Combine Two Morpho Objects

Description

This function merges two 'morpho' objects, combining their sequences, model parameters, and transition histories, while ensuring tree and fossil consistency.

Usage

combine.morpho(x, y)

Arguments

Value

A combined 'morpho' object.

Examples

phy <- ape::rtree(10)

# simulate characters along the branches of the tree
morpho1 <-  sim.morpho(tree = phy,
                           k = c(2,3,4),
                           trait.num = 20,
                           ancestral = TRUE,
                           partition = c(10,5,5),
                           ACRV = "gamma",
                           variable = TRUE,
                           ACRV.ncats = 4,
                           define.Q = NULL)

morpho2 <-  sim.morpho(tree = phy,
                           k = c(2,3,4),
                           trait.num = 20,
                           ancestral = TRUE,
                           partition = c(10,5,5),
                           ACRV = "gamma",
                           variable = TRUE,
                           ACRV.ncats = 4,
                           define.Q = NULL)

combined <- combine.morpho(morpho1, morpho2)

Determines the number of convergently evolved traits

Description

Identifies which traits have evolved independently multiple times (convergent evolution) in a morpho object.

Usage

convergent_evol(data = NULL)

Arguments

Value

A data.frame listing convergent traits, their state, and number of transitions

Determines the route (nodes and branches) for a tip in a phylogenetic tree

Description

Traverses the tree to determine the evolutionary path (branches) from root to a given tip.

Usage

find_path_to_tip(tree, tip)

Arguments

Value

A matrix with columns parent and child representing the path

Examples

phy <- ape::rtree(10)
route_n <- find_path_to_tip(phy, "t2")

Add reconstructed tree and matrix to morpho object

Description

Function to add the reconstructed tree and corresponding reconstructed matrix to an existing morpho object

Usage

get.reconstructed(data)

Arguments

Value

a 'morpho object'

Examples

# simulate tree
lambda = 0.1
mu = 0.05
tips = 10
t = TreeSim::sim.bd.taxa(n = tips, numbsim = 1, lambda = lambda, mu = mu)[[1]]

# Simulate fossils and extant taxa
rate = 0.1 # poisson sampling rate
f = FossilSim::sim.fossils.poisson(rate = rate, tree = t, root.edge = FALSE)
rho = 0.5
f2 = FossilSim::sim.extant.samples(fossils = f, tree = t, rho = rho)
morpho_data <-  sim.morpho(k = c(2,3),
                           time.tree = t,
                           trait.num = 6,
                           ancestral = TRUE,
                           br.rates = 0.1,
                           partition = c(4,2),
                           ACRV = "gamma",
                           variable = TRUE,
                           ACRV.ncats = 4,
                           fossil = f2)

re <- get.reconstructed(morpho_data)

Get discrete gamma rates

Description

Computes a set of discrete gamma rates for rate variation across sites or characters. This function is adapted from the phangorn package.

Usage

get_gamma_rates(alpha, k)

Arguments

Value

Numeric vector of length k representing the discrete gamma rates.

Examples

get_gamma_rates(alpha = 0.5, k = 4)

Get discrete log-normal rates

Description

Computes a set of discrete log-normal rates for rate variation across sites or characters. The rates are normalized so that the mean rate equals 1.

Usage

get_lognormal_rates(meanlog, sdlog, k)

Arguments

Value

Numeric vector of length k representing the discrete log-normal rates.

Examples

get_lognormal_rates(meanlog = 0, sdlog = 1, k = 4)

Morpho object

Description

Create a morpho object.

Usage

morpho(
  sequences = NULL,
  trees = NULL,
  model = NULL,
  transition_history = NULL,
  root.states = NULL,
  fossil = NULL
)

as.morpho(
  sequences,
  trees,
  model = NULL,
  transition_history = NULL,
  root.states = NULL,
  fossil = NULL
)

is.morpho(sequences)

Arguments

Value

An object of class "morpho" containing the simulated morphological data and associated information. The object includes the simulated sequences, phylogenetic trees and branch rates used for the simulation, model parameters, root states, fossil information (if provided), and the character transition history.

Example morpho dataset

Description

Small example dataset for testing morpho functions.

Usage

data(morpho_data)

Format

A list with components:

sequences

List of sequences for each taxon

trees

List containing the evolutionary tree

Match sampled ancestor labels

Description

Match the sampled ancestor labels from Morphsim and Fossilsim

Usage

morphsim_fossilsim(data = NULL)

Arguments

Value

A character matrix mapping sampled ancestor labels between the naming conventions used by Morphsim and Fossilsim

Examples

data(morpho_data)
morphsim_fossilsim <- function(data = morpho_data)

Plot full evolutionary history

Description

This function creates a plot showing continuous evolution of discrete traits.

