Chapterbib package

Here is useful information on the "chapterbib" package.

The trick to get it working is to run bibtex on each chapter and then run latex on the main document.

What makes Android revolutionary

Very good post.

Easy_install utility for Python libraries

The "easy_install" tool is very convenient to install Python libraries, especially on Linux platform. I used it to get "rpy" to work on my computers.

Python resources

Here is a good list of python resources.

Cool Blog

A cool blog on math, programming, etc.

JVM-based R

Renjin, a jvm-based R interpreter. Looks interesting.

Why don't we hire .NET programmers

Good article, well said!

Rosetta code

Rosetta code provides some interesting programming demos.

Random computation

This blog has some interesting materials related to stochastic computation.

Real world clojure

A list of real world Clojure application.

Data sorcery with Clojure

Some useful examples using Incanter for data analysis.

The future of computing in China

An insightful article.

Clojure demos

Here are some cool Clojure demos. By the way the IntelliJ community edition works really well with Clojure (with plugin, of course). It's free and open source.

Jamsim

Jamsim is a microsimulation took utilizing R and Java. It looks fascinating. Its documentation can improve in the future.

Lisp outside the box

An interesting book, with a few free chapters.

Game of life

Implemented in various languages, including R.

Here is a Python version.

Another one.

Beijing air quality

This is an interesting post.

I ran the script today and got this:

What's going on?

Here comes a longer term trend:

Gimp

I am not a graphics person, but this really amazes me.

Linux blog

Refining Linux is an interesting Linux-related blog site.

E-book resource

This place has some e-books collection.

Lisp and python

This helps understanding both better.

Bibtex vs. biblatex

Here is a comprehensive discussion on the relative strengths and weaknesses of each approach. Here are some instruction about how to switch from bibtex to biblatex.

R vs. python

Fascinating discussions here.

Mint 12 is out

I will give it a try. The next release should be stable enough as my main workstations OS.

Free software

This is a comprehensive analysis of the status of free software, may be helpful for my own research.

Dev-C++

The Dev-C++ project seems to have come back.

ESS + ECB

Lush

The lush project looks interesting. Here is an informative post. This is another one.

Debian does not seem to like freepascal and lazarus

After installing the new freepascal 2.4.4 from the debian repository, my mint debian box began to show all kind of problems: chromium stopped working, the usual "./configure, make, make install" stopped working, R stopped working ... Things went back to normal after I uninstalled fp and lazarus.

Gcc and debian testing

The new gcc (4.6.2) was just out a couple of weeks ago and Debian testing has already included it.

Linux, Minix, and BSD

The interview and all the follow-ups are educational as well as entertaining ...

Debugging tutorial for StatET

Here is a brief introduction to the visual debugger of StatET, which I find very useful.

ESS tracebug module

The ESS tracebud module is a very powerful debug tool for R. I spent some time playing with it last night and really like it. Based on its project web site announcement, it will become an integrated component for the future ESS releases.

Programming fonts

Here are 5 good programming fonts. I like droid sans mono too.

One little problem with the new StatET

The new StatET looks great, and the visual debugger is really cool. However, after playing with it for a little while, I realized that the outline function (which works on LaTeX source file) still does not work on .Rnw file. The StatET group probably thinks that this is something that the TeXLipse group should do, while the TeXlipse group probably thinks this is not a LaTeX-related issue.

Linux Mint pulls ahead of Ubuntu

This should not be a surprise, especially since I myself have made the transition from Ubuntu to Mint Debian.

Linux Mint pulls ahead of Ubuntu

This should not be a surprise, especially since I myself have made the transition from Ubuntu to Mint Debian.

More than one columns in Beamer slide

Sometimes it is helpful to have more than one columns in a Beamer slide. This post shows how to do that.

Software review for semi-parametric shared frailty model

This paper is helpful.

How to repair the swap partition in Ubuntu

The post may be useful when one needs to reset the swap partition.

MGSE

Looks like the folks at Mint are planning some seriously different from Unity and Gnome3 Shell.

R, ADMB, and SAS

This (and all the follow-ups) is the most interesting live discussion about software comparison recently. I read Zhang et al. paper some time ago but did not find it very interesting. But this ongoing discussion that triggered by that paper is really interesting.

