R Source Code Blocks in Org Mode

Setup and configuration

Adapted from org-mode official site.

Install R with binary or source code Comprehensive R Archive Network for Arch Linux, following documents here.

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sudo pacman -S r
# and rstudio IDE
pacaur -y rstudio-desktop-bin
Install ESS (Emacs Speak Statistics) Mode

Follow instruction here.

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(add-to-list 'load-path "~/.emacs.d/ESS/lisp")
(require 'ess-site)
Finally, you’ll need to ensure that org-babel-load-languages includes an entry for R.

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(org-babel-do-load-languages
'org-babel-load-languages
'((R . t)))
Org Mode supports graphical output for LaTeX documents using the PGF and TikZ graphics system for TeX. In order to use this facility your R installation will need the tikzDevice package. One way to ensure that this device is loaded is to put the following lines in .Rprofile:

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old <- getOption("defaultPackages")
options(defaultPackages = c(old, "tikzDevice"))

Use ESS to step through evaluation line-by-line

Use C-c C-c to execute the block

Use C-c ' to visit the edit buffer for your code block

Use ess-eval-line-and-step to evaluate each line in turn

Header arguments for output

does not produce a file -as you see it does here?

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#+begin_src R :file 1.png :results value graphics
library(lattice)
xyplot(1:10 ~ 1:10)
#+end_src
does produce a file, by printing object

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#+begin_src R :file 2.png :results value graphics
library(lattice)
print(xyplot(1:10 ~ 1:10))
#+end_src
does produce a file, by using :results output

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#+begin_src R :file 3.png :results output graphics
library(lattice)
xyplot(1:10 ~ 1:10)
#+end_src
does produce a file, by evaluating in :session

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#+begin_src R :file 4.png :session :results graphics
library(lattice)
xyplot(1:10 ~ 1:10)
#+end_src

share var across blocks

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#+BEGIN_SRC R :session

test <- head(mtcars)

#+END_SRC

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#+RESULTS:

| 21 | 6 | 160 | 110 | 3.9 | 2.62 | 16.46 | 0 | 1 | 4 | 4 |

| 21 | 6 | 160 | 110 | 3.9 | 2.875 | 17.02 | 0 | 1 | 4 | 4 |

| 22.8 | 4 | 108 | 93 | 3.85 | 2.32 | 18.61 | 1 | 1 | 4 | 1 |

| 21.4 | 6 | 258 | 110 | 3.08 | 3.215 | 19.44 | 1 | 0 | 3 | 1 |

| 18.7 | 8 | 360 | 175 | 3.15 | 3.44 | 17.02 | 0 | 0 | 3 | 2 |

| 18.1 | 6 | 225 | 105 | 2.76 | 3.46 | 20.22 | 1 | 0 | 3 | 1 |

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#+BEGIN_SRC R :session :file 4.png :results graphics

test

plot(pressure)

#+END_SRC

Org Mode Output

from R with Ascii package

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> library(ascii)

> options(asciiType = "org")

> counts <- c(18, 17, 15, 20, 10, 20, 25, 13, 12)

> outcome <- gl(3, 1, 9)

> treatment <- gl(3, 3)

> d.AD <- data.frame(treatment, outcome, counts)

> glm.D93 <- glm(counts ~ outcome + treatment, family = poisson())

> ascii(glm.D93)

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|-------------+----------+------------+---------+----------------------|

| (Intercept) | 3.04 | 0.17 | 17.81 | 0.00 |

| outcome2 | -0.45 | 0.20 | -2.25 | 0.02 |

| outcome3 | -0.29 | 0.19 | -1.52 | 0.13 |

| treatment2 | 0.00 | 0.20 | 0.00 | 1.00 |

| treatment3 | 0.00 | 0.20 | 0.00 | 1.00 |

from org-mode R block

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#+BEGIN_SRC R :results output org

library(ascii)

a <- runif(100)

c <- "Quantiles of 100 random numbers"

b <- ascii(quantile(a),header=T,include.colnames=T,caption=c)

print(b,type="org")

rm(a,b,c)

#+END_SRC

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#+CAPTION: Quantiles of 100 random numbers

| 0% | 25% | 50% | 75% | 100% |

|------+------+------+------+------|

| 0.01 | 0.28 | 0.56 | 0.76 | 1.00 |

Warning messages:

1: In rep(rownames, length = nrow(x)) :

'x' is NULL so the result will be NULL

2: In rep(colnames, length = ncol(x)) :

'x' is NULL so the result will be NULL

latex code from R

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#+begin_src R :results output latex

library(xtable)

x <- rnorm(100)

y <- x + rnorm(100)

xtable(summary(lm(y ~ x)))

#+end_src

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#+RESULTS:

#+BEGIN_EXPORT latex

% latex table generated in R 3.4.0 by xtable 1.8-2 package

% Thu May 25 16:07:05 2017

\begin{table}[ht]

\centering

\begin{tabular}{rrrrr}

\hline

& Estimate & Std. Error & t value & Pr($>$$|$t$|$) \\

\hline

(Intercept) & -0.0308 & 0.1013 & -0.30 & 0.7617 \\

x & 0.9268 & 0.0930 & 9.96 & 0.0000 \\

\hline

\end{tabular}

\end{table}

#+END_EXPORT

Blog

Setup and configuration

Use ESS to step through evaluation line-by-line

Header arguments for output

share var across blocks

Org Mode Output

from R with Ascii package

from org-mode R block

latex code from R

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