R

library() see the list of installed packages. library(class) load the package class. search() see the list of loaded packages. install.packages() and update.packages() install and update packages.

To start ESS session, run command S. ESS will create a command interface as a buffer. Execute ?foo will open the R-doc for the function foo.

There's a babel in org mode for R, so just C-c C-c would work. This will prompt to create a session. One special for this babel is you can evaluate by line, using C-<RET> in the edit buffer.

Keep the session using the header:

#+PROPERTY: session *R*

To export a graph:

:file image.png :results output graphics :exports both

To export ordinary result:

:exports both

To export some summary data:

:exports both :results output org

We need to know what's going on in the current workspace. getwd() and setwd() get and set the current dir. ls() list the objects currently stored. rm(x, y, z) remove objects rm(list=ls()) remove all objects. objects() create and store current objects.

We can perform some IO by save.image("mydata.Rdata") and load("mydata.Rdata") will save and load workspace in current directory respectively. source("a.R") loads a script. sink("a.lis") redirects the output to a file, and sink() restore that to standard output.

You can view documentation by calling help help(lm). ?lm and ??solve also shows documentation, while example(topic), as its name indicates, shows the examples. help.start() opens the html documentation page.

Finally, q() quit R.

• str show the structure of arbitrary type
• summary print the summary

To see the data, you can use:

• dim()
• length()
• head()
• tail()
• summary(dataset) shows some information like max,min,mean
• class(data$col) get type
• levels(data$col) if it is factor, get the values

Create a vector by c: c(10.4, 5.6, 3.1). This connects elements end to end, e.g. c(x, 0, x). By a sequence 1:30: the same as: c(1, 2, ..., 29, 30). Colon operator can also specify a backward sequence: 30:1 Colon operator has higher priority: 2*1:15 is the same as c(2, 4, …, 28, 30) The colon operator works, if you want a more flexible and powerful expression, seq is what you want:

• seq(2,10) produces 2:10.
• seq(-5, 5, by=.2)
• seq(length=51, from=-5, by=.2)

Repeating can be done by rep:

• x <- c(1,2,3)
• rep(x, times=5) : [1,2,3,1,2,3,...]
• rep(x, each=5) : [1,1,1,1,1,2,2,2,2,2,...]

Inside [], it can be a number or character, or a vector of them. For vectors, [] returns the element. For lists, [] will return the the element inside a list, while [[]] will return the single element. [] does not allow a vector as index.

If the index is integer, will select based on the position, start from 1. If it is negative, it means the elements other than those index. The index 0 will return empty. Other numeric values will be converted to integer towards zero.

The index can be a integer vector, which selects a bunch of values.

If the index is logical vector, the true ones will be returned. If the index is character, it is compared, partially, with the names attributes of the vector. $ can be used for indexing with character. The empty index [] will returns the entire vector with irrelevant attributes removed. The only retained ones are the names, dim and dimnames attributes.

fruit <- c(5, 10, 1, 20)
names(fruit) <- c("orange", "banana", "apple", "peach")
lunch <- fruit[c("apple","orange")]
# matrix
dim(z) <- c(3,5,100)~
z[2,,]
z[,,]

Matrix can be created by the matrix function.

matrix(1:9, nrow=3,byrow=TRUE)

na.omit

can omit the NA values in data frame

A data frame is a list of equal-length vectors. When getting the data from read.csv, the result is a data frame. Use names to work on data frames will emit the names.

• Since it is a list, using [] to index will give also the list, a.k.a. data frame, retaining names. You can use a vector as index.
• Using [[]] to index will give the value, dropping names. You cannot use a vector as index.

if

if (STMT) STMT else if (STMT) STMT else STMT

Switch

switch (STMT, LIST)

• the STMT is first evaluated
• if the value is within 1 and the length of the LIST, evaluate LIST[i], and return
• return NULL
• Notice that the LIST can be a comma separated argument of switch … which means switch actually accepts ...

for

for (NAME in VECTOR) STMT

while

=while (STMT) STMT

repeat

repeat STMT

break, next

 fm = lm(y ~ x1 + x2, data = mydataframe)

The fitted model in the variable fm can be accessed by:

coef

extract the coefficients

deviance

the Residual Sum of Square

formula

extract the model formula

plot

produce four plots: residuals, fitted values, diagnostics.

predict(OBJECT, newdata=DATA.FRAME)

use the model to predict

residuals

extract the residuals

The models can be updated, if the formula only changes a little bit. In the following example, the . means the corresponding part of the original formula.

fs <- lm(y~x1 + x2, data=mydata)
fs <- update(fs, . ~ . + x3)
fs <- update(fs, sqrt(.) ~ .)

• box
• axis
• las attribute
• legend
• par
• text
• mtext
• points

When outputting some image, you have to tell R which format you want to use. The default on linux is X11, that's why it opens a image immediately after plotting. To use a device, call the device function, and after that all graphics output will be sent to that device.

• X11
• pdf
• png
• jpeg

When you have finished with a device, terminate it by dev.off().

To output to a file TODO to open plot in emacs:

  pdf("test1.pdf")
  dev.control(displaylist = "enable")
  plot(1:10)
  dev.copy(pdf, "test2.pdf")
  dev.off()
  # should now have a valid test2.pdf
  dev.off() # finished

Possible ... arguments:

• type what type of plot:
  • p for points,
  • l for lines,
  • b for both,
  • h for histogram like (or high-density) vertical lines,
• main an overall title for the plot: see title.
• xlab a title for the x axis: see title.
• ylab a title for the y axis: see title.

A Grammar of Data Manipulation https://cran.r-project.org/web/packages/dplyr/index.html https://cran.rstudio.com/web/packages/dplyr/vignettes/introduction.html