In stenw/BST02R: Supporting Material for the R Course of the NIHES (BST02)

knitr::opts_chunk$set(
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R as a calculator

One of the most simple things we can do with R is to use it as a kind of calculator. We can do all elementary arithmetic operations:

>1 + 1
[1] 2
>1 - 1
[1] 0
>2 * 3
[1] 6
>2 / 3
[1] 0.6666667

Here we use '>' to denote the R prompt. It is used in the console to indicate that R is ready for a new command. The lines in between is the output given by R.

Most of the functionality in R comes from its functions. There are many functions we can use including the standard mathematical ones:

cos(3.1415) [1] -1 exp(0) [1] 1 log(1) [1] 0

We will discuss functions later on in this text in much more detail.

Variables

The results above are displayed but not stored. To do this we must give a name to the result. That is, we store the result in a variable. The results are now no longer displayed but using the variable name we can refer to it later.

Assigning a result in a variable is done using <-. For example:

>five <- 3+2
> five
[1] 5
> five + 1
[1] 6

Each variable has a class that determines for a large extend what we can do with it.

R packages and the library command

As mentioned above R is a modular language that we can extend using packages. We can load a package using the command library(). So if we want to load the survival package (in order to do survival analysis ) we type:

>library(survival)

Before we can load a library it must be installed. This can be done using the command install.packages(packagename) where packagename is the name of the package between single or double quotes. For example:

>install.packages('gamlss')

Some useful packages are lme4 for analyses with repeated measurements and mice for multiple imputation.

Documentation

The functions help and ? can be used to read the documentation on a particular subject (mostly functions). The package in which the function is defined must be loaded unless you use the package parameter ofn the help function. For example: help('survreg' , package='survival').

Using help.search and ?? we can search the documentation files in a more general way. The documentation for all installed packages is searched for topics that have specific words in the title.

>?library
>help(install.packages)
>help.search('logistic regression')

Some R packages are also documented with so called vignettes. You can browse the vignettes of a package using the function browseVignettes, for example browseVignettes(package="survival").

Using the function RSiteSearch you can search the documentation of all packages that are on CRAN (so it is like a google for R).

Another great source of help is the site 'Stack Overflow'. A site were people can ask all kinds of programming related questions.

stenw/BST02R documentation built on May 26, 2019, 4:35 a.m.