model_adequacy_hbds: Check if a birth-death-sampling model adequately explains a...

In castor: Efficient Phylogenetics on Large Trees

Check if a birth-death-sampling model adequately explains a timetree.

Description

Given a rooted timetree and a homogenous birth-death-sampling model (e.g., as used in molecular epidemiology), check if the model adequately explains various aspects of the tree, such as the branch length and node age distributions and other test statistics. The function uses bootstrapping to simulate multiple hypothetical trees according to the model and then compares the distribution of those trees to the original tree. This function may be used to quantify the "goodness of fit" of a birth-death-sampling model to a timetree. For background on the HBDS model see the documentation for generate_tree_hbds.

Usage

model_adequacy_hbds(tree,
                    models,
                    splines_degree      = 1,
                    extrapolate         = FALSE,
                    Nbootstraps         = 1000,
                    max_sim_attempts    = 1000,
                    Nthreads            = 1,
                    max_extant_tips     = NULL,
                    max_model_runtime   = NULL)

Arguments

tree	A rooted timetree of class "phylo".
models	Either a single HBDS model or a list of HBDS models, specifying the pool of models from which to randomly draw bootstraps. Every model should itself be a named list with some or all of the following elements: stem_age: Numeric, the age (time before present) at which the HBDS process started. If NULL, this is automatically set to the input tree's root age. end_age : Numeric, the age (time before present) at which the HBDS process halted. This will typically be 0 (i.e., at the tree's youngest tip), however it may also be negative if the process actually halted after the youngest tip was sampled. ages: Numeric vector, specifying discrete ages (times before present) in ascending order, on which all model variables (e.g., \lambda, \mu and \psi) will be specified. Age increases from tips to root; the youngest tip in the input tree has age 0. The age grid must cover stem_age and end_age. lambda: Numeric vector of the same length as ages, listing the speciation rate (\lambda) of the HBDS model at the corresponding ages. Between grid points, the speciation rate is assumed to either be constant (if splines_degree=0), or linearly (if splines_degree=1) or quadratically (if splines_degree=2) or cubically (if splines_degree=3). mu: Numeric vector of the same length as ages, listing the extinction rate (\mu) of the HBDS model at the corresponding ages. Between grid points, the extinction rate is assumed to either be constant (if splines_degree=0), or linearly (if splines_degree=1) or quadratically (if splines_degree=2) or cubically (if splines_degree=3). Note that in epidemiological models \mu usually corresponds to the recovery rate plus the death rate of infected hosts. If mu is not included, it is assumed to be zero. psi: Optional numeric vector of the same length as ages, listing the Poissonian sampling rate (\mu) of the HBDS model at the corresponding ages. Between grid points, the sampling rate is assumed to either be constant (if splines_degree=0), or linearly (if splines_degree=1) or quadratically (if splines_degree=2) or cubically (if splines_degree=3). If psi is not included, it is assumed to be zero. kappa: Optional numeric vector of the same length as ages, listing the retention probability upon sampling (\kappa) of the HBDS model at the corresponding ages. Between grid points, the retention probability is assumed to either be constant (if splines_degree=0), or linearly (if splines_degree=1) or quadratically (if splines_degree=2) or cubically (if splines_degree=3). Note that since kappa are actual probabilities, they must all be between 0 and 1. If kappa is not included, it is assumed to be zero. CSA_ages: Numeric vector listing the ages (time before present) of concentrated sampling attempts, in ascending order. If empty or NULL, no concentrated sampling attempts are included, i.e. all sampling is assumed to be done according to the Poissonian rate \psi. CSA_probs: Optional numeric vector, of the same length as CSA_ages, specifying the sampling probabilities for each concentrated sampling attempt listed in CSA_ages. Hence, a lineage extant at age CSA_ages[k] has probability CSA_probs[k] of being sampled. Note that since CSA_probs are actual probabilities, they must all be between 0 and 1. CSA_probs must be provided if and only if CSA_ages is provided. CSA_kappas: Optional numeric vector, of the same length as CSA_ages, specifying the retention probability upon sampling for each concentrated sampling attempt listed in CSA_ages. Note that since CSA_kappas are actual probabilities, they must all be between 0 and 1. CSA_kappas must be provided if and only if CSA_ages is provided. If you are assessing the adequacy of a single model with specific parameters, then models can be a single model. If you want to assess the adequacy of a distribution of models, such as sampled from the posterior distribution during a Bayesian analysis, models should list those posterior models.
splines_degree	Integer, one of 0, 1, 2 or 3, specifying the polynomial degree of the model parameters \lambda, \mu, \psi and \kappa between age-grid points. For example, splines_degree=0 means piecewise constant, splines_degree=1 means piecewise linear and so on.
extrapolate	Logical, specifying whether to extrapolate the model variables \lambda, \mu, \psi and \kappa (as constants) beyond the provided age grid all the way to stem_age and end_age if needed.
Nbootstraps	Integer, the number of bootstraps (simulations) to perform for calculating statistical significances. A larger number will increase the accuracy of estimated statistical significances.
max_sim_attempts	Integer, maximum number of simulation attempts per bootstrap, before giving up. Multiple attempts may be needed if the HBDS model has a high probability of leading to extinction early on.
Nthreads	Integer, number of parallel threads to use for bootstrapping. Note that on Windows machines this option is ignored.
max_extant_tips	Integer, optional maximum number of extant tips per simulation. A simulation is aborted (and that bootstrap iteration skipped) if the number of extant tips exceeds this threshold. Use this to avoid occasional explosions of runtimes, for example due to very large generated trees.
max_model_runtime	Numeric, optional maximum computation time (in seconds) to allow for each HBDS model simulation (per bootstrap). Use this to avoid occasional explosions of runtimes, for example due to very large generated trees. Aborted simulations will be omitted from the bootstrap statistics. If NULL or <=0, this option is ignored.

