updated to rocker/tidyverse:3.6.0 and modified project template

.gitignore

@@ -1 +1,2 @@
 certs/localhost
+.Rproj.user

README.md

@@ -3,7 +3,7 @@ RStudio
 
 A containerized RStudio instance from the rocker base image:
 
-    rocker/tidyverse:3.5.3
+    rocker/tidyverse:3.6.0
 
 This container comes with a `nginx` reverse proxy (access via. port 80)
 and the Tidyverse collection of packages pre-installed by default.
@@ -19,11 +19,21 @@ The projects directory is pre-configured with a project template (00_next_projec
 that is useful for projects that conform to the principles of reproducible research
 and "project-as-a-package".
 
-### Default login
+### Suggested R Packages
+
+`install.packages(c("lubridate", "ProjectTemplate"))`
+
+### Default R Studio login
 
 username: rstudio
+password: rstudio1
+
+Update password in `docker-compose.yml` at the following location:
 
-Default password: rstudio1
+```
+environment:
+ - PASSWORD=rstudio1
+```
 
 ## Docker Ubuntu Server Installation/Set-up
 
@@ -53,7 +63,7 @@ Default password: rstudio1
 ## HTTPS encryption
 
 [These instructions](https://medium.com/@pentacent/nginx-and-lets-encrypt-with-docker-in-less-than-5-minutes-b4b8a60d3a71)
-were used to set up a secure HTTPS connection to RStuido with Certbot SSL
+were used to set up a secure HTTPS connection to RStudio with Certbot SSL
 certificates. Also see [here](https://github.com/wmnnd/nginx-certbot).
 
 This will not work out of the box, the NGINX configuration file will need to be

docker-compose.yml

@@ -6,7 +6,7 @@ services:
     container_name: nginx
     restart: on-failure
     networks:
-      - tki-net
+      - net
     volumes:
       - ./nginx.conf:/etc/nginx/nginx.conf
       - ./data/certbot/conf:/etc/letsencrypt
@@ -26,7 +26,7 @@ services:
     entrypoint: "/bin/sh -c 'trap exit TERM; while :; do certbot renew; sleep 12h & wait $${!}; done;'"
 
   rstudio:
-    image: rocker/tidyverse:3.5.3
+    image: rocker/tidyverse:3.6.0
     container_name: rstudio
     restart: on-failure
     volumes:
@@ -44,15 +44,15 @@ services:
         volume:
           no-copy: true
     networks:
-      - tki-net
+      - net
     environment:
       - PASSWORD=rstudio1
     expose:
       - 8787
 
 networks:
   tki-net:
-    name: tki-net
+    name: net
 
 volumes:
   r_libs:

nginx.conf

@@ -7,32 +7,33 @@ http {
         server rstudio:8787;
     }
 
-    #### START REMOVE - remove this block of code if SSL certification is not wanted ####
-    server {
-      listen 80;
-      server_name example.org;  #### UPDATE example.org to your domain name ####
-      server_tokens off;
-
-      location /.well-known/acme-challenge/ {
-          root /var/www/certbot;
-      }
-
-      location / {
-        return 301 https://$host$request_uri;
-      }
-    }
-    #### END REMOVE ####
+#    #### START BLOCK - uncomment this block to enable SSL encryption ####
+#    server {
+#      listen 80;
+#      server_name example.org;  #### UPDATE example.org to your domain name ####
+#      server_tokens off;
+#
+#      location /.well-known/acme-challenge/ {
+#          root /var/www/certbot;
+#      }
+#
+#      location / {
+#        return 301 https://$host$request_uri;
+#      }
+#    }
+#    #### END BLOCK ####
 
     server {
-      listen 443 SSL; # listen 80; #### remove "listen 443 SSL; #" statement if SSL certification is not wanted ####
+      listen 80; #### remove this line if SSL certification is enabled ####
+#     listen 443 SSL; #### uncomment this line if SSL certification is enabled ####
       server_name example.org; #### UPDATE example.org to your domain name ####
 
