# Removing Uncited References in a Tex File (with R)

Last week, with @3wen, we were working a the revised version of our work on smoothing densities of spatial processes (with edge correction). Usually, once you have revised the paper, some references were added, others were droped. But you need to spend some time, to check that all references are actually mentioned in the paper. For instance, consider the following compiled tex file :

# Generating your own normal distribution table

It might sounds incredibly old fashion, but for my the exam for the ACT2121 probability course (to prepare for the exam P of the Society of Actuaries), I will provide a standard normal distribution table. The problem is that it is never the one we’re looking for (sometimes it is the survival function, sometimes it is the cumulative distribution function, sometimes we consider only positive values, etc). Here is the one that will be given for the exam, this Friday.

Now, here is the code to generate it.

I did use the following code to generate the table (in a latex format),

> u=seq(0,3.09,by=0.01)
> p=pnorm(u)
> m=matrix(p,ncol=10,byrow=TRUE

We have here the table that we wish to have in our table,

> options(digits=4)
> m
[,1]   [,2]   [,3]   [,4]   [,5]   [,6]   [,7]   [,8]   [,9]  [,10]
[1,] 0.5000 0.5040 0.5080 0.5120 0.5160 0.5199 0.5239 0.5279 0.5319 0.5359
[2,] 0.5398 0.5438 0.5478 0.5517 0.5557 0.5596 0.5636 0.5675 0.5714 0.5753
[3,] 0.5793 0.5832 0.5871 0.5910 0.5948 0.5987 0.6026 0.6064 0.6103 0.6141
[4,] 0.6179 0.6217 0.6255 0.6293 0.6331 0.6368 0.6406 0.6443 0.6480 0.6517
[5,] 0.6554 0.6591 0.6628 0.6664 0.6700 0.6736 0.6772 0.6808 0.6844 0.6879
[6,] 0.6915 0.6950 0.6985 0.7019 0.7054 0.7088 0.7123 0.7157 0.7190 0.7224
[7,] 0.7257 0.7291 0.7324 0.7357 0.7389 0.7422 0.7454 0.7486 0.7517 0.7549
[8,] 0.7580 0.7611 0.7642 0.7673 0.7704 0.7734 0.7764 0.7794 0.7823 0.7852
[9,] 0.7881 0.7910 0.7939 0.7967 0.7995 0.8023 0.8051 0.8078 0.8106 0.8133
[10,] 0.8159 0.8186 0.8212 0.8238 0.8264 0.8289 0.8315 0.8340 0.8365 0.8389
[11,] 0.8413 0.8438 0.8461 0.8485 0.8508 0.8531 0.8554 0.8577 0.8599 0.8621
[12,] 0.8643 0.8665 0.8686 0.8708 0.8729 0.8749 0.8770 0.8790 0.8810 0.8830
[13,] 0.8849 0.8869 0.8888 0.8907 0.8925 0.8944 0.8962 0.8980 0.8997 0.9015
[14,] 0.9032 0.9049 0.9066 0.9082 0.9099 0.9115 0.9131 0.9147 0.9162 0.9177
[15,] 0.9192 0.9207 0.9222 0.9236 0.9251 0.9265 0.9279 0.9292 0.9306 0.9319
[16,] 0.9332 0.9345 0.9357 0.9370 0.9382 0.9394 0.9406 0.9418 0.9429 0.9441
[17,] 0.9452 0.9463 0.9474 0.9484 0.9495 0.9505 0.9515 0.9525 0.9535 0.9545
[18,] 0.9554 0.9564 0.9573 0.9582 0.9591 0.9599 0.9608 0.9616 0.9625 0.9633
[19,] 0.9641 0.9649 0.9656 0.9664 0.9671 0.9678 0.9686 0.9693 0.9699 0.9706
[20,] 0.9713 0.9719 0.9726 0.9732 0.9738 0.9744 0.9750 0.9756 0.9761 0.9767
[21,] 0.9772 0.9778 0.9783 0.9788 0.9793 0.9798 0.9803 0.9808 0.9812 0.9817
[22,] 0.9821 0.9826 0.9830 0.9834 0.9838 0.9842 0.9846 0.9850 0.9854 0.9857
[23,] 0.9861 0.9864 0.9868 0.9871 0.9875 0.9878 0.9881 0.9884 0.9887 0.9890
[24,] 0.9893 0.9896 0.9898 0.9901 0.9904 0.9906 0.9909 0.9911 0.9913 0.9916
[25,] 0.9918 0.9920 0.9922 0.9925 0.9927 0.9929 0.9931 0.9932 0.9934 0.9936
[26,] 0.9938 0.9940 0.9941 0.9943 0.9945 0.9946 0.9948 0.9949 0.9951 0.9952
[27,] 0.9953 0.9955 0.9956 0.9957 0.9959 0.9960 0.9961 0.9962 0.9963 0.9964
[28,] 0.9965 0.9966 0.9967 0.9968 0.9969 0.9970 0.9971 0.9972 0.9973 0.9974
[29,] 0.9974 0.9975 0.9976 0.9977 0.9977 0.9978 0.9979 0.9979 0.9980 0.9981
[30,] 0.9981 0.9982 0.9982 0.9983 0.9984 0.9984 0.9985 0.9985 0.9986 0.9986
[31,] 0.9987 0.9987 0.9987 0.9988 0.9988 0.9989 0.9989 0.9989 0.9990 0.9990
> rownames(m)=seq(0,3,b=.1)
> colnames(m)=seq(0,.09,by=.01)

