Description Usage Arguments Value
View source: R/default_params_doc.R
Defailt parameter documentation
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time,
M,
pars,
replicates,
divdepmodel,
nonoceanic_pars,
num_guilds,
prop_type2_pool,
replicates_apply_type2,
sample_freq,
plot_sims,
verbose,
area_pars,
hyper_pars,
dist_pars,
ext_pars,
island_ontogeny,
sea_level,
extcutoff,
shift_times,
mainland_n,
island_replicates,
island_spec,
stt_table,
rates,
max_rates,
timeval,
totaltime,
possible_event,
maxspecID,
mainland_spec,
max_area,
proportional_peak_t,
peak_sharpness,
total_island_age,
sea_level_amplitude,
sea_level_frequency,
island_gradient_angle,
d_0,
x,
alpha,
beta,
D,
simulation_outputs,
plot_plus_one,
type,
plot_lists,
...,
datalist,
datatype,
initparsopt,
idparsopt,
idparsfix,
parsfix,
idparsnoshift,
idparsmat,
res,
ddmodel,
cond,
eqmodel,
x_E,
x_I,
tol,
maxiter,
methode,
optimmethod,
CS_version,
tolint,
datatable,
island_age,
number_clade_types,
list_type2_clades,
epss,
t,
initEI,
data_table,
endmc,
archipelago,
phylo_data,
archipelago_data,
gam,
laa,
lac,
mu,
K,
num_spec,
num_immigrants,
global_min_area_time,
global_max_area_time,
distance_type,
distance_dep,
parallel,
cpus,
pars1,
pars2,
tvec,
initprobs,
pb,
island,
title,
plot_lists_simulations,
plot_lists_simulations_MLE,
kind_of_plot,
resolution,
trait_pars
)
|
time |
Numeric defining the length of the simulation in time units. For examples, if an island is known to be 4 million years old, setting time = 4 will simulate the entire life span of the island; setting time = 2 will stop the simulation at the mid-life of the island. |
M |
Numeric defining the size of mainland pool, i.e. the number of species that can potentially colonize the island. |
pars |
A numeric vector containing the model parameters:
The elements 6:10 are required only when type 2 species are included or in the rate shift model. |
replicates |
Number of island replicates to be simulated. |
divdepmodel |
Option divdepmodel = 'CS' runs a model with clade-specific carrying capacity, where diversity-dependence operates only within single clades, i.e. only among species originating from the same mainland colonist. Option divdepmodel = 'IW' runs a model with island-wide carrying capacity, where diversity-dependence operates within and among clades. Option divdepmodel = 'GW' runs a model with diversity-dependence operates within a guild. |
nonoceanic_pars |
A vector of length two with:
|
num_guilds |
The number of guilds on the mainland. The number of
mainland species is divided by the number of guilds when |
prop_type2_pool |
Fraction of mainland species that belongs to the
second subset of species (type 2). Applies only when two types of species
are simulated (length(pars) = 10). For |
replicates_apply_type2 |
Applies only when two types of species are being simulated. Default replicates_apply_type2 = TRUE runs simulations until the number of islands where a type 2 species has colonised is equal to the specified number of replicates. This is recommended if prop_type2_pool is small or if the rate of immigration of type two species (pars[9]) is low, meaning that more replicates are needed to achieved an adequate sample size of islands with type 2 species. Setting replicates_apply_type2 = FALSE simulates islands up to the specified number of replicates regardless of whether type 2 species have colonised or not. |
sample_freq |
Numeric specifing the number of units times should be divided by for plotting purposes. Larger values will lead to plots with higher resolution, but will also run slower. |
plot_sims |
Default = TRUE plots species-through-time (STT) plots. It detects how many types of species are present. If only one type of species is present, STT is plotted for all species. If two types are present, three plots are produced: STT for all, STT for type 1 and STT for type 2. |
verbose |
In simulation and dataprep functions a logical,
|
area_pars |
A named list containing area and sea level parameters as
created by
|
hyper_pars |
A named list of numeric hyperparameters for the rate
calculations as returned by
|
dist_pars |
A named list of a numeric distance from the mainland as
created by
|
ext_pars |
A numeric vector:
|
island_ontogeny |
In |
sea_level |
In |
extcutoff |
A numeric with the cutoff for the the maximum extinction rate preventing it from being too large and slowing down simulation. |
shift_times |
a numeric vector specifying when the rate shifts occur before the present. |