Usage

## S3 method for class 'morpho'
plot(
  x = NULL,
  trait = NULL,
  timetree = FALSE,
  show.fossil = FALSE,
  reconstructed = FALSE,
  root.edge = FALSE,
  edge.width = 1,
  label.offset = 0.05,
  e.cex = 0.5,
  f.cex = 1,
  box.cex = 4,
  col = c("#fdfdfd", "lightgray", "lightblue", "pink", "yellow", "green", "orange"),
  col.timescale = "darkgrey",
  ...
)

Arguments

Value

No return value, called for its side effect of producing a plot.

Examples

# simulate a phylogenetic tree
data(morpho_data)
plot(morpho_data, trait = 4, timetree = FALSE, show.fossil = FALSE,
     root.edge = FALSE, reconstructed = FALSE)

Plots morphological matrix

Description

This function plots the full morphological matrix assocaited with the character data at the tips of a tree. Requires a morpho object as input.

Usage

plotMorphoGrid(
  data = NULL,
  timetree = FALSE,
  seq = "tips",
  num.trait = "all",
  col = c("lavender", "white", "lightskyblue1", "pink", "gold2", "forestgreen", "coral")
)

Arguments

Value

No return value, called for its side effect of producing a plot.

Examples

data(morpho_data)
# plot the character matrix
plotMorphoGrid(data = morpho_data, seq = "tips", num.trait = "all")

Get reconstructed matrix

Description

This function returns the moprhological matrix for tips in the reconstructed tree.

Usage

reconstruct.matrix(data)

Arguments

Color branches for plotting a reconstructed tree

Description

This function generates colors for branches when plotting a reconstructed tree from a morpho object containing fossil data. Branches that are part of the reconstructed tree or have fossils along them are colored black; all others are grey.

Usage

reconstruct.tree(data)

Arguments

Value

A list of length 2:

Remove morphological character data

Description

This function removes characters from a morphological matrix simulated using morphsim

Usage

sim.missing.data(
  data = NULL,
  seq = NULL,
  method = NULL,
  probability = NULL,
  traits = NULL,
  taxa = NULL
)

Arguments

Value

An object of class morpho.

Examples

#' # simulate a phylogenetic tree
phy <- ape::rtree(10)

# simulate characters along the branches of the tree
morpho_data <-  sim.morpho(tree = phy,
                           k = c(2,3,4),
                           trait.num = 20,
                           ancestral = TRUE,
                           partition = c(10,5,5),
                           ACRV = "gamma",
                           variable = TRUE,
                           ACRV.ncats = 4,
                           define.Q = NULL)

# randomly remove data
missing.data <- sim.missing.data(data = morpho_data,
                                  method = "random",
                                  seq = "tips",
                                  probability = 0.5)


# remove data based on the partition
missing.data <- sim.missing.data(data = morpho_data,
                                 method = "partition",
                                 seq = "tips",
                                 probability = c(0.7, 0, 0.5))

# remove data based on the rate it was simulated under
missing.data <- sim.missing.data(data = morpho_data,
                                        method = "rate",
                                        seq = "tips",
                                        probability = c(0,0,0.2,1))

# remove  characters from specific traits
missing.data <- sim.missing.data(data = morpho_data,
                                 method = "trait",
                                 seq = "tips",
                                 probability = 1,
                                 traits = c(1,2,5))

# remove  characters from specific taxa
missing.data <- sim.missing.data(data = morpho_data,
                                 method = "taxa",
                                 seq = "tips",
                                 probability = 1,
                                 taxa = c("t1", "t2"))

Simulate characters along branches in a tree

Description

This function simulates discrete character data along the branches of a phylogentic tree. It can be used with either a time tree or a tree with branch lengths in evolutionary distance. If using a time tree branch rates can be specified, either as one values for all branches or as a vector with different rates per branch. If no branch rates are specified a default of 0.1 is applied to all branches.

