whale_BAMM_object: Dataset summarizing 1000 posterior samples of BAMM for extant...
In deepSTRAPP: Test for Differences in Diversification Rates over Time
whale_BAMM_object R Documentation
Dataset summarizing 1000 posterior samples of BAMM for extant whales
Description
An object of class "bammdata" containing information of 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 of diversification dynamics
of extant ponerine ants (Ponerinae subfamily) modeled with BAMM.
Phylogeny-related elements used to plot a phylogeny with ape::plot.phylo():
-
$edge Matrix of integers. Defines the tree topology by providing rootward and tipward node ID of each edge.
-
$Nnode Integer. Number of internal nodes.
-
$tip.label Vector of character strings. Labels of all tips.
-
$edge.length Vector of numerical. Length of edges/branches.
BAMM internal elements used for tree exploration:
-
$begin Vector of numerical. Absolute time since root of edge/branch start (rootward).
-
$end Vector of numerical. Absolute time since root of edge/branch end (tipward).
-
$downseq Vector of integers. 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 Vector of integer. 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 branches.
-
$tipStates List of integer vectors. One per posterior sample. Record regime ID per tips.
-
$tipLambda List of numerical vectors. One per posterior sample. Record speciation rates per tips.
-
$tipMu List of numerical vectors. One per posterior sample. Record extinction rates per tips.
-
$eventBranchSegs List of matrix of numerical. One per posterior sample. Record regime ID per segments of branches.
-
$meanTipLambda Vector of numerical. Mean tip speciation rates across all posterior configurations of tips.
-
$meanTipMu Vector of numerical. 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 Vector of integers. 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 holds a single entry describing
this mean diversification history.
-
$MSC_indices Vector of integers. 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 holds 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/
deepSTRAPP documentation built on Jan. 20, 2026, 1:06 a.m.
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| whale_BAMM_object | R Documentation |
Dataset summarizing 1000 posterior samples of BAMM for extant whales
Description
An object of class "bammdata" containing information of 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 of diversification dynamics
of extant ponerine ants (Ponerinae subfamily) modeled with BAMM.
Phylogeny-related elements used to plot a phylogeny with ape::plot.phylo():
-
$edgeMatrix of integers. Defines the tree topology by providing rootward and tipward node ID of each edge. -
$NnodeInteger. Number of internal nodes. -
$tip.labelVector of character strings. Labels of all tips. -
$edge.lengthVector of numerical. Length of edges/branches.
BAMM internal elements used for tree exploration:
-
$beginVector of numerical. Absolute time since root of edge/branch start (rootward). -
$endVector of numerical. Absolute time since root of edge/branch end (tipward). -
$downseqVector of integers. Order of node visits when using a pre-order tree traversal. -
$lastvisitID of the last node visited when starting from the node in the corresponding position in$downseq.
BAMM elements summarizing diversification data:
-
$numberEventsVector of integer. Number of events/macroevolutionary regimes (k+1) recorded in each posterior configuration. k = number of shifts. -
$eventDataList of data.frames. One per posterior sample. Records shift events and macroevolutionary regimes parameters. 1st line = Background root regime. -
$eventVectorsList of integer vectors. One per posterior sample. Record regime ID per branches. -
$tipStatesList of integer vectors. One per posterior sample. Record regime ID per tips. -
$tipLambdaList of numerical vectors. One per posterior sample. Record speciation rates per tips. -
$tipMuList of numerical vectors. One per posterior sample. Record extinction rates per tips. -
$eventBranchSegsList of matrix of numerical. One per posterior sample. Record regime ID per segments of branches. -
$meanTipLambdaVector of numerical. Mean tip speciation rates across all posterior configurations of tips. -
$meanTipMuVector of numerical. Mean tip extinction rates across all posterior configurations of tips. -
$typeCharacter string. Set the type of data modeled with BAMM. Here, type = "diversification".
Additional elements providing key information for downstream analyses:
-
$expectedNumberOfShiftsInteger. The expected number of regime shifts used to set the prior in BAMM. -
$MSP_treeObject of classphylo. List of 4 elements duplicating information from the Phylogeny-related elements above, except$MSP_tree$edge.lengthis recording the Marginal Shift Probability of each branch (i.e., the probability of a regime shift to occur along each branch) -
$MAP_indicesVector of integers. 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 holds a single entry describing this mean diversification history. -
$MSC_indicesVector of integers. The indices of the Maximum Shift Credibility (MSC) configurations among the posterior samples. -
$MSC_BAMM_objectList 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 holds 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/
R Package Documentation
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We want your feedback!
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