eel_cat_3lvl_data: Data summarizing the evolution of feeding habits in eels...
In deepSTRAPP: Test for Differences in Diversification Rates over Time

eel_cat_3lvl_data

R Documentation

Data summarizing the evolution of feeding habits in eels using a 3-level factor as categorical trait

Description

A list containing feeding habits data of eels mapped on the phylogeny, modeled with geiger::fitDiscrete. This object was obtained with prepare_trait_data(). Initial data was altered arbitrarily to create three categories, adding a "kiss" feeding habit to the initial "bite" and "suction" data. This is NOT real biological 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. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1038/ncomms6505")}

Usage

data(eel_cat_3lvl_data)

Format

A list with 6 elements.

Details

A list of five objects containing information on the evolution of feeding habits in eels. This object was obtained with prepare_trait_data().

⁠$densityMaps⁠ List of objects of class ⁠"densityMap⁠ that contains a phylogenetic tree and associated mapping of probability to harbor a given state/range along branches. The list contains one ⁠"densityMap⁠ per state/range found in the tip_data.
⁠$trait_data_type⁠ Character string. Record the type of trait data. Here: "categorical".
⁠$simmaps⁠ List of 100 stochastic mapping simulations for trait evolution. Each element is a "simmap" object (see phytools::make.simmap) representing a possible evolutionary history that fits states observed on tips, infered ACE at internal nodes, and transition rates as estimated from the best fit model.
⁠$ace⁠ Numerical matrix that record the posterior probabilities of ancestral states/ranges (characters) estimates (ACE) at internal nodes. Rows are internal nodes. Columns are states/ranges. Values are posterior probabilities of each state per node.
⁠$best_model_fit⁠ List that provides the output of the best fitting model (Here: ER model).
⁠$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. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1038/ncomms6505")}