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Data summarizing the evolution of geographic ranges in eels

Source: R/datasets_doc.R
eel_biogeo_data.Rd

A list containing (fake) geographic ranges data of eels mapped on the phylogeny, modeled with R package BioGeoBEARS. This object was obtained with prepare_trait_data(). Initial data based on feeding habits was altered to be transformed into range "A" and "B", and then adding arbitrarily multi-area "AB" ranges. This is NOT real biogeographic data. Please refer to the initial article for real data.

Original data source: Collar, D. C., P. C. Wainwright, M. E. Alfaro, L. J. Revell, and R. S. Mehta (2014) Biting disrupts integration to spur skull evolution in eels. Nature Communications, 5, 5505. https://doi.org/10.1038/ncomms6505

Usage

data(eel_biogeo_data)

Format

A list with 9 elements.

Details

A list of 9 elements containing information on the evolution of geographic ranges in eels. This object was obtained with prepare_trait_data().

  • $densityMaps List of objects of class "densityMap that contains a phylogenetic tree and associated mapping of probability to harbor a given range along branches. The list contains only a "densityMap per unique areas because split_multi_area_ranges was set to TRUE.

  • $densityMaps_all_ranges List of objects of class "densityMap that contains a phylogenetic tree and associated mapping of probability to harbor a given range along branches. The list contains one "densityMap per range found along branches during the simulated biogeographic histories.

  • $trait_data_type Character string. Record the type of trait data. Here: "biogeographic".

  • $ace Numerical matrix that record the posterior probabilities of ancestral ranges estimated at internal nodes. Only unique areas are considered among the ranges. Multi-area ranges have been split among unique ranges. Rows are internal nodes. Columns are ranges. Values are posterior probabilities of each range per node.

  • $ace_all_ranges Numerical matrix that record the posterior probabilities of ancestral ranges estimated at internal nodes. All ranges observed along branches during the simulated biogeographic histories are present. Rows are internal nodes. Columns are ranges. Values are posterior probabilities of each range per node.

  • $BSM_output List of two lists that contains summary information of cladogenetic ($RES_caldo_events_tables) and anagenetic ($RES_ana_events_tables) events recording across the 1000 simulations of biogeographic histories performed during Biogeographic Stochastic Mapping (BSM). Each element of the list is a data.frame recording events occurring during one simulation.

  • $simmaps List of 1000 objects of class "simmap". Each simmap object is a phylogeny with one simulated biogeographic history (i.e., transitions in geographic ranges) mapped along branches.

  • $best_model_fit List that provides the output of the best fitting model (Here: DEC+J model).

  • $model_selection_df Data.frame that summarizes model comparisons used to select the best fitting model.

References

Collar, D. C., P. C. Wainwright, M. E. Alfaro, L. J. Revell, and R. S. Mehta (2014) Biting disrupts integration to spur skull evolution in eels. Nature Communications, 5, 5505. https://doi.org/10.1038/ncomms6505

See also

prepare_trait_data()