If you are using Ubuntu/Linux, you can install
libcurl4-gnutls-dev and problem solved!
In your shell:
sudo apt-get install libcurl4-openssl-dev
sudo apt-get install libssl-dev
sudo apt-get install libcurl4-gnutls-dev
sudo apt-get install libxml2-dev
Archive for the ‘ R ’ Category
Problems installing the devtools package (Ubuntu)
Author: Fabio FajardoNov 25
R online!
Author: Fabio FajardoJul 1
Todo mundo sabe da importância das linguagens de programação no mundo moderno e mais ainda para análise das dados. R é um ambiente computacional e uma linguagem de programação cuja popularidade cresce rapidamente. A linguagem é ótima para o tratamento, análise e visualização gráfica de dados. Hoje é considerado o melhor ambiente computacional para essa finalidade.
Existem milhares de sites que disponibilizam material para aprender a programar no R (https://blog.ufes.br/fabiomolinares/2017/04/26/free-100-online-tutorials-for-r-programming-statistics-and-graphics/). Mas, o acesso online pode facilitar a vida de um iniciante quando tenta usá-lo num equipamento que não o tenha instalado ou ainda está no celular e quer fazer uso rápido do R.
Vou listar algumas alternativas que já usei:
- https://rnotebook.io/ (Roda Jupyter R notebooks online)
- http://www.r-fiddle.org/ (or https://cdn.datacamp.com/dcl-react-prod/example.html)
- https://repl.it/languages/rlang
- https://www.jdoodle.com/execute-r-online
- https://www.tutorialspoint.com/execute_r_online.php
- https://rweb.stat.umn.edu/Rweb/Rweb.general.html
- https://rdrr.io/snippets/
- https://rextester.com/l/r_online_compiler
Free 100 Online tutorials for R programming, Statistics and Graphics
Author: Fabio FajardoApr 26
Here is a list of FREE R tutorials hosted in official website of universities around the world. The tutorials are listed in no particular order, actually based on when I have discovered it. They will be categorised soon. Please kindly suggest me other university-hosted online R tutorials by email to me@pairach.com.
A list of R tutorials, which are not hosted in the webpages of academic institutes can be found here.
- University of Oxford
Modern Applied Statistics with S, 4edn (On-line material)[url]
by W. N. Venables and B. D. Ripley - University of California at Davis
Getting Started with the R Data Analysis Package [url]
by Norm Matloff - Clarkson University
R Tutorial [url]
by Kelly Black - York University
Getting started with R [url] - University of Waterloo
R Tutorial For Windows and Unix Environment [url] - University of California at Los Angles, UCLA
Resources to help you learn and use R [url] - University of California at Riverside
Programming in R [url] - University of Illinois
A Brief Introduction to R [url] - University of Texas at Austin
R Tutorial Videos [url]
by Brandon K. Vaughn - University of California at Berkeley
An Introduction to R (pdf)
by Phil Spector - Chiang Mai University
Econometrics with R (in Thai) [url]
by Pairach Piboonrungroj - University of California at Santa Babara
R Programming Resource Centre [url]
by National Center for Ecological Analysis and Synthesis - University of Carnegie Mellon
A Tutorial: Some Fundamentals of R [url]
by Bruce E. Trumbo - University of Illinois State
R Tutorial [url]
by Dong-Yun Kim - University of MacMaster
Introduction to the R Statistical Computing Environment [url]
by John Fox. - University of Princeton
Introducing R [url]
by Germán Rodríguez - University of Amsterdam
How to draw graphs with R (Graphics) [url]
