A minimal example of APA manuscript preparation, integrating text & analysis code, using Rmarkdown and papaja
R is a statistical programming language which is increasingly popular with psychologists. It can import and process your data, fit statistical models (from simple t-tests to state of the art such as bayesian multilevel model fitting). It also makes nice plots. RStudio is a way of editing R scripts and running R analysis. RMarkdown is a way of using RStudio to produce documents (e.g. as webpages, MS Word or PDF). Another advantage is that you can include R code in your document file - so no more running your analysis in SPSS and copying the results into your document (and making errors / forgetting which version of the analysis you ran etc). This is an example document which integrates all the functions of Rmarkdown - running analysis, formatting references, etc. It uses an add-on for Rmarkdown called papaja which helps us make nicely APA formatted documents