# Cut the phylogeny and posterior probability mapping of a categorical trait for a given focal time in the past Cuts off all the branches of the phylogeny which are younger than a specific time in the past (i.e. the `focal_time`). Branches overlapping the `focal_time` are shorten to the `focal_time`. Likewise, remove posterior probability mapping of the categorical trait for the cut off branches by updating the `$tree$maps` and `$tree$mapped.edge` elements. ```r cut_densityMap_for_focal_time(densityMap, focal_time, keep_tip_labels = TRUE) ``` ## Arguments - `densityMap`: Object of class `"densityMap"`, typically generated with `phytools::densityMap()`, that contains a phylogenetic tree and associated posterior probability mapping of a categorical trait. The phylogenetic tree must be rooted and fully resolved/dichotomous, but it does not need to be ultrametric (it can includes fossils). - `focal_time`: Numerical. The time, in terms of time distance from the present, for which the tree and mapping must be cut. It must be smaller than the root age of the phylogeny. - `keep_tip_labels`: Logical. Specify whether terminal branches with a single descendant tip must retained their initial `tip.label`. Default is `TRUE`. ## Returns The function returns the cut densityMap as an object of class `"densityMap"` with three elements. It contains a `$tree` element of classes `"simmap"` and `"phylo"`. This function updates and adds multiple useful sub-elements to the `$tree` element. * `$maps` An updated list of named numerical vectors. Provides the mapping of posterior probability of the state along each remaining edge. * `$mapped.edge` An updated matrix. Provides the evolutionary time spent across posterior probabilities (columns) along the remaining edges (rows). * `$root_age` Integer. Stores the age of the root of the tree. * `$nodes_ID_df` Data.frame with two columns. Provides the conversion from the `new_node_ID` to the `initial_node_ID`. Each row is a node. * `$initial_nodes_ID` Vector of character strings. Provides the initial ID of internal nodes. Used to plot internal node IDs as labels with `ape::nodelabels()`. * `$edges_ID_df` Data.frame with two columns. Provides the conversion from the `new_edge_ID` to the `initial_edge_ID`. Each row is an edge/branch. * `$initial_edges_ID` Vector of character strings. Provides the initial ID of edges/branches. Used to plot edge/branch IDs as labels with `ape::edgelabels()`. The `$col` element describes the colors used to map each possible posterior probability value from 0 to 1000. The `$states` element provide the name of the states. Here, the first value is the absence of the state labeled as "Not X" with X being the state. The second value is the name of the state. High posterior probability reflects high likelihood to harbor the state. Low probability reflects high likelihood to NOT harbor the state. ## Details The phylogenetic tree is cut for a specific time in the past (i.e. the `focal_time`). When a branch with a single descendant tip is cut and `keep_tip_labels = TRUE`, the leaf left is labeled with the tip.label of the unique descendant tip. When a branch with a single descendant tip is cut and `keep_tip_labels = FALSE`, the leaf left is labeled with the node ID of the unique descendant tip. In all cases, when a branch with multiple descendant tips (i.e., a clade) is cut, the leaf left is labeled with the node ID of the MRCA of the cut-off clade. The posterior probability mapping of a categorical trait is updated accordingly by removing mapping associated with the cut off branches. ## Examples ```r # ----- Prepare data ----- # # Load mammals phylogeny and data from the R package motmot included within deepSTRAPP # Data source: Slater, 2013; DOI: 10.1111/2041-210X.12084 data("mammals", package = "deepSTRAPP") # Obtain mammal tree mammals_tree <- mammals$mammal.phy # Convert mass data into categories mammals_mass <- setNames(object = mammals$mammal.mass$mean, nm = row.names(mammals$mammal.mass))[mammals_tree$tip.label] mammals_data <- mammals_mass mammals_data[seq_along(mammals_data)] <- "small" mammals_data[mammals_mass > 5] <- "medium" mammals_data[mammals_mass > 10] <- "large" table(mammals_data) # (May take several minutes to run) # Produce densityMaps using stochastic character mapping based on an equal-rates (ER) Mk model mammals_cat_data <- prepare_trait_data(tip_data = mammals_data, phylo = mammals_tree, trait_data_type = "categorical", evolutionary_models = "ER", nb_simulations = 100, plot_map = FALSE) # Set focal time focal_time <- 80 # Extract the density map for small mammals (state 3 = "small") mammals_densityMap_small <- mammals_cat_data$densityMaps[[3]] # ----- Example 1: keep_tip_labels = TRUE ----- # # Cut densityMap to 80 Mya while keeping tip.label # on terminal branches with a unique descending tip. updated_mammals_densityMap_small <- cut_densityMap_for_focal_time( densityMap = mammals_densityMap_small, focal_time = focal_time, keep_tip_labels = TRUE) # Plot node labels on initial stochastic map with cut-off phytools::plot.densityMap(mammals_densityMap_small, fsize = 0.7, lwd = 2) ape::nodelabels(cex = 0.7) abline(v = max(phytools::nodeHeights(mammals_densityMap_small$tree)[,2]) - focal_time, col = "red", lty = 2, lwd = 2) # Plot initial node labels on cut stochastic map phytools::plot.densityMap(updated_mammals_densityMap_small, fsize = 0.8) ape::nodelabels(cex = 0.8, text = updated_mammals_densityMap_small$tree$initial_nodes_ID) # ----- Example 2: keep_tip_labels = FALSE ----- # # Cut densityMap to 80 Mya while NOT keeping tip.label updated_mammals_densityMap_small <- cut_densityMap_for_focal_time( densityMap = mammals_densityMap_small, focal_time = focal_time, keep_tip_labels = FALSE) # Plot node labels on initial stochastic map with cut-off phytools::plot.densityMap(mammals_densityMap_small, fsize = 0.7, lwd = 2) ape::nodelabels(cex = 0.7) abline(v = max(phytools::nodeHeights(mammals_densityMap_small$tree)[,2]) - focal_time, col = "red", lty = 2, lwd = 2) # Plot initial node labels on cut stochastic map phytools::plot.densityMap(updated_mammals_densityMap_small, fsize = 0.8) ape::nodelabels(cex = 0.8, text = updated_mammals_densityMap_small$tree$initial_nodes_ID) ``` ## See Also `cut_phylo_for_focal_time()` `extract_most_likely_trait_values_for_focal_time()` `extract_most_likely_states_from_densityMaps_for_focal_time()` For a guided tutorial, see this vignette: `vignette("cut_phylogenies", package = "deepSTRAPP")` ## Author(s) Maël Doré

cut_densityMap_for_focal_time function