

sample_b() 
Sample from any birth model
Type : Sampling algorithm Title : sample_b Usage : see sample Function: Samples trees from a pure birth model Returns : see sample Args : %algorithm_options requires the field: rate => sampling rate 
sample_bd() 
Sample from any birth and death model for which nstar exists
Type : Sampling algorithm Title : sample_bd Usage : see sample Function: Samples trees from a birth and death model Returns : see sample Args : %algorithm_options requires the fields: nstar => once a tree has nstar species there should be a negligible chance of returning to tree_size species rate => sampling rate 
sample_incomplete_sampling_bd() 
Sample from any birth and death model with incomplete taxon sampling
Type : Sampling algorithm Title : sample_incomplete_sampling_bd Usage : see sample Function: Samples trees from a birth and death model with incomplete taxon sampling Returns : see sample Args : %algorithm_options requires the fields: rate => sampling rate nstar => once a tree has nstar species there should be a negligible chance of returning to mstar species mstar => trees with more than mstar species form a negligible contribution to the final sample. sampling_probability => see below. sampling_probability
vector: must have length (mstartree_size+1) The ith element gives the probability of not sampling i species. scalar: the probability of sampling any individual species. Is used to calculate a vector as discussed in the paper. 
sample_memoryless_b() 
Sample from a memoryless birth model
Type : Sampling algorithm Title : sample_memoryless_b Usage : see sample Function: Samples trees from a memoryless birth model Returns : see sample Args : %algorithm_options with fields: pendant_dist => function reference for generating random shortest pendant edges NB: The function pointed to by pendant_dist is given model_options as it’s input argument with an added field tree_size. It must return a random value from the probability density for the shortest pendant edges. 
sample_constant_rate_bd() 
Sample from a constant rate birth and death model
Type : Sampling algorithm Title : sample_constant_rate_bd Usage : see sample Function: Samples trees from a memoryless birth model Returns : see sample Args : no specific algorithm options but see below NB: This algorithm only applies to constant rate birth and death processes. Consequently a model does not need to be specified (and will be ignored if it is). But birth_rate and death_rate model options must be given. 
All evolutionary models take a options hash as their input argument and return a Bio::Phylo::Forest::Tree. This tree may contain extinct lineages (lineages that end prior to the end of the tree).The options hash contains any model specific parameters (see the individual model descriptions) and one or both terminating conditions: tree_size => the number of extant species at which to terminate the tree tree_age => the age of the tree at which to terminate the process
Note that if the model stops due to the tree_size condition then the tree ends immediately after the speciation event that created the last species.
constant_rate_birth() A constant rate birth model (Yule/ERM)
Type : Evolutionary model Title : constant_rate_birth Usage : $tree = constant_rate_birth(%options) Function: Produces a tree from the model terminating at a given size/time Returns : Bio::Phylo::Forest::Tree Args : %options with fields: birth_rate The birth rate parameter (default 1) tree_size The size of the tree at which to terminate tree_age The age of the tree at which to terminate NB: At least one of tree_size and tree_age must be specifiedexternal_model() A dummy model that takes as input a set of newick_trees and randomly samples these.
Type : Evolutionary model Title : external_model Usage : $tree = $external_model(%options) Function: Returns a random tree that was given as input Returns : Bio::Phylo::Forest::Tree Args : %options with fields: trees An array of newick strings. One of these is returned at random. NB: The usual parameters tree_size and tree_age will be ignored. When sampling using this model the trees array must contain trees adhering to the requirements of the sampling algorithm. This is NOT checked automatically.constant_rate_birth_death() A constant rate birth and death model
Type : Evolutionary model Title : constant_rate_birth_death Usage : $tree = constant_rate_birth_death(%options) Function: Produces a tree from the model terminating at a given size/time Returns : Bio::Phylo::Forest::Tree Args : %options with fields: birth_rate The birth rate parameter (default 1) death_rate The death rate parameter (default no extinction) tree_size The size of the tree at which to terminate tree_age The age of the tree at which to terminate NB: At least one of tree_size and tree_age must be specifieddiversity_dependent_speciation() A birth and death model with speciation rate dependent on diversity as per Etienne et. al. 2012
Type : Evolutionary model Title : diversity_dependent_speciation Usage : $tree = diversity_dependent_speciation(%options) Function: Produces a tree from the model terminating at a given size/time Returns : Bio::Phylo::Forest::Tree Args : %options with fields: maximal_birth_rate The maximal birth rate parameter (default 1) death_rate The death rate parameter (default no extinction) K_dash The modified carrying capacity (no default) tree_size The size of the tree at which to terminate tree_age The age of the tree at which to terminate NB: At least one of tree_size and tree_age must be specifiedReference: Rampal S. Etienne, Bart Haegeman, Tanja Stadler, Tracy Aze, Paul N. Pearson, Andy Purvis and Albert B. Phillimore. Diversitydependence brings molecular phylogenies closer to agreement with the fossil record doi: 10.1098/rspb.2011.1439
constant_rate_birth_death() A temporal shift birth and death model
Type : Evolutionary model Title : temporal_shift_birth_death Usage : $tree = constant_rate_birth_death(%options) Function: Produces a tree from the model terminating at a given size/time Returns : Bio::Phylo::Forest::Tree Args : %options with fields: birth_rates The birth rates death_rates The death rates rate_times The times after which the rates apply (first element must be 0) tree_size The size of the tree at which to terminate tree_age The age of the tree at which to terminate NB: At least one of tree_size and tree_age must be specifiedevolving_speciation_rate() An evolutionary model featuring evolving speciation rates. Each daughter species is assigned its parent’s speciation rate multiplied by a normally distributed noise factor.
Type : Evolutionary model Title : evolving_speciation_rate Usage : $tree = evolving_speciation_rate(%options) Function: Produces a tree from the model terminating at a given size/time Returns : Bio::Phylo::Forest::Tree Args : %options with fields: birth_rate The initial speciation rate (default 1) evolving_std The standard deviation of the normal distribution from which the rate multiplier is drawn. tree_size The size of the tree at which to terminate tree_age The age of the tree at which to terminate NB: At least one of tree_size and tree_age must be specifiedclade_shifts() A constant rate birthdeath model with punctuated changes in the speciation and extinction rates. At each change one lineage receives new prespecified speciation and extinction rates.
Type : Evolutionary model Title : clade_shifts Usage : $tree = clade_shifts(%options) Function: Produces a tree from the model terminating at a given size/time Returns : Bio::Phylo::Forest::Tree Args : %options with fields: birth_rates The speciation rates death_rates The death rates rate_times The times at which the rates are introduced to a new clade. The first time should be zero. The remaining must be in ascending order. tree_size The size of the tree at which to terminate tree_age The age of the tree at which to terminate NB: At least one of tree_size and tree_age must be specifiedbeta_binomial() An evolutionary model featuring evolving speciation rates. From Blum2007
Type : Evolutionary model Title : beta_binomial Usage : $tree = beta_binomial(%options) Function: Produces a tree from the model terminating at a given size/time Returns : Bio::Phylo::Forest::Tree Args : %options with fields: birth_rate The initial speciation rate (default 1) model_param The parameter as defined in Blum2007 tree_size The size of the tree at which to terminate tree_age The age of the tree at which to terminate NB: At least one of tree_size and tree_age must be specified
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