-      #### START REMOVE - remove this block of code if SSL certification is not wanted ####
-      ssl_certificate       /etc/letsencrypt/live/example.org/fullchain.pem; #### UPDATE example.org to your domain name ####
-      ssl_certificate_key   /etc/letsencrypt/live/example.org/privkey.pem; #### UPDATE example.org to your domain name ####
-      include               /etc/letsencrypt/options-ssl-nginx.conf;
-      ssl_dhparam           /etc/letsencrypt/ssl-dhparams.pem;
-      #### END REMOVE ####
+#      #### START BLOCK - uncomment this block to enable SSL encryption ####
+#      ssl_certificate       /etc/letsencrypt/live/example.org/fullchain.pem; #### UPDATE example.org to your domain name ####
+#      ssl_certificate_key   /etc/letsencrypt/live/example.org/privkey.pem; #### UPDATE example.org to your domain name ####
+#      include               /etc/letsencrypt/options-ssl-nginx.conf;
+#      ssl_dhparam           /etc/letsencrypt/ssl-dhparams.pem;
+#      #### END BLOCK ####
 
       location / {
         proxy_pass         http://rstudio;

projects/00_next_project/.Rbuildignore

@@ -0,0 +1,2 @@
+^.*\.Rproj$
+^\.Rproj\.user$

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

@@ -1,9 +1,24 @@
-# Reads raw delimited data and saves as RDS files in data folder
-# created 25-May-2018 by Paul Stevenson
+#' Reads raw delimited data and saves as RDS files in data folder
+#' created 25-May-2018 by Paul Stevenson
+#' updated 27-May-2019 by Paul Stevenson
 
+#### libraries ----
+
+library(dplyr)
 library(readr)
 library(readstata13)
 
+#### helper functions ----
+
+source("R/99-helper.R")
+
+#### load data ----
+
 dat <- read_csv("data-raw/file.csv")
 
-devtools::use_data("var_name", overwrite = T)
+#### Data cleaning ----
+
+
+#### save data ----
+
+save(dat, file = "data/dat.RData")

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

@@ -1,10 +1,27 @@
-# This is the starting point for the project. load.project will load the
-# data and run any scripts in the munge directory.
-# Created by Paul Stevenson 17-May-2018
+#' This is the starting point for the project. load.project will load the
+#' data and run any scripts in the munge directory.
+#' Created by Paul Stevenson 17-May-2018
+#' Updated 27-May-2019 by Paul Stevenson
 
-library('repmis')
+#### libraries ----
 
-LoadandCite(pkgs = c("tidyverse", "lubridate", "ProjectTemplate", "repmis", "biometrics"),
-            file = "report/assets/bib/packages.bib")
+library(ProjectTemplate)
+library(dplyr)
+
+#### Project automation with Project Template ----
 
 load.project(munging = TRUE, data_loading = TRUE)
+
+#### load data ----
+
+# load("data/dat.RData")
+# load("cache/dat.RData")
+
+#### helper functions ----
+
+source("R/99-helper.R")
+
+#### Data wrangling/cleaning ----
+
+
+#### Analysis ----

projects/00_next_project/config/global.dcf

@@ -1,4 +1,4 @@
-version: 0.8.2
+version: 0.9.0
 data_loading: TRUE
 data_loading_header: TRUE
 data_ignore:
@@ -9,8 +9,8 @@ logging: FALSE
 logging_level: INFO
 load_libraries: FALSE
 libraries: stats, reshape2, plyr, tidyverse
-as_factors: TRUE
-data_tables: FALSE
+as_factors: FALSE
 attach_internal_libraries: FALSE
-cache_loaded_data:  FALSE
+cache_loaded_data: FALSE
 sticky_variables: NONE
+tables_type: tibble

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

@@ -1 +1,23 @@
-# Example preprocessing script.
+#' Example preprocessing script.
+#' Created 21-May-2019 by Paul Stevenson
+#' Updated 27-May-2019 by Paul Stevenson
+
+#### libraries ----
+
+library(ProjectTemplate)
+library(dplyr)
+
+#### helper functions ----
+
+source("R/99-helper.R")
+
+#### load data ----
+
+load("data/dat.RData")
+
+#### Data wrangling ----
+
+
+#### save data ----
+
+cache("dat")