Minzhao Liu's Blog

R Command Abbreviations by Jeromy Anglim

May 10th, 2010 Minzhao No comments

From: http://jeromyanglim.blogspot.com/2010/05/abbreviations-of-r-commands-explained.html

R Command	Abbreviation Expanded	Comments	Type
`ls`	[L]i[S]t objects	common command in Unix-like operating systems	Basics
`rm`	[R]e[M]ove objects	common command in Unix-like operating systems	Basics
`str`	[STR]ucture		Basics
`unz`	[UNZ]ip		Basics
`getwd`	[GET] [W]orking [D]irectory		Basics
`dir`	[DIR]ectory		Basics
`sprintf`	[PRINT] [F]ormatted	S for String of Silently?	Basics
`c`	[C]ombine values		Basics
`regexpr`	[REG]ular [EXPR]ession	Why “regular”? See regular sets, regular language	Strings
`diag`	[DIAG]onal values of a matrix		Basics
`col`	[COL]umn		Basics
`lapply`	[APPLY] to each element of a list or vector and return a [L]ist	L is for List	Basics
`sapply`	[APPLY ]to each element of a list or vector and attempt to [S]implify the returned object to a vector	S is for Simplify	Basics
`mapply`	[M]ultivariate version of s[APPLY]		Basics
`tapply`	[T]able [APPLY] function to sets of values as defined by an index		Basics
`apply`	[APPLY] function to sets of values as defined by an index		Basics
`MARGIN = 1 or 2 in apply`	rows [1] come before columns [2]	e.g., a 2 x 3 matrix has 2 rows and 3 columns (note: row count is stated first)	Basics
`rmvnorm`	[R]andom number generator for [M]ulti[V]ariate [NORM]al data		Basics
`rle`	[R]un [L]ength [E]ncoding		Basics
`ftable`	[F]ormat [TABLE]		Basics
`xtabs`	Cross (i.e., [X]) [TAB]ulation	[X] is the symbol of a cross; [X] is sometimes spoken as “by”. Cross-tabulating means to cross one variable with another	Basics
`xtable`	[TABLE] of the object [X]		Basics
`formatC`	[FORMAT] using [C] style formats	i.e., [C] the programming language	Basics
`Sweave`	[WEAVE] [S] code in a LaTeX document	The R Programming language is a dialect of S	Basics
`cor`	[COR]relation		analyses
`ancova`	[AN]alysis [O]f [COVA]riance		analyses
`manova`	[M]ultivariate [AN]alysis [O]f [COVA]riance		analyses
`aov`	[A]nalysis [O]f [V]ariance		analyses
`TukeyHSD`	[T]ukey’s [H]onestly [S]ignificant [D]ifference		analyses
`hclust`	[H]ierarchical [CLUST]er analysis		analyses
`cmdscale`	[C]lassical metric [M]ulti[D]imensional [SCAL]ing		analyses
`factanal`	[FACT]or [ANAL]ysis		analyses
`princomp`	[PRIN]cipal [COMP]onents analysis		analyses
`prcomp`	[PR]incipal [COMP]onents analysis		analyses
`lme`	[L]inear [M]ixed [E]ffects model		analyses
`resid`	[RESID]uals		models
`ranef`	[RAN]dom [EF]fects		models
`anova`	[AN]alysis [O]f [VA]riance		models
`fixef`	[FIX]ed [EF]ffects		models
`vcov`	[V]ariance-[COV]ariance matrix		models
`logLik`	[LOG] [LIK]elihood		models
`BIC`	[B]ayesian [I]nformation [C]riteria		models
`mcmcsamp`	[M]arkov [Chain] [Monte] [C]arlo [SAMP]ling		models
`eval`	[EVAL]uate an R expression		Basics
`cat`	con[CAT]enate	standard Unix command	Basics
`apropos`	Search documentation for a purpose or on a topic (i.e., [APROPOS])	Unix command for search documentation;	Basics
`read.csv`	[READ] a file in [C]omma [S]eperated [V]alues format	i.e., in each row of the data commas separate values for each variable	Basics
`read.fwf`	[READ] a file in [F]ixed [W]idth [F]ormat		Basics
`seq`	Generate [SEQ]uence		Basics
`rep`	[REP]licate values of x	perhaps also [REP]eat	Basics
`dim`	[DIM]ension of an object	Typically, number of rows and columns in a matrix	Basics
`gl`	[G]enerate factor [L]evels		Basics
`rbind`	[BIND] [R]ows together		Basics
`cbind`	[BIND] [C]olumns together		Basics
`is.na`	[IS] [N]ot [A]vailable		Basics
`nrow`	[N]umber of [ROW]s		Basics
`ncol`	[N]umber of [COL]umns		Basics
