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To install the R package LEMAD, make sure you have devtools installed and then type from R (Rstudio):
library(devtools)
remotes::install_github("leonelhalsina/lemad")
It is likely that the latest Rtools needs to be installed. We recommend to have the latest R (it works perfectly with R 4.2.1). Also, package rgal might cause issues.
For MAC users, it is being reported that installing gfortran 11.2 could be useful.
We have prepared a vignette (a sort of manual with chunks of code) that can be called once you load the library:
library(lemad)
devtools::install(build_vignettes = TRUE)
browseVignettes("lemad")
You can also see the Vignette by clicking on link located in the right hand side of this wiki page.
1- On November 8th 2022 we have released a version 2.1.0 where c++ code (from Thijs Janzen, University of Groningen) is used to reduce computation time. It is a shame that we could not include this nice feature at the time of publishing the paper three months ago. In the paper we mentioned that a 66-species tree and 3 areas (which means it is total of 7 areas because all combinations) takes 10 minutes to complete analysis. With this c++ improvement, that time is shorted. It now takes 5 seconds.
2- On December 7th 2022 we have release a version 2.1.1 to be able to include an region "with no modern species" into the analysis. Additionally, LEMAD can take a tailored matrix to define what dispersal/extirpation events can take place. Vignette is updated.
3- On January 25th 2023: user can choose between simplex and subplex routines to maximize the likelihood.
4.- On August 4th 2023: lemad alphabetically sorts the areas
5.- On August 7th 2023: lemad offers a function to plot the output.
When using lemad, please cite:
Herrera-Alsina L, Algar A. C., Lancaster L.T., Ornelas J. F., Bocedi G, Papadopulos A. S. T., Gubry-Rangin C., Osborne O. G., Mynard P., Sudiana I. M., P Lupiyaningdyah P., Juliandi B. & Travis J.M.J. (2022). The Missing Link in Biogeographic Reconstruction: Accounting for Lineage Extinction Rewrites History. Journal of Biogeography https://doi.org/10.1111/jbi.14489
- Reconstructing ancient dispersal through Antarctica: A case study of stream-inhabiting beetles: https://doi.org/10.1111/jbi.14702