RRphylogeography code and data

1.     One of the main goals of historical biogeography is understanding where species originated, and how climate change and ecological interactions shaped their distribution. The task is complicated by both active and passive mechanisms, including habitat tracking, the separation of species into metapopulations of variably interconnected demes, and long-distance dispersal which may all obscure the geographic signature of species origin.
2.     Current historical biogeography tools use phylogenies to infer the area of origin. They work by discretizing the geographic range occupied by the species into distinct areas and then applying ancestral character estimation to identify the area occupied at speciation. These methods are powerful and can account for different modes of speciation. Yet, they are bound to assume that the discrete areas currently occupied by the species are faithful representation of their climatic and historic affiliation and ignore metapopulation structures. Still, m..., Literature overview and simulations (the data), R coding (the software), , Supporting Code and Data to replicate RRphylogeography simulations and
compare them to other historical biogeography methods.

**IMPORTANT NOTICE**: Please unzip compressed files and store them as
individual folders named as the corresponding zip file. Then, gather the
RRgeo R package, supporting code files and data in the same folder. The
final “RRphylogeography code and data” folder should include:

gen3sis: folder

clim_variables: folder

occurrences_data: folder

input_mask: tiff file

Workspace: folder

R_functions: folder

RRgeo: zipped R package

## Repository content:

### 1. Guidance vignettes (including annotated and explained code lines):

Simulation-instructions (.pdf)

RRphylogeography-routine (.pdf)

Herodotools-and-BioGeoBEARS-routine (.pdf)

Machuruku-routine (.pdf)

Machuruku-RRphylo-routine (.pdf)

### 2. Data (automatically loaded into the R workspace by executing the scripts):

gen3sis: part of the example data provided within the gen3sis package
which we used to sim...