`attr`	[ATTR]ibute		Basics
`rev`	[REV]erse		Basics
`diff`	[DIFF]erence between x and a lag of x		Math
`prod`	[PROD]uct		Math
`var`	[VAR]iance		Math
`sd`	[S]tandard [D]eviation		Math
`cumsum`	[CUM]ulative [SUM]		Math
`cumprod`	[CUM]ulative [PROD]uct		Math
`setdiff`	[DIFF]erence between two [SET]s		Math
`intersect`	[INTERSECT]ion		Math
`Re`	[RE]al part of a number		Math
`Im`	[IM]aginary part of a number		Math
`Mod`	[MOD]ulo opertion	remainder of division of one number by another	Math
`t`	[T]ranspose of a vector or matrix		Math
`substr`	Return [SUBSTR]ing		Strings
`strsplit`	[SPLIT] a [STR]ing vector		Strings
`grep`	[G]lobal / [R]egular [E]xpression / [P]rint	Etymology based on text editor instructions in programs such as ed	Strings
`sub`	[SUB]stitute identified pattern found in string		Strings
`gsub`	[G]lobal [SUB]stitute identified pattern found in string		Strings
`pmatch`	[P]artial string [MATCH]ing		Strings
`nchar`	[N]umber of [CHAR]acters in a string		Strings
`ps.options`	[OPTIONS] for [P]ost-[S]cript		Graphic Devices
`win.metafile`	[WIN]dows [METAFILE] graphic		Graphic Devices
`dev.off`	[DEV]ice [OFF]		Graphic Devices
`dev.cur`	[CUR]rent [DEV]ice		Graphic Devices
`dev.set`	[SET] the current [DEV]ice		Graphic Devices
`hist`	[HIST]ogram		base graphics
`pie`	[PIE] Chart		base graphics
`coplot`	[CO]nditioning [PLOT]		base graphics
`matplot`	[PLOT] colums of [MAT]rices		base graphics
`assocplot`	[ASSOC]iation [PLOT]		base graphics
`plot.ts`	[PLOT] [T]ime [S]eries		base graphics
`qqnorm`	[Quantile]-[Q]uantile [P]lot based on normal distribution		base graphics
`persp`	[PERSP]ective [P]lot		base graphics
`xlim`	[LIM]it of the [X] axis		base graphics parameter
`ylim`	[LIM]it of the [Y] axis		base graphics parameter
`xlab`	[LAB]el for the [X] axis		base graphics parameter
`ylab`	[LAB]el for the [Y] axis		base graphics parameter
`main`	[MAIN] title for the plot		base graphics parameter
`sub`	[SUB] title for the plot		base graphics parameter
`mtext`	[M]argin [TEXT]		base graphics parameter
`abline`	[LINE] on plot often of the form y = [A] + [B] x		base graphics parameter
`h argument in abline`	[H]orizontal line		base graphics parameter
`v argument in abline`	[V]ertical line		base graphics parameter
`par`	Graphics [PAR]ameter		base graphics parameter
`adj`	[ADJ]ust text [J]ustification		base graphics parameter
`bg`	[B]ack[G]round colour		base graphics parameter
`bty`	[B]ox [TY]pe		base graphics parameter
`cex`	[C]haracter [EX]tension or [EX]pansion of plotting objects		base graphics parameter
`cex.sub`	[C]haracter [EX]tension or [EX]pansion of [SUB]title		base graphics parameter
`cex.axis`	[C]haracter [EX]tension or [EX]pansion of [AXIS] annotation		base graphics parameter
`cex.lab`	[C]haracter [EX]tension or [EX]pansion X and Y [LAB]els		base graphics parameter
`cex.main`	[C]haracter [EX]tension or [EX]pansion of [MAIN] title		base graphics parameter
`col`	Default plotting [COL]our		base graphics parameter
`las`	[L]abel of [A]xis [S]tyle		base graphics parameter
`lty`	[L]ine [TY]pe		base graphics parameter
`lwd`	[L]ine [W]i[D]th		base graphics parameter
`mar`	[MAR]gin width		base graphics parameter
`mfg`	Next [G]raph for [M]atrix of [F]igures		base graphics parameter
`mfcol`	[M]atrix of [F]igures entered [COL]umn-wise		base graphics parameter
`mfrow`	[M]atrix of [F]igures entered [ROW]-wise		base graphics parameter
`pch`	[P]lotting [CH]aracter		base graphics parameter
`ps`	[P]oint [S]ize of text	Point is a printing measurement	base graphics parameter
`pty`	[P]lot region [TY]pe		base graphics parameter
`tck`	Length of [T]i[CK] marks		base graphics parameter
