mebioda

Introduction to the week and to R

Lectures

• Traits, phenotypes, and functional diversity
• Characters, homology, and data integration
• Topological analysis: tree shape, diversification, PD
• Phylogenetic comparative analysis

Practicals

• R basics, RMarkdown, data I/O
• topological analysis
• character analysis
• functional trait analysis
• functional and phylogenetic diversity

R syntax

• syntax basics
• data import
• data transformation
• data wrangling
• additional cheat sheets

Interacting with the R environment

• Through the R engine
• In RStudio
• On the shell, e.g.:
  • R CMD BATCH script.R - redirects STDOUT to file script.Rout
  • Rscript script.R - no redirection

Installing R packages

• in RStudio
• on the REPL CLI
• with devtools from github

R packages

• ape
• geiger
• diversitree
• phytools
• phangorn
• rmarkdown
• knitr
• picante
• FD
• VEGAN
• TreeSim
• TreePar
• molaR
• geomorph
• Rvcg
• Morpho
• rgl

R communities

• rOpenSci
• r-sig-phylo

Software

• phylocom

Databases

• TRY
• BIEN
• PanTHERIA
• APG-III

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