If you haven’t already, please install both R and RStudio following the instructions in this video
This setting will cause you issues in the future if you don’t change it now. Set R/RStudio to not automatically an RData file:
For an extremely detailed introduction, please see
help.start()
In this documentation, the above command will be executed at the command prompt, see below.
From help.start()
:
R is a free software environment for statistical computing and graphics.
and from https://www.rstudio.com/products/RStudio/:
RStudio is an integrated development environment (IDE) for R.
In contrast to many other statistical software packages that use a
point-and-click interface, e.g. SPSS, JMP, Stata, etc, R has a
command-line interface. The command line has a command prompt,
e.g. >
, see below.
>
This means, that you will be entering commands on this command line and hitting enter to execute them, e.g.
help()
Use the up arrow to recover past commands.
hepl()
help() # Use up arrow and fix
Most likely, you are using a graphical user interface (GUI) and therefore, in addition, to the command line, you also have a windowed version of R with some point-and-click options, e.g. File, Edit, and Help.
In particular, there is an editor to create a new R script. So rather
than entering commands on the command line, you will write commands in a
script and then send those commands to the command line using
Ctrl-R
(PC) or Command-Enter
(Mac).
a = 1
b = 2
a + b
## [1] 3
Multiple lines can be run in sequence by selecting them and then
using Ctrl-R
(PC) or Command-Enter
(Mac).
One of the most effective ways to use this documentation is to cut-and-paste the commands into a script and then execute them.
Cut-and-paste the following commands into a new
script and then run those commands directly from the script
using Ctrl-R
(PC) or Command-Enter
(Mac).
x <- 1:10
y <- rep(c(1,2), each=5)
m <- lm(y~x)
s <- summary(m)
Now, look at the result of each line
x
y
m
s
s$r.squared
x
## [1] 1 2 3 4 5 6 7 8 9 10
y
## [1] 1 1 1 1 1 2 2 2 2 2
m
##
## Call:
## lm(formula = y ~ x)
##
## Coefficients:
## (Intercept) x
## 0.6667 0.1515
s
##
## Call:
## lm(formula = y ~ x)
##
## Residuals:
## Min 1Q Median 3Q Max
## -0.4242 -0.1667 0.0000 0.1667 0.4242
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 0.6667 0.1880 3.546 0.00756 **
## x 0.1515 0.0303 5.000 0.00105 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 0.2752 on 8 degrees of freedom
## Multiple R-squared: 0.7576, Adjusted R-squared: 0.7273
## F-statistic: 25 on 1 and 8 DF, p-value: 0.001053
s$r.squared
## [1] 0.7575758
All basic calculator operations can be performed in R.
1+2
## [1] 3
1-2
## [1] -1
1/2
## [1] 0.5
1*2
## [1] 2
2^3 # same as 2**3
## [1] 8
For now, you can ignore the [1] at the beginning of the line, we’ll learn about that when we get to vectors.
Many advanced calculator operations are also available.
(1+3)*2 + 100^2 # standard order of operations (PEMDAS)
## [1] 10008
sin(2*pi) # the result is in scientific notation, i.e. -2.449294 x 10^-16
## [1] -2.449294e-16
sqrt(4)
## [1] 2
log(10) # the default is base e
## [1] 2.302585
log(10, base = 10)
## [1] 1
A real advantage to using R rather than a calculator (or calculator app) is the ability to store quantities using variables.
a = 1
b = 2
a + b
## [1] 3
a - b
## [1] -1
a / b
## [1] 0.5
a * b
## [1] 2
b ^ 3
## [1] 8
When assigning variables values, you can also use arrows <- and -> and you will often see this in code, e.g.
a <- 1 # recommended
2 -> b # uncommon, but sometimes useful
c = 3 # similar to other languages
Now print them.
a
## [1] 1
b
## [1] 2
c
## [1] 3
While using variables alone is useful, it is much more useful to use informative variables names.
# Rectangle
length <- 4
width <- 3
area <- length * width
area
## [1] 12
perimeter <- 2 * (length + width)
# Circle
radius <- 2
area <- pi*radius^2 # this overwrites the previous `area` variable
circumference <- 2*pi*radius
area
## [1] 12.56637
circumference
## [1] 12.56637
# (Right) Triangle
opposite <- 1
angleDegrees <- 30
angleRadians <- angleDegrees * pi/180
(adjacent <- opposite / tan(angleRadians)) # = sqrt(3)
## [1] 1.732051
(hypotenuse <- opposite / sin(angleRadians)) # = 2
## [1] 2
Suppose an individual tests positive for a disease, what is the probability the individual has the disease? Let
The above probability can be calculated using Bayes’ Rule:
\[ P(D|+) = \frac{P(+|D)P(D)}{P(+|D)P(D)+P(+|N)P(N)} = \frac{P(+|D)P(D)}{P(+|D)P(D)+(1-P(-|N))\times(1-P(D))} \]
where
Calculate the probability the individual has the disease if the test is positive when
specificity <- 0.95
sensitivity <- 0.99
prevalence <- 0.001
probability <- (sensitivity*prevalence) / (sensitivity*prevalence + (1-specificity)*(1-prevalence))
probability
## [1] 0.01943463
Objects in R can be broadly classified according to their dimensions:
and according to the type of variable they contain:
Scalars have a single value assigned to the object in R.