`tcl`	[T]i[C]k mark length		base graphics parameter
`xaxs`	[X] [AX]is [S]tyle		base graphics parameter
`yaxs`	[Y] [AX]is [S]tyle		base graphics parameter
`xaxt`	[X] [AX]is [T]ype		base graphics parameter
`yaxt`	[Y] [AX]is [T]ype		base graphics parameter
`asp`	[ASP]ect ratio		base graphics parameter
`xyplot`	[X] [Y] [PLOT]	[X] for horizontal axis; [Y] for vertical axis	lattice
`bwplot`	[B]ox and [W]hisker plot		lattice
`qq`	[Q]uantile-[Quantile] plot’		lattice
`splom`	[S]catter[PLO]t [M]atrix		lattice
`optim`	[OPTIM]isation		analyses
`lm`	[L]inear [M]odel		analyses
`glm`	[G]eneralised [L]inear [M]odel		analyses
`nls`	[N]onlinear [L]east [S]quare parameter esetimation		analyses
`loess`	[LO]cally [E]stimated [S]catterplot [S]moothing		analyses
`prop.test`	[TEST] null hypothesis that [PROP]ortions in several gropus are the same		analyses
`rnorm`	[R]andom number drawn from [NORM]al distribution		distributions
`dnorm`	[D]ensity of a given quantile in a [NORM]al distribution		distributions
`pnorm`	[D]istribution function for [NORM]al distribution returning cumulaive [P]robability		distributions
`qnorm`	[Q]uantile function based on [NORM]al distribution		distributions
`rexp`	[R]andom number generation from [EXP]onential distribution		distributions
`rgamma`	[R]andom number generation from [GAMMA] distribution		distributions
`rpois`	[R]andom number generation from [POIS]on distribution		distributions
`rweibull`	[R]andom number generation from [WEIBULL] distribution		distributions
`rcauchy`	[R]andom number generation from [CAUCHY] distribution		distributions
`rbeta`	[R]andom number generation from [BETA] distribution		distributions
`rt`	[R]andom number generation from [t] distribution		distributions
`rf`	[R]andom number generation from [F] distribution	F for Ronald [F]isher	distributions
`rchisq`	[R]andom number generation from [CHI] [SQ]uare distribution		distributions
`rbinom`	[R]andom number generation from [BINOM]ial distribution		distributions
`rgeom`	[R]andom number generation from [EXP]onential distribution		distributions
`rhyper`	[R]andom number generation from [HYPER]geometric distribution		distributions
`rlogis`	[R]andom number generation from [LOGIS]tic distribution		distributions
`rlnorm`	[R]andom number generation from [L]og [NOR]mal distribution		distributions
`rnbinom`	[R]andom number generation from [N]egative [BINOM]ial distribution		distributions
`runif`	[R]andom number generation from [UNIF]orm distribution		distributions
`rwilcox`	[R]andom number generation from [WILCOX]on distribution		distributions
`ggplot`	[G]rammar of [G]raphics [PLOT]	See Leland Wilkinson (1999)	Graphics
`x as argument`	[X] is common letter for unknown variable in math		Basics
`FUN as argument`	[FUN]ction		Basics
`pos as argument`	[POS]ition		Basics
`lib.loc in library`	[LIB]rary folder [LOC]ation		Basics
`sep as argument`	[SEP]erator character		Basics
`comment.char in read.table`	[COMMENT] [CHAR]acter(s)		Basics
`I`	[I]nhibit [I]nterpretation		Basics
`T value`	[T]rue		Basics
`F value`	[F]alse		Basics
`na.rm`	[N]ot [A]vailable values are to be [R]e[M]oved		Basics
`fivenum`	[FIVE] [NUM]ber summary		Basics
`IQR`	[I]nter [Q]uartile [R]ange		Basics
`coef`	Model [COEF]ficients		Basics
`dist`	Compute [DIST]ance matrix		Basics
`df`	[D]egrees of [F]reedom		Basics
`mad`	[M]edian [A]bsolute [D]eviation		Basics
`sink`	Divert R output to a connection (i.e., like connecting a pipe to a [SINK])		Basics
`eol in write.table`	[End] [O]f [L]ine character(s)		Basics
`R`	[R]oss Ihaka and [R]obert Gentleman or [R] is letter before S		Basics
`CRAN`	[C]omprehensive [R] [A]rchive [N]etwork		Basics

