Description Usage Arguments Note Author(s)
View source: R/default_params_doc.R
This function does nothing. It is intended to inherit is parameters' documentation.
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alignment,
alignment_params,
bd_mutation_rate,
bd_tree,
bd_tree_filename,
bins,
brts,
chain_length,
clock_model,
cond,
crown_age,
error_measure_params,
experiment_type,
experiments,
fasta_filename,
filename,
folder_name,
init_speciation_rate,
init_extinction_rate,
lambda,
lambdas,
mbd_l_matrix,
mbd_mutation_rate,
mbd_params,
mbd_paramses,
mbd_params_interval,
mbd_sim_rng_seed,
mbd_tree,
mcmc_chain_length,
misc_params,
model_type,
mu,
mus,
mutation_rate,
n_replicates,
nu,
nus,
nu_events,
parameters,
parameter_filename,
parameters_filename,
phylo,
pir_params,
posterior_trees,
precision,
project_folder_name,
q,
qs,
razzo_params,
razzo_paramses,
rng_seed,
sample_interval,
seed,
seed_folder,
sequence_length,
sim_pars,
sim_phylo,
site_model,
sub_chain_length,
tree,
tree_type,
tree_filename,
trees_filename,
twinning_params,
verbose
)
|
alignment |
a DNA alignment |
alignment_params |
parameters for creating an alignment,
as can be created by |
bd_mutation_rate |
the mutation rate when creating an alignment from a BD tree |
bd_tree |
a phylogent of class |
bd_tree_filename |
name of the file that stores a BD twin tree |
bins |
how many bins in the histograms? |
brts |
set of branching times |
chain_length |
something |
clock_model |
Name of the clock model that has to be used for the inference. Valid names are 'strict' and 'rln'. |
cond |
conditioning as specified in |
crown_age |
The crown age of the tree. |
error_measure_params |
parameters to set how the error
between given tree and inferred trees in measure,
as can be created by |
experiment_type |
the type of experiment,
can be either |
experiments |
provides information on how the experiment has to be set
up. To create it use |
fasta_filename |
name of a FASTA file |
filename |
the file's name, without the path |
folder_name |
name of the main folder |
init_speciation_rate |
a speciation rate |
init_extinction_rate |
an extinction rate |
lambda |
per-lineage speciation rate. See |
lambdas |
per-lineage speciation rates. See |
mbd_l_matrix |
the L matrix of an MBD tree |
mbd_mutation_rate |
the mutation rate when creating an alignment from a MBD tree |
mbd_params |
MBD parameter set |
mbd_paramses |
data frame with one MBD parameter set per row. If a simulation with one MBD parameter set has 10 replicates, this data frame will hold 10 rows, each with different seeds |
mbd_params_interval |
data frame with one MBD parameter set per row. If a simulation with one MBD parameter set has 10 replicates, this data frame will hold 10 rows, each with different seeds |
mbd_sim_rng_seed |
rng seed to simulate a mbd tree |
mbd_tree |
an MBD tree |
mcmc_chain_length |
length of an MCMC |
misc_params |
additional parameters for razzo. They contain tree_filename to store the original given tree and mbd_sim_rng_seed for when an mbd tree is simulated |
model_type |
the type of inference model, must be
|
mu |
per-species extinction rate. See |
mus |
per-species extinction rates. See |
mutation_rate |
something |
n_replicates |
number of replicates |
nu |
the rate at which a multiple-birth specation is triggered.
See |
nus |
the rates at which a multiple-birth specation is triggered.
See |
nu_events |
the number of nu-triggered events that have to be present in the simulated tree |
parameters |
the razzo parameters |
parameter_filename |
full path to a |
parameters_filename |
full path to a |
phylo |
a phylogeny |
pir_params |
a parameter set for one |
posterior_trees |
phylogenetic trees in a BEAST2 posterior,
of class |
precision |
define the precision of the approximation. |
project_folder_name |
project folder name,
will be the full path to |
q |
per-species speciation probability in case of occurrance of
a multiple event. See |
qs |
per-species speciation probabilities in case of occurrance of
a multiple event. See |
razzo_params |
a parameter set for one |
razzo_paramses |
a list of |
rng_seed |
a random number generator seed |
sample_interval |
the interval at which the MCMC algorithm makes a measurement |
seed |
a random number generator seed |
seed_folder |
the folder where the data for a specific seed is stored |
sequence_length |
the length of each DNA sequence in an alignment |
sim_pars |
something |
sim_phylo |
something |
site_model |
Name of the site model that has to be used for the inference. Valid names are 'jc69' and 'gtr'. |
sub_chain_length |
length of the sub-chain used by the Nested Sampling algorithm to estimate the marginal likelihood |
tree |
an ultrametric phylogenetic tree of class |
tree_type |
can be 'true' or 'twin' |
tree_filename |
name of the phylogeny file |
trees_filename |
name of the BEAST2 posterior phylogenies file |
twinning_params |
parameters for creating a twin tree,
as can be created by |
verbose |
give more output |
This is an internal function, so it should be marked with
@noRd
. This is not done, as this will disallow all
functions to find the documentation parameters
Documentation by Giovanni Laudanno, use of this function by Richel J.C. Bilderbeek
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