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updated to rocker/tidyverse:3.6.0 and modified project template
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‎.gitignore

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certs/localhost
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.Rproj.user

‎README.md

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A containerized RStudio instance from the rocker base image:
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rocker/tidyverse:3.5.3
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rocker/tidyverse:3.6.0
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This container comes with a `nginx` reverse proxy (access via. port 80)
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and the Tidyverse collection of packages pre-installed by default.
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that is useful for projects that conform to the principles of reproducible research
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and "project-as-a-package".
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### Default login
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### Suggested R Packages
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`install.packages(c("lubridate", "ProjectTemplate"))`
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### Default R Studio login
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username: rstudio
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password: rstudio1
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Update password in `docker-compose.yml` at the following location:
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Default password: rstudio1
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```
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environment:
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- PASSWORD=rstudio1
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```
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## Docker Ubuntu Server Installation/Set-up
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## HTTPS encryption
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[These instructions](https://medium.com/@pentacent/nginx-and-lets-encrypt-with-docker-in-less-than-5-minutes-b4b8a60d3a71)
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were used to set up a secure HTTPS connection to RStuido with Certbot SSL
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were used to set up a secure HTTPS connection to RStudio with Certbot SSL
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certificates. Also see [here](https://github.com/wmnnd/nginx-certbot).
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This will not work out of the box, the NGINX configuration file will need to be

‎docker-compose.yml

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container_name: nginx
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restart: on-failure
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networks:
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- tki-net
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- net
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volumes:
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- ./nginx.conf:/etc/nginx/nginx.conf
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- ./data/certbot/conf:/etc/letsencrypt
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entrypoint: "/bin/sh -c 'trap exit TERM; while :; do certbot renew; sleep 12h & wait $${!}; done;'"
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rstudio:
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image: rocker/tidyverse:3.5.3
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image: rocker/tidyverse:3.6.0
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container_name: rstudio
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restart: on-failure
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volumes:
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volume:
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no-copy: true
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networks:
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- tki-net
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- net
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environment:
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- PASSWORD=rstudio1
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expose:
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- 8787
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networks:
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tki-net:
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name: tki-net
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name: net
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volumes:
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r_libs:

‎nginx.conf

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server rstudio:8787;
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}
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#### START REMOVE - remove this block of code if SSL certification is not wanted ####
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server {
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listen 80;
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server_name example.org; #### UPDATE example.org to your domain name ####
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server_tokens off;
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location /.well-known/acme-challenge/ {
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root /var/www/certbot;
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}
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location / {
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return 301 https://$host$request_uri;
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}
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}
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#### END REMOVE ####
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# #### START BLOCK - uncomment this block to enable SSL encryption ####
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# server {
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# listen 80;
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# server_name example.org; #### UPDATE example.org to your domain name ####
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# server_tokens off;
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#
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# location /.well-known/acme-challenge/ {
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# root /var/www/certbot;
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# }
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#
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# location / {
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# return 301 https://$host$request_uri;
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# }
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# }
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# #### END BLOCK ####
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server {
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listen 443 SSL; # listen 80; #### remove "listen 443 SSL; #" statement if SSL certification is not wanted ####
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listen 80; #### remove this line if SSL certification is enabled ####
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# listen 443 SSL; #### uncomment this line if SSL certification is enabled ####
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server_name example.org; #### UPDATE example.org to your domain name ####
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#### START REMOVE - remove this block of code if SSL certification is not wanted ####
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ssl_certificate /etc/letsencrypt/live/example.org/fullchain.pem; #### UPDATE example.org to your domain name ####
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ssl_certificate_key /etc/letsencrypt/live/example.org/privkey.pem; #### UPDATE example.org to your domain name ####
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include /etc/letsencrypt/options-ssl-nginx.conf;
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ssl_dhparam /etc/letsencrypt/ssl-dhparams.pem;
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#### END REMOVE ####
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# #### START BLOCK - uncomment this block to enable SSL encryption ####
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# ssl_certificate /etc/letsencrypt/live/example.org/fullchain.pem; #### UPDATE example.org to your domain name ####
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# ssl_certificate_key /etc/letsencrypt/live/example.org/privkey.pem; #### UPDATE example.org to your domain name ####
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# include /etc/letsencrypt/options-ssl-nginx.conf;
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# ssl_dhparam /etc/letsencrypt/ssl-dhparams.pem;
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# #### END BLOCK ####
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location / {
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proxy_pass http://rstudio;

‎projects/00_next_project/.Rbuildignore

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^.*\.Rproj$
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^\.Rproj\.user$

‎projects/00_next_project/R/00-cleaner.R

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# Reads raw delimited data and saves as RDS files in data folder
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# created 25-May-2018 by Paul Stevenson
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#' Reads raw delimited data and saves as RDS files in data folder
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#' created 25-May-2018 by Paul Stevenson
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#' updated 27-May-2019 by Paul Stevenson
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#### libraries ----
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library(dplyr)
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library(readr)
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library(readstata13)
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#### helper functions ----
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source("R/99-helper.R")
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#### load data ----
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dat <- read_csv("data-raw/file.csv")
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devtools::use_data("var_name", overwrite = T)
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#### Data cleaning ----
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#### save data ----
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save(dat, file = "data/dat.RData")

‎projects/00_next_project/R/01-main.R

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# This is the starting point for the project. load.project will load the
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# data and run any scripts in the munge directory.
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# Created by Paul Stevenson 17-May-2018
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#' This is the starting point for the project. load.project will load the
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#' data and run any scripts in the munge directory.
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#' Created by Paul Stevenson 17-May-2018
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#' Updated 27-May-2019 by Paul Stevenson
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library('repmis')
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#### libraries ----
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LoadandCite(pkgs = c("tidyverse", "lubridate", "ProjectTemplate", "repmis", "biometrics"),
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file = "report/assets/bib/packages.bib")
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library(ProjectTemplate)
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library(dplyr)
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#### Project automation with Project Template ----
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load.project(munging = TRUE, data_loading = TRUE)
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#### load data ----
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# load("data/dat.RData")
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# load("cache/dat.RData")
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#### helper functions ----
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source("R/99-helper.R")
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#### Data wrangling/cleaning ----
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#### Analysis ----

‎projects/00_next_project/config/global.dcf

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version: 0.8.2
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version: 0.9.0
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data_loading: TRUE
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data_loading_header: TRUE
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data_ignore:
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logging_level: INFO
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load_libraries: FALSE
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libraries: stats, reshape2, plyr, tidyverse
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as_factors: TRUE
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data_tables: FALSE
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as_factors: FALSE
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attach_internal_libraries: FALSE
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cache_loaded_data: FALSE
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cache_loaded_data: FALSE
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sticky_variables: NONE
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tables_type: tibble

‎projects/00_next_project/munge/01-munge.R

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# Example preprocessing script.
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#' Example preprocessing script.
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#' Created 21-May-2019 by Paul Stevenson
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#' Updated 27-May-2019 by Paul Stevenson
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#### libraries ----
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library(ProjectTemplate)
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library(dplyr)
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#### helper functions ----
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source("R/99-helper.R")
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#### load data ----
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load("data/dat.RData")
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#### Data wrangling ----
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#### save data ----
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cache("dat")

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