Search

Riinu's scripting diary

If it ain't broke, you're outdated

Add abcd labels on ggplot facets

Rplot

How long did my R script run?

This to the beginning:

strt<-Sys.time()

And this to the end:

print(Sys.time()-strt)

Example output:

> print(Sys.time()-strt)
Time difference of 16.39691 secs

 

Adding space between rows in LaTex tables

By default, LaTex tables are very tight:

\usepackage{booktabs}

\begin{table}[]
\centering
\caption{My caption}
\label{my-label}
\begin{tabular}{@{}lll@{}}
\toprule
Rows  & Column 1 & Column 2 \\ \midrule
Row 1 & 1234     & 2345     \\
Row 2 & 3456     & 4567     \\
Row 3 & 5678     & 6789     \\
Row 4 & 7890     & 8901     \\
Row 5 & 9012     & 10000    \\ \bottomrule
\end{tabular}
\end{table}


Screen Shot 2016-04-11 at 11.28.54

Adding this to the document preamble will add space between the rows:

\renewcommand{\arraystretch}{1.7}

Screen Shot 2016-04-11 at 11.24.26

And this command can be used to add space between rows manually:

\vspace{1cm}

Screen Shot 2016-04-11 at 11.25.38

My minimal LaTex preamble

My minimal example:

\documentclass[a4paper]{article}

%%% FIGURES AND TABLES %%%%
\usepackage{graphicx} %gives the \includegraphics[width=0.5\textwidth]{my_image}



%%% PAGE AND TEXT SET-UP %%%%
\usepackage{fullpage} %gets rids of the wide default borders
\renewcommand{\baselinestretch}{1.5} %space between lines


\begin{document}

Hello hello hello


\end{document}



And then one that is not so minimal, but still pretty basic and useful:

 

\documentclass[a4paper]{article}

%%% FIGURES AND TABLES %%%%
\usepackage{graphicx} %gives the \includegraphics[width=0.5\textwidth]{my_image}
\usepackage{booktabs} %for nicer tables
\usepackage{tabu} %advanced control over tables

\renewcommand{\thetable}{S\arabic{table}} %if this is supplement (this numbers figures as S1, S2...), comment out if main
\renewcommand{\thefigure}{S\arabic{figure}} %if this is supplement, replace S with A if Appendix



%%% SPECIAL CHARACTERS %%%%
\usepackage{amsmath} % amsmath provides extra maths symbols
\newcommand{\degree}{\ensuremath{^\circ}} %for some reason I can't find a degree symbol from other packages or the packages I do find it from clash with some others
\usepackage{times} %these packages will make texttildelow look normal
\usepackage{textcomp}

%%% REFERENCES $$$
\usepackage{natbib} %references as citet (textual) or citep (parenthetical)

%%% PAGE AND TEXT SET-UP %%%%
\usepackage{fullpage} %gets rids of the wide default borders
\usepackage{caption} 
\captionsetup[table]{skip=10pt} %this adds space between the table caption and the table itself
\renewcommand{\baselinestretch}{1.5} %space between lines




\begin{document}

Hello hello hello



\bibliographystyle{apalike}
\bibliography{mybibfile.bib}

\end{document}

(Syntax highlighting with http://markup.su/highlighter/)

How to “increase” array resolution in R (replicate each element both column-wise and row-wise)

One picture says more than a thousand words. You have what is one the left, and you want what is on the right.

resolution_cut

my_matrix = matrix(c(1, 2, 3, 4, 5, 6, 7, 8, 9), nrow=3)
 
#matrix is a 2D array, this next row creates a third dimension,
#duplicating the data
my_array = array(my_matrix, dim = c(3,3,2))

There are a few different ways to do this, but by far the cleanest and quickest way is to just select the rows and columns multiple times, by replicating row and column numbers (instead of actually replicating each element):

#2D:
increased_matrix = my_matrix[rep(1:nrow(my_matrix), each=3), rep(1:ncol(my_matrix, each=3)]
 
#3D (same really, just one extra comma for the third dimension):
increased_array = my_array[rep(1:nrow(my_array), each=3), rep(1:ncol(my_array, each=3), ]

Note that by default, in rep(something, n) the n is times so equivalent to rep(something, times=n), but in this case we need to use each instead of times.