mainland_n |
A numeric stating the number of mainland species, that is the number of species that can potentially colonize the island. If using a clade-specific diversity dependence, this value is set to 1. If using an island-wide diversity dependence, this value is set to the number of mainland species. |
island_replicates |
List output from
|
island_spec |
Matrix with current state of simulation containing number of species. |
stt_table |
Matrix with number of species at each time step. |
rates |
named list of numeric rates as returned by
|
max_rates |
named list of numeric max rates as returned by
|
timeval |
Numeric defining current time of simulation. |
totaltime |
Numeric defining the length of the simulation in time units. |
possible_event |
Numeric defining what event will happen. |
maxspecID |
Current species IDs. |
mainland_spec |
Number of mainland species. |
max_area |
Numeric defining maximum area. |
proportional_peak_t |
Numeric value from 0 to 1 indicating where in the island's history the peak area is achieved. |
peak_sharpness |
Numeric defining sharpness of peak. |
total_island_age |
Numeric defining total island age. |
sea_level_amplitude |
Numeric defining amplitude of area fluctuation from sea level. |
sea_level_frequency |
Numeric defining frequency of sine wave of area change from sea level. |
island_gradient_angle |
Numeric defining the angle in degrees specifying the slope of the island. |
d_0 |
Numeric defining the scaling parameter for exponent for calculating cladogenesis rate. |
x |
Numeric defining the exponent for calculating extinction rate. |
alpha |
Numeric defining the exponent for calculating the immigration rate. |
beta |
Numeric defining the exponent for calculating the anagenesis rate. |
D |
A numeric defining the distance parameters for the rate calculations. |
simulation_outputs |
A list with matrices and vectors of simulation produced by DAISIE_sim functions. |
plot_plus_one |
Boolean to indicate to plot all values plus one.
Set to |
type |
String to indicate if stt of all species or all possible stt
should be plotted. Default is |
plot_lists |
List of lists containing average and quantile species through time. |
... |
Any arguments to pass on to plotting functions. |
datalist |
Data object containing information on colonisation and
branching times. This object can be generated using the DAISIE_dataprep
function, which converts a user-specified data table into a data object, but
the object can of course also be entered directly. It is an R list object
with the following elements. |
datatype |
Sets the type of data: 'single' for a single island or archipelago treated as one, and 'multiple' for multiple archipelagoes potentially sharing the same parameters. |
initparsopt |
The initial values of the parameters that must be optimized, they are all positive. |
idparsopt |
The ids of the parameters that must be optimized. The ids
are defined as follows: |
idparsfix |
The ids of the parameters that should not be optimized, e.g. c(1,3) if lambda^c and K should not be optimized. |
parsfix |
The values of the parameters that should not be optimized. |
idparsnoshift |
For datatype = 'single' only: The ids of the parameters that should not be different between two groups of species; This can only apply to ids 6:10, e.g. idparsnoshift = c(6,7) means that lambda^c and mu have the same values for both groups. |
idparsmat |
For datatype = 'multiple' only: Matrix containing the ids
of the parameters, linking them to initparsopt and parsfix. Per island
system we use the following order: |
res |
Sets the maximum number of species for which a probability must be computed, must be larger than the size of the largest clade. |
ddmodel |
Sets the model of diversity-dependence: |
cond |
cond = 0 : conditioning on island age |
eqmodel |
Sets the equilibrium constraint that can be used during the
likelihood optimization. Only available for datatype = 'single'. |
x_E |
Sets the fraction of the equlibrium endemic diversity above which the endemics are assumed to be in equilibrium; only active for eqmodel = 13 or 15. |
x_I |
Sets the fraction of the equlibrium non-endemic diversity above which the system is assumed to be in equilibrium; only active for eqmodel = 15. |
tol |
Sets the tolerances in the optimization. Consists of: |
maxiter |
Sets the maximum number of iterations in the optimization. |
methode |
Method of the ODE-solver. See package deSolve for details. Default is "lsodes". |
optimmethod |
