default_params_doc: Documentation for function arguments in the DAISIEmainland...

In joshwlambert/DAISIEmainland: Simulates Data for Phylogenetic Data on Islands for DAISIE with the Addition of Mainland Dynamics

Documentation for function arguments in the DAISIEmainland package

Description

Documentation for function arguments in the DAISIEmainland package

Usage

default_params_doc(
  branch_code,
  branching_times,
  event_times,
  missing_species,
  stac,
  timeval,
  total_time,
  gam,
  laa,
  lac,
  mu,
  k,
  num_spec,
  num_immigrants,
  mainland_n,
  island_tbl,
  multi_mainland_clade,
  mainland_clade,
  mainland_spec,
  mainland_sample_prob,
  mainland_sample_type,
  m,
  verbose,
  rates,
  island_pars,
  mainland_ex,
  replicates,
  possible_event,
  max_spec_id,
  mainland_scenario,
  anc_branch_t_bp,
  subset_island,
  daisie_mainland_data,
  daisie_data,
  ideal_daisie_data,
  empirical_daisie_data,
  ideal_or_empirical_island,
  species_type,
  ideal_ml,
  empirical_ml,
  sim_params,
  param_set,
  data_folder_path,
  output_file_path,
  param_space,
  parameter,
  plotting_data,
  breaks,
  num_breaks,
  signif,
  scientific,
  transform,
  mainland,
  age,
  multi_daisie_data,
  analysis_result,
  analysis_results,
  labels,
  branch_colour
)

