All functions |
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Create a multi-regime Gaussian model (MixedGaussian) |
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