Method used in likelihood optimization. Default is "subplex" (see subplex package). Alternative is 'simplex' which was the method in previous versions. |
CS_version |
For internal testing purposes only. Default is 1, the original DAISIE code. |
tolint |
Vector of two elements containing the absolute and relative tolerance of the integration. |
datatable |
Data frame (table) with user-specified data. See file
Galapagos_datatable.Rdata for a template of an input table. Each row on the
table represents and independent colonisation event. Table has the following
four columns. |
island_age |
Age of island in appropriate units. In
|
number_clade_types |
Number of clade types. Default: number_clade_types = 1 all species are considered to belong to same macroevolutionary process. If number_clade_types = 2, there are two types of clades with distinct macroevolutionary processes. |
list_type2_clades |
If number_clade_types = 2, list_type2_clades specifies the names of the clades that have a distinct macroevolutionary process. The names must match those in the $Clade_name column of the source data table (e.g. list_type2_clades = "Finches"). If number_clade_types = 1, then list_type2_clades = NA should be specified (default) |
epss |
Default= 1E-5 should be appropriate in most cases. This value is used to set the maximum age of colonisation of "Non_endemic_MaxAge" and "Endemic_MaxAge" species to an age that is slightly younger than the island for cases when the age provided for that species is older than the island. The new maximum age is then used as an upper bound to integrate over all. |
t |
The time at which the expectations need to be computed. |
initEI |
The initial values for the number of endemics and
non-endemics. In |
data_table |
data table |
endmc |
Numeric for how many simulations should run. |
archipelago |
something |
phylo_data |
something |
archipelago_data |
something |
gam |
A numeric with the per capita immigration rate. |
laa |
A numeric with the per capita anagenesis rate. |
lac |
A numeric with the per capita cladogenesis rate. |
mu |
A numeric with the per capita extinction rate. |
K |
A numeric with carrying capacity. |
num_spec |
A numeric with the current number of species. |
num_immigrants |
A numeric with the current number of non-endemic species (a.k.a non-endemic species). |
global_min_area_time |
stub |
global_max_area_time |
stub |
distance_type |
Use 'continent' if the distance to the continent should be used, use 'nearest_big' if the distance to the nearest big landmass should be used, and use 'biologically_realistic' if the distance should take into account some biologically realism, e.g. an average of the previous two if both are thought to contribute. |
distance_dep |
Sets what type of distance dependence should be used. Default is a power law, denoted as 'power'. Alternatives are an exponantial relationship denoted by 'exp' or sigmoids, either 'sigmoidal_col' for a sigmoid in the colonization, 'sigmoidal_ana' for sigmoidal anagenesis, 'sigmoidal_clado' for sigmoidal cladogenesis, and 'sigmoidal_col_ana' for signoids in both colonization and anagenesis. |
parallel |
Sets whether parallel computation should be used. Use 'no' if no parallel computing should be used, 'cluster' for parallel computing on a unix/linux cluster, and 'local' for parallel computation on a local machine. |
cpus |
Number of cpus used in parallel computing. Default is 3. Will not have an effect if parallel = 'no'. |
pars1 |
Vector of model parameters: |
pars2 |
Vector of settings: |
tvec |
The times at which the probabilities need to be computed. |
initprobs |
The initial probability distribution for the number of endemics and non-endemics; either this or initEI must be NULL. |
pb |
Probability distribution in matrix format as output by
|
island |
Island data object. Can be in DAISIE list format (see Galapagos_datalist and DAISIE_data_prep for examples) or in table format (see Galapagos_datatable for an example). |
title |
Title of the plot |
plot_lists_simulations |
List with simulation output after parsing by
|
plot_lists_simulations_MLE |
List with simulation output after parsing
by |
kind_of_plot |
Character vector stating how STT plot resulting from MLE
based simulations should be plotted. Default is |
resolution |
numeric indicating resolution of plot. Should be < 0. |
trait_pars |
A named list containing diversification rates considering
two trait states created by
|
Nothing
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