Using externally generated multiply imputed data sets with Zelig

This post provides some hints. This may be what I need to improve my infant mortality paper.

The same can be achieved using the "mi()" function provided by the Zelig package.

Free scientific software

The large number of free scientific software included in the Sage package gives a pretty good idea about what is available.

SabreR

SabreR just released an update. It is another software package that can estimate multivariate multilevel model (other options are aML, MCMCglmm, etc.). They seem to also have a book dedicated to the software, which be worth checking out.

It will be great if the author can incorporate some plotting function into the package.

Mint-coated Debian is great

I really like my Mint-coated Debian system (running xfce). For experimentation, one can simply enable the Debian testing software repository; for production use on my primary workstation, it may be a good idea to use the Mint software repository because the Mint folks promised to ensure that the update pack they issued won't break the system.

Sakura

On my Mint Xfce box, the xfce terminal started and responded more slowly than gnome terminal. This is quite strange and I have been using the gnome terminal instead. Today I found sakura, another gtk-based terminal emulator and really like it.

Upgrading Mint Debian with Debian source

I finally got tired waiting for the Mint guy to release their next update pack. I just added the Debian testing source and did a complete update. The system is running well so far and shows no sign of breakage.

The new StatET looks promising

StatET plugin for Eclipse just reached its 2.0 release, which is a big jump from the previous one. The new version seems to have quite a few new features that worth being considered seriously.

I like Emace+ESS, Rstudio, and Eclipse+StatET. Choice is a good thing!

Interesting "emacs vs. vi" blog

This one actually has some quite useful information ...

A few free books

1. Advanced Linux Programming;
2. Free for All;
3. Two Bits;
4. ...

Good R technical resources

Can be found here.

Doing email from within emacs

Here is a tutorial. A different one here.

Performance difference between Stata and R

With respect to multinomial logit model, the performance difference between the two packages are quite large, based on this post.

Stallman's comment on Jobs's death

Here. Very short and controversial. Here is a good analysis. Comments from Eric Raymond.

This guy, Larry, tried to start a war but got beaten up pretty bad.

Martin jetpack

Isn't this cool?

GEE using Stata vs. R

I am running GEE logistic regression model for my fetal loss paper. As usual, I compare results between Stata and R and make sure they are consistent. To my surprise, the models assuming independent correlation structure give similar results but the models assuming exchangeable correlation structure give drastically different results.

It turns out that there is only one woman in my sample who reported a total number of eleven pregnancies (all others reported ten or less) and the presence of this single observation had huge influence on the algorithm used in R but not the one used in Stata. After excluding this single observation, the two sets of results look identical.

Maximum likelihood example

Here is one and here is another one. This one is also helpful.

Updated examples that combine Rcpp and CppBugs

This example is very informative in illustrating how to use CppBugs module with Rcpp to conduct fast MCMC simulation in R.

Free software directory

There are some amazing stuff inside.

Rcpp examples in one place

Very convenient.

Installing the Scythe library

I manged to installed the Scythe statistical library on my Mint system. The authors commented out the line "#include " in the "matrix.h" file, which causes trouble during compiling, but that was easy to fix: just remove the comment mark. 


This article is very good in helping people to get started with the library. 

SBCL + Slime setup tutorial

This is helpful. This post is also very helpful (particularly the last paragraph about the caveat). Here is another one.

Mint Debian vs. Mint Ubuntu

Comparing software selection between the Debian-based and Ubuntu-based Mint distros is interesting. On the one hand, the Debian-based distro has the up-to-date packages for Emacs, SBCL, GCC, etc., but outdated version for Firefox, Thunderbird, etc., while the Ubuntu-based distro has updated Firefox, Thunderbird but outdated Emacs, SBCL, etc.

Mint Debian Upgrade

My Mint Debian installation seemed to have survived the first serious upgrade. The only visible problem I can see is that the configuration for Xfce window manager stopped responding. I can live with the default one but it will be nice to get it back.

Using Inkscape to Post-edit Labels in R Graphs

Here are some helpful tips.

Numerical Methods of Statistics

This is a very useful book.

X file explorer

Xfe is a flexible and lightweight file manager. It can be changed to a two-panel layout just like total commander under windows.

Get rid of unwanted items from the Xfce application menu

If removing an application leaves a zombie item in the Xfce application menu, the easiest way is to go to the /usr/share/application folder and delete the item there.