Categories: R Tags: R

Using LaTeX to Split PDF Files

May 8th, 2010 Minzhao No comments

Motivation

LaTeX is not only a tool to type literatures, but also a tool to do other things. For example, if I wanna extract one or several pages from one or more pdf files, I could use that with some pdf editor , but by some packages in LaTeX, you could also make that.

Usage

Suppose your source pdf is source.pdf, you wanna draw the 2nd and 4th page from that, by

\usepackage{pdfpages}
\includepdf[page={2,4}]{source}

pdflatex -> voila, here you are.

Reference

For more details, see pdfpages package.

Categories: LaTeX Tags: LaTeX, package, pdf

firemacs by Kazu Yamamoto ( a emacs(vi)-like plugin for firefox)

May 2nd, 2010 Minzhao No comments

Introduction

This plugin helps you browse website via firefox without moving your hands up and down. That does not mean you could discard your mouse, but if combined with thinkpad little red point on your keyboard, it’s pretty awesome that you could leave your cordless mouse alone.

Basic Usage

My basic use is :

h : go to previous tab
l : go to next tab
j : scroll up
k : scroll down
b: page up
u: page down
C-v: page down
M-v: page up
C-b: go to previous
C-f: go to next tab
C-n: go to next line
C-p: go to previous line
C-x k: kill current tab
C-s: search
C-w: cut
C-y: paste
M-w: copy
C-a: go to the head of current line

Reference

https://addons.mozilla.org/en-US/firefox/addon/4141

Categories: Emacs, Web Tags: Emacs, firefox, plugin

Recent-jump.el for Emacs by ChunYe Wang

April 27th, 2010 Minzhao No comments

Reference: Written by ChunYe Wang, here’s the file I got originally.

Motivation

recent-jump.el written by ChunYe Wang, is such a implementation for Emacs that it helps you to jump where you visit recently. Sometimes it’s annoying to move up and down while revising your papers, usually I forgot to mention something in the previous paragraph, or have to copy some code from other buffer.

I used to play ido.el and ibuffer.el , which are extremely useful and helpful to switch between buffers. Now combined with recent-jump.el, you could not only jump between lines, but jump between buffers as well, even the very point you just edit in the last several buffer. Here’s how to do it.

