fixed merge

Merge branch 'master' of git.soton.ac.uk:ba1e12/workflow

Conflicts:
	docs/basicReport.html

Rmd/basicReport.Rmd

@@ -29,6 +29,7 @@ bibliography: '`r here::here("bibliography.bib")`'
 ---
 
 ```{r knitrSetup, include=FALSE}
+startTime <- proc.time()
 knitr::opts_chunk$set(echo = FALSE) # by default turn off code echo
 ```
 
@@ -56,17 +57,16 @@ There's quite a lot of data...
 drake::readd(gWPlot)
 ```
 
-# Runtime
+# R environment
 
 ```{r check runtime, include=FALSE}
+# within Rmd timing
 t <- proc.time() - startTime
 elapsed <- t[[3]]
 ```
 
 Report generated in `r round(elapsed,2)` seconds ( `r round(elapsed/60,2)` minutes) using [knitr](https://cran.r-project.org/package=knitr) in [RStudio](http://www.rstudio.com) with `r R.version.string` running on `r R.version$platform`.
 
-# R environment
-
 ## R packages used
 
  * base R [@baseR]

_drake_basicReport.R

+# basic drake makefile
+
+# Libraries ----
+library(woRkflow) # remember to build it first :-)
+woRkflow::setup() # load env.R set up the default paths etc
+
+reqLibs <- c("data.table", # data munching
+             "drake", # what's done stays done
+             "here", # here
+             "lubridate", # dates and times
+             "ggplot2", # plots
+             "skimr" # for skim
+)
+# load them
+woRkflow::loadLibraries(reqLibs)
+
+# Parameters ----
+
+# Some data to play with:
+# https://data.nationalgrideso.com/carbon-intensity1/historic-generation-mix/r/historic_gb_generation_mix
+
+urlToGet <- "http://data.nationalgrideso.com/backend/dataset/88313ae5-94e4-4ddc-a790-593554d8c6b9/resource/7b41ea4d-cada-491e-8ad6-7b62f6a63193/download/df_fuel_ckan.csv"
+update <- "please" # edit this in any way (at all) to get drake to re-load the data from the url
+rmdFile <- "basicReport" # <- name of the .Rmd file to run at the end 
+title <- "UK Electricity Generation"
+subtitle <- "UK ESO grid data"
+authors <- "Ben Anderson"
+
+# Functions ----
+# for use in drake
+getData <- function(f,update){
+  # gets the data
+  message("Getting data from: ", f)
+  dt <- data.table::fread(f)
+  return(dt)
+}
+
+makeGWPlot <- function(dt){
+  message("Rebuilding plot")
+  # expects the eso data as a data.table
+  # draws a plot
+  dt[, rDateTime := lubridate::ymd_hms(DATETIME)] # hurrah, somebody read https://speakerdeck.com/jennybc/how-to-name-files?slide=21
+  dt[, weekDay := lubridate::wday(rDateTime, label = TRUE)]
+  # draw a megaplot for illustrative purposes
+  p <- ggplot2::ggplot(dt, aes(x = rDateTime, 
+                               y = GENERATION/1000,
+                               colour = weekDay)) +
+    geom_point() +
+    theme(legend.position = "bottom") +
+    labs(x = "Time",
+         y = "Generation (GW - mean per halfhour?)",
+         caption = "Source: UK Grid ESO (http://data.nationalgrideso.com)")
+  return(p)
+}
+
+makeReport <- function(f){
+  message("Re-running report: ", f)
+  # default = html
+  rmarkdown::render(input = paste0(here::here("Rmd", f),".Rmd"), # we love here:here() - it helps us find the .Rmd to use
+                    params = list(title = title,
+                                  subtitle = subtitle,
+                                  authors = authors),
+                    output_file = paste0(here::here("docs", f),".html") # where the output goes
+  )
+}
+
+# Set the drake plan ----
+# Clearly this will fail if you do not have internet access...
+plan <- drake::drake_plan(
+  esoData = getData(urlToGet, update), # returns data as data.table. If you edit 'update' in any way it will reload - drake is watching you!
+  skimTable = skimr::skim(esoData), # create a data description table
+  gWPlot = makeGWPlot(esoData), # make a plot
+  out = makeReport(rmdFile)
+)
+
+drake::drake_config(plan, verbose = 2)
+

make_basicReport.R

+# make file for drake
+# see https://books.ropensci.org/drake/projects.html#usage
+
+# Set up ----
+startTime <- proc.time()
+
+# use r_make to run the plan inside a clean R session so nothing gets contaminated
+drake::r_make(source = "_drake_basicReport.R") # where we keep the drake plan etc
+
+# we don't keep this in /R because that's where the package functions live
+# we don't use "_drake.R" because we have lots of different plans
+
+# Finish off ----
+
+t <- proc.time() - startTime # how long did it take?
+elapsed <- t[[3]]
+
+print("Done")
+print(paste0("Completed in ", round(elapsed/60,3), " minutes using ",
+             R.version.string, " running on ", R.version$platform))
\ No newline at end of file