To put it in a nice latex format, we can use

> library(xtable)
> newm=xtable(m,digits=4)
> print.xtable(newm, type="latex", file="nor1.tex")

We now have a simple tex file containing a table.

\begin{table}[ht]
\centering
\begin{tabular}{rrrrrrrrrrr}
\hline
& 0 & 0.001 & 0.002 & 0.003 & 0.004 & 0.005 & 0.006 & 0.007 & 0.008 & 0.009 \\
\hline
0 & 0.5000 & 0.5040 & 0.5080 & 0.5120 & 0.5160 & 0.5199 & 0.5239 & 0.5279 & 0.5319 & 0.5359 \\
0.1 & 0.5398 & 0.5438 & 0.5478 & 0.5517 & 0.5557 & 0.5596 & 0.5636 & 0.5675 & 0.5714 & 0.5753 \\
0.2 & 0.5793 & 0.5832 & 0.5871 & 0.5910 & 0.5948 & 0.5987 & 0.6026 & 0.6064 & 0.6103 & 0.6141 \\
0.3 & 0.6179 & 0.6217 & 0.6255 & 0.6293 & 0.6331 & 0.6368 & 0.6406 & 0.6443 & 0.6480 & 0.6517 \\
0.4 & 0.6554 & 0.6591 & 0.6628 & 0.6664 & 0.6700 & 0.6736 & 0.6772 & 0.6808 & 0.6844 & 0.6879 \\
0.5 & 0.6915 & 0.6950 & 0.6985 & 0.7019 & 0.7054 & 0.7088 & 0.7123 & 0.7157 & 0.7190 & 0.7224 \\
0.6 & 0.7257 & 0.7291 & 0.7324 & 0.7357 & 0.7389 & 0.7422 & 0.7454 & 0.7486 & 0.7517 & 0.7549 \\
0.7 & 0.7580 & 0.7611 & 0.7642 & 0.7673 & 0.7704 & 0.7734 & 0.7764 & 0.7794 & 0.7823 & 0.7852 \\
0.8 & 0.7881 & 0.7910 & 0.7939 & 0.7967 & 0.7995 & 0.8023 & 0.8051 & 0.8078 & 0.8106 & 0.8133 \\
0.9 & 0.8159 & 0.8186 & 0.8212 & 0.8238 & 0.8264 & 0.8289 & 0.8315 & 0.8340 & 0.8365 & 0.8389 \\
1 & 0.8413 & 0.8438 & 0.8461 & 0.8485 & 0.8508 & 0.8531 & 0.8554 & 0.8577 & 0.8599 & 0.8621 \\
1.1 & 0.8643 & 0.8665 & 0.8686 & 0.8708 & 0.8729 & 0.8749 & 0.8770 & 0.8790 & 0.8810 & 0.8830 \\
1.2 & 0.8849 & 0.8869 & 0.8888 & 0.8907 & 0.8925 & 0.8944 & 0.8962 & 0.8980 & 0.8997 & 0.9015 \\
1.3 & 0.9032 & 0.9049 & 0.9066 & 0.9082 & 0.9099 & 0.9115 & 0.9131 & 0.9147 & 0.9162 & 0.9177 \\
1.4 & 0.9192 & 0.9207 & 0.9222 & 0.9236 & 0.9251 & 0.9265 & 0.9279 & 0.9292 & 0.9306 & 0.9319 \\
