name.check
(Package: geiger) :
Compares taxa in data and tree
This function is a general tool for checking for concordance between a data file and a phylogenetic tree. For the data, names can be specified as the names of objects in the vector, rownames of the data array or as 'data.names'. The name.check function finds and lists all taxa present in data set but not in the tree, and vice-versa. The treedata function returns a list containing both the tree and the data after pruning out any species that are not found in both.
● Data Source:
CranContrib
● Keywords: arith
● Alias: name.check
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A package for macroevolutionary simulation and estimating parameters related to diversification from comparative phylogenetic data.
● Data Source:
CranContrib
● Keywords:
● Alias: geiger, geiger-package
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Runs a user defined number of calibration simulations (Wegmann et al. 2009) to generate tuning parameters MECCA's ABC-MCMC. The function takes a large number of arguments but in most cases these can remain at default settings.
● Data Source:
CranContrib
● Keywords:
● Alias: calibrate.mecca
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fitContinuous
(Package: geiger) :
model fitting for continuous comparative data
fitting macroevolutionary models to phylogenetic trees
● Data Source:
CranContrib
● Keywords: arith, models
● Alias: fitContinuous
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Computes Akaike's Information Criterion for MCMC samples (AICM: see Raftery et al. 2007). Can be used to perform model selection using output from fitContinuousMCMC.
● Data Source:
CranContrib
● Keywords:
● Alias: aicm
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performs posterior predictive checks for models of quantitative trait evolution. At present, only BM, EB, and clade.shift models are implemented
● Data Source:
CranContrib
● Keywords:
● Alias: pp.mcmc
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working with systematic reference tables and phylogenies
● Data Source:
CranContrib
● Keywords: data, graphs, manip
● Alias: glomogram.phylo, lookup.phylo, nodelabel.phylo, phylo.clades, phylo.lookup
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rc
(Package: geiger) :
relative cladogenesis test
conducting the relative cladogenesis test for all slices through a tree
● Data Source:
CranContrib
● Keywords: arith
● Alias: rc
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This function takes the output of calibrateMecca along with observed data and partial least squares loadings and outputs starting values and tuning parameters for the ABC-MCMC (Wegmann et al. 2009).
● Data Source:
CranContrib
● Keywords:
● Alias: startingpt.mecca
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geiger-example functions are used solely for demonstrative purposes
● Data Source:
CranContrib
● Keywords:
● Alias: ex.jumpsimulator, ex.ratesimulator, ex.traitgram
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providing 
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