/) 후 [대시보드](https://github.com/zarathucorp/kweatherdashboard) 만들기

[![](dashboard.png)](http://app.zarathu.com)

---

# 범용 서비스

---
# 공개 웹

* [일반 데이터](http://app.zarathu.com/basic)

* [반복측정 데이터](http://app.zarathu.com/repeated) - 한 사람이 여러번 측정함

* [서베이(survey) 데이터](http://app.zarathu.com/survey) - 샘플가중치 존재(ex: 국건영)

* [프로펜시티 점수 분석]((http://app.zarathu.com/ps)(experimental)
]

---
# R 패키지 개발

3개의 패키지를 [CRAN](https://cran.r-project.org/)에 배포.

- [jstable](https://github.com/jinseob2kim/jstable): 논문용 테이블 만들기

- [jskm](https://github.com/jinseob2kim/jskm): kaplan-meier 생존곡선 그리기

- [jsmodule](https://github.com/jinseob2kim/jsmodule): 위 2 패키지를 적용한 통계분석 웹

[RUCK 2019 발표](https://ruck2019.r-kor.org/speakers/zarathu/)

---
# [jstable](https://github.com/jinseob2kim/jstable): table 1

```r
library(jstable)
*tb1 <- CreateTableOneJS(names(mtcars), strata = "vs", data = mtcars, factorVars = c("vs", "am", "gear", "carb"))
datatable(tb1$table[, -6], caption = tb1$caption)
```

<div id="htmlwidget-9af30f7b7b4b83c8347b" style="width:100%;height:auto;" class="datatables html-widget"></div>
<script type="application/json" data-for="htmlwidget-9af30f7b7b4b83c8347b">{"x":{"filter":"none","caption":"<caption>Stratified by vs<\/caption>","data":[["n","mpg ","cyl ","disp ","hp ","drat ","wt ","qsec ","vs (%)","","am (%)","","gear (%)","","","carb (%)","","","","",""],["","","","","","","","","0","1","0","1","3","4","5","1","2","3","4","6","8"],["    18"," 16.62 (3.86)","  7.44 (1.15)","307.15 (106.77)","189.72 (60.28)","  3.39 (0.47)","  3.69 (0.90)"," 16.69 (1.09)","    18 (100.0) ","     0 (  0.0) ","    12 ( 66.7) ","     6 ( 33.3) ","    12 ( 66.7) ","     2 ( 11.1) ","     4 ( 22.2) ","     0 (  0.0) ","     5 ( 27.8) ","     3 ( 16.7) ","     8 ( 44.4) ","     1 (  5.6) ","     1 (  5.6) "],["    14"," 24.56 (5.38)","  4.57 (0.94)","132.46 (56.89)"," 91.36 (24.42)","  3.86 (0.51)","  2.61 (0.72)"," 19.33 (1.35)","     0 (  0.0) ","    14 (100.0) ","     7 ( 50.0) ","     7 ( 50.0) ","     3 ( 21.4) ","    10 ( 71.4) ","     1 (  7.1) ","     7 ( 50.0) ","     5 ( 35.7) ","     0 (  0.0) ","     2 ( 14.3) ","     0 (  0.0) ","     0 (  0.0) "],["","<0.001","<0.001","<0.001","<0.001"," 0.013"," 0.001","<0.001","<0.001",""," 0.556",""," 0.001","",""," 0.002","","","","",""],["","","","","","","","","","","","","exact","","","exact","","","","",""]],"container":"<table class=\"display\">\n  <thead>\n    <tr>\n      <th> <\/th>\n      <th>level<\/th>\n      <th>0<\/th>\n      <th>1<\/th>\n      <th>p<\/th>\n      <th>test<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"pageLength":5,"order":[],"autoWidth":false,"orderClasses":false,"columnDefs":[{"orderable":false,"targets":0}],"lengthMenu":[5,10,25,50,100]}},"evals":[],"jsHooks":[]}</script>

---
# [jstable](https://github.com/jinseob2kim/jstable): regression

```r
model.logisic <- glm(vs ~ wt + qsec, data = mtcars)
*res.logistic <- glmshow.display(model.logisic)
*out.logistic <- LabelepiDisplay(res.logistic)
datatable(out.logistic, caption = res.logistic$first.line)
```

<div id="htmlwidget-3f5d087092db9a043853" style="width:100%;height:auto;" class="datatables html-widget"></div>
<script type="application/json" data-for="htmlwidget-3f5d087092db9a043853">{"x":{"filter":"none","caption":"<caption>Linear regression predicting vs\n<\/caption>","data":[["wt","qsec","No. of observations","R-squared","AIC value"],["-0.29 (-0.44,-0.13)","0.21 (0.14,0.28)","32","0.7405","10.7788"],["< 0.001","< 0.001","","",""],["-0.23 (-0.32,-0.13)","0.19 (0.14,0.24)","","",""],["< 0.001","< 0.001","","",""],["**","**",null,null,null]],"container":"<table class=\"display\">\n  <thead>\n    <tr>\n      <th> <\/th>\n      <th>crude coeff.(95%CI)<\/th>\n      <th>crude P value<\/th>\n      <th>adj. coeff.(95%CI)<\/th>\n      <th>adj. P value<\/th>\n      <th>sig<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"dom":"rt","order":[],"autoWidth":false,"orderClasses":false,"columnDefs":[{"orderable":false,"targets":0}]}},"evals":[],"jsHooks":[]}</script>

---
# [jskm](https://github.com/jinseob2kim/jskm)

---
# [jsmodule](https://github.com/jinseob2kim/jsmodule)

<center>
<figure>
<a href="https://github.com/jinseob2kim/jsmodule"><img src="https://github.com/jinseob2kim/jsmodule/raw/master/vignettes/figures/addin.gif" width=100%></a>
<figurecaption>Rstudio Addins: jsmodule packages</figurecaption>
</figure>
</center>

통계분석 웹 : http://app.zarathu.com/

---

# 기타

---
# 개발 & 배포환경

개발, 맞춤형 앱

* 대학원 서버에 [Docker 이미지](https://cloud.docker.com/u/jinseob2kim/repository/docker/jinseob2kim/docker-rshiny) 설치하여 기생.
    + R, Rstudio server, shiny server와 자주 쓰는 패키지를 미리 설치.
    
--

범용 앱

* AWS에 [Docker swarm](https://github.com/jinseob2kim/swarm-setting) 환경 구축.
    + 부하정도에 따라 자동으로 인스턴스 추가/삭제. 현재 1대면 충분..
    
--

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/)
    
---
# [shinykorea](https://github.com/shinykorea/Meetup) 밋업

---
# 오픈채팅

---
# Executive Summary

* 의학연구자들에게 [맞춤형 통계 웹](http://app.zarathu.com)을 제공.

* 범용으로 쓰일만한 것들을 [웹](http://app.zarathu.com)과 [R 패키지](https://github.com/jinseob2kim/jsmodule)로 배포.

모임 소개

* [<span><i class="fab  fa-github faa-float animated "></i>shinykorea</span>](https://github.com/shinykorea/Meetup) 밋업 후원: [R](https://www.r-project.org/) 웹만들기 지식 공유

* 카카오 오픈채팅: 프로그래밍 갤러리 R사용자 모임
]

---

# END