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R Project

Starting R from cmd line (R bin folder added to the %PATH%): R, Rgui.

q() : quit. q("no") to quit without saving.

Help !

  • R Project Getting Help page

  • R documentation

  • R Language Documentation

  • R Open (Microsoft

  • help.start(): start the help (entry points to Manuals, Reference, Miscellaneous Material, ...)

  • Package Documentation: help(package = "datasets")

  • demo(): package demos "graphics", "colors". demo(package = .packages(all.available = TRUE) to list all demos available.

  • ? = help(): ?plot, help(plot), help("plot") display help on object.

    • ?* help on arithmetic opertaor, ?NA, ?log, ...
    • help("bs", try.all.packages = TRUE)
    • help("bs", package = "splines")
    • example(): run example from an online help topic (that is valid entry in the online help. ?colnames -> example("colnames")

  • ?? = help.search(): search for help in all installed packages. ??xyplot

    • use help.search("xyplot", rebuild = TRUE) to refresh help DB (useful when new packages have been installed)

  • str(a) # display the internal structure of an R object

  • system.file(): Finds the full file names of files in package

    • system.file("examples", package="shiny") [1] "T:/PortableApps/R/R_lib_32/shiny/examples"

Help! : apropos(), find() to find object by (partial) name

apropos() and find() search objects in the loaded packages matching expression.

apropos("GLM")` # objects with name containg GLM
[1] "glm"           "glm.control"   "glm.fit"       "predict.glm"  
[5] "residuals.glm" "summary.glm"

> apropos("^cor", ignore.case='TRUE') # objects beginning with cor
[1] "cor"      "cor.test"

# the R 1-2-letter things
apropos("^..?$")

# the R 8-and-more letter things
apropos("^.{8,}$")
table(nchar(apropos("^.{8,}$")))

find() returns packages where objects of a given name can be found

find("plot")
[1] "package:graphics"

find("^plot", simple.words = FALSE)
[1] "package:stats"    "package:graphics"

cor <- 1:3
find("cor")
[1] ".GlobalEnv"    "package:stats"

find("cor", numeric = TRUE)                     # package position in search path (search())
find("cor", numeric = FALSE, mode = "function")  # [1] "package:stats"
rm(cor)

R Session

R Workspace (R session image -> .RData / .rda)

  • ls(): list objects in the workspace / search path
  • ls.str(pat="data_"): list objects with their structures
  • attach(): Attach set of R Objects to Search Path
name <- "Carmen"; n1 <- 10; n2 <- 100; m <- 0.5
ls(pat = "ˆm")
ls.str() # display details of in memory objects
> ls.str()
# m :  num 0.5
# name :  chr "Carmen"
lsf.str() # functions in memory

# rm(): remove an object
rm(a)
rm(a, b, c)
rm(list=ls()) # remove all workspace objects from memory

history(): R commands history

a <- rnorm(10^7)
object.size(a)                     ##80000024 bytes
print(object.size(a),units="b")    ##80000024 bytes
print(object.size(a),units="Kb")   ##78125 Kb
print(object.size(a),units="Mb")   ##76.3 Mb
print(object.size(a),units="Gb")   ##0.1 Gb
print(object.size(a),units="auto") ##76.3 Mb

save & load workspace image

load("T:\\SW Dev\\R project\\statsTeachR\\introR_21_1.0\\introR\\source\\labs\\.RData")      
save.image("c:\\users\\family\\Desktop\\wk_img.RData")
# <=> save(list=ls(all=TRUE), file="c:\\...\wk_img.RData")

save.image(file="~/Logiciels/R/test.rda")
load("~/Logiciels/R/test.rda")

Working Dir

-getwd(): Get Working Dir -setwd("C:/data"): Set the working dir

setwd("T:/SW Dev/R project/statsTeachR/introR_21_1.0")
source("lab1_code1.R")

#set working dir to user's home dir
path.expand("~") # ~ -> $HOME
setwd("~")
setwd("~/Desktop")
getwd()
## [1] "d:/urrutiaa/My Documents"

# Lists the content of the working directory
dir()
list.files()

R datasets

  • data() : list datasets from loaded packages
  • data(package="datasets") # lists all the datasets in the "datasets" package
  • data(iris) : load iris data
    • ?iris # Help for the "iris" Datasets
    • str(iris) # structure

R Programming

  • page(lm): opens a new editor window and prints the code of the function in this editor.
  • trCopy(): function in the TinnR package to copy the code of the function. Then you just have to paste it in a text editor to have a look at it.
  • args(round): display function's arguments
  • Debug : debug(f), undebug(f), debugonce(), isdebugged(f)
  • traceback()
  • browser(): Debug > by inserting this function in the code you will be able to inspect objects, traceback, and run step by step.
    • trace("myfunc", browser, at = 4): add the browser() function within your func at line 4. untrace() to remove it.
    • trace() can also be used to trace a function call. ex: trace(sum); hist(stats::rnorm(100)) will trace each call to sum. untrace(sum).
  • options(error = recover), recover(). browse directly on any of the currently active function calls. options(error = NULL)

R Utils

system() gives access to the system (DOS or unix)

system("convert W:/toto.ps W:/toto.png") # converts toto.ps to toto.png
system("D:/Stata10/stata.exe do D:/pgm.do", wait = F) # opens Stata and run pgm.do
system("pdflatex.exe -shell-escape file.tex") # runs pdflatex
system("open file.pdf") # opens the pdf
system("open M:/.../doc/*.pdf") # opens all the pdf in a directory

File mgmt

  • file.info("taille.txt")
  • file.edit(), file.show()
  • file.remove(dir(path="directoryname", pattern="*.log"))
Sys.sleep(5)

browseURL("http://en.wikibooks.org/wiki/R_Programming")

# For example, we download "http://en.wikibooks.org/wiki/R_Programming/Text_Processing" on our Desktop
download.file(url="http://en.wikibooks.org/wiki/R_Programming/Text_Processing", destfile= "~/Desktop/test_processing.html")
# You can also read it into R using readLines()
text <- readLines("http://en.wikibooks.org/wiki/R_Programming/Text_Processing")

Performances. (see also microbenchmark package adv-r Performance)

system.time(x<-rnorm(10^6))
   # user  system elapsed
   # 0.11    0.00    0.11

debut <- proc.time()
x <- rnorm(10^6)
proc.time()-debut   
   # user  system elapsed
   # 0.11    0.00    0.10

R References

Stats with R

Data Mining / Statistics