Tips

Useful Rstudio shortcuts

replace Cmd (macOS) by Ctrl for PC

• Scripting
  • Alt + -: insert <-
  • Cmd + Shift + M: insert %>%
  • Cmd + Alt + I: insert code chunk
  • Alt + ↑ or ↓: move line up / down
  • Cmd + Alt + ↑ or ↓: copy line up / down
  • Ctrl + Alt + ↑ or ↓: multi-line edition
• Running
  • Cmd + Enter: run code (highlighted lines or all pipeline if not)
  • Cmd + Shift + P: re-run Previous code
  • Cmd + Shift + Enter: run Current chunk
  • Cmd + Shift + K: Knit document
• Files
  • Cmd + .: find files or functions in a project

For projects

• for all projects, data must be loaded. Either from a file or querying the NCBI server. In all cases to avoid depending on the internet access, you should download those data on your hard drives and load those local files while testing. Only at the end, you can run the whole workflow using the remote data loading process.

url <- "https://rworkshop.uni.lu/lectures/data/example.csv"
url_file <- here::here("data", basename(url))
url_file

## [1] "/builds/aurelien.ginolhac/rworkshop/data/example.csv"

# download if file is not present
if (!file.exists(url_file)) {
  message(paste("downloading", url, "to", url_file))
  download.file(url, url_file)
}

## downloading https://rworkshop.uni.lu/lectures/data/example.csv to /builds/aurelien.ginolhac/rworkshop/data/example.csv

## Warning in download.file(url, url_file): URL https://rworkshop.uni.lu/lectures/
## data/example.csv: cannot open destfile '/builds/aurelien.ginolhac/rworkshop/
## data/example.csv', reason 'No such file or directory'

## Warning in download.file(url, url_file): download had nonzero exit status

message("testing again, no download this time")

## testing again, no download this time

if (!file.exists(url_file)) {
  message(paste("downloading", url, "to", url_file))
  download.file(url, url_file)
}

## downloading https://rworkshop.uni.lu/lectures/data/example.csv to /builds/aurelien.ginolhac/rworkshop/data/example.csv

## Warning in download.file(url, url_file): URL https://rworkshop.uni.lu/lectures/
## data/example.csv: cannot open destfile '/builds/aurelien.ginolhac/rworkshop/
## data/example.csv', reason 'No such file or directory'

## Warning in download.file(url, url_file): download had nonzero exit status

• check that the knitting process works, classic mistakes:
  • install.packages() in un-commented line or in a chunk not tagged as eval = FALSE
  • missing library() calls of necessary package. You can use as first chunk with include = FALSE to avoid loading messages but loading all necessary packages
  • incorrect file paths. Please use a RStudio project, here and relative paths to have a share-able project

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