initial commit

.Rbuildignore

+^\.gitlab-ci\.yml$
+^.*\.Rproj$
+^\.Rproj\.user$

.dockerignore

+.drake
+artifacts
+.git
\ No newline at end of file

.gitignore

+
+# Created by https://www.gitignore.io/api/r
+# Edit at https://www.gitignore.io/?templates=r
+### R ###
+# History files
+.Rhistory
+.Rapp.history
+# Session Data files
+.RData
+# User-specific files
+.Ruserdata
+# Example code in package build process
+*-Ex.R
+# Output files from R CMD build
+/*.tar.gz
+# Output files from R CMD check
+/*.Rcheck/
+# RStudio files
+.Rproj.user/
+# produced vignettes
+vignettes/*.html
+vignettes/*.pdf
+# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
+.httr-oauth
+# knitr and R markdown default cache directories
+*_cache/
+/cache/
+# Temporary files created by R markdown
+*.utf8.md
+*.knit.md
+### R.Bookdown Stack ###
+# R package: bookdown caching files
+/*_files/
+# End of https://www.gitignore.io/api/r
+
+.drake
+artifacts/*.*
+!artifacts/.gitkeep
\ No newline at end of file

.gitlab-ci.yml

+stages:
+  - build-image
+  - fit
+  - deploy
+
+build-testing-image:
+  stage: build-images
+  image: docker:19.03.1
+  services:
+    - docker:19.03.1-dind
+  variables:
+    DOCKER_HOST: tcp://docker:2375/
+  before_script:
+    - echo $CI_REGISTRY_PASSWORD | docker login -u $CI_REGISTRY_USER --password-stdin $CI_REGISTRY
+  script:
+    - docker pull $CI_REGISTRY_IMAGE:latest || true
+    - docker build --cache-from $CI_REGISTRY_IMAGE:latest --tag $CI_REGISTRY_IMAGE:$CI_COMMIT_SHA --tag $CI_REGISTRY_IMAGE:latest .
+    - docker push $CI_REGISTRY_IMAGE:$CI_COMMIT_SHA
+    - docker push $CI_REGISTRY_IMAGE:latest
+  only:
+    changes:
+      - "DESCRIPTION"
+      - "Dockerfile"
+  when: always
+  
+run-drake:
+  stage: fit
+  image: $CI_REGISTRY_IMAGE:latest
+  cache:
+    paths:
+      - .drake
+  artifacts:
+    name: "$CI_JOB_NAME"
+    paths:
+      - artifacts/
+  before_script:
+    - Rscript -e "remotes::install_deps()"
+  script:
+    - make.R
+  when: always
+
+
+

DESCRIPTION

+Package: repel-drake
+Title: What the Package Does (One Line, Title Case)
+Version: 0.0.0.9000
+Authors@R: 
+    person(given = "First",
+           family = "Last",
+           role = c("aut", "cre"),
+           email = "first.last@example.com",
+           comment = c(ORCID = "YOUR-ORCID-ID"))
+Description: What the package does (one paragraph).
+License: What license it uses
+Encoding: UTF-8
+LazyData: true
+Imports: 
+    drake,
+    tidyverse,
+    knitr,
+    rmarkdown,
+    visNetwork
\ No newline at end of file

Dockerfile

+FROM rocker/verse:3.6.1
+
+RUN apt-get update && apt-get install -y --allow-downgrades --allow-remove-essential --allow-change-held-packages --allow-unauthenticated --no-install-recommends --no-upgrade \
+  curl
+
+## Install packages
+RUN install2.r -s remotes
+COPY DESCRIPTION /pkg/DESCRIPTION
+RUN Rscript -e "remotes::install_deps(pkgdir = '/pkg/', dependencies=TRUE, upgrade = 'always', force = FALSE, quiet = FALSE)"

R/functions.R

+# This file contains all the functions of the workflow.
+# If needed, you could split it up into multiple files.
+
+# Pick a random subset of n rows from a dataset
+random_rows <- function(data, n){
+  data[sample.int(n = nrow(data), size = n, replace = TRUE), ]
+}
+
+# Bootstrapped datasets from mtcars.
+simulate <- function(n){
+  # Pick a random set of cars to bootstrap from the mtcars data.
+  data <- random_rows(data = mtcars, n = n)
+  
+  # x is the car's weight, and y is the fuel efficiency.
+  data.frame(
+    x = data$wt,
+    y = data$mpg
+  )
+}
+
+# Try a couple different regression models.
+
+# Is fuel efficiency linearly related to weight?
+reg1 <- function(d){
+  lm(y ~ + x, data = d)
+}
+
+# Is fuel efficiency related to the SQUARE of the weight?
+reg2 <- function(d){
+  d$x2 <- d$x ^ 2
+  lm(y ~ x2, data = d)
+}

R/packages.R

+# Here, load the packages you need for your workflow.
+
+library(drake)
+library(knitr)
+library(tidyverse)
+library(htmlwidgets)

R/plan.R

+# This is where you set up your workflow plan,
+# a data frame with the steps of your analysis.
+
+###################
+### THE NEW WAY ###
+###################
+
+# drake >= 7.0.0 has a new interface for generating plans.
+# Read about it at https://ropenscilabs.github.io/drake-manual/plans.html
+
+my_plan <- drake_plan(
+  report = knit(knitr_in("report.Rmd"), file_out("artifacts/report.md"), quiet = FALSE),
+  small = simulate(48),
+  large = simulate(64),
+  regression1 = target(
+    reg1(data),
+    transform = map(data = c(small, large), .tag_out = reg)
+  ),
+  regression2 = target(
+    reg2(data),
+    transform = map(data, .tag_out = reg)
+  ),
+  summ = target(
+    suppressWarnings(summary(reg$residuals)),
+    transform = map(reg)
+  ),
+  coef = target(
+    suppressWarnings(summary(reg))$coefficients,
+    transform = map(reg)
+  ),
+  model = target(
+    saveRDS(reg, file_out(!!file.path("artifacts", paste0(.id_chr, ".rds")))),
+    transform = map(reg)
+  )
+)
+