Biogeobears r package

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August undefined, 2024

WebDec 11, 2014 · 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. WebPackage ‘BioGeoBEARS’ was removed from the CRAN repository. Formerly available versions can be obtained from the archive. Archived on 2024-01-28 as check issues …

rexpokit: R Wrappers for EXPOKIT; Other Matrix Functions

WebApr 3, 2024 · Such packages may be found on GitHub, R-Forge, Bioconductor, or authors’ websites. At least ten packages start as phy* in this domain, including two pairs of similarly named packages (phytools and phylotools, phylobase and phybase); users are encouraged to read and distinguish carefully between package names. WebNov 17, 2014 · Package ‘BioGeoBEARS’ July 2, 2014 Type Package Title BioGeography with Bayesian (and Likelihood) Evolutionary Analysis in R Scripts Version 0.2.1 Date … north central university programs

Bayesian estimation of the global biogeographical history of …

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 … WebSep 1, 2024 · We used these climatic clusters to estimate ancestral ranges using the ‘BioGeoBEARS’ R package. A lineage through time plot was calculated using the R package ‘APE’. We used Bayesian diversification models (compound Poisson process on mass extinction times) to test hypotheses on how late Cenozoic uplift and climatic … WebThe default, cornercoords_loc="manual", will not allow split states to be plot. The R script plot_phylo3_nodecoords.R is located in the BioGeoBEARS extension data directory, extdata/a_scripts. You should be able to get the full path with list.files (system.file ("extdata/a_scripts", package="BioGeoBEARS"), full.names=TRUE). northcentral university registrar

Progress on R-spatial evolution, Apr 2024

nmatzke/BioGeoBEARS: BioGeoBEARS: BioGeography with …

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 … http://phylo.wikidot.com/biogeobears northcentral university reputationWebOct 12, 2024 · : InternetOpenUrl failed: 'The operation timed out' Warning in download.packages(pkgs, destdir = tmpd, available = available, : download of package ‘GEOquery’ failed package ‘rlang’ successfully unpacked and MD5 sums checked package ‘tidyselect’ successfully unpacked and MD5 sums checked package ‘plogr’ successfully … northcentral university phd mft

"WebBioGeoBEARS allows probabilistic inference of both historical biogeography (ancestral geographic ranges on a phylogeny) as well as comparison of different models of range … Details. Summary: This package performs model-based statistical inference for … " - Biogeobears r package

Biogeobears r package

BioGeoBEARS: BioGeography with Bayesian (and …

WebJul 27, 2012 · Details. Summary: This package performs model-based statistical inference for historical biogeography. This includes inference of model parameters, ancestral states, and model comparison. This package performs ML (maximum-likelihood) based inference, but the same functions can easily be integrated into a Bayesian analysis via use of … WebA new R package, BioGeoBEARS, implements many models in a common likelihood framework, so that standard statistical model selection procedures can be applied to let …

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WebWe used the R package ‘BioGeoBEARS’ (Matzke, 2013) to compare biogeographical models and estimate ancestral ranges in the Solanaceae. ‘BioGeoBEARS’ implements maxi-mum likelihood (ML) methods that replicate the key assumptions of three most commonly used methods in his-torical biogeography, namely DEC (dispersal–extinction– WebMay 29, 2024 · BioGeoBEARS_model_object_to_params_upper: Produce the upper limit on the parameters from a BioGeoBEARS... BioGeoBEARS-package: BioGeography with Bayesian (and likelihood) Evolutionary... BioGeoBEARS_run-class: An object of class BioGeoBEARS_run holding the model inputs; calc_AICc_column: Calculate AICc values …

WebBioGeoBEARS is an R package, authored by Nicholas J. Matzke, that is designed to perform inference of biogeographic history on phylogenies, and also model testing and … WebApr 10, 2024 · This is the third report on the R-spatial evolution project. The project involves the retirement (archiving) of rgdal, rgeos and maptools during 2024. The first report set out the main goals of the project. The second report covered progress so far, steps already taken, and those remaining to be accomplished. A talk at the University of Chicago ...

WebJan 2, 2014 · BioGeoBEARS allows probabilistic inference of both historical biogeography (ancestral geographic ranges on a phylogeny) as well as comparison of different models … 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 behavior.

WebApr 12, 2024 · We exported the maximum clade credibility tree inferred in BEAST and a geographical range file into R for historical biogeography reconstruction using the package BioGeoBears (Matzke, 2013). We used six defined regions for our phylogeny: Africa, Asia, Europe, North America, South America and Australia.

WebFigure 1: The processes assumed by di erent historical biogeography methods. Each of these processes is controlled by the speci ed parameter(s) in the BioGeoBEARS … north central university music north central university pseoWeb# When R packages contain extra files, they are stored in the "extdata" directory # inside the installed package. # # BioGeoBEARS contains various example files and scripts in its extdata directory. # # Each computer operating system might install BioGeoBEARS in a different place, # depending on your OS and settings. # northcentral university registrar officeWebMay 9, 2024 · The R package BioGeoBEARS provides a framework for testing maximum likelihood and Bayesian models to reconstruct ancestral ranges (Matzke 2013a). The ability to customize models within this package allows new model types to be compared in addition to more widely used models. north central university skyline loginhttp://phylo.wikidot.com/ how to reset my googleWebAug 14, 2014 · By default, BioGeoBEARS uses the R package optimx (Nash and Varadhan 2011; 2012) to perform ML estimation of the free parameters, using the quasi-Newton method with box constraints (Byrd et al. 1995). Once the ML estimate of the parameters has been made, BioGeoBEARS estimates the probability of each possible ancestral state at … how to reset my google authenticatorWebMay 17, 2024 · In this article, we present and test a new extension of the R package BioGeoBEARS in which macroevolutionary dispersal probability can be affected by a discrete trait that is itself evolving. We apply the model to southern-hemisphere conifers belonging to the families Podocarpaceae and Araucariaceae to test whether the seed … how to reset my fitbit charge