Download

borrowed from bigFang

recent-jump

Usage

installation:
put recent-jump.el in your emacs load path.

configuration:

(setq recent-jump-threshold 4)
(setq recent-jump-ring-length 10)
(global-set-key (kbd "C-o") 'recent-jump-jump-backward)
(global-set-key (kbd "M-o") 'recent-jump-jump-forward)
(require 'recent-jump)

even if you do not know anything about emacs lisp language, it ’s still quite easy to understand what those codes mean. Use C-o to jump backward, and M-o to jump forward.

Enjoy.

Categories: Emacs Tags: Emacs

Calc2LaTeX Plug-in for Making LaTeX Tables

April 27th, 2010 Minzhao No comments

Motivation

It’s really disgusting to make complicated tables when you are typing LaTeX, here’s one method helping you to get LaTeX code for whatever table you want.

The basic idea is to take advantage of those WYSIWYG software like Excel or OpenOffice Spreadsheet. There’s a plug-in called Excel2Latex which could transform your excel table into LaTeX code. While for free OpenOffice Spreadsheet, the calc2latex plug-in is quite helpful. By that, you will no longer worry about how to make multicolumn, multirow, all kinds of weird tables in LaTeX.

Download

Download from this url.

Usage

after installation
make your table in OpenOffice Spreadsheet
mark your table and click tools, ‘Macros’ -> ‘run Macro’
choose ‘My Macros’,-> ‘Calc2LaTeX’ -> ‘Calc2LaTeX’ -> Main -> Run
choose your setup

then you could copy the results into your LaTeX file. Easy~

Reference

http://calc2latex.sourceforge.net/

Categories: LaTeX Tags: LaTeX, openoffice, table

Get BibTeX from Google Scholar

April 15th, 2010 Minzhao No comments

1. go to www.google.com/scholar.

2. scholar preference

3.Bibliography Manager: choose BibTeX

4. search for paper and click ‘ import into BibTeX’

5. copy that in your bib file.

But the problem is that there’s still some error in the bibtex from google scholar, for example ,

http://scholar.google.com/scholar.bib?q=info:Kb5Zq_JwPi0J:scholar.google.com/&output=citation&hl=en&as_sdt=40000&ct=citation&cd=2

@article{alan2002categorical,
  title={{Categorical data analysis}},
  author={Alan, A.},
  journal={Editorial John Willey \& Sons},
  year={2002}
}

actually, the author is Dr. Alan Agresti, and the publisher is John Wiley & Sons. Well, anyone has better suggestions?

Categories: Emacs, LaTeX, Study Tags: LaTeX

A nice ggplot2 web interface by Jeroen Ooms

April 12th, 2010 Minzhao No comments

http://www.yeroon.net/ggplot2/

pretty , just give a try.

Categories: R, Study Tags: ggplot2

How to add CC license into LaTeX file and how to build LaTeX package

March 29th, 2010 Minzhao No comments

Introduction

This article will introduce how to add CC into $\LaTeX$ file and how to build your own $\LaTeX$ package.

What is CC

CC is short for Creative Commons, which provides various kinds of licenses. Basically, CC license announces some rights reserved or some perticular rights reserved instead of All rights reserved. On their website, you could customize the license you want, just by clicking some buttons. Convenient html code will be produced.

CC license in $\LaTeX$ slides

However, those codes are only for html, in order to embed CC license into $\LaTeX$ slides, usually beamer slides, I found the following historical, ugly, but ready-eat $\LaTeX$ package cclicenses CTAN. Here’s how it works:

put the following code in the preamble,

\usepackage{cclicenses}

then follow the instruction in the help pdf for cclicenses package above.

Fortunately, I found this post by Sebastian Pipping. Here’s the screenshot.

ccbeamer

One thing Sebastian Pipping mentioned is that it’s not a real $\LaTeX$ package, thus to be a legitimate lazy man, I modified his package a little and built this ccbeamer $\LaTeX$ package.