a <- 3.14159265
b <- "STAT 587 (Eng)"
c <- TRUE
Print the objects
a
## [1] 3.141593
b
## [1] "STAT 587 (Eng)"
c
## [1] TRUE
The c()
function creates a vector in R
a <- c(1, 2, -5, 3.6)
b <- c("STAT", "587", "(Eng)")
c <- c(TRUE, FALSE, TRUE, TRUE)
To determine the length of a vector in R use
length()
length(a)
## [1] 4
length(b)
## [1] 3
length(c)
## [1] 4
To determine the type of a vector in R use class()
class(a)
## [1] "numeric"
class(b)
## [1] "character"
class(c)
## [1] "logical"
Create a numeric vector that is a sequence using : or
seq()
.
1:10
## [1] 1 2 3 4 5 6 7 8 9 10
5:-2
## [1] 5 4 3 2 1 0 -1 -2
seq(from = 2, to = 5, by = .05)
## [1] 2.00 2.05 2.10 2.15 2.20 2.25 2.30 2.35 2.40 2.45 2.50 2.55 2.60 2.65 2.70
## [16] 2.75 2.80 2.85 2.90 2.95 3.00 3.05 3.10 3.15 3.20 3.25 3.30 3.35 3.40 3.45
## [31] 3.50 3.55 3.60 3.65 3.70 3.75 3.80 3.85 3.90 3.95 4.00 4.05 4.10 4.15 4.20
## [46] 4.25 4.30 4.35 4.40 4.45 4.50 4.55 4.60 4.65 4.70 4.75 4.80 4.85 4.90 4.95
## [61] 5.00
Another useful function to create vectors is rep()
rep(1:4, times = 2)
## [1] 1 2 3 4 1 2 3 4
rep(1:4, each = 2)
## [1] 1 1 2 2 3 3 4 4
rep(1:4, each = 2, times = 2)
## [1] 1 1 2 2 3 3 4 4 1 1 2 2 3 3 4 4
Arguments to functions in R can be referenced either by position or by name or both. The safest and easiest to read approach is to name all your arguments. I will often name all but the first argument.
Elements of a vector can be accessed using brackets, e.g. [index].
a <- c("one","two","three","four","five")
a[1]
## [1] "one"
a[2:4]
## [1] "two" "three" "four"
a[c(3,5)]
## [1] "three" "five"
a[rep(3,4)]
## [1] "three" "three" "three" "three"
Alternatively we can access elements using a logical vector where only TRUE elements are accessed.
a[c(TRUE, TRUE, FALSE, FALSE, FALSE)]
## [1] "one" "two"
You can also see all elements except some using a negative sign
-
.
a[-1]
## [1] "two" "three" "four" "five"
a[-(2:3)]
## [1] "one" "four" "five"
You can assign new values to elements in a vector using = or <-.
a[2] <- "twenty-two"
a
## [1] "one" "twenty-two" "three" "four" "five"
a[3:4] <- "three-four" # assigns "three-four" to both the 3rd and 4th elements
a
## [1] "one" "twenty-two" "three-four" "three-four" "five"
a[c(3,5)] <- c("thirty-three","fifty-five")
a
## [1] "one" "twenty-two" "thirty-three" "three-four" "fifty-five"
Matrices can be constructed using cbind()
,
rbind()
, and matrix()
:
m1 <- cbind(c(1,2), c(3,4)) # Column bind
m2 <- rbind(c(1,3), c(2,4)) # Row bind
m1
## [,1] [,2]
## [1,] 1 3
## [2,] 2 4
all.equal(m1, m2)
## [1] TRUE
m3 <- matrix(1:4, nrow = 2, ncol = 2)
all.equal(m1, m3)
## [1] TRUE
m4 <- matrix(1:4, nrow = 2, ncol = 2, byrow = TRUE)
all.equal(m3, m4)
## [1] "Mean relative difference: 0.4"
m3
## [,1] [,2]
## [1,] 1 3
## [2,] 2 4
m4
## [,1] [,2]
## [1,] 1 2
## [2,] 3 4
Elements of a matrix can be accessed using brackets separated by a comma, e.g. [row index, column index].
