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.