A Publication Workflow for Organising Files and Directories

The following describes my workflow for publishing journal articles. It defines a set of rules for organising the files and directories associated with writing and publishing a peer-reviewed journal article.

It covers issues of file organisation, version control, and collaboration. It embodies a number of lessons that I've learnt while publishing journal articles. It also helps to have a standardised approach.

Home, End, Page Up, Page Down Keys in OSX

Shortcut keys for navigation are inconsistent in OSX across applications. Notionally the home and end keys are Fn + Left / Right and Page Up / Page Down are Fn + Up/Down. However, this does not always achieve the same navigational effect, especially for programs ported from Windows.

Ways that closed access academic publishers could improve

Accessing journal articles has certainly got easier over the years. Nonetheless, there are still many issues with how closed-access journals provide access. This hampers the scientific process.

Accessing a journal article that my institution has paid for should be as simple as going to the standard publications home page (with  one more click to download the pdf).

While from a broader societal level, there are many reasons to like open access publishing. However, for working scientists with institutional access to most journals, the day-to-day issue with closed access publishers is usability related. Here are a few things that I wish all publishers would do:

Generating APA style tables in R: Current challenges

This post reviews some aspects of generating formatted tables using R suitable for inclusion in a manuscript conforming to APA style. I review my current workflow that involves a large amount of manual formatting in Excel. I then discuss what it would take to automate more of these manual steps in R.

Suggestions for how R and RStudio could improve auto-completion and usability of R

RStudio has improved the power of auto-completion in R and generally increased usability. However, there remains the potential to improve discoverability and usability. There are also coding practices that R package authors can adopt both to work better with auto-complete and make the features of their R package more discoverable.  After using and teaching R for the last ten years, this post outlines what I see as major areas for potential improvement.

Workflow for Completing a Revise and Resubmit of a Journal Article in Psychology

This post discusses my workflow for completing a revise and resubmit.
I have a template document for representing revise and resubmit responses.
See my templates page on github and specifically see the file "response-to-reviewers.dotx".

Managing Timeframes from Initial Submission to Final Acceptance of Journal Articles in Psychology

This post discusses issues related to the managing the timeframe from an initial submission to a journal to final acceptance at that or another journal. They are personal notes that pertain to my experiences in psychology. I post them here in case they might be useful for others.

Customising ProjectTemplate in R

This post talks about my workflow for getting started with a new data analysis project using the ProjectTemplate package.

Using R to replicate common SPSS multiple regression output

The following post replicates some of the standard output you might get from a multiple regression analysis in SPSS. A copy of the code in RMarkdown format is available on github. The post was motivated by this previous post that discussed using R to teach psychology students statistics.

Writing a Concise Introduction to a Psychology Journal Article: An Article Deconstruction

I often talk about article deconstruction as a useful method for extracting principles for writing journal articles. The following is an article deconstruction of the introduction section of Fujita and Diener (2005). The writing principles extracted may be relevant to others writing introductions to journal articles in psychology.

How to convert manual APA references to Endnote references in Word

When collaborating on a journal article with colleagues I sometimes get Word documents that have manually formatted references. I often want to convert the manual references to Endnote references. The following post discusses a workflow for doing this.

Tutorials, Answers, and Data Files for Multivariate Research Methods Course using SPSS and Amos

I recently developed a set of tutorials for teaching research methods using SPSS and Amos to I/O psychology students. I thought they might be useful for other instructors or people learning intermediate multivariate research methods to social and behavioural science students. Thus, I have made the resources available as a downloadable repository.

Evaluating the Potential Incorporation of R into Research Methods Education in Psychology

I was recently completing some professional development activities that required me to write a report on a self-chosen topic related to diversity in student backgrounds. I chose to use the opportunity to reflect on the potential for using R to teach psychology students research methods. I thought I'd share the report in case it interests anyone.

Google Reader Replacements: Feedly and The Old Reader

This post discusses the impending demise of Google Reader and configuring Feedly as a replacement.

Beamer presentations using pandoc, markdown, LaTeX, and a makefile

This post discusses the creation of beamer presentations using a combination of markdown, pandoc, and LaTeX. This workflow offers the potential to reduce typing and increase readability of beamer presentation source code. Source code for an example presentation is provided containing markdown and LaTeX source code along with a makefile for building the beamer PDF.

