Hadley's vocabulary with additional definitions and reproducible examples

hadley_vocabulary.rmd

# Hadley's vocabulary with additional definitions and reproducible examples

This document takes the original [Vocabulary chapter](https://github.com/hadley/devtools/wiki/Vocabulary) from Hadley Wickham's in progress book "[Advanced R development: making reusable code](https://github.com/hadley/devtools/wiki)" and adds definitions and reproducible examples using [knitr](http://yihui.name/knitr/). Unless otherwise noted, the examples come straight from the help for each function or are modified versions from those examples.

```{r}
library("knitr")
```



##The basics


### The first functions to learn

`?` help on functions and datasets

```{r}
?cat
``` 



`str` displays the internal str_ucture of an R object
```{r}
a <- c(1:10)
str(a)
b <- c("a", "b", "c")
str(b)
```


### Important operators and assignment
`%in%` demonstrates which elements of the vector on the right match the vector on the left. this function is similar to `match` but with a different syntax

```{r}
1:10 %in% c(1,3,5,9)
sstr <- c("c","ab","B","bba","c",NA,"@","bla","a","Ba","%")
sstr[sstr %in% c(letters, LETTERS)]
```

`match` returns a vector of the positions of (first) matches of its first argument in its second
a <- c(1:10)
b <- c(7:20)
match(a, b)


`=` indicates an assignment
```{r}
a = 1
a
```


`<-` indicates an assignment
```{r}
a <- 1
a
```

`<<-` used in functions to search through the environment for an existing definition of the variable being assigned.  If such a variable is found (and its binding is not locked) then its value is redefined, otherwise assignment takes place in the global environment
```{r}
a <<- 1
a
```


`$`

`[`

`[[`

`head`


`tail`


`subset`

`with`

`assign`

`get`



### Comparison
`all`

`equal`

`identical`


`!=`

`==`

`>`

`>=`

`<`

`<=`

`is.na`

`complete.cases`

`is.finite`



### Basic math
`*`

`+`

`-`

`/`

^

%%

%/%

abs

sign


acos

asin

atan

atan2

sin

cos

tan

ceiling

floor

round

trunc

signif

exp

log

log10

log2

sqrt

max

min

prod

sum

cummax

cummin

cumprod

cumsum

diff

pmax

pmin

range

mean

median

cor

sd

var

rle

### Functions
function
missing
on.exit
return

invisible

### Logical & sets 
&

|

!

xor

all

any

intersect

union

setdiff

setequal

which



### Vectors and matrices
c
matrix

### automatic coercion rules character > numeric > logical
length
dim

ncol

nrow

cbind

rbind

names

colnames

rownames

t

diag

sweep

as.matrix

data.matrix



### Making vectors 
c

rep

rep_len

seq

seq_len, seq_along
rev
sample
choose, factorial, combn
(is/as).(character/numeric/logical/...)

### Lists & data.frames 
list, unlist
data.frame, as.data.frame
split
expand.grid

### Control flow 
if, &&, || (short circuiting)
for, while
next, break
switch
ifelse


## Common data structures


### Date time
ISOdate


ISOdatetime

strftime

strptime

date

difftime

julian

months

quarters

weekdays

library(lubridate)

### Character manipulation 
grep

agrep

gsub

strsplit

chartr

nchar

tolower

toupper

substr

paste

library(stringr)



### Factors 
factor

levels

nlevels

reorder

relevel

cut

findInterval

interaction

options(stringsAsFactors = FALSE)

### Array manipulation

array

dim

dimnames

aperm

library(abind)


## Statistics
### Ordering and tabulating 
duplicated

unique

merge

order

rank

quantile

sort

table

ftable

### Linear models 
fitted

predict

resid

rstandard

lm

glm

hat

influence.measures

logLik

df

deviance

formula

~

I

anova

coef

confint

vcov


contrasts

### Miscellaneous tests
apropos("\\.test$")

### Random variables 
(q, t, d, r) * (beta, binom, cauchy, chisq, exp, f, gamma, geom, 
  hyper, lnorm, logis, multinom, nbinom, norm, pois, signrank, t, 
  unif, weibull, wilcox, birthday, tukey)

### Matrix algebra 
crossprod

tcrossprod


eigen

qr

svd
%*%

%o%

outer
rcond
solve


## Working with R
### Workspace 
ls

exists

rm

getwd

setwd

q

source

install.packages



library calls a package
```{r}
library("ggplot2")
```


require is identical to library, but it tends to be used inside functions since it will give you a warning and continue if the package is not found. In contrast, library will give you an error

```{r}
require("ggplot2")
```

### Help
help

? <!-- this is redundant -->

help.search

apropos

RSiteSearch

citation

demo

example

vignette

### Debugging
traceback

browser

recover

options(error = )

stop

warning

message

tryCatch

try

I/O



### Output
print

cat

message

warning

dput

format

sink

capture.output



### Reading and writing data

data

count.fields

read.csv

write.csv,

read.delim

write.delim

read.fwf

readLines

writeLines

readRDS

saveRDS

load

save


library(foreign)

### Files and directories 
dir
basename, dirname, tools::file_ext
file.path
path.expand, normalizePath
file.choose
file.copy, file.create, file.remove, file.rename, dir.create
file.exists, file.info
tempdir, tempfile
download.file, library(downloader)