 

Cut a time period from netCDF with nco

ncks -d time,start_time,end_time in.nc out.nc

start_time and end_time are integers.

Add -F, if you want to use Fortran indexing (to start from 1).

No space between dimension name and start-end points!

Converting R Markdown to Latex

Install Pandoc: http://pandoc.org/

library(knitr)
 
knit('report.Rmd') #This creates 'report.md'

 

Open the Terminal, Command Prompt (search for cmd) or Windows Powershell, go to the folder and do:

pandoc -s report.md -o report.tex

And that’s it!

(Read this, if you want vector images.)

Reordering factor levels in R and what could go wrong

I’ve recently started using ggplot2 in addition to lattice (see this post that I made a while ago, explaining how I got into using lattice in the first place). Hint: when using ggplot2, you’ll need to use of the reshape2 package (also written by the amazing Hadley Wickham) to get your data into a form that ggplot2 works best with. Another thing that you’ll want to think about when using ggplo2 is factor levels. This post will show how to (and also how not to) rearrange factor levels in R.

Let’s create a quick barplot with strings as x labels.

library(ggplot2)
 
#create dummy data
a = paste('my', 1:11)
b = 1:11
df = data.frame(a, b)
df
qplot(a, b, data=df, geom='bar', stat='identity') + 
  theme(axis.text=element_text(size=16, angle=45))

 

barplot1

As df$a is an array of strings, R sets the factor levels alphabetically: my 1, my 10, my 11, my 2…which is not what we want, so let’s rearrange factor levels:

df$a = factor(df$a, levels = paste('my', 1:11))
df$a
qplot(a, b, data=df, geom='bar', stat='identity') + 
  theme(axis.text=element_text(size=16, angle=45))

 

barplot2

And finally, the wrong way to rearrange factor levels would be by using the levels() function:

df = data.frame(a, b)
levels(df$a) = paste('my', 1:11)
qplot(a, b, data=df, geom='bar', stat='identity') + 
  theme(axis.text=element_text(size=16, angle=45))

 

barplot3

So be careful – if your data is not as obvious as this example and you are a bit new to factors and levels, you might end up plotting wrong results (like on the last example, “my 2” and “my 3” were plotted with the values 10 and 11).

Latex tables: column widths and alignments

Firstly, start off your table in http://www.tablesgenerator.com/.

Tables Generator will do a lot for you. Its most useful features are importing from .csv and merging cells. The Booktabs table style (alternative to default table style from the menu) looks a bit nicer and is “publication quality”. Note that publication quality tables should not contain vertical lines.

Screen shoti of Tables Generator
Screen shot of Tables Generator
Code#1

Code #1 is the code from Tables Generator with the addition of caption, label and Latex document begin-end (so it’s compilable). Continuing from that table, let’s centre the contents of columns 1-3 and the whole table in your document, by adding \centering and changing the table specs from l’s to c’s: Code #2.

Code#2

Finally, if your cell contents are long and need wrapping:

table 3

 Note that if your table is too wide for your document margins, then LaTex issues a warning, not an error. So you need check for warnings like “Overfull \hbox (9.75735pt too wide) in paragraph at lines 55–63” in your compilation log. A quick solution to wide cells is like this (Code#4):

Code#4
Code#4

But this solution does not include decent central alignment. Using m (so m{2cm} instead of p{2cm}) would do the vertical centering (e.g. look how the first row is alligned), but still not horizontal. So following this StackOverflow post, I started defining column types and widths using the array package. See Code#5.

Code#5
Code#5

Next time I might write a post on how to add extra space between lines.

Powered by WordPress.com.

Up ↑