by Angelos-Miltiadis Krypotos - University of North Texas
Do it yourself – Introduction to R (Intro) [url] - University of Warwick
R programming page [url]
(Biosciences: Molecular Organisation and Assembly in Cells)
by Peter Cock. - University of Illinois at Urbana-Champaign
R tutorial for Applied Econometrics [url]
by Prof. Roger Koenker
- Coastal Carolina University
R tutorials (General) [url]
by William B. King - University of Colorado Denver
R Tutorial (General)[url]
by Stephanie Santorico and Mark Shin - Stanford School of Medicine (Biomedical Informatics)
R Tutorial (VDO on Introduction + Translational Bioinformatics (url) - Harding University
Producing Simple Graphs with R (basic graphic e.g., line, bar, hist, line) (url)
by Frank McCown - University of Kentucky, Department of Statistics
Use Software R to do Survival Analysis and Simulation [pdf]
by Mai Zhou - University of Pittsburgh, Department of Statistics
Time Series Analysis and Its Applications: With R Examples[url]
by R.H. Shumway & D.S. Stoffer - University of Toronto
R Tutorial (for Ecology) [url]
by the Cadotte Lab - Florida State University
Use R for Climate research [url]
by James B. Elsner & Thomas H. Jagger - University of Washington
Introduction to R [url]
by Jinyoung Kim - Lancaster University (UK)
R tutorial [url]
by Joe Whittaker - University of Georgia Athens
A short R tutorial [pdf]
by Steven M. Holland - University of Twente
R tutorials [url]
(more than 1o tutorials about R in pdf + data & code)
by D G Rossiter - Vrijie University Amsterdam, Netherlands
Handleiding R (in Dutch) [pdf]
by A.W. van der Vaart - University of Wisconsin-Madison
Introduction to R [url]
by Karl W Broman - City University of New York
simpleR Using R for Introductory Statistics [url]
by John Verzani - Pomona College
An R tutorial [pdf]
by Jo Hardin - University of Alaska Fairbanks
Using R [url]
by the Biology & Wildlife Department computer - University of Bath
Practical Regression and Anova using R [pdf]
Julian J. Faraway - University of Goettingen
Time Series Analysis with R – Part I [pdf]
by Walter Zucchini and Oleg Nenadíc
Statistical Analysis with R – a quick start – [pdf]
by Oleg Nenadíc and Walter Zucchini - University of Washington, Department of Economics
Working with Time Series Data in R [pdf]
by Eric Zivot - University of Liège, Faculty of Engineering
Using R for Linear regression [pdf, 9 pages]
by Kristel Van Steen - University of Cambridge
Local tips for R [url] – in both statistics & graphics
by Rudolf Cardinal - Montana State University, Department of Mathematical Sciences
Introduction to Sweave (R+LaTeX) [url]
by Jim Robison-Cox - Stanford University
Social Network Analysis in R [url] including source R files and outputs
by McFarland, Daniel A., Solomon Messing, Michael Nowak and Sean J. Westwood. - Ludwig-Maximilians-University Munich (Germany)
Sweave (R + LaTeX) [url] including manuals and example files
by Friedrich Leisch - Ecole Polytechnique Fédérale de Lausanne
Sweave = R • LaTeX^2 (pdf, slides)
by Nicola Sartori - University of Auckland
Four course on Statistical Computing and Graphics including document, R codes (pdf)
by Ross Ihaka - Nova Southeastern University
Many R tutorials using Tegrity-based video tutorials (url)
by Thomas W. MacFarland - Penn State University
– Introduction to R (get started) [url]
– Welcome to STAT 497C – Topics in R Statistical Language! [url] - Carnegie Mellon University