-------- Edited on Dec. 11, 2014 ------------

Here is a better solution.

Browser problem on Mint Debian

Neither Chrome nor Opera works flawlessly on the new Mint Debian: sometimes they crashed, sometimes they took a long time to load, and sometimes they stopped responding. This is not a show stopper, but it is a weird problem.

Resources for learning C++ and R

Here are a few online resources that I found useful for the purpose of learning C++ and R:

1. University of British Columbia;
2. Purdue University

Armadillo in Linux Mint Debian (Xfce)

It took me a while to figure out that I need to specify "g++ -Wall -o "%e" "%f"  -larmadillo -lblas" instead of "g++ -Wall -o "%e" "%f" -larmadillo" to compile the example program provided by the armadillo tar ball under Mint Linux Debian edition.

New Mint Linux Debian is finally here

Looks very promising.

Here is a helpful post about Mint XFCE.

Advanced C++ template techniques

I found this materials very helpful.

COMPUTING FOR NUMERICAL METHODS USING VISUAL C++

An interesting Wiley book. The source code for console applications can compile using g++ with very minor modifications.

Linux partition guid

Here is a short but useful guide showing how to partition a hard drive for a new Linux installation.

Configuring AUCTeX

This post explains how to configure AUCTeX to use different PDF file viewers.

Ra vs. compiler package

R seems to have two byte code compilers: the Ra add-on module (and the accompanying "jit" package) and the "compiler" package came with the default installation. I wonder how they differentiate from each other and what the strengths and weaknesses of each are.

CppBugs

A simple way to get CppBugs to work is to copy the "cppbugs" folder to "/usr/local/include". On my Ubuntu 10.04 system, I also need to modify the make file located in the test file directory and replace the "ARMADILLO_LIBS = llapack" with "ARMADILLO_LIBS = -larmadillo".

As a BUGS/JAGS user, I think this project is very promising and extremely interesting. It will be even more attractive if CppBugs can be integrated with R (maybe through Rcpp) in the similar way that R2WinBUGS integrates WinBUGS with R.

Using Rcpp for faster MCMC simulation

Here is a very informative blog post showing how to use Rcpp to speed up MCMC simulation.

OpenGeoDa, again

Another new release of OpenGeoDa is out, but the same problems persists: while the Linux version opened .shp files with Chinese names without problems, the windows version crashed.

Now the new version also works on Ubuntu 11.04 64-bit.

The "rube" package

The "rube" package is very promising. It builds upon the "R2WinBUGS" package and adds some very useful features. I hope it further extends to the JAGS engine because JAGS is apparently the future of the BUGS famine.

R for programmer

This is a useful document.

WebOS is gone

So that's it, HP has decided to ditch its short-lived tablet, smartphone etc.

Ibus mode

Ibus mode for Emacs allows the use of Ibus input method in Emacs. Very convenient.

13 greatest error messages of all time

Here is a fun post.

Tango color theme for Emacs

I like the Tango color theme for Emacs

Get predicted values from GAM models

I used to rely on the default plot produced  by the GAM command; now I realized that it is quite simple to produce and plot predicted predicted values using the "predict.gam()" function in the "mcgv" package.

Interaction effect plot

I am glad to find out that the "effects" package can now handle mixed effect model results from "lme4".

How to get marginal effects with "mvrs"

I found this very helpful post by Ryan sometime ago about how to get marginal effect from estimated models with "mvrs" command, very helpful.

Stata 12

There are two things I like Stata 12 most: (1) automatic memory management, and (2) a decent program editor for Linux (I know the editor has been available on the Windows platform since version 11, but I am a Linux person). The updated "margin" commands also look good.

A few things to do after installing Linux Mint

To make Linux Mint more comfortable.

Dong MCMC using Rcpp

Here is an interesting example.

OpenGeoDa

The Linux version of the OpenGeoDa seems to be more stable than the Windows version: I was able to open some shape files with Chinese file names under Ubuntu Linux but not under Windows 7 (simply crashed).

Updated on August 18. 2011: 

Now the problem is that OpenGeoDa does not seem to run on Ubuntu 11.04 64-bit: no error messages and no hints, really weird...

Mint Linux Debian edition

It is highly regarded here, and may provide a way from Ubuntu to Debian.