1.5 & 0.9332 & 0.9345 & 0.9357 & 0.9370 & 0.9382 & 0.9394 & 0.9406 & 0.9418 & 0.9429 & 0.9441 \\
1.6 & 0.9452 & 0.9463 & 0.9474 & 0.9484 & 0.9495 & 0.9505 & 0.9515 & 0.9525 & 0.9535 & 0.9545 \\
1.7 & 0.9554 & 0.9564 & 0.9573 & 0.9582 & 0.9591 & 0.9599 & 0.9608 & 0.9616 & 0.9625 & 0.9633 \\
1.8 & 0.9641 & 0.9649 & 0.9656 & 0.9664 & 0.9671 & 0.9678 & 0.9686 & 0.9693 & 0.9699 & 0.9706 \\
1.9 & 0.9713 & 0.9719 & 0.9726 & 0.9732 & 0.9738 & 0.9744 & 0.9750 & 0.9756 & 0.9761 & 0.9767 \\
2 & 0.9772 & 0.9778 & 0.9783 & 0.9788 & 0.9793 & 0.9798 & 0.9803 & 0.9808 & 0.9812 & 0.9817 \\
2.1 & 0.9821 & 0.9826 & 0.9830 & 0.9834 & 0.9838 & 0.9842 & 0.9846 & 0.9850 & 0.9854 & 0.9857 \\
2.2 & 0.9861 & 0.9864 & 0.9868 & 0.9871 & 0.9875 & 0.9878 & 0.9881 & 0.9884 & 0.9887 & 0.9890 \\
2.3 & 0.9893 & 0.9896 & 0.9898 & 0.9901 & 0.9904 & 0.9906 & 0.9909 & 0.9911 & 0.9913 & 0.9916 \\
2.4 & 0.9918 & 0.9920 & 0.9922 & 0.9925 & 0.9927 & 0.9929 & 0.9931 & 0.9932 & 0.9934 & 0.9936 \\
2.5 & 0.9938 & 0.9940 & 0.9941 & 0.9943 & 0.9945 & 0.9946 & 0.9948 & 0.9949 & 0.9951 & 0.9952 \\
2.6 & 0.9953 & 0.9955 & 0.9956 & 0.9957 & 0.9959 & 0.9960 & 0.9961 & 0.9962 & 0.9963 & 0.9964 \\
2.7 & 0.9965 & 0.9966 & 0.9967 & 0.9968 & 0.9969 & 0.9970 & 0.9971 & 0.9972 & 0.9973 & 0.9974 \\
2.8 & 0.9974 & 0.9975 & 0.9976 & 0.9977 & 0.9977 & 0.9978 & 0.9979 & 0.9979 & 0.9980 & 0.9981 \\
2.9 & 0.9981 & 0.9982 & 0.9982 & 0.9983 & 0.9984 & 0.9984 & 0.9985 & 0.9985 & 0.9986 & 0.9986 \\
3 & 0.9987 & 0.9987 & 0.9987 & 0.9988 & 0.9988 & 0.9989 & 0.9989 & 0.9989 & 0.9990 & 0.9990 \\
\hline
\end{tabular}
\end{table}

and the following code to get a graph, illustrating was was actually computed, in the table (see a previous post for more details)

