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Dataset summarizing 1000 posterior samples of BAMM for extant whales

Source: R/datasets_doc_for_CRAN.R
whale_BAMM_object.Rd

An object of class "bammdata" containing information on diversification dynamics of extant whales (Cetacea order) modeled with BAMM.

Source: Steeman, M. E., M. B. Hebsgaard, R. E. Fordyce, S. Y. W. Ho, D. L. Rabosky, R. Nielsen, C. Rahbek, H. Glenner, M. V. Sorensen, and E. Willerslev (2009) Radiation of extant cetaceans driven by restructuring of the oceans. Systematic Biology, 58, 573-585.

Usage

data(whale_BAMM_object)

Format

A list with 24 elements.

Details

An object of class "bammdata" containing information on diversification dynamics of extant whales (Cetacea order) modeled with BAMM.

Phylogeny-related elements used to plot a phylogeny with ape::plot.phylo():

  • $edge Integer matrix. Defines the tree topology by providing rootward and tipward node ID of each edge.

  • $Nnode Integer. Number of internal nodes.

  • $tip.label Character vector. Labels of all tips.

  • $edge.length Numeric vector. Length of edges/branches.

BAMM internal elements used for tree exploration:

  • $begin Numeric vector. Absolute time since root of edge/branch start (rootward).

  • $end Numeric vector. Absolute time since root of edge/branch end (tipward).

  • $downseq Integer vector. Order of node visits when using a pre-order tree traversal.

  • $lastvisit ID of the last node visited when starting from the node in the corresponding position in $downseq.

BAMM elements summarizing diversification data:

  • $numberEvents Integer vector. Number of events/macroevolutionary regimes (k+1) recorded in each posterior configuration. k = number of shifts.

  • $eventData List of data.frames. One per posterior sample. Records shift events and macroevolutionary regimes parameters. 1st line = Background root regime.

  • $eventVectors List of integer vectors. One per posterior sample. Record regime ID per branch.

  • $tipStates List of integer vectors. One per posterior sample. Record regime ID per tip.

  • $tipLambda List of numeric vectors. One per posterior sample. Record speciation rates per tip.

  • $tipMu List of numeric vectors. One per posterior sample. Record extinction rates per tip.

  • $eventBranchSegs List of numeric matrices. One per posterior sample. Record regime ID per segment of branches.

  • $meanTipLambda Numeric vector. Mean tip speciation rates across all posterior configurations of tips.

  • $meanTipMu Numeric vector. Mean tip extinction rates across all posterior configurations of tips.

  • $type Character string. Set the type of data modeled with BAMM. Here, type = "diversification".

Additional elements providing key information for downstream analyses:

  • $expectedNumberOfShifts Integer. The expected number of regime shifts used to set the prior in BAMM.

  • $MSP_tree Object of class phylo. List of 4 elements duplicating information from the Phylogeny-related elements above, except $MSP_tree$edge.length is recording the Marginal Shift Probability of each branch (i.e., the probability of a regime shift to occur along each branch)

  • $MAP_indices Integer vector. The indices of the Maximum A Posteriori probability (MAP) configurations among the posterior samples.

  • $MAP_BAMM_object List of 18 elements of class "bammdata" recording the mean rates and regime shift locations found across the Maximum A Posteriori probability (MAP) configurations. All BAMM elements summarizing diversification data hold a single entry describing this mean diversification history.

  • $MSC_indices Integer vector. The indices of the Maximum Shift Credibility (MSC) configurations among the posterior samples.

  • $MSC_BAMM_object List of 18 elements of class "bammdata" recording the mean rates and regime shift locations found across the Maximum Shift Credibility (MSC) configurations. All BAMM elements summarizing diversification data hold a single entry describing this mean diversification history.

References

Steeman, M. E., M. B. Hebsgaard, R. E. Fordyce, S. Y. W. Ho, D. L. Rabosky, R. Nielsen, C. Rahbek, H. Glenner, M. V. Sorensen, and E. Willerslev (2009) Radiation of extant cetaceans driven by restructuring of the oceans. Systematic Biology, 58, 573-585.

See also

BAMM software website: http://bamm-project.org/