Skip to contents

Update diversification rates/regimes mapped on a phylogeny up to a given time in the past

Source: R/update_rates_and_regimes_for_focal_time.R
update_rates_and_regimes_for_focal_time.Rd

Updates an object of class "bammdata" to obtain the diversification rates/regimes found along branches at a specific time in the past (i.e. the focal_time). Optionally, the function can update the object to display a mapped phylogeny such as branches overlapping the focal_time are shorten to the focal_time.

Usage

update_rates_and_regimes_for_focal_time(
  BAMM_object,
  focal_time,
  update_rates = TRUE,
  update_regimes = TRUE,
  update_tree = FALSE,
  update_plot = FALSE,
  update_all_elements = FALSE,
  keep_tip_labels = TRUE,
  verbose = TRUE
)

Arguments

BAMM_object

Object of class "bammdata", typically generated with prepare_diversification_data(), that contains a phylogenetic tree and associated diversification rate mapping across selected posterior samples. 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, at which the tree and rate mapping must be cut. It must be smaller than the root age of the phylogeny.

update_rates

Logical. Specify whether diversification rates stored in $tipLambda (speciation) and $tipMu (extinction) must be updated to summarize rates found along branches at focal_time. Default is TRUE.

update_regimes

Logical. Specify whether diversification regimes stored in $tipStates must be updated to summarize regimes found along branches at focal_time. Default is TRUE.

update_tree

Logical. Specify whether to update the phylogeny such as all branches that are younger than the focal_time are cut-off. Default is FALSE.

update_plot

Logical. Specify whether to update the phylogeny AND the elements used by plot_BAMM_rates() to plot diversification rates on the phylogeny such as all branches that are younger than the focal_time are cut-off. Default is FALSE. If set to TRUE, it will override the update_tree parameter and update the phylogeny.

update_all_elements

Logical. Specify whether to update all the elements in the object, including rates/regimes/phylogeny/elements for plot_BAMM_rates()/all other elements. Default is FALSE. If set to TRUE, it will override other update_* parameters and update all elements.

keep_tip_labels

Logical. Should terminal branches with a single descendant tip retain their initial tip.label on the updated phylogeny and diversification rate mapping? Default is TRUE. If set to FALSE, the tipward node ID will be used as label for all tips.

verbose

Logical. Should progression be displayed? A message will be printed for every batch of 100 BAMM posterior samples updated. Default is TRUE.

Value

The function returns a list as an updated BAMM_object of class "bammdata".

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, including fossils older than focal_time if present.

    • If keep_tip_labels = TRUE, cut-off branches with a single descendant tip retain their initial tip.label.

    • If keep_tip_labels = FALSE, all cut-off branches are labeled using their tipward node ID.

  • $edge.length Vector of numerical. Length of edges/branches.

  • $node.label Vector of character strings. Labels of all internal nodes. (Present only if present in the initial BAMM_object)

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 named integer vectors. One per posterior sample. Record regime ID per tips present at focal_time. Updated if update_regimes = TRUE.

  • $tipLambda List of named numerical vectors. One per posterior sample. Record speciation rates per tips present at focal_time. Updated if update_rates = TRUE.

  • $tipMu List of named numerical vectors. One per posterior sample. Record extinction rates per tips present at focal_time. Updated if update_rates = TRUE.

  • $eventBranchSegs List of matrix of numerical. One per posterior sample. Record regime ID per segments of branches.

  • $meanTipLambda Vector of named numerical. Mean tip speciation rates across all posterior configurations of tips present at focal_time (does not includes older fossils).

  • $meanTipMu Vector of named numerical. Mean tip extinction rates across all posterior configurations of tips present at focal_time (does not includes older fossils).

  • $type Character string. Set the type of data modeled with BAMM. Should be "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) whose origin is older that focal_time.

  • $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) configuration. All BAMM elements summarizing diversification data holds a single entry describing this the mean diversification history, updated for the focal_time`.