> library("tikzDevice")
> options(tikzMetricPackages = c("\\usepackage[utf8]{inputenc}",
+ "\\usepackage[T1]{fontenc}", "\\usetikzlibrary{calc}", "\\usepackage{amssymb}"))
+ tikz("normal-dist.tex", width = 8, height = 4,
+ standAlone = TRUE,
+ packages = c("\\usepackage{tikz}",
+ "\\usepackage[active,tightpage,psfixbb]{preview}",
+ "\\PreviewEnvironment{pgfpicture}",
+ "\\setlength\\PreviewBorder{0pt}",
+ "\\usepackage{amssymb}"))
> u=seq(-3,3,by=.01)
> plot(u,dnorm(u),type="l",axes=FALSE,xlab="",ylab="",col="white")
> axis(1)
> I=which((u<=1))
> polygon(c(u[I],rev(u[I])),c(dnorm(u)[I],rep(0,length(I))),col="red",border=NA)
> lines(u,dnorm(u),lwd=2,col="blue")
> text(-1.5, dnorm(-1.5)+.17, "$\\textcolor{blue}{X\\sim\\mathcal{N}(0,1)}$", cex = 1.5)
> text(1.75, dnorm(1.75)+.25,
+ "$\\textcolor{red}{\\mathbb{P}(X\\leq x)=\\displaystyle{ + \\int_{-\\infty}^x \\varphi(t)dt}}$", cex = 1.5)
> dev.off()

Now we have the graph in another tex file. It is possible to embed the code in a tex file, or to compile the tex file to get a pdf file. I did generate the pdf file.

Here is the tex file I finally get. It is now extremely simple to get your own normal distribution table. Now, I guess it could be possible to use sweave, or knitr. Once I’ll get a copy of Yihui’s book, I’ll try to use it to generate distribution table for my courses !

# LaTeX in R graphs

A nice post was recently published on the rsnippets blog, about the tikzDevice R package. This package is – indeed – awesome. Even if it has been removed from the CRAN website. Of course, it can be download from the archive folder, on http://cran.r-project.org/…, but also (for a more recent version)  on http://download.r-forge.r-project.org/…. But first, it is necessary to install the following package.

> install.packages("filehash")

Then, we can load the library

> library("tikzDevice")

If we want to use nice LaTeX formulas, it might be necessary to upload some (LaTeX) libraries and to specify the encoding format

> "options(tikzMetricPackages = c("\\usepackage[utf8]{inputenc}",
+ "\\usepackage[T1]{fontenc}", "\\usetikzlibrary{calc}", "\\usepackage{amssymb}"))

(this is detailed, e.g. in  http://yihui.name/…), then, we write a code to plot a graph. The idea is to produce a tex file which contains the graph, or more precisely which will produce a pdf graph when we compile it. We start with

> tikz("normal-dist.tex", width = 8, height = 4,
+ standAlone = TRUE,
+ packages = c("\\usepackage{tikz}",
+ "\\usepackage[active,tightpage,psfixbb]{preview}",
+ "\\PreviewEnvironment{pgfpicture}",
+ "\\setlength\\PreviewBorder{0pt}",
+ "\\usepackage{amssymb}"))

We will produce a 8×4 graph. The graph is the following,

> u=seq(-3,3,by=.01)
> plot(u,dnorm(u),type="l",axes=FALSE,xlab="",ylab="",col="white")
> axis(1)
> I=which((u>=0)&(u<=1))
> polygon(c(u[I],rev(u[I])),c(dnorm(u)[I],rep(0,length(I))),col="red",border=NA)
> lines(u,dnorm(u),lwd=2,col="blue")

We can add text (or TeX based text)

> text(-1.5, dnorm(-1.5)+.17, "$\\textcolor{blue}{X\\sim\\mathcal{N}(0,1)}$", cex = 1.5)
> text(1.75, dnorm(1.75)+.25,
+ "$\\textcolor{red}{\\mathbb{P}(X\\in[0,1])=\\displaystyle{\\int_0^1 \\varphi(x)dx}}$", cex = 1.5)

And we end the file with a standard

> dev.off()

This will produce a .tex file. If we compile this file, we can generate a pdf file, that can be inserted in lecture notes, slides or articles,

Nice, isn’t it ?

