Biogeobears tutorial
WebOct 30, 2013 · Dr. Nicholas Matzke discusses special cases of a supermodel implemented in BioGeoBEARS, a new R package that implements the most popular biogeographical mode... WebOct 15, 2024 · October 15, 2024 Software Open Access . nmatzke/BioGeoBEARS: BioGeoBEARS: BioGeography with Bayesian (and likelihood) Evolutionary Analysis with R Scripts. Nicholas J. Matzke
Biogeobears tutorial
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WebApr 10, 2024 · BioGeoBEARS adds an additional cladogenic event: founder-event speciation (the new species jumps to a range outside of the ancestral range), and also allows the relative weighting of the different sorts of events to be made into free parameters, allowing optimization and standard model choice procedures to pick the best model. ... WebFeb 27, 2024 · This tutorial provides a brief background in some of these models, then describes how to perform Bayesian inference of historical biogeography using RevBayes. ... Founder-event speciation in …
WebThe starting parameters are d=0.01 and e=0.01. All of the. #' other BioGeoBEARS models can be created by modifying the setup of the DEC model. #' (adding free parameters, changing the weight of different cladogenesis events, etc.). #' This does \emph {not} mean that all of these models are special cases of DEC. The. WebMar 6, 2024 · Results from BioGeoBEARS showing AIC for each biogeographic model estimating ancestral area for reticulating phylogenies broken into parental major (Tree 1) and minor sister clades (Tree 2) of Lampropeltis. Table_S2.BioGeoBears_results.txt. ... BioGEOBEARS_Tutorial_Lamps .R. Data 4. Geographic areas used for …
WebMay 26, 2011 · R packages. BioGeoBEARS — inference and model choice in historical/phylogenetic biogeography. See also Publications using BioGeoBEARS.. rexpokit — accessory package for BioGeoBEARS, does fast matrix exponentiation with the FORTRAN package EXPOKIT (Sidje 1998). cladoRcpp — accessory package for … Webadd_corners: Iterate up through a plotted tree, getting the coordinates of... addslash: Add a slash to a directory name if needed add_to_downpass_labels: Iterate up and down a tree in C++ LAGRANGE downpass order adf: Convert to data.frame, without factors adf2: Convert to data.frame, without factors AICstats_2models: Calculate all the AIC and LRT stats …
WebMay 15, 2024 · A tag already exists with the provided branch name. Many Git commands accept both tag and branch names, so creating this branch may cause unexpected …
WebNov 13, 2013 · The main goals of the workshop are for participants to (1) understand the different historical biogeography methods, and understand what assumptions they are making, (2) to learn how to run BioGeoBEARS and do statistical model comparison and ancestral range estimation, and hopefully (3) try it out on their own data. new orleans community resource guideWebThe utility of the legend is also debatable, as plot_BioGeoBEARS_results plots the colors and state/range names directly onto the plot. Any legend will get unwieldy above perhaps … new orleans comic conventionWebMay 29, 2024 · add_corners: Iterate up through a plotted tree, getting the coordinates of... addslash: Add a slash to a directory name if needed add_to_downpass_labels: Iterate up and down a tree in C++ LAGRANGE downpass order adf: Convert to data.frame, without factors adf2: Convert to data.frame, without factors AICstats_2models: Calculate all the … new orleans community developmentWebApr 3, 2024 · BioGeoBEARS allows probabilistic inference of both historical biogeography (ancestral geographic ranges on a phylogeny) as well as comparison of different models of range evolution. Epidemiology. See the Epidemiology task view for details about packages useful for epidemiology, including phylogenetic epidemiology. Omics neworleans.comhttp://mnh.scu.edu.cn/soft/blog/RASP/index.html new orleans community print shopWebManually modify the states_list. This strategy can allow/disallow any combination of states/ranges that you like, in any time bin, but it requires you to understand how to … introduction to lighting pptWebThe utility of the legend is also debatable, as plot_BioGeoBEARS_results plots the colors and state/range names directly onto the plot. Any legend will get unwieldy above perhaps 32 states, which is just 5 areas with no constraints (see numstates_from_numareas, or type numstates_from_numareas (numareas5, maxareas5, include_null_range=TRUE). new orleans community foundation