---
title: "A.1 -- Using R"
author: "Martin Morgan "
date: "11 - 12 September 2017"
output:
BiocStyle::html_document:
toc: true
toc_depth: 2
vignette: >
% \VignetteIndexEntry{A.1 -- Using R}
% \VignetteEngine{knitr::rmarkdown}
---
```{r style, echo = FALSE, results = 'asis'}
knitr::opts_chunk$set(
eval=as.logical(Sys.getenv("KNITR_EVAL", "TRUE")),
cache=as.logical(Sys.getenv("KNITR_CACHE", "TRUE")))
```
# _RStudio_: A Quick Tour
Panes
Options
Help
Environment, History, and Files
# _R_: First Impressions
Type values and mathematical formulas into _R_'s command prompt
```{r plus}
1 + 1
```
Assign values to symbols (variables)
```{r values-symbols}
x = 1
x + x
```
Invoke functions such as `c()`, which takes any number of values and
returns a single _vector_
```{r vector}
x = c(1, 2, 3)
x
```
_R_ functions, such as `sqrt()`, often operate efficiently on vectors
```{r vectorized}
y = sqrt(x)
y
```
There are often several ways to accomplish a task in _R_
```{r skinning-the-cat}
x = c(1, 2, 3)
x
x <- c(4, 5, 6)
x
x <- 7:9
x
10:12 -> x
x
```
Sometimes _R_ does 'surprising' things that can be fun to figure out
```{r surprise}
x <- c(1, 2, 3) -> y
x
y
```
## _R_ Data types: vector and list
'Atomic' vectors
- Types include integer, numeric (float-point; real), complex,
logical, character, raw (bytes)
```{r atomic-vectors}
people <- c("Lori", "Nitesh", "Valerie", "Herve")
people
```
- Atomic vectors can be named
```{r named-vectors}
population <- c(Buffalo=259000, Rochester=210000, `New York`=8400000)
population
log10(population)
```
- Statistical concepts like `NA` ("not available")
```{r NA-concept}
truthiness <- c(TRUE, FALSE, NA)
truthiness
```
- Logical concepts like 'and' (`&`), 'or' (`|`), and 'not' (`!`)
```{r logical-concept}
!truthiness
truthiness | !truthiness
truthiness & !truthiness
```
- Numerical concepts like infinity (`Inf`) or not-a-number (`NaN`,
e.g., 0 / 0)
```{r numerical-concept}
undefined_numeric_values <- c(NA, 0/0, NaN, Inf, -Inf)
undefined_numeric_values
sqrt(undefined_numeric_values)
```
- Common string manipulations
```{r string-manipulation}
toupper(people)
substr(people, 1, 3)
```
- _R_ is a green consumer -- recycling short vectors to align with
long vectors
```{r greenery}
x <- 1:3
x * 2 # '2' (vector of length 1) recycled to c(2, 2, 2)
truthiness | NA
truthiness & NA
```
- It's very common to nest operations, which can be simultaneously
compact, confusing, and expressive (`[`: subset; `<`: less than)
```{r nested-operations}
substr(tolower(people), 1, 3)
population[population < 1000000]
```
Lists
- The list type can contain other vectors, including other lists
```{r lists}
frenemies = list(
friends=c("Larry", "Richard", "Vivian"),
enemies=c("Dick", "Mike")
)
frenemies
```
- `[` subsets one list to create another list, `[[` extracts a list element
```{r list-subset}
frenemies[1]
frenemies[c("enemies", "friends")]
frenemies[["enemies"]]
```
Factors
- Character-like vectors, but with values restricted to specific levels
```{r factors}
sex = factor(c("Male", "Male", "Female"),
levels=c("Female", "Male", "Hermaphrodite"))
sex
sex == "Female"
table(sex)
sex[sex == "Female"]
```
## Classes: data.frame and beyond
Variables are often related to one another in a highly structured way,
e.g., two 'columns' of data in a spreadsheet
```{r related-variables}
x = rnorm(1000) # 1000 random normal deviates
y = x + rnorm(1000) # another 1000 deviates, as a function of x
plot(y ~ x) # relationship between x and y
```
Convenient to manipulate them together
- `data.frame()`: like columns in a spreadsheet
```{r data.frame}
df = data.frame(X=x, Y=y)
head(df) # first 6 rows
plot(Y ~ X, df) # same as above
```
- See all data with `View(df)`. Summarize data with `summary(df)`
```{r data.frame-summary}
summary(df)
```
- Easy to manipulate data in a coordinated way, e.g., access column
`X` with `$` and subset for just those values greater than 0
```{r data.frame-subset}
positiveX = df[df$X > 0,]
head(positiveX)
plot(Y ~ X, positiveX)
```
- _R_ is introspective -- ask it about itself
```{r introspection}
class(df)
dim(df)
colnames(df)
```
- `matrix()` a related class, where all elements have the same type (a
`data.frame()` requires elements within a column to be the same
type, but elements between columns can be different types).
A scatterplot makes one want to fit a linear model (do a regression
analysis)
- Use a _formula_ to describe the relationship between variables
- Variables found in the second argument
```{r lm-formula}
fit <- lm(Y ~ X, df)
```
- Visualize the points, and add the regression line
```{r lm-plot}
plot(Y ~ X, df)
abline(fit, col="red", lwd=3)
```
- Summarize the fit as an ANOVA table
```{r anova}
anova(fit)
```
- N.B. -- 'Type I' sums-of-squares, so order of independent variables
matters; use `drop1()` for 'Type III'. See [DataCamp Quick-R][]
- Introspection -- what class is `fit`? What _methods_ can I apply to
an object of that class?
```{r class-method-introspection}
class(fit)
methods(class=class(fit))
```
## Help!
Help available in _Rstudio_ or interactively
- Check out the help page for `rnorm()`
```{r, eval=FALSE}
?rnorm
```
- 'Usage' section describes how the function can be used
```
rnorm(n, mean = 0, sd = 1)
```
- Arguments, some with default values. Arguments matched first by
name, then position
- 'Arguments' section describes what the arguments are supposed to be
- 'Value' section describes return value
- 'Examples' section illustrates use
- Often include citations to relevant technical documentation,
reference to related functions, obscure details
- Can be intimidating, but in the end actually _very_ useful
[DataCamp Quick-R]: http://www.statmethods.net/stats/anova.html