Here is another positive review.

Gnome 3 looks nice

I tweaked my ubuntu 11.04 and replaced the default window manager with Gnome 3. It took a while to get used to it but eventually I like it a lot. I think part of the reason ubuntu is turning to unity instead of the old gnome2 is that the new gnome represents such a drastic shift away from the old gnome2, which is no longer under active development.

The overall experience is positive. I expect the next release will get rid of the few annoyance such as the lack of easy-to-use configuration tool to tweak things like screensaver, sound, etc.

Touchpad review

Here is a not so favorable review of HP Touchpad. Here is another one. It is interesting to see how Ipad and Galaxy tab were often used as reference of comparison.

Use JAGS with ggplot2

Here is a short demo of how to use JAGS with ggplot2.

Course materials for spatial analysis using R

The PDF slides are very informative.

List of PDF reader for Android

Here is the list.

Using shape files in R

Here is a good demo. Here is another one.

Qgis and google map

Here is an illustration of how to combine them together. This post explains how to do geocoding.

Info on open source GIS

This provides some helpful information.

Legends in ggplot2

A simple plot takes a few lines of coding:


g1 <- ggplot(d, aes(birth.year))


g2 <- g1 + geom_line(aes(y=alive0, linetype="Famale")) + 
geom_line(aes(y=alive1, linetype="Male")) + scale_linetype_discrete(name = "")


g3 <- g2 + geom_point(aes(y=alive0, shape="Famale")) + 
geom_point(aes(y=alive1, shape="Male")) + scale_x_continuous("") + scale_y_continuous("Proportion Alive in 1982") + opts(legend.position=c(.24, .95), legend.justification = c(1, 1)) + scale_shape_discrete(name="")


g4 <- g3 + labs(fill="")

LaTeX template for NSF proposal

Since I am beginning to work on a NSF grant proposal, I started to look for suitable LaTeX templates. Here is one. And here are some useful tips as well as examples.

Here is an official resource, and here are some very useful LaTeX resources.

A good blog on programming

In Chinese.

Replicating multilevel analysis Mplus results

Since I am relatively unfamiliar with Mplus, The first step toward building a complicated model is to replicate some simpler results using statistical packages I have more knowledge on such Stata and R, then build it up piece by piece. 

As the effort to understand the multilevel mixture modeling capacity of Mplus, I have decided to use the Mplus sample data set, "ex10.1.dat", to try alternative model specifications in both Mplus, Stata and R. I am going to post a series of code and results. 

As the first step, I try this really simple Mplus code: 

-----------------------------------------------------------

DATA: FILE IS ex10.1.dat;

VARIABLE: NAMES ARE y x1 x2 w class clus;

USEVARIABLES = y x1 x2;

WITHIN = x1 x2;

CLUSTER = clus;

ANALYSIS: TYPE = TWOLEVEL;

STARTS = 0;

MODEL:

%WITHIN%

y ON x1 x2;

%BETWEEN%

y ON ;

-----------------------------------------------------------

which gives exactly the same results as the following Stata code: 

-----------------------------------------------------------

xtreg y x1 x2, i(clus) mle

-----------------------------------------------------------

China map

Here is a list of China maps.

Mtable extension as a package

This looks promising.

Mplus for Bayesian analysis

The new Mplus has a quite rich set of Bayesian analysis feature. I cannot wait to play with it.

Extension to mtable function

Here are some useful extension to the "mtable" function in the memisc package.

22 free tools for data visualization and analysis

Good information here.

WinBUGS to ADMB

I found the short article published on the ADMB newsletter about how to translate WinBUGS code into ADMB very educational.

UPX

I did a simple random effect model in ADMB. The resulted Linux binary file is about 1.5M. I was able to shrink it to slightly over .5M using UPX. This is quite amazing.

Estimating a linear regression using MLE

Here is an informative demo. This is another interesting post.

Ess-tracebug

A nice debugger for ESS and R, here.

Interesting post regarding Freepascal and Lazarus

Here is an interesting post about Freepascal and Lazarus project.

Laplace's Demon

This is a serious attempt to code a general purpose MCMC sampling engine in R.

10 Myths About Introverts 10 Myths About Introverts

Here is an interesting post.

A blog on bayesian computatin

This is an interesting blog.