Usage

sim.morpho(
  tree = NULL,
  time.tree = NULL,
  k = 2,
  trait.num,
  partition = NULL,
  br.rates = NULL,
  ACRV = NULL,
  alpha.gamma = 1,
  ACRV.ncats = 4,
  meanlog = NULL,
  sdlog = NULL,
  define.ACRV.rates = NULL,
  variable = FALSE,
  ancestral = TRUE,
  fossil = NULL,
  define.Q = NULL
)

Arguments

Value

An object of class 'morpho', with the following components:

sequences

A list containing up to 3 elements: morphological data for the 'tips' of the tree, the 'nodes', and, if provided, the sampled ancestors ('SA'). For 'SA', the naming scheme differs from that of 'FossilSim': the morphological data are named using the specimen number ('data$fossil$specimen') and the branch number along which the fossil was sampled.

tree

A list containing up to 3 elements: the 'EvolTree' (branch lengths in genetic distance), the 'TimeTree' (branch lengths in time units), and 'BrRates' (the evolutionary rate per branch).

model

Information about the model used to simulate the data. 'Specified' states the exact model used per partition, as well as the number of traits and character states respectively. 'RateVar' contains the relative rates used to simulate the data, and 'RateVarTrait' contains information about which rate category was used to simulate each trait. These values are listed from lowest rate (1) to highest.

transition_history

A list containing *n* data frames, where *n* is the number of simulated traits. Each data frame contains information about transitions that occurred for that trait, including the branch number ('edge'), the new state number ('state'), and the point along the branch where the transition occurred ('hmin').

root.states

A vector of root states for each trait.

fossil

The fossil object provided to 'morphsim' from 'FossilSim'. The naming scheme therefore matches that of 'FossilSim'.

Examples

# simulated tree
phy <- ape::rtree(10)

# simulate characters along the branches of the tree
morpho_data <-  sim.morpho(tree = phy,
                           k = c(2,3,4),
                           trait.num = 20,
                           partition = c(10,5,5),
                           ACRV = "gamma",
                           ACRV.ncats = 4,
                           variable = TRUE,
                           ancestral = TRUE,
                           define.Q = NULL)

# To simulate ordered characters:
# First define a Q-matrix. The following is for ordered characters where transitions can only occur
# between states 0 and 1 and 1 and 2

ord_Q <- matrix(c(
-0.5, 0.5, 0.0,
0.3333333, -0.6666667, 0.3333333,
0.0, 0.5, -0.5
), nrow = 3, byrow = TRUE)

# This Q matrix can be then used to simulate character data.

morpho_data <- sim.morpho(tree = phy,
                          k = 3,
                          trait.num = 20,
                          ancestral = TRUE,
                          ACRV = "gamma",
                          variable = TRUE,
                          ACRV.ncats = 4,
                         define.Q = ord_Q)

Calculates statistics for a morpho object

Description

Computes three key pieces of information for a morpho object: 1. The Consistency Index (CI) and Retention Index (RI) based on the tip sequence data. 2. Convergent traits, identifying traits that have evolved independently multiple times. 3. Summary information about the size and structure of the tree.

Usage

stats.morpho(data)

Arguments

Value

A list with three elements: - Statistics: data.frame with CI and RI - Convergent_Traits: data.frame listing convergent traits - Tree: data.frame summarizing extant/extinct tips and sampled ancestors

Examples

data(morpho_data)
summary <- stats.morpho(data = morpho_data)

Generate a symmetric Q matrix

Description

Creates a K x K symmetric rate matrix (Q matrix) with equal transition rates between states. The diagonal elements are set such that each row sums to zero.

Usage

symmetric.Q.matrix(K)

Arguments

Value

A K x K numeric matrix representing the symmetric Q matrix.

Examples

symmetric.Q.matrix(4)

Write reconstructed character matrix to file

Description

Write the character matrix for the reconstructed tree to a nexus file

Usage

write.recon.matrix(data, file = NULL)

Arguments

Value

No return value, called for its side effect of writing data to a file.

Examples

data(morpho_data)
tmp <- tempfile(fileext = ".nex")
write.recon.matrix(data = morpho_data, file = tmp)

Write reconstructed tree to file

Description

Write the reconstructed tree to Newick string

Usage

write.recon.tree(data = NULL, file = NULL)

Arguments

Value

No return value, called for its side effect of writing data to a file.

Examples

data(morpho_data)
tmp <- tempfile(fileext = ".tre")
write.recon.tree(data = morpho_data, file = tmp)

Write the taxa ages of reconstructed tree

Description

Writes the ages of the specimen in the reconstructed tree to a file. The tsv format used here is directly compatible with RevBayes

Usage

write.recon.tsv(data, file, uncertainty = 0)

Arguments

Value

No return value, called for its side effect of writing data to a file.

Examples

data(morpho_data)
tmp <- tempfile(fileext = ".tsv")
write.recon.tsv(data = morpho_data, file = tmp)

Write the taxa ages

Description

Writes the ages of the specimens in the true tree to a file. The tsv format used here is directly compatible with RevBayes

Usage

write.tsv(data, file, uncertainty = 0)

Arguments

Value

No return value, called for its side effect of writing data to a file.

Examples

data(morpho_data)
tmp <- tempfile(fileext = ".tsv")
write.tsv(data = morpho_data, file = tmp)