Video: knitr, R Markdown, and R Studio: Introduction to Reproducible Analysis

This post presents the video of a talk that I presented in July 2012 at Melbourne R Users on using knitr, R Markdown, and R Studio to perform reproducible analysis. I also provide links to a github repository where the R markdown examples can be examined and the slides can be downloaded.

Converting Sweave LaTeX to knitr LaTeX: A case study

The following post documents the steps I needed to take in order to convert a project using Sweave LaTeX into one using knitr LaTeX.

How to Convert Sweave LaTeX to knitr R Markdown: Winter Olympic Medals Example

The following post shows how to manually convert a Sweave LaTeX document into a knitr R Markdown document. The post (1) reviews many of the required changes; (2) provides an example of a document converted to R Markdown format based on an analysis of Winter Olympic Medal data up to and including 2006; and (3) discusses the pros and cons of LaTeX and Markdown for performing analyses.

Example Reproducible Report using R Markdown: Analysis of California Schools Test Data

This is a quick set of analyses of the California Test Score dataset. The post was produced using R Markdown in RStudio 0.96. The main purpose of this post is to provide a case study of using R Markdown to prepare a quick reproducible report. It provides examples of using plots, output, in-line R code, and markdown. The post is designed to be read along side the R Markdown source code, which is available as a gist on github.

Getting Started with R Markdown, knitr, and Rstudio 0.96

This post examines the features of R Markdown using knitr in Rstudio 0.96. This combination of tools provides an exciting improvement in usability for reproducible analysis. Specifically, this post (1) discusses getting started with R Markdown and knitr in Rstudio 0.96; (2) provides a basic example of producing console output and plots using R Markdown; (3) highlights several code chunk options such as caching and controlling how input and output is displayed; (4) demonstrates use of standard Markdown notation as well as the extended features of formulas and tables; and (5) discusses the implications of R Markdown. This post was produced with R Markdown. The source code is available here as a gist. The post may be most useful if the source code and displayed post are viewed side by side. In some instances, I include a copy of the R Markdown in the displayed HTML, but most of the time I assume you are reading the source and post side by side.

How to plot three categorical variables and one continuous variable using ggplot2

This post shows how to produce a plot involving three categorical variables and one continuous variable using ggplot2 in R.

Getting Started with JAGS, rjags, and Bayesian Modelling

This post provides links to various resources on getting started with Bayesian modelling using JAGS and R. It discusses: (1) what is JAGS; (2) why you might want to perform Bayesian modelling using JAGS; (3) how to install JAGS; (4) where to find further information on JAGS; (5) where to find examples of JAGS scripts in action; (6) where to ask questions; and (7) some interesting psychological applications of Bayesian modelling.

New Psychology and Cognitive Science Question and Answer Site: COGSCI.SE

There is now a new website for researchers to ask and answer questions on topics related to psychology and cognitive science. The site is cogsci.stackexchange.com. From the success of earlier released sites in the Stack Exchange network such as those on programming, statistics, and latex, the site for psychology and cognitive science has the potential be a great resource for researchers. I'm actively contributing on the site. So, if you are a researcher in psychology, I hope you'll check it out. The rest of this post sets out (a) a little history of Stack Exchange question and answer sites as they relate to psychology and statistics; (b) why I think this new site for psychology and cognitive science has so much potential; and (c) why, if you are a professional or student researcher in psychology, you might want to get involved.

Tips for Undergraduates Interested in a Career in Organisational Psychology: Australian Perspective

Undergraduate psychology students often ask me about careers in organisational psychology. This post aims to provide a few links and resources to assist such students to learn about the profession and the career pathways. The post includes (a) a basic description of organisational psychology, (b) links to Australian educational and professional society resources, (c) discussion of PhD and academic options, and (d) additional resources to learn more about the profession.

Correlation Resources: SPSS, R, Causality, Interpretation, and APA Style Reporting

This post provides links to a range of resources related to the use and interpretation of correlations. I wanted to provide a page with links to a number of additional resources that would be useful both for those of my students who might be keen to learn more and for anyone else who might be interested. Specifically, this post provides links to: (a) introductory book-style chapters on correlation, (b) resources related to assorted issues in correlation (i.e., discussion of causal inference, correlation with various variable types, range restriction, statistical power, correlation interpretation, and significance testing), (c) tutorials on computing correlations using SPSS and R, and (d) tips for reporting correlations in APA Style.

