benchmark {DAISIEprep}

Performance analysis of the extract_island_species() function Uses system.time() for timing for reasons explained here: https://radfordneal.wordpress.com/2014/02/02/inaccurate-results-from-microbenchmark/ # nolint

Description

Performance analysis of the extract_island_species() function Uses system.time() for timing for reasons explained here: https://radfordneal.wordpress.com/2014/02/02/inaccurate-results-from-microbenchmark/ # nolint

Usage

benchmark(
  phylod,
  tree_size_range,
  num_points,
  prob_on_island,
  prob_endemic,
  replicates,
  extraction_method,
  asr_method,
  tie_preference,
  log_scale = TRUE,
  parameter_index = NULL,
  verbose = FALSE
)

Arguments

phylod

A phylo4d object from the package phylobase containing phylogenetic and endemicity data for each species.

tree_size_range

Numeric vector of two elements, the first is the smallest tree size (number of tips) and the second is the largest tree size

num_points

Numeric determining how many points in the sequence of smallest tree size to largest tree size

prob_on_island

Numeric vector of each probability on island to use in the parameter space

prob_endemic

Numeric vector of each probability of an island species being endemic to use in the parameter space

replicates

Numeric determining the number of replicates to use to account for the stochasticity in sampling the species on the island and endemic species

extraction_method

A character string specifying whether the colonisation time extracted is the minimum time (min) (before the present), or the most probable time under ancestral state reconstruction (asr).

asr_method

A character string, either "parsimony" or "mk" determines whether a maximum parsimony or continuous-time markov model reconstructs the ancestral states at each node. See documentation in castor::asr_max_parsimony() or castor::asr_mk_model() in castor R package for details on the methods used.

tie_preference

Character string, either "island" or "mainland" to choose the most probable state at each node using the max.col() function. When a node has island presence and absence equally probable we need to decide whether that species should be considered on the island. To consider it on the island use ties.method = "last" in the max.col() function, if you consider it not on the island use ties.method = "first". Default is "island".

log_scale

A boolean determining whether the sequence of tree sizes are on a linear (FALSE) or log (TRUE) scale

parameter_index

Numeric determining which parameter set to use (i.e which row in the parameter space data frame), if this is NULL all parameter sets will be looped over

verbose

Boolean. States if intermediate results should be printed to console. Defaults to FALSE

Value

Data frame