Interesting blog post about Maxima and R

This is an interesting post about R and Maxima.

Some Emacs lisp tricks

This is very helpful.

Verbosus

Verbosus is another online LaTeX composing environment. Looks promising.

Eigen

Eigen is a mature and well documented matrix class.

Introduction to Probability and Statistics Using R

The author has done an amazing job maintaining this web site and the book.

Popularity of R

R is gaining popularity, according to this post.

Scientific Linux seems worth trying

According to this post, Scientific Linux seems worth trying.

Solar laptop charger

Here is a review of solar laptop chargers.

Remove the dock, back to normal

I played with the Cairo dock for over a month. I finally decided to remove it and go back to the plain Gnome interface.

Labels and legends in ggplot2 figure

I struggled with getting the labels and legends right in my ggplot2 figure and found this web page very helpful.

Here are some discussions about how to change the font size for the labels.

R GUI

A list of 7 R GUI.

Git with Emacs

A useful places to get the information on how to use Git with Emacs.

Ask R not to create a local directory tree

I don't like R to create a local directory tree in my home directory because new packages will automatically be installed into that directory. The way to do this is to modify the "/usr/local/lib64/R/etc/Renviron" and mark the line "R_LIBS_USER=${R_LIBS_USER-'~/R/x86_64-unknown-linux-gnu-library/2.12'}" off. Simple as that.

Mastering Emacs

This is a good site for Emacs user.

Here is another one.

Emacs 23.3

Just installed the new Emacs 23.3 from source. It seemed to solve the problem I had before using SyncTeX for forward search in Evince.

PAC manager

PAC manager is a GUI client for SSH. It feels like secureCRT from long time ago.

RedNotebook

Free software for daily journal. First impression is positive.

DID resources

This is a list of resources showing how DID works:

1. In Stata;
2. A PowerPoint slide;
3. 
   

Use github

The introduction is generally helpful, but they forgot to say that you also need to run "ssh-add" after you generate the keys etc., as described here.

Rstudio

Rstudio, an open source cross-platform IDE for R, seems to be really attractive. It probably will not drag me away from Emacs, but having more options is always a good thing.

The only downside of it is that it automatically installs R from the Ubuntu software repository, even though I have already had a manually compiled version installed on the system. It will be better if Rstudio does not try to install a version of R as default but gives the choice to the user.

I think this IDE is an excellent choice for teaching purpose: by now the only reason I am hesitating to teach my students using R as opposed to other statistical package is the lack of a "modern" IDE. I mean, Emacs + ESS suites me just fine, but I cannot imagine what will happen if I try to make my undergraduate students learn to do this on their Windows machine!

After a few tweaks, and many thanks to the guys working on Rstudio, I was able to compile and install the source distribution.

Commands used:

1. git clone git@github.com:rstudio/rstudio.git
2. git submodule update --init --recursive
3. cmake -DRSTUDIO_TARGET=Desktop -DCMAKE_BUILD_TYPE=Release
4. sudo make install

LibreOffice 3.3.1

LibreOffice 3.3.1 has a much improved startup performance, compared to both LibreOffice 3.3 and OpenOffice. This improvement has real significance for an ordinary user.

Simulate parameters

This blog shows how to simulate parameters from a tobit model with a few line of R code.

Population Studies

Population Studies is one of my favorite academic journals. Only recently it started to accepts PDF submission. This is a very positive development.

R Graphics Manual

Very useful web site for R graphics.

A few summary functions used by ggplot2

I could not quite figure out what the summary function "mean_sdl" stands for, so I took at a look at the source code "stat-summary.r". It turns out that this is a wrapper function of the "smean_sdl()" of the Hmisc package, as well as the "median_hilow", "mean_cl_normal" and "mean_cl_boot".