Transition to Linux and Ubuntu: The Experience of a Quantitative Social Scientist

This post discusses my experience migrating to Ubuntu from Windows from the perspective of a quantitatively oriented researcher in psychology. It discusses (a) my general transition to open source tools for doing research; (b) examination of Cygwin; (c) choosing a Linux distribution; (d) preparing for installation of Ubuntu; (e) initial reflections on installing Ubuntu; and (f) a long list of various solutions to specific problems that I encountered whilst getting started with Ubuntu.

Guide to Getting Started with R: 2011 Update

In mid-2009, I wrote a post on getting started with R. A lot has happened in the world of R over the last two years. New books, videos, online documentation, blogs and other resources have emerged. New community structures have emerged. As such I've given the guide a major overhaul both to increase its usability and acknowledge the many exciting changes in the world of R. The updated Guide to Getting Started with R is available here..

Case Study in Customising Syntax Highlighting and Folding in Vim for a Niche Scripting Language Called Inquisit

This post presents my efforts to setup a productive environment for editing Inquisit scripts in Vim. In addition to being relevant to people who write Inquisit scripts, the post is designed as a general case study in customising Vim for a niche programming language. Specifically, the post discusses how to setup in Vim: (a) code folding using a custom expression, (b) custom syntax highlighting, and (c) interactions with the command-line.

Using Vim and VimOutliner as a Brainstorming and Outlining Tool

This post discuses using Vim as an outlining tool. It focuses particularly on VimOutliner. In particular the post (a) discusses reasons why I like outlining tools, (b) presents some links for getting started and installing VimOutliner, (c) presents my verdict on the personal utility of VimOutliner, and (d) presents an assortment of little issues that I encountered and resolved while learning to use VimOutliner.

How to Ask Me a Statistics Question

This post includes instructions on how to ask me a written statistics question.

R Optimisation Tips using Optim and Maximum Likelihood

This post summarises some R modelling tips I picked up at AMPC2011.

R versus Matlab in Mathematical Psychology

I recently attended the 2011 Australasian Mathematical Psychology Conference. This post summarises a few thoughts I had on the use of R, Matlab and other tools in mathematical psychology flowing from discussions with researchers at the conference.

Reasons for Transitioning to Vim: Bringing LaTeX, R, Sweave and More under One Roof

This post describes the reasons for my transition to Vim.

2010 in Review: 99 Most Popular Pages on Jeromy Anglim's Blog

In the spirit of taking stock of the year that's been, and in the spirit of festive television repeats, this post reviews 2010 for this blog.

Question and Answer Sites on Statistics, Computing, Research, and Psychology

This post sets out some of my favourite question and answer sites on topics related to statistics, computing, research, and psychology.

Video of Reproducible Research with R: Melbourne R Users 1st Dec 2010

As previously mentioned I gave a talk at Melbourne R Users Group titled "Reproducible Research and R Workflow". It covered technologies including LaTeX, Sweave, R, make, Eclipse, and git. This post shares the video.

R Workflow: Slides from a Talk at Melbourne R Users (1st Dec 2010)

I gave a presentation at Melbourne R Users on the topic of R Workflow. The presentation covered R code organisation, and useful R related tools including Eclipse, StatET, Git, make, Sweave and LaTeX. Also, the slides from the presentation provide links to four complete examples of using R, Sweave, LaTeX, and make.

Sweave Tutorial 3: Console Input and Output - Multiple Choice Test Analysis

This post provides an example of using Sweave to perform an item analysis of a multiple choice test. It is designed as a tutorial for learning more about using Sweave in a mode where console input and output is displayed. Copies of all source code and the final PDF report is provided.

Sweave Tutorial 2: Batch Individual Personality Reports using R, Sweave, and LaTeX

This post documents an example of using Sweave to generate individualised personality reports based on responses to a personality test. Each report provides information on both the responses of the general sample and responses of the specific respondent. All source code is provided, and selected aspects are discussed, including makefiles use of \Sexpr, figures, and LaTeX tables using Sweave.

Getting Started with Git, EGit, Eclipse, and GitHub: Version Control for R Projects

This post provides information on
(a) installing Git using the Eclipse plugin Egit. (b) uploading repositories to GitHub, and (c) links to resources on Git, Git and LaTeX, and Git and R. The focus is on version control for people working on R, Sweave, and LaTeX related projects.