m <- matrix(1:12, nrow=3, ncol=4)
m
## [,1] [,2] [,3] [,4]
## [1,] 1 4 7 10
## [2,] 2 5 8 11
## [3,] 3 6 9 12
m[2,3]
## [1] 8
Multiple elements can be accessed at once
m[1:2,3:4]
## [,1] [,2]
## [1,] 7 10
## [2,] 8 11
If no row (column) index is provided, then the whole row (column) is accessed.
m[1:2,]
## [,1] [,2] [,3] [,4]
## [1,] 1 4 7 10
## [2,] 2 5 8 11
Like vectors, you can eliminate rows (or columns)
m[-c(3,4),]
## [,1] [,2] [,3] [,4]
## [1,] 1 4 7 10
## [2,] 2 5 8 11
Be careful not to forget the comma, e.g.
m[1:4]
## [1] 1 2 3 4
When you install R, you actually install several R packages. When you initially start R, you will load the following packages
You can find this information by running the following code and looking at the attached base packages.
sessionInfo()
## R version 4.2.2 (2022-10-31)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.2
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## loaded via a namespace (and not attached):
## [1] digest_0.6.29 R6_2.5.1 jsonlite_1.8.0 magrittr_2.0.3
## [5] evaluate_0.15 stringi_1.7.6 rlang_1.0.2 cli_3.3.0
## [9] rstudioapi_0.13 jquerylib_0.1.4 bslib_0.3.1 rmarkdown_2.14
## [13] tools_4.2.2 stringr_1.4.0 xfun_0.31 yaml_2.3.5
## [17] fastmap_1.1.0 compiler_4.2.2 htmltools_0.5.2 knitr_1.39
## [21] sass_0.4.1
These packages provide a lot of functionality and have been in existence (almost as they currently are) from the early days of R.
While a lot of functionality exist in these packages, much more functionality exists in user contributed packages. On the comprehensive R archive network (CRAN), there are (as of 2023/01/29) 19,122 packages available for download. On Bioconductor, there are an additional 2,183. There are also additional packages that exist outside of these repositories.
To install packages from CRAN, use the install.packages
function. For example,
install.packages("tidyverse")
or, to install all the packages needed for this class,
install.packages(c("tidyverse",
"gridExtra",
"rmarkdown",
"knitr"))
R packages almost always depend on other packages. When you use the
install.packages()
function, R will automatically install
these dependencies.
You may run into problems during this installation process. Sometimes
the dependencies will fail. If this occurs, try to install just that
dependency using install.packages()
.
Sometimes you will be asked whether you want to install a newer version of a package from source. My general advice (for those new to R) is to say no and instead install the older version of the package. If you want to install from source, you will need Rtools (Windows) or Xcode (Mac). Alternatively, you can wait a couple of days for the newer version to be pre-compiled.
The installation only needs to be done once. But we will need to load the packages in every R session where we want to use them. To load the packages, use
library("dplyr")
library("tidyr")
library("ggplot2")
alternatively, you can load the entire (not very big)
tidyverse
.
library("tidyverse")
## ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.2 ──
## ✔ ggplot2 3.3.6 ✔ purrr 0.3.4
## ✔ tibble 3.1.7 ✔ dplyr 1.0.9
## ✔ tidyr 1.2.0 ✔ stringr 1.4.0
## ✔ readr 2.1.2 ✔ forcats 0.5.1
## ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
## ✖ dplyr::filter() masks stats::filter()
## ✖ dplyr::lag() masks stats::lag()
To learn R, you may want to try the swirl package. To install, use
install.packages("swirl")
After installation, use the following to get started
library("swirl")
swirl()
Also, the R 4 Data Science book is extremely helpful.
As you work with R, there will be many times when you need to get help.
My basic approach is
In all cases, knowing the R keywords, e.g. a function name, will be extremely helpful.
If you know the function name, then you can use
?<function>
, e.g.
?mean
The structure of help is
If you cannot remember the function name, then you can use
help.search("<something>")
, e.g.
help.search("mean")
Depending on how many packages you have installed, you will find a lot or a little here.
I google for <something> R
, e.g.
calculate mean R
Some useful sites are
Although the general R help can still be used, e.g.
?ggplot
?geom_point
It is much more helpful to google for an answer
geom_point
ggplot2 line colors
The top hits will all have the code along with what the code produces.
These sites all provide code. The first two also provide the plots that are produced.