R for reproducible scientific analysis

Seeking help

Learning objectives

To know where to look for help.
To become familiar with R help files for functions and special operators.
To be able to use CRAN task views to identify packages to solve a problem.
To be able to seek help from your peers.

Reading Help files

R and add-on packages provide help files for functions. To load the help page for a specific function:

?function_name
help(function_name)

These functions will display the requested help page at the bottom left panel in RStudio (or as plain text in R).

Each help page is broken down into sections:

Description: an extended description of what the function does.
Usage: the arguments of the function and their default values.
Arguments: an explanation of the data each argument expects.
Details: any important details to be aware of.
Value: the data the function returns and in which type.
See Also: any related functions you might find useful.
Examples: some examples on how to use the function.

Different functions might have different sections, but these are the main ones you should be aware of.

Special Operators

To seek help on special operators, use quotes:

?"+"

Getting help on packages

Many packages come with “vignettes”: tutorials and extended example documentation. Without any arguments, vignette() will list all vignettes for all installed packages; vignette(package="package-name") will list all available vignettes for package-name, and vignette("vignette-name") will open the specified vignette.

If a package doesn’t have any vignettes, you can usually find help by typing help("package-name").

When you kind of remember the function

If you’re not sure what package a function is in, or how it’s specifically spelled you can do a fuzzy search:

??function_name

When you have no idea where to begin

If you don’t know what function or package you need to use CRAN Task Views is a specially maintained list of packages grouped into fields. This can be a good starting point.

When your code doesn’t work: seeking help from your peers

If you’re having trouble using a function, 9 times out of 10, the answers you are seeking have already been answered on Stack Overflow. You can search using the [r] tag.

If you can’t find the answer, there are a few useful functions to help you ask a question from your peers:

?dput

Will dump the data you’re working with into a format so that it can be copied and pasted by anyone else into their R session.

sessionInfo()

R version 3.2.0 (2015-04-16)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.9.5 (Mavericks)

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
[1] knitr_1.10.12

loaded via a namespace (and not attached):
 [1] XML_3.98-1.2         digest_0.6.8         bitops_1.0-6        
 [7] rmarkdown_0.7        tools_3.2.0          Biobase_2.28.0      
[10] RCurl_1.95-4.6       yaml_2.1.13          htmltools_0.2.6

Will print out your current version of R, as well as any packages you have loaded. This can be useful for others to help reproduce and debug your issue.

Challenge 1

Look at the help for the paste function. You’ll need to use this later. What is the difference between the sep and collapse arguments?

Other ports of call

Challenge solutions

Solution to challenge 1

Look at the help for the paste function. You’ll need to use this later.

help("paste")
?paste