Open & Free Course on Statistics (with applications in R among other software) [url] - Centre for Mathematical Sciences, Lund University
Exception handling in R [url]
Object-oriented programming with references using S3/UseMethod [url]
by Henrik Bengtsson - University of Edinburgh
Data Mining and Exploration (with examples with R) [url]
by Charles Sutton - University of Washington
Survey analysis in R [url]
by Thomas Lumley - Department of Psychology, University of Pennsylvania
Notes on the use of R for psychology experiments and questionnaires [url]
by Jonathan Baron and Yuelin Li - College of Staten Island, Department of Mathematics
simpleR: Using R for Introductory Statistics [url]
By John Verzani - Vanderbilt University
rApache Manual [url] - University of Aarhus, Department of Computer Science – Daimi, Faculty of Science
RPy — R from Python [url] - University of Auckland
Many documents and links about R [url]
By Paul Murrell - National Institute of Genetics (Japan)
R Graphical Manual [url]
By Osamu Ogasawara and IMS Lab Inc. Japan - Montana State University
R Labs for Vegetation Ecologists [url] - University of Auckland
Introduction to Data Technologies: Basic introduction to a number of computer technologies for working with data (HTML, XML, Databases, SQL, regular expressions, and R) [url]
by Paul Murrell - Department of Statistics and Actuarial Science, SFU
Technical Notes on the R programming language [url]
by Sigal Blay - University of Vienna
Stattconn Project [url]
by Thomas Baier and Erich Neuwirth - Gunma University (Japan)
R による統計処理 [url]
by Shigenobu AOKI - Tsukuba Office, Agriculture, Forestry and Fisheries Research Council Secretariat
R Tips (in Japancese) [url] - University of Western Ontario, Department of Statistical & Actuarial Sciences
Debugging in R [url]
by Duncan Murdoch - University of Sunderland
Programming in R [url]
by Harry Erwin - Smith College, Department of Mathematics and Statistics
Use of R as a toolbox for mathematical statistics exploration [url]
by Nicholas J. Horton, Elizabeth R.Brown and Linjuan Qian - Katholieke Universiteit Leuven
R and Statistics [url]
by Guido Wyseure - Iowa State University
Introduction to R [url]
by Di Cook - Cambridge University
Graph redesign in R [url]
by Stephen J. Murdoch - Trinity College Dublin
R Podcasts [url]
by Andrew Jackson - University of Arizona
Introduction to R [url]
by Caroline R.H. Wiley - Cambridge University
ESS: Emacs Speak Statistics [url]
by Stephen Eglen - Columbia University
Running WinBugs and OpenBugs from R [url]
Andrew Gelman - University of Bremen
vim R plugin for Linux/Unix [url]
Johannes Ranke - Montana State University
R Web: Statistical Analysis on the web. [url]
by Jeff Banfield - University of Florida
R for Categorical data analysis [html]
by Brett D. Presnell - University of Auckland
An S (and R) Programming Workshop in 2003 (including slides, data and codes) [html]
by The Quartet (affiliations at that moment)
(1) Bill Venables (CSIRO, Australia)
(2) Robert Gentleman (Harvard University)
(3) Ross Ihaka (University of Auckland)
(4) Paul Murrell (University of Auckland) - Australian National University , Mathematical Science Institute
Data Analysis and Graphics Using R – An Example-Based Approach [url]
by John Maindonald and John Braun - The Hebrew University
Introduction to Statistical Thinking (With R, Without Calculus) [pdf]
by Benjamin Yakir - Basel Institute for Clinical Epidemiology and Biostatistics
Tutorial: ggplot2 [pdf, 14 p.]