# Animation, from R to LaTeX

Just a short post, to share some codes used to generate animated graphs, with R. Assume that we would like to illustrate the law of large number, and the convergence of the average value from binomial sample. We can generate samples $X_{i,j}\sim\mathcal{B}(1/2)$ using

> n=200
> k=1000
> set.seed(1)
> X=matrix(sample(0:1,size=n*k,replace=TRUE),n,k)

Each row $\boldsymbol{X}_{i}=(X_{i,1},\cdots,X_{i,n},\cdots)$ will be a trajectory of heads and tails. For each trajectory, define the mean $\bar{X}_{i,n}=n^{-1}(X_{i,1}+\cdots+X_{i,n})$, which will denote the mean of the first $n$ values. Such a matrix can be computed using

> cummean=function(M){
+ U=matrix(M[,1],nrow(M),1)
+ 	for(i in 2:ncol(M)){
+ 	U=cbind(U,(U[,i-1]*(i-1)+M[,i])/i)}
+ return(U)
+ }

Define then

> Xbar=cummean(X)

Now, to generate an animated gif, the way I usually do it is to generate graphs (png graphs) using a loop,

> S=trunc(10^seq(1,3,by=.05))
> for(j in 1:length(S)){
+ 	s=S[j]
+ 	Xhist=hist(Xbar[,s],breaks=seq(0,1,by=.05),plot=FALSE)
+ 	nfile=paste("LLN-",100+j,".png",sep="")
+ 	png(nfile,600,350)
+ 	layout(matrix(c(3,0,1,2),2,2,byrow=TRUE), c(3,1), c(1,3), TRUE)
+ 	plot(1:s,Xbar[1,1:s],type="l",col="light blue",ylim=0:1,xlab="",ylab="",axes=FALSE,
+ 		 xlim=c(10,k),log="x")
+ 	axis(1)
+ 	axis(2)
+ 	for(i in 2:(n-1)) lines(1:s,Xbar[i,1:s],col="light blue")
+ 	lines(1:s,Xbar[n,1:s],col="red",lwd=2)
+ 	abline(v=s)
+ 	barplot(Xhist$counts, axes=TRUE,horiz=TRUE,col="light green",xlim=c(0,n/2*1.05)) + dev.off() + } I start at 100 because afterwards, when merging files, it is better to have (really) consecutive numbers, since sometimes, the lexical order is used, i.e. after 1 is 10, then 100, etc. Then I use Terminal commands Here, the delay is in /100 seconds, and I use an infinite loop. The graph is here It is possible to use > library(animation) > ani.options(interval=.15) > saveGIF({ }) But the loop can be used also to generate several graphs, and to produce an animated graph in a pdf document (slides or lecture notes). The idea is to use the same code, but the output is here a pdf graph. > S=trunc(10^seq(1,3,by=.1)) > for(j in 1:length(S)){ + s=S[j] + Xhist=hist(Xbar[,s],breaks=seq(0,1,by=.05),plot=FALSE) + nfile=paste("LLN-",j,".pdf",sep="") + pdf(nfile,10,6) + layout(matrix(c(3,0,1,2),2,2,byrow=TRUE), c(3,1), c(1,3), TRUE) + plot(1:s,Xbar[1,1:s],type="l",col="light blue",ylim=0:1,xlab="",ylab="",axes=FALSE, + xlim=c(10,k),log="x") + axis(1) + axis(2) + for(i in 2:(n-1)) lines(1:s,Xbar[i,1:s],col="light blue") + lines(1:s,Xbar[n,1:s],col="red",lwd=2) + abline(v=s) + barplot(Xhist$counts, axes=TRUE,horiz=TRUE,col="light green",xlim=c(0,n/2*1.05))
+ 	dev.off()
+ }

We can then import them in LaTeX,

\documentclass[a4]{article}
\usepackage{graphicx}
\usepackage{animate}
\begin{document}
\begin{center}
\animategraphics[height=3.1in,palindrome]{1}{/Users/UQAM/LLN-}{1}{21}
\end{center}
\end{document}

This will generate the following pdf file. This animate package is described in several forums, e.g. http://www.geogebra.org/…