class: center, middle, inverse, title-slide # Reproducible science: Module2 ## Bridging the gap among actors ### <a href="dossa@xtbg.org.cn">Gbadamassi G.O. Dossa</a> ### Xishuangbanna Tropical Botanical Garden, XTBG-CAS ### 2021/09/20 (updated: 2022-06-27) --- class: center, middle # Acknowledgements The content of this module are based on materials from: .pull-right[  ] .pull-right[ [Roger D. Peng's materials](https://publichealth.jhu.edu/faculty/1549/roger-d-peng) ] --- class: center, middle # Where is the Gap?  --- class: center # How can we bridge the gap?  --- class: center # Research pipeline  Please examine again this pipeline. --- class: center # Recent developments in reproducible research  --- class: center # What do we need for reproducible research? -- .left[ - Analytic data are available; ] -- .left[ - Analytic code are available; ] -- .left[ - Documentation of code and data; ] -- .left[ - Standard means of distribution. ] --- class: center # Who are the players? .left[ - Authors: -> Want to make their research reproducible -> Want tools for RR to make their lives easier (or at least not much harder) ] -- .left[ - Readers: -> Want to reproduce (and perhaps expand upon) interesting findings -> Want tools for RR to make their lives easier ] --- class: center # Existing chalenges .left[ - Authors must undertake considerable effort to put data/results on the web (may not have resources like a web server); - Readers must download data/results individually and piece together which data go with which code sections, etc.; - Readers may not have the same resources as authors; - Few tools to help authors/readers (although toolbox is growing!). ] --- class: center # Responses to challenges: in reality .left[ - Authors -> Just put stuff on the web -> (Infamous) Journal supplementary materials -> There are some central databases for various fields (e.g. biology, ICPSR) ] -- .left[ - Readers -> Just download the data and (try to) figure it out -> Piece together the software and run it ] --- class: center # Literate (statistical) programming .left[ - An article is a stream of text and code; - Analysis code is divided into text and code chunks; - Each code chunk loads data and computes results. ] -- .left[ - Presentation code formats results (tables, figures, etc.); - Article text explains what is going on; - Literate programs can be weaved to produce human-readable documents and tangled to produce machine-readable documents. ] --- class: center # Literate (statistical) programming 2 .left[ Literate programming is a general concept that requires: - A documentation language (human readable); - A programming language (machine readable): 1. Sweave uses L^AT^EX and R as the documentation and programming languages 2. Sweave was developed by Friedrich Leisch (member of the R Core) and is maintained by R core [Sweave's main web site](http://www.statistik.lmu.de/~leisch/Sweave). ] --- class: center # Sweave Limitations .left[ Sweave has many limitations: - Focused primarily on LaTeX language, a difficult to learn markup language used only by weirdos; - Lacks features like caching, multiple plots per chunk, mixing programming languages and many other technical items; - Not frequently updated or very actively developed. ] -- .left[So is there any alternative to Sweave? ] --- class: center # Alternative to Sweave: knitr .left[ - Yes, there is knitr is an alternative (more recent) package to Sweave developed by [**Yihui Xie**](https://yihui.org/en/about/); - Brings together many features added on to Sweave to address limitations; - knitr uses R as the programming language and variety of documentation languages LaTeX, Markdown, HTML; - knitr was developed by Yihui Xie (while a graduate student in statistics at Iowa State); - See [*knitr*](http://yihui.name/knitr/) for more and in lectures later. ] --- class: center # Does reproducibility consume more time? <div class="figure" style="text-align: center"> <img src="img/time-saving.png" alt="Reproducibilit equals effecient use of time" width="80%" /> <p class="caption">Reproducibilit equals effecient use of time</p> </div> --- class: center # Summary .left[ - Reproducible research is important as a minimum standard, particularly for studies that are difficult to replicate; - Infrastructure is needed for creating and distributing reproducible documents, beyond what is currently available; - There is a growing number of tools for creating reproducible documents. ] --- class: center, middle # Thank you for listening! Any questions now or email me at [**dossa@xtbg.org.cn**](http://people.ucas.edu.cn/~Dossa?language=en) Slides created via the R package [**xaringan**](https://github.com/yihui/xaringan). The chakra comes from [remark.js](https://remarkjs.com), [**knitr**](https://yihui.org/knitr/), and [R Markdown](https://rmarkdown.rstudio.com).