by Ramon Saccilotto, Universitätsspital Basel - UC, Davis: Bioinformatics
Data Analysis and Visualization Course, 2012 (links to many sessions during two days of the course)
by Vince Buffalo, Joe Fass, Jie Peng and Dawei Lin - University of Warwick
R useR! Conference 2011 (links to materials and documents of the tutorials, invited talks and presentations)
by Department of Statistics, University of Warwick - Vanderbilt University
R useR! Conference 2012 (links to materials and documents of short courses, tutorials, invited talks and presentations)
by Department of Statistics, Vanderbilt University - Technische Universität Wien, Vienna, Austria
useR! 2004: The 5th International R useRs Conference (links to materials of the conference)
DSC 1999: The 1st conference for the developers of statistical software and researchers in statistical computing
DSC 2001: The 2nd conference for the developers of statistical software and researchers in statistical computing
DSC 2003: The 3rd conference for the developers of statistical software and researchers in statistical computing
by Department of Statistics and Probability Theory,Technische Universität Wien - The University of Auckland
DSC 2007: The 5th conference for the developers of statistical software and researchers in statistical computing
(Workshops, Program, papers and posters)
by Department of Statistics, The University of Auckland - University of Oxford
APTS Computer-Intensive Statistics 2012 (html) – Lecture note, datasets and codes
by Prof. Brain Ripley - Simon Fraser University
Technical Notes on the R programming language
by Sigal Blay - University of Florida
Introducing Monte Carlo Methods with R (pdf)
by Christian P. Robert George Casella - University of Tennessee
pbdR — Programming with Big Data in R (html)
Remote Data Analysis and Visulization Center - National Center for Ecological Analysis and Synthesis
The Regents of the University of California
– Integrate C Language Functions into R With an R Package
– R: A self-learn tutorial - Ghent University
Teaching materials (slides, codes and datasets) for using lavaan package for Structural Equation Modeling (link)
by Yves Rosseel - Calvin College
Computational Statistics Using R and R Studio – An Introduction for Scientists (pdf)
by Randall Pruim - Department of Mathematical Sciences
Aalborg University, Denmark
Graphical Models with R (pdf)
Soren Hojsgaard - Statistics Department
Carnegie Mellon University
Writing R Functions (pdf)
by Cosma Shalizi - Institute for Environmental Sciences
University Koblenz-Landau
Lecture “Applied Multivariate Statistics” 2011/2012 (url)
by Ralf Schäfer - University of Groningen, The Netherlands
R Tutorial for Applied Statistics (URL)
by Anne Boomsma - University of Florida
Tutorial on Making Simple R Packages (URL) - University of Göttingen – Georg-August-Universität Göttingen
Time Series Analysis with R – Part I (PDF)
by Walter Zucchini, Oleg Nenadi´c - Harvard University
Quick Introduction to Graphics in R Introduction to the R language (pdf)
by Aedin Culhane - University of Pennsylvania
R Study Group (General guide to R) (URL)
Josef Fruehwald
Problems installing the devtools package in Ubuntu
Author: Fabio FajardoJun 7
You want to use the devtools
package. Suposse that you have run the following commands:
> install.packages("devtools", dependencies = TRUE)
...
> library(devtools)
Error in library(devtools) : there is no package
called ‘devtools’
The 'devtools' package was not installed!
Solution:
I installed libcurl4-gnutls-dev and the
problem was solved.
In your shell:
apt-get -y build-dep libcurl4-gnutls-dev
apt-get -y install libcurl4-gnutls-dev
How to update R software in windows?
Author: Fabio FajardoFeb 9
- Install the package using install.packages(“installr”)
- Load package with library(“installr”)
- Use the function updateR() to update!
- It checks for a newer version of R.
- If one exists, the function will download the most updated R version and run its installer.
- Once done, the function will offer to copy (or move) all of the packages from the old R library to the new R library.
- It will then offer to update the moved packages, offer to open the new Rgui, and lastely, it will quit the old R.
A sphere in R using rgl package
Author: Fabio FajardoJun 3
The rgl.spheres function is a fantastic way to plot spheres! Look at!
library("rgl") rgl.spheres(1,1,1,radius=1,color="blue")
It’s possible to read command line parameters from an R script?
Author: Fabio FajardoJun 2
YES! yes, it’s very simple. I will describe the procedure:
1. You should create the file with code R. Command-line parameters are accessible via commandArgs()
.
2. You can use Rscript
on all platforms, including Windows. It will support commandArgs()
, for example: In the terminal
Rscript myscript.R arg1 arg2 arg3
arg1, arg2 and arg3 are arguments into your R script. If your args are strings with spaces in them, enclose within double quotes. There are two add-on packages on CRAN — getopt and optparse — which were both written for command-line parsing.
