R commands

See also why use R and the RSS feed of posts labelled R.

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R mailing list: Use < - data-blogger-escaped-assignment="" data-blogger-escaped-comment----="" data-blogger-escaped-for="" data-blogger-escaped-functions="">

Set operations

x = letters[1:3]
y = letters[3:5]

union(x, y)
## [1] "a" "b" "c" "d" "e"
intersect(x, y)
## [1] "c"
setdiff(x, y)
## [1] "a" "b"
setdiff(y, x)
## [1] "d" "e"
setequal(x, y)
## [1] FALSE

Information about your R system

sessionInfo()

installed.packages()

Handling files

getwd()
list.files(tempdir()) 
dir.create("blabla")
read.csv("data.csv")

Lists

Given a list structure x, unlist simplifies it to produce a vector which contains all the atomic components which occur in x.

l1 <- a="a" b="2," c="pi+2i)" font="" list="" nbsp="">

unlist(l1) # a character vector

x<- 1="" br="">
x<-1

S3 methods

x<-1



List all available methods for a class:


methods(class="lm")

 One liners

Remove all objects in the workspace except one :


rm(list=ls()[!ls()=="object_to_keep"])

knitr

Those 2 commands are different.
Sets the options for chunk, within a knitr chunk inside the .Rmd document


opts_chunk$set(fig.width=10)

 Sets the options for knitr outside the .Rmd document


opts_knit$set()

dplyr

pipes

cars %>%
  group_by(speed) %>%
  print %>%
  summarise(numberofcars = n(),
            min = min(dist),
            mean = mean(dist),
            max = max(dist))

group_by() creates a tbl_df objects which is a wrapper around a data.frame to enable some functionalities. Note that print returns its output on a tbl_df object. So print() can be used inside the pipe without stopping the workflow.

 plyr (I replaced it with dplyr)

progress bar


l_ply(1:100000, identity, .progress = "win")

Rename items in a dataframe with revalue


sawnwood$item <- br="" item="" revalue="" sawnwood="">    c("Sawnwood (C)" = "Sawnwood Coniferous",
   "Sawnwood (NC)" = "Sawnwood Non Coniferous"))

Rename column names by their names





rename(mtcars, c("disp" = "displacement"))

Plotting with ggplot2

• geom_bar
• geom_tile + a gradient produce heat maps

JabRef to manage a bibliography

Jabref is a free software than can save a bibliography in bibtex format. This format can be used to import citation in windows or latex based text editing system such as Lyx.

Link to PDF or other files

Jabref can automatically create links for files for which you have an entry, if they are located under the main file directory. To change the main file directory: 

Options -> Preferences -> External programs -> Main file directory

But the main file directory can also be specified for each bibtex database under:

File -> Database properties -> General file directory and PDF directory

Creating PDF reports with R on Ubuntu

Texi2pdf

Texi2pdf is a function from the tools package that Compiles LaTeX Files into PDFs.

Using the R command:

> texi2pdf("docs/rapports/draft/template2.tex")

Prompted the error:

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  :
  Running 'texi2dvi' on 'docs/rapports/draft/template2.tex' failed.
Messages:
sh: 1: /usr/bin/texi2dvi: not found

Installing texlive and texinfo fixed this error.

sudo apt-get install texinfo

sudo apt-get install texlive

For info the source of the texi2dvi bash script was mentioned by this blogger.

Accents

There was an issue with accents not rendered.
Loading this package fixes it:

 \usepackage[utf8]{inputenc}

devtools

 opts_knit$get() showed me options that don't exist any-more in the current version of the knitr package. I wanted to install the latest version of knitr.
I needed the package devtools.
But I couldn't install devtools because of this message

Cannot find curl-config

As explained in this mail, installing the package  "libcurl4-gnutls-dev" fixes this. I could then install the package devtools and load it.

To install the latest version of knitr:

library(devtools)
install_github(repo = "knitr", username = "yihui")

xtable

The xtable galery explains how to do longtable and tables in landscape format.It also demonstrates how to rotate column names and how to print a table of linear model coefficients.