MorphSim (version 0.1.0)

sim.missing.data: 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
)

Value

An object of class morpho.

Arguments

data

A `morpho` object with sequence data.

seq

Character. Which sequence data to use: "tips", "nodes", or "SA".

method

Character. Method for removing data. Options:

• "random": removes characters randomly across the matrix.

• "partition": removes characters by partition (probabilities per partition).

• "rate": removes characters by rate category (probabilities per rate category).

• "trait": removes characters from specific traits.

• "taxa": removes characters from specific taxa.

• "extinct": removes data from extinct taxa only. Note: This refers to characters from the tips.

probability

Numeric. Probability of missing data (single value or vector depending on method).

traits

When method = "trait", indices of traits to remove.

taxa

When method = "taxa", indices of taxa to remove.

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"))