The accompanying R Notebook is a simple example that combines R code chunks, Python code chunks, and BibTeX literature citations in one R Markdown document. For additional information please see RStudio as a Research and Writing Platform. Click here to read the notebook.
Making maps on a computer has traditionally required the use of desktop geographic information system (GIS) software such as ArcGIS or QGIS. An alternative is to use R, a free software environment for statistical computing and graphics. R has many features that allow it to read GIS data and produce both static and interactive maps. This document (which is an R Notebook) shows how to make maps with R and RStudio, using R base graphics and the maps and mapdata packages, in addition to the leaflet and tmap packages.
The R Notebook Habitat structure and phenotypic variation in the invading butterfly Coenonympha tullia is a mockup of a scientific paper (although the field data are real) to illustrate the use of R Notebooks as a means of creating reproducible research. The objective is to produce publication-quality output, in HTML, PDF, and Microsoft Word formats, with text, literature citations, a formatted bibliography, statistical analyses, tables, and graphics, all from one, plain-text R Notebook.