  • $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, updated for the focal_time`.

New elements added to provide update information:

  • $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().

  • $dtrates List of three elements.

    • 1/ $dtrates$tau Numerical. Resolution factor describing the fraction of each segment length used in plot_BAMM_rates() compared to the full depth of the initial tree (i.e., the root_age)

    • 2/ $dtrates$rates List of two numerical vectors. Speciation and extinction rates along segments used by plot_BAMM_rates().

    • 3/ $dtrates$tmat Matrix of numerical. Start and end times of segments in term of distance to the root.

  • $initial_colorbreaks List of three vectors of numerical. Rate values of the percentiles delimiting the bins for mapping rates to colors with BAMMtools::plot.bammdata(). Each element provides values for different type of rates ($speciation, $extinction, $net_diversification).

  • $focal_time Integer. The time, in terms of time distance from the present, at which the rates/regimes were extracted and the tree was eventually cut.

Details

The object of class "bammdata" (BAMM_object) is cut-off at a specific time in the past (i.e. the focal_time) and the current diversification rate values of the overlapping edges/branches are extracted.

—– Update diversification rate data —–

If update_rates = TRUE, diversification rates of branches overlapping with focal_time will be updated. Each cut-off branches form a new tip present at focal_time with updated associated diversification rate data. Fossils older than focal_time do not yield any data.

  • $tipLambda contains speciation rates.

  • $tipMu contains extinction rates.

If update_regimes = TRUE, diversification regimes of branches overlapping with focal_time will be updated. Each cut-off branches form a new tip present at focal_time with updated associated diversification regime ID found in $tipStates. Fossils older than focal_time do not yield any data.

—– Update the phylogeny —–

If update_tree = TRUE, elements defining the phylogeny, as in an "phylo" object will be updated such as all branches that are younger than the focal_time are cut-off:

  • $edge defines the tree topology.

  • $Nnode defines the number of internal nodes.

  • $tip.label provides the labels of all tips, including fossils older than focal_time if present.

  • $edge.length provides length of all branches.

  • $node.label provides the labels of all internal nodes. (Optional)

—– Update the plot from plot_BAMM_rates() —–

If update_plot = TRUE, elements used to plot diversification rates on the phylogeny using plot_BAMM_rates() will be updated such as all branches that are younger than the focal_time are cut-off:

  • $begin provides absolute time since root of edge/branch start (rootward).

  • $end provides absolute time since root of edge/branch end (tipward).

  • $eventVectors provides regime membership per branches in each posterior sample configuration.

  • $eventBranchSegs provides regime membership per segments of branches in each posterior sample configuration.

  • $dtrates provides mean speciation and extinction rates along segments of branches, and resolution fraction (tau) describing the fraction of each segment length compared to the full depth of the initial tree (i.e., the root_age).

See also

cut_phylo_for_focal_time() plot_BAMM_rates()