Tiny example: script.R
options(echo=TRUE) # To see commands in output file
args <- commandArgs(trailingOnly = TRUE)
# trailingOnly=TRUE means that only your
# arguments are returned
print(args)
start_date <- as.Date(args[1]) # First argument
figure_name <- args[2] # Second argument
n <- as.integer(args[3]) # Third argument
rm(args)
# Some computations:
x <- rnorm(n)
postscript(paste(figure_name,".eps",sep=""))
plot(start_date+(1L:n), x,type="l")
dev.off()
summary(x)
To run:
Rscript script.R 02/06/2015 figure 1000
Booktabs package and Sweave
Author: Fabio FajardoMay 30
The booktabs package in latex makes really beautiful tables. This package provide some additional commands to enhance the quality of table in LaTeX, especially if there is math in your table that might run up against the regular \hline
in the tabular environment. I created a table with the following code:
% file: example.Rnw % require xtable \documentclass{article} \usepackage{booktabs} \begin{document} \begin{table}[!h] \centering \caption{This is my table.} \label{tab:table1} <<mytable,echo=F,results=tex>>= mat <- as.data.frame(matrix(runif(25),nrow=5)) colnames(mat) <- c("$\\alpha$","$\\beta$", "$\\gamma$","$\\delta$","$\\frac{\\epsilon}{2}$") rownames(mat) <- c(‘A’,’B’,’C’,’D’,’E’) mat <- xtable::xtable(mat,digits=rep(5,ncol(mat)+1)) print(mat, sanitize.text.function = function(x){x}, floating=FALSE, hline.after=NULL, add.to.row=list(pos=list(-1,0, nrow(mat)), command=c('\\toprule\n', '\\midrule\n','\\bottomrule\n'))) @ \end{table} \end{document}
You can use to compile:
$ R CMD Sweave example.Rnw $ pdflatex example.tex
The definition of \toprule, \midrule and \bottomrule from
booktabs package is:
\def\toprule{\noalign{\ifnum0=`}\fi \@aboverulesep=\abovetopsep \global\@belowrulesep=\belowrulesep \global\@thisruleclass=\@ne \@ifnextchar[{\@BTrule}{\@BTrule[\heavyrulewidth]}}
\def\midrule{\noalign{\ifnum0=`}\fi \@aboverulesep=\aboverulesep \global\@belowrulesep=\belowrulesep \global\@thisruleclass=\@ne \@ifnextchar[{\@BTrule}{\@BTrule[\lightrulewidth]}}
\def\bottomrule{\noalign{\ifnum0=`}\fi \@aboverulesep=\aboverulesep \global\@belowrulesep=\belowbottomsep \global\@thisruleclass=\@ne \@ifnextchar[{\@BTrule}{\@BTrule[\heavyrulewidth]}}
Adding regression line equation and R Square on graph
Author: Fabio FajardoMay 30
set.seed(34567)
x <- runif(10); y <- 4*x+rnorm(10) fit <- lm(y~x) r2 <- summary(fit)$r.squared # plot data and regression line plot(x, y) abline(fit, col=2) # add text to plot with legend()
legend('topleft', title='option 1', legend=sprintf("y = %3.2fx %+3.2f, R\UB2 = %3.2f",
coef(fit)[2]
,
coef(fit)[1]
, r2), bty='n', cex=0.7) # if you prefer a space between plus/minus and b b<-
coef(fit)[1]
if(b<0) {b_sign='-'; b=-b} else {b_sign= '+'} legend('topright', title='option 2', legend=sprintf("y = %3.2f x %s %3.2f, R\UB2 = %3.2f", coef(fit)[2],b_sign,b,r2), bty='n',cex=0.7)
Important: R\UB2B2 defined R square symbol. B2 is the hex code for UTF-8 character ² and \U is a control sequence that will call that character.
Decimal places in R plot legend?
Author: Fabio FajardoMay 30
For specifying the number of digits, tipically we use the command round, for example:
round(pi, digits=2)
[1] 3.14
However, we can also use sprintf
command to deal with both the number of digits and the + or – in your equation, for example:
sprinf(“%3.2f”,pi)
[1] “3.14”
Note that,
forces the + or – sign in a equation.3.2f
controls the number of digits and the symbol %