Simulating second difference using Zelig

I am trying to simulate second difference using Zelig, here is my code:
--------------------------------------------------------

data(turnout)


# estimation


z.out <- zelig(vote ~ race*age + educate + income,
               model = "logit", data = turnout)


summary(z.out)


# first difference


x.low <- setx(z.out, educate = 12)
x.high <- setx(z.out, educate = 16)


s.out <- sim(z.out, x = x.low, x1 = x.high)


s.low <- sim(z.out, x=x.low)
s.high <- sim(z.out, x=x.high)


dif <- (s.high$qi$ev - s.low$qi$ev)


# second difference


x.low.low <- setx(z.out, educate = 12, age = 20)
x.low.high <- setx(z.out, educate = 12, age = 30)
x.high.low <- setx(z.out, educate = 16, age = 20)
x.high.high <- setx(z.out, educate = 16, age = 30)


s1 <- sim(z.out, x = x.low.low, x1 = x.low.high)
s2 <- sim(z.out, x = x.high.low, x1 = x.high.high)


did1 <- s1$qi$fd - s2$qi$fd


# or equivalent


s3 <- sim(z.out, x = x.low.low, x1 = x.high.low)
s4 <- sim(z.out, x = x.low.high, x1 = x.high.high)


did2 <- s3$qi$fd - s4$qi$fd

---------------------------------------------------------

It would be great if Zelig can do this directly though. 

R, windows, linux, etc.

For some reasons I had to work on a Windows machine for the last couple of days. So I installed Revolution R and played with it. It is an elegant piece of software with clearly defined targeted user group. It fits the Windows world well. On the other hand, this means that it has distanced itself from the free software world as represented by Linux and R: while Linux and R make it easy for you to gets your hands dirty by playing with the C/C++ code under the surface and blur the distinction between "developer" and "user", the distinction is so prominent in the Windows world (I assume in the Mac world too) and by making view, changing, and compiling source code very difficult, binary files are deified.

How can I graph the results of the margins command?

A useful post from UCLA ATS Computing explaining how to plot the results from the "margins" command. This one explains how to explain interaction results. More generally, the "Stata Frequently Asked Questions" section is also helpful.

LibreOffice

As the first stable version of LibreOffice got out today, I immediately uninstall the old OpenOffice and replace with the new LibreOffice following the procedures described here.

The reason... I think this post summarized really well.

Post-estimation results manipulation: Stata vs. R

Stata's new "margins" command is as powerful as "Zelig" package for R for the purpose of conducting post-estimation manipulation of the results (e.g. producing predicted probabilities, confidence intervals, etc.). While "margins" uses delta method, "Zelig" uses predictive simulation. The best thing is that the results produced by one package can be checked against the other to ensure the consistency.

GlmmADMB

The package "glmmADMB" is a good demonstration of the power and flexibility of ADMB: with two well structured C++ template files (1427 and 434 lines of code), the package is as almost as powerful as full scale commercial software such as HLM.

PGF/TikZ related resources

Many useful resources related to PGF/TikZ can be found here.

Some useful tips using shell commands

Here are a list of useful tips using shell commands (in Chinese).

ADMB 10

I just found out that ADMB 10 is out! The new release makes it much easier to compile and install from source (was possible in the previous release but took some tweak).

The R package to interface between R and ADMB, R2admb, developed by Ben Bolker , seems mature enough for serious use.

Booktabs with longtable

I finally figured out how to use "booktabs" with "longtable". The "esttab" can be used to produce preliminary output, but the output needs to be manually tuned to get the desired look. Here are come tips., and here is a helpful example. Below is the preamble:


{
\begin{center}
\def\sym#1{\ifmmode^{#1}\else\(^{#1}\)\fi}
\begin{longtable}{l*{4}{c}}
\caption{Something}\\
\toprule
                    &\multicolumn{1}{c}{Model 1}    &\multicolumn{1}{c}{Model 2}    &\multicolumn{1}{c}{Model 3}    &\multicolumn{1}{c}{Model 4}    \\
\endfirsthead
\caption[]{(Continued)} \\
                \toprule
                    &\multicolumn{1}{c}{Model 1}    &\multicolumn{1}{c}{Model 2}    &\multicolumn{1}{c}{Model 3}    &\multicolumn{1}{c}{Model 4}    \\
                \midrule
\endhead
                \midrule \multicolumn{5}{r}{\emph{Continued on next page}}
\endfoot
\endlastfoot
\midrule

...

\end{center}

\end{longtable}

}

Cairo dock

I installed Cairo dock on one of my Ubuntu machine. I was not sure what I was getting at first, but the experience was surprisingly pleasant. Now I understand why many people like similar things on Mac. I decide to keep it at least for a while.

Handbook of Open Source Tools

Very handy reference book about open source software tools.