Beyond the availability of data and methods, reproducible science requires the traceability of analyses. Whether it is for yourself or for collaborators, as series of tools and good practices can facilitate your work flow, simplify analyses, and prevent the loss of data and results. This lecture provides an introduction to reproducibility using . Slides Click on the image below to access the slides: Related packages knitr knitr provides excellent resources for literate programming mixing with LaTeX or markdown. ...

This practical aims to illustrate the basics of phylogenetic reconstruction using R, with an emphasis on how the methods work, how their results can be interpreted, and the relative advantages and limitations of the methods. Three main classes of phylogenetic approaches are introduced, namely distance-based, maximum parsimony, and maximum likelihood methods. We also illustrate how to assess the reliability of individual nodes using bootstrap, and show how a simple linear model can be used to estimate a molecular clock in rooted phylogenies. ...

leaflet (function() { // If window.HTMLWidgets is already defined, then use it; otherwise create a // new object. This allows preceding code to set options that affect the // initialization process (though none currently exist). window.HTMLWidgets = window.HTMLWidgets || {}; // See if we're running in a viewer pane. If not, we're in a web browser. var viewerMode = window.HTMLWidgets.viewerMode = /\bviewer_pane=1\b/.test(window.location); // See if we're running in Shiny mode. ...

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