Author

Maël Doré

Examples

# ----- Example 1: Extant whales (87 taxa) ----- #

## Load the BAMM_object summarizing 1000 posterior samples of BAMM
data(whale_BAMM_object, package = "deepSTRAPP")

## Set focal-time to 5 My
focal_time = 5

## Update the BAMM object
whale_BAMM_object_5My <- update_rates_and_regimes_for_focal_time(
   BAMM_object = whale_BAMM_object,
   focal_time = 5,
   update_rates = TRUE, update_regimes = TRUE,
   update_tree = TRUE, update_plot = TRUE,
   update_all_elements = TRUE,
   keep_tip_labels = TRUE,
   verbose = TRUE)
#> 2025-10-22 14:34:18.595919 - Tip states/rates updated for BAMM posterior sample n°100/1000
#> 2025-10-22 14:34:18.821238 - Tip states/rates updated for BAMM posterior sample n°200/1000
#> 2025-10-22 14:34:19.067507 - Tip states/rates updated for BAMM posterior sample n°300/1000
#> 2025-10-22 14:34:19.28706 - Tip states/rates updated for BAMM posterior sample n°400/1000
#> 2025-10-22 14:34:19.456503 - Tip states/rates updated for BAMM posterior sample n°500/1000
#> 2025-10-22 14:34:19.645893 - Tip states/rates updated for BAMM posterior sample n°600/1000
#> 2025-10-22 14:34:19.824692 - Tip states/rates updated for BAMM posterior sample n°700/1000
#> 2025-10-22 14:34:20.039497 - Tip states/rates updated for BAMM posterior sample n°800/1000
#> 2025-10-22 14:34:20.218913 - Tip states/rates updated for BAMM posterior sample n°900/1000
#> 2025-10-22 14:34:20.398334 - Tip states/rates updated for BAMM posterior sample n°1000/1000

# Add "phylo" class to be compatible with phytools::nodeHeights()
class(whale_BAMM_object) <- unique(c(class(whale_BAMM_object), "phylo"))
root_age <- max(phytools::nodeHeights(whale_BAMM_object)[,2])
# Remove temporary "phylo" class
class(whale_BAMM_object) <- setdiff(class(whale_BAMM_object), "phylo")

## Plot initial BAMM_object for t = 0 My
plot_BAMM_rates(whale_BAMM_object, add_regime_shifts = TRUE,
                labels = TRUE, legend = TRUE, cex = 0.5,
                par.reset = FALSE) # Keep plotting parameters in memory to use abline().
abline(v = root_age - focal_time,
      col = "red", lty = 2, lwd = 2)


## Plot updated BAMM_object for t = 5 My
plot_BAMM_rates(whale_BAMM_object_5My, add_regime_shifts = TRUE,
                labels = TRUE, legend = TRUE, cex = 0.8)


# ----- Example 2: Extant Ponerinae (1,534 taxa) ----- #

## Load the BAMM_object summarizing 1000 posterior samples of BAMM
data(Ponerinae_BAMM_object, package = "deepSTRAPP")

## Set focal-time to 10 My
focal_time = 10

if (FALSE) { # \dontrun{
## Update the BAMM object (May take several minutes to run)
Ponerinae_BAMM_object_10My <- update_rates_and_regimes_for_focal_time(
  BAMM_object = Ponerinae_BAMM_object,
  focal_time = focal_time,
  update_rates = TRUE, update_regimes = TRUE,
  update_tree = TRUE, update_plot = TRUE,
  update_all_elements = TRUE,
  keep_tip_labels = TRUE,
  verbose = TRUE) } # }

## Load results to save time
data(Ponerinae_BAMM_object_10My, package = "deepSTRAPP")

## Extract root age
# Add temporarily the "phylo" class to be compatible with phytools::nodeHeights()
class(Ponerinae_BAMM_object) <- unique(c(class(Ponerinae_BAMM_object), "phylo"))
root_age <- max(phytools::nodeHeights(Ponerinae_BAMM_object)[,2])
# Remove temporary "phylo" class
class(Ponerinae_BAMM_object) <- setdiff(class(Ponerinae_BAMM_object), "phylo")

## Plot diversification rates on the initial tree
plot_BAMM_rates(Ponerinae_BAMM_object,
                legend = TRUE, labels = FALSE)
abline(v = root_age - focal_time,
       col = "red", lty = 2, lwd = 2)


## Plot diversification rates and regime shifts on the updated tree (cut-off for 10 My)
# Keep the initial color scheme
plot_BAMM_rates(Ponerinae_BAMM_object_10My, legend = TRUE, labels = FALSE,
                colorbreaks = Ponerinae_BAMM_object_10My$initial_colorbreaks$net_diversification)


# Use a new color scheme mapped on the new distribution of rates
plot_BAMM_rates(Ponerinae_BAMM_object_10My, legend = TRUE, labels = FALSE)