Details

In addition to model selection, the adequacy of any chosen model should also be assessed in absolute terms, i.e. not just relative to other competing models (after all, all considered models might be bad). This function essentially determines how probable it is for hypothetical trees generated by a candidate model (or a distribution of candidate models) to resemble the tree at hand, in terms of various test statistics. In particular, the function uses a Kolmogorov-Smirnov test to check whether the probability distributions of edge lengths and node ages in the tree resemble those expected under the provided models. All statistical significances are calculated using bootstrapping, i.e. by simulating trees from the provided models. For every bootstrap, a model is randomly chosen from the provided models list.

Note that even if an HBDS model appears to adequately explain a given timetree, this does not mean that the model even approximately resembles the true diversification history (i.e., the true speciation, extinction and sampling rates) that generated the tree (Louca and Pennell 2020). Hence, it is generally more appropriate to say that a given model "congruence class" rather than a specific model explains the tree.

Note that here "age" refers to time before present, i.e. age increases from tips to roots and the youngest tip in the input tree has age 0. In some situations the process that generated the tree (or which is being compared to the tree) might have halted after the last tip was sampled, in which case end_age should be negative. Similarly, the process may have started prior to the tree's root (e.g., sampled tips coalesce at a later time than when the monitoring started), in which case stem_age should be greater than the root's age.

For convenience, it is possible to specify a model without providing an explicit age grid (i.e., omitting ages); in such a model \lambda, \mu, \psi and \kappa are assumed to be time-independent, and hence lambda, mu, psi and kappa must be provided as single numerics (or not provided at all).

Value

A named list with the following elements:

success	Logical, indicating whether the model evaluation was successful. If FALSE, then an additional return variable, error, will contain a description of the error; in that case all other return variables may be undefined. Note that success does not say whether the model explains the tree, but rather whether the computation was performed without errors.
Nbootstraps	Integer, the number of bootstraps used.
tree_Ntips	Integer, the number of tips in the original tree.
bootstrap_mean_Ntips	Numeric, mean number of tips in the bootstrap trees.
PNtips	Numeric, two-sided statistical significance of the tree's number of tips under the provided null model, i.e. the probability that abs(bootstrap_mean_Ntips-tree_Ntips) would be as large as observed.
tree_Colless	Numeric, Colless imbalance statistic (Shao and Sokal, 1990) of the original tree.
bootstrap_mean_Colless	Numeric, mean Colless statistic across all bootstrap trees.
PColless	Numeric, two-sided statistical significance of the tree's Colless statistic under the provided null model, i.e. the probability that abs(bootstrap_mean_Colless-tree_Colless) would be as large as observed.
tree_Sackin	Numeric, Sackin statistic (Sackin, 1972) of the original tree.
bootstrap_mean_Sackin	Numeric, median Sackin statistic across all bootstrap trees.
PSackin	Numeric, two-sided statistical significance of the tree's Sackin statistic under the provided null model, i.e. the probability that abs(bootstrap_mean_Sackin-tree_Sackin) would be as large as observed.
tree_edgeKS	Numeric, Kolmogorov-Smirnov (KS) statistic of the original tree's edge lengths, i.e. the estimated maximum difference between the tree's and the model's (estimated) cumulative distribution function of edge lengths.
bootstrap_mean_edgeKS	Numeric, mean KS statistic of the bootstrap trees' edge lengths.
PedgeKS	Numeric, the one-sided statistical significance of the tree's edge-length KS statistic, i.e. the probability that the KS statistic of any tree generated by the model would be larger than the original tree's KS statistic. A low value means that the probability distribution of edge lengths in the original tree differs strongly from that expected based on the model.
tree_tipKS	Numeric, Kolmogorov-Smirnov (KS) statistic of the original tree's tip ages (sampling times before present), i.e. the estimated maximum difference between the tree's and the model's (estimated) cumulative distribution function of tip ages.
bootstrap_mean_tipKS	Numeric, mean KS statistic of the bootstrap trees' tip ages.
PtipKS	Numeric, the one-sided statistical significance of the tree's tip-age KS statistic, i.e. the probability that the KS statistic of any tree generated by the model would be larger than the original tree's KS statistic. A low value means that the probability distribution of tip ages in the original tree differs strongly from that expected based on the model.
tree_nodeKS	Numeric, Kolmogorov-Smirnov (KS) statistic of the original tree's node ages (divergence times before present), i.e. the estimated maximum difference between the tree's and the model's (estimated) cumulative distribution function of node ages.
bootstrap_mean_nodeKS	Numeric, mean KS statistic of the bootstrap trees' node ages.
PnodeKS	Numeric, the one-sided statistical significance of the tree's node-age KS statistic, i.e. the probability that the KS statistic of any tree generated by the model would be larger than the original tree's KS statistic. A low value means that the probability distribution of node ages in the original tree differs strongly from that expected based on the model.
statistical_tests	Data frame, listing the above statistical test results in a more compact format (one test statistic per row).
LTT_ages	Numeric vector, listing ages (time before present) on which the tree's LTT will be defined.
tree_LTT	Numeric vector of the same length as LTT_ages, listing the number of lineages in the tree at every age in LTT_ages.
bootstrap_LTT_CI	Named list containing the elements means, medians, CI50lower, CI50upper, CI95lower and CI95upper. Each of these elements is a numeric vector of length equal to LTT_ages, listing the mean or a specific percentile of LTTs of bootstrap trees at every age in LTT_ages. For example, bootstrap_LTT_CI$CI95lower[10] and bootstrap_LTT_CI$CI95upper[10] define the lower and upper bound, respectively, of the 95% confidence interval of LTTs generated by the model at age LTT_ages[10].
fraction_LTT_in_CI95	Numeric, fraction of the tree's LTT contained within the equal-tailed 95%-confidence interval of the distribution of LTT values predicted by the model. For example, a value of 0.5 means that at half of the time points between the present-day and the root, the tree's LTT is contained with the 95%-CI of predicted LTTs.

Author(s)

Stilianos Louca

References

S. Louca and M. W. Pennell (2020). Extant timetrees are consistent with a myriad of diversification histories. Nature. 580:502-505.

O. G. Pybus and P. H. Harvey (2000). Testing macro-evolutionary models using incomplete molecular phylogenies. Proceedings of the Royal Society of London. Series B: Biological Sciences. 267:2267-2272.

M. J. Sackin (1972). "Good" and "Bad" Phenograms. Systematic Biology. 21:225-226.

K.T. Shao, R. R. Sokal (1990). Tree Balance. Systematic Biology. 39:266-276.

See Also

simulate_deterministic_hbds, generate_tree_hbds, model_adequacy_hbd

Examples

## Not run: 
# generate a tree based on a simple HBDS process
max_time = 10
gen = castor::generate_tree_hbds(max_time           = max_time,
                                 lambda             = 1,
                                 mu                 = 0.1,
                                 psi                = 0.1,
                                 no_full_extinction = TRUE)
if(!gen$success) stop(sprintf("Could not generate tree: %s",gen$error))
tree     = gen$tree
root_age = castor::get_tree_span(tree)$max_distance

# determine age of the stem, i.e. when the HBDS process started
stem_age = gen$root_time + root_age

# determine age at which the HBDS simulation was halted.
# This might be slightly negative, e.g. if the process
# halted after the last sampled tip
end_age = root_age - (gen$final_time-gen$root_time)

# compare the tree to a slightly different model
model = list(stem_age    = stem_age,
             end_age     = end_age,
             lambda      = 1.2,
             mu          = 0.1,
             psi         = 0.2)
adequacy = model_adequacy_hbds( tree, 
                                models = model,
                                Nbootstraps = 100)
if(!adequacy$success){
    cat(sprintf("Adequacy test failed: %s\n",adequacy$error))
}else{
    print(adequacy$statistical_tests)
}

## End(Not run)

castor documentation built on Aug. 18, 2023, 1:07 a.m.