Arguments

branch_code	a species' branching pattern, as checked by check_branch_code, e.g. A, AB, AABA.
branching_times	island age and stem age of the population/species in the case of Non-endemic, Non-endemic_MaxAge and Endemic anagenetic species. For cladogenetic species these should be island age and branching times of the radiation including the stem age of the radiation. See check_branching_times for a more detailed description.
event_times	the island age, stem age of species, and -for cladogenetic species- speciation times, as checked by check_event_times
missing_species	the number of island species that were not sampled for particular clade (only applicable for endemic clades), as can be checked by check_missing_species
stac	the status of the colonist, see stac_to_str for values and meanings
timeval	Numeric defining current time of simulation.
total_time	Numeric defining the length of the simulation in time units.
gam	Numeric with the per capita immigration rate.
laa	Numeric with the per capita anagenesis rate.
lac	Numeric with the per capita cladogenesis rate.
mu	Numeric with the per capita extinction rate.
k	Numeric with carrying capacity.
num_spec	Numeric with the current number of species.
num_immigrants	Numeric with the current number of non-endemic species.
mainland_n	Numeric stating the number of mainland species that can colonize the island.
island_tbl	Data frame with current state of simulation containing number of species, see create_test_island_tbl()
multi_mainland_clade	A list of data frames each data frame is an mainland_clade
mainland_clade	Data frame with state of mainland, see create_test_mainland_clade()
mainland_spec	Numeric focal species on the mainland
mainland_sample_prob	Numeric between zero and one determining the probability of an extant mainland species being sampled.
mainland_sample_type	String either "unsampled" for unsampled known species on the mainland, "undiscovered" for undiscovered species on the mainland, or "complete" if the mainland sampling probability is one.
m	Numeric defining the size of mainland pool.
verbose	Logical, determining if progress output should be printed during the simulation.
rates	named list of numeric rates as returned by calc_rates.
island_pars	A numeric vector containing the parameters for the island: island_pars[1]: lambda^c (cladogenesis rate) island_pars[2]: mu (extinction rate) island_pars[3]: K (carrying capacity), set K=Inf for diversity independence. island_pars[4]: gamma (immigration rate) island_pars[5]: lambda^a (anagenesis rate)
mainland_ex	Numeric parameter for mainland extinction rate.
replicates	Integer specifying number of island replicates to be simulated.
possible_event	Numeric defining what event will happen.
max_spec_id	Current species IDs.
mainland_scenario	Integer determining which mainland clade scenario is produced
anc_branch_t_bp	Numeric ancestral branching time before the present of the immigrant species ancestor and its extant relative on the mainland
subset_island	Data frame of island species that originated from a single colonisation event
daisie_mainland_data	list containing data of a DAISIE simulation with mainland dynamics, as produced by sim_island_with_mainland and checked by check_daisie_mainland_data A daisie_mainland_data has two elements: ideal_multi_daisie_data: the ideal data set produced in a simulation, see check_multi_daisie_data for more details empirical_multi_daisie_data: the empirical data sets produced in a simulation see check_multi_daisie_data for more details
daisie_data	a DAISIE datalist, as can be checked by check_daisie_data. To quote the DAISE doc: A datalist is an object containing information on colonisation and branching times. This object can be generated using DAISIE_dataprep, which converts a user-specified data table into a datalist, but the object can of course also be entered directly. A datalist is a list with the following elements: The first element of the list has two or three components: $island_age - the island age Then, depending on whether a distinction between types is made, we have: $not_present - the number of mainland lineages that are not present on the island or: $not_present_type1 - the number of mainland lineages of type 1 that are not present on the island $not_present_type2 - the number of mainland lineages of type 2 that are not present on the island The remaining elements of the datalist each contains information on a single colonist lineage on the island and has 5 components: $colonist_name - the name of the species or clade that colonized the island $branching_times - island age followed by stem age of the population/species in the case of Non-endemic, Non-endemic_MaxAge species and Endemic species with no close relatives on the island. For endemic clades with more than one species on the island (cladogenetic clades/ radiations) these should be island age followed by the branching times of the island clade including the stem age of the clade $stac - the status of the colonist, see stac_to_str for values and descriptions $missing_species - number of island species that were not sampled for particular clade (only applicable for endemic clades) $type1or2 - whether the colonist belongs to type 1 or type 2
ideal_daisie_data	a list, of which each element contains the history of a DAISIE simulation with mainland dynamics, with a length that equals the number of replicates. The simulated history is recorded perfectly, resulting in ideal data. The list elements are of type DAISIE::datalist, as checked by check_daisie_data and can be used by DAISIE (e.g. DAISIE_ML_CS)
empirical_daisie_data	a list, of which each element contains the history of a DAISIE simulation with mainland dynamics, with a length that equals the number of replicates The simulated history is recorded as an empiricist would, resulting in imperfect data. The list elements are of type DAISIE::datalist, as checked by check_daisie_data and can be used by DAISIE (e.g. DAISIE_ML_CS)
ideal_or_empirical_island	the evolutionary history of an island from ideal or empirical data, as created by sim_island ideal_or_empirical_island is a list containing 3 components: ⁠$branching_times⁠: island age, species stem age and speciation times. See check_branching_times for more details ⁠$stac⁠: the status of the colonist, see stac_to_str for values and meanings ⁠$missing_species⁠: number of island species that were not sampled for particular clade (only applicable for endemic clades) For recolonising lineages, there is an extra element, all_colonisations per list element. It is comprised of ⁠$event_times⁠ and ⁠$species_type⁠: ⁠$event_times⁠ ordered numeric vectors containing all events for each extant recolonising lineage. This includes all colonisation and branching times. Each vector pertains to one colonising lineage. ⁠$species_type⁠ a string. Can be "A", "C" or "I" depending on whether the extant clade is of anagenetic, cladogenetic or immigrant origin, respectively.
species_type	a string. Can be "A", "C" or "I" depending on whether the extant clade is of anagenetic, cladogenetic or immigrant origin, respectively.
ideal_ml	List containing maximum likelihood estimates from DAISIE fitted to ideal data produced from sim_island_with_mainland. Output from DAISIE::DAISIE_ML_CS
empirical_ml	List containing maximum likelihood estimates from DAISIE fitted to empirical data produced from sim_island_with_mainland. Output from DAISIE::DAISIE_ML_CS
sim_params	Vector of five numerics for the values of cladogenesis, extinction, carrying capacity, immigration and anagenesis used to simulate data
param_set	Numeric for the index of the parameter set from the parameter space
data_folder_path	String specifying the directory the data is read from
output_file_path	String specifying the directory the file is saved in, if NULL the file is returned to console and not saved
param_space	String specifying which parameter space results to read. Either "general", "mainland_ex", or "mainland_sample_prob"
parameter	String specifying which parameter is plotted. "mainland_ex" plots mainland extinction as the variable, "mainland_sample_prob" plots mainland sampling probability as the variable and "both" plots all the data
plotting_data	Numeric vector of data points
breaks	A vector of numerics
num_breaks	A numeric specifying how many breaks are wanted on the plot axes
signif	A numeric specifying how many significant figures the axes labels have when plotting
scientific	A boolean determining whether the axis labels will be converted to scientific notation
transform	Either NULL or "ihs" to specify no transformation of the data or an inverse hyperbolic sine (ihs) transformation
mainland	the evolutionary history of the mainland species, as created by sim_mainland. Use plot_mainland to visualise the that evolutionary history.
age	Numeric defining age of singleton species
multi_daisie_data	A list of daisie_data elements
analysis_result	A list containing ouput from the run_analysis script. The list can be checked with check_analysis_result
analysis_results	A list of analysis_result elements which can be checked with check_analysis_result
labels	A string or vector of strings to label the plotting grid
branch_colour	A string, either "unique_species_id" or "clade_id" to colour the branches of the mainland tree(s) with one of the attributes.

Value

Nothing

Author(s)

Joshua W. Lambert

joshwlambert/DAISIEmainland documentation built on July 14, 2024, 5:40 p.m.