How to make your own $\LaTeX$ package

Referring to this web page, I did as follows:

Rename Sebastian’s ccbeamer.tex to ccbeamer.sty (used to put all your command into .sty file)
For your $\TeX$ distribution, (mine is TeXlive 2009) , find where $\LaTeX$ packages are installed. (mine is usr/local/texlive/2009/texmf-dist/tex/latex)
make directory, and put creative commons and ccbeamer.sty in.
use texhash to refresh your $\LaTeX$ database.

so if you download my modified ccbeamer $\LaTeX$ package, what you need to do is just to extract the zip file into where your $\LaTeX$ packages are installed, and refresh the database, put

\usepackage{ccbeamer}

in your preamble.

For more options, read the ccbeamer.sty file.

Download

ccbeamer

Categories: Emacs, Study Tags: Creative Commons, LaTeX, package

How to establish your own blog

March 29th, 2010 Minzhao No comments

Motivation

In this article, I will give a brief introduction about how to build a blog with WordPress.

What you need and how to do

domain
First you need to register the url you wanna use. For example, my domain is got from www.godaddy.com, just for $1. Godaddy always has some deals and coupons from time to time. The domain, like your home address, should be impressive and easy to remember.
host
Host is like a server, where you put all your website files and data. In order to use WordPress, the host has to support PHP, MySQL and so on. Usually, you could get your host where you get the domain,like Bluehost, Dreamhost, Godaddy and so forth, but basically they are not free. Actually there does exist many free hosting service, which also means less stable and volumn. For example, mine is from 000Webhsot.
WordPress
WordPress is an open source blog publishing application powered by PHP and MySQL which can also be used for content management. It’s free and user-friendly. Actually, you can design your blog, your website, even forum after obtaining host and domain, but I am a lazy man, WordPress is just the tool for me to publish my notes without taking time on css design or whatever, they have a lot of plugins and themes which are extremely useful. I would write an article about recommended WordPress plugins.

How to combine WordPress with your host

Log in your host server, and find CPanel.
Find Software/Service, MySQL
Create new database and user, then right now, you would have
- database name
- database username
- database host (some would give you its own host , otherwise, it’s localhost)
Back to CPanel, and find Files
Use web file manager or FTP method, to upload WordPress to /public_html
- for standard CPanel, you could download WordPress zip or gz file, and upload it directly, then standard CPanel would extract it.
- for nonstandard CPanel, you could download WordPress zip or gz file on your local desktop, and extract it by yourself, then upload the whole directory onto /public_html
On your web browser, type in your domain (your website). Voila, here’s your website. If everything is fine, you will be informed that you lack a configuration. Following those clicks, input your database name, username, password, host address( most do not need to change), and so on, then get a temporary password, do remember that, change it later.
Voila, it works.

Categories: Web Tags: cpanel, Web, wordpress

Minzhao Liu's Blog

R Command Abbreviations by Jeromy Anglim

Using LaTeX to Split PDF Files

Motivation

Usage

Reference

firemacs by Kazu Yamamoto ( a emacs(vi)-like plugin for firefox)

Introduction

Basic Usage

Reference

Recent-jump.el for Emacs by ChunYe Wang

Reference: Written by ChunYe Wang, here’s the file I got originally.

Motivation

Download

Usage

Calc2LaTeX Plug-in for Making LaTeX Tables

Motivation

Download

Usage

Reference

Get BibTeX from Google Scholar

A nice ggplot2 web interface by Jeroen Ooms

How to add CC license into LaTeX file and how to build LaTeX package

Introduction

What is CC

CC license in $\LaTeX$ slides

How to make your own $\LaTeX$ package

Download

How to establish your own blog

Motivation

What you need and how to do

How to combine WordPress with your host

Categories

Tag Cumulus

Recent Comments

Categories

Blogroll

Meta

Motivation

Usage

Reference

Introduction

Basic Usage

Reference

Reference: Written by ChunYe Wang, here’s the file I got originally.

Motivation

Download

Usage

Motivation

Download

Usage

Reference

Introduction

What is CC

CC license in slides

How to make your own package

Download

Motivation

What you need and how to do

How to combine WordPress with your host

Categories

Tag Cumulus

Recent Comments

Categories

Blogroll

Meta

CC license in $\LaTeX$ slides

How to make your own $\LaTeX$ package