R Documentation

• R documentation Hub

Packages Documentation

Look for websites

A convenient and nicer way to browse package’s documentation.

Get started

Usually a short tutorial that demonstrates main package features.

Function Reference

Lists all the packages functions and links to documentation pages.

Articles / Tutorials

Task-specific tutorials and more information.

Search Feature

All packages websites built with {pkgdown} have a powerful built-in search box, use it !

Getting Help From the R console

Almost all the website content is also accessible within your r session:

• vignette("[pkgName]") will open “Get started” page in the Help tab,

• When typing a function use tab⇥ to see all available options.

• When typing functions arguments, use tab⇥ to see all available arguments.

• When using a function, use F1 key to open help page (or use ?[function] ).

Internal Resources

Packages Websites

All our packages have dedicated websites. You can find the links in GitHub repositories (or in Bluespice)

r.esqlabs.com

A collection of presentation/workshop material developed internally.

ESQlabs R Guidelines website

AI assistants

You can try to ask questions, generate or explain code chunks and even debug your own code.

You’re not alone

Someone else probably had the same/similar question before.

• Posit Community Forum,

• Stack Overflow,

• R support Teams Channel (Modeling and Simulation | R Support) (use the search feature),

• GitHub issues.

How to ask for help ?

Do not share screenshots

Do not Copy Paste from Console

library(dplyr)
library(readxl)
setwd("/Users/NoOne/Documents/my_work_folder/project_1/data")
data <- read_xlsx("Export 2024-01-02 V5.xlsx")
data %>%
  mutate(year = case_when(date <= "2020-12-31" & date >= "2020-01-01" ~ 2020,
                          is.na(date) ~ NA))
Error: Problem with `mutate()` input `year`.
x must be a double vector, not a logical vector.
ℹ Input `year` is `case_when(...)`.

Others must make fiddly edits to run the code.

How to ask for help ?

What is a reprex ?

• A code chunk,
• reproduce a problem,
• minimalist,
• self-contained,
• shows outputs,
• easy to run.

Why should I reprex ?

Making a minimal, reproducible example can take time. It can be easy to convince yourself to skip the process and “just get the help I need”. But the time is ultimately worth spending.

• 80% of the time creating a reprex reveals the source of your problem. The process of writing up a self-contained and minimal example allows you to learn and answer your own question.

• 20% of time you will have captured the essence of your problem in a way that is easy for others to play with.

Help yourself and help others help you !

How to reprex ?

install.packages("reprex")
library(reprex)

Write your reproducible minimal example inside reprex() function

reprex({
  (y <- 1:4)
  mean(y)
})

A nicely rendered HTML preview will display in RStudio’s Viewer and a piece of markdown will be added to your clipboard

(y <- 1:4)
#> [1] 1 2 3 4
mean(y)
#> [1] 2.5

A good reprex needs

• Libraries☝️

• Data ✌️

• Code 👌

Librairies ☝

reprex({
  library(ospsuite)
  
  filePath <- system.file("extdata", 
                          "Diclofenac_PK_data_complete.xlsx", 
                          package = "ospsuite.parameteridentification")
  
  importConfig <- createImporterConfigurationForFile(filePath = filePath)
  
  obsData <- loadDataSetsFromExcel(xlsFilePath = filePath,
                                   importerConfigurationOrPath = importConfig,
                                   importAllSheets = TRUE)
})

• A reprex is isolated from your working environment

  • All needed libraries need to be loaded explicitly,

  • Variable defined in a reprex will not interact with the ones defined in your working environment,

Data✌️

reprex({
  library(ospsuite)
  
  filePath <- system.file("extdata", 
                          "Diclofenac_PK_data_complete.xlsx", 
                          package = "ospsuite.parameteridentification")
  
  importConfig <- createImporterConfigurationForFile(filePath = filePath)
  
  obsData <- loadDataSetsFromExcel(xlsFilePath = filePath,
                                   importerConfigurationOrPath = importConfig,
                                   importAllSheets = TRUE)
})

• When possible, try to use example or built-in data (mtcars dataset, aciclovir simulation, etc.)

• For {esqlabsR} projects, attach project configuration files

🔥Never use setwd() 🔥

setwd("C:\Users\absolutelyNoOne\path\that\only\I\have")

The chances that setwd() works on another computer are approximately 0%.

Use RStudio Projects instead 😉

Code 👌

reprex({
  library(ospsuite)
  
  filePath <- system.file("extdata", 
                          "Diclofenac_PK_data_complete.xlsx", 
                          package = "ospsuite.parameteridentification")
  
  importConfig <- createImporterConfigurationForFile(filePath = filePath)
  
  obsData <- loadDataSetsFromExcel(xlsFilePath = filePath,
                                   importerConfigurationOrPath = importConfig,
                                   importAllSheets = TRUE)
})

• Try to remove all unnecessary code to make it easy for other to understand what your code does,

• If you are not sure where the error occurs, add lines one by one until the code fails.

Output

The Output will automatically appear in the Viewer pan, and a Markdown sample will be added to your clipboard, ready to be pasted.

library(ospsuite)
#> Loading required package: rSharp
#> 
#> Attaching package: 'ospsuite'
#> The following object is masked from 'package:base':
#> 
#>     %||%

filePath <- system.file("extdata", 
                        "Diclofenac_PK_data_complete.xlsx", 
                        package = "ospsuite.parameteridentification")

importConfig <- createImporterConfigurationForFile(filePath = filePath)
#> Error in do.call(".External", c(list("r_call_method", self$pointer, methodName), : Type:    OSPSuite.Infrastructure.Import.Core.UnsupportedFileTypeException
#> Message: The type of file that you are trying to open is not currently supported
#> ...

obsData <- loadDataSetsFromExcel(xlsFilePath = filePath,
                                 importerConfigurationOrPath = importConfig,
                                 importAllSheets = TRUE)
#> Error in eval(expr, envir, enclos): object 'importConfig' not found

Share it !

You can now paste this in the R Support Teams Channel

1. Create a Code block,

2. Paste (Pick “Plain Text”),
   

3. Add short description of what you are trying to do and attach necessary files,
4. Post.

A great reprex needs

• Libraries☝️

• Data ✌️

• Code 👌

• Session Infos 🤟

Session Info 🤟

reprex({
  library(ospsuite)
  
  filePath <- system.file("extdata", 
                          "Diclofenac_PK_data_complete.xlsx", 
                          package = "ospsuite.parameteridentification")
  
  importConfig <- createImporterConfigurationForFile(filePath = filePath)
  
  obsData <- loadDataSetsFromExcel(xlsFilePath = filePath,
                                   importerConfigurationOrPath = importConfig,
                                   importAllSheets = TRUE)
  }, 
  session_info = TRUE)

References

• reprex documentation: https://reprex.tidyverse.org/index.html

• Ariel Muldoon “How to reprex” presentation: https://aosmith16.github.io/spring-r-topics/slides/week09_reprex.html#1

• Jenny Bryan “Creating reproducible example with reprex”: https://speakerdeck.com/jennybc/reprex-reproducible-examples-with-r

• R Language collective answer on StackOverflow: https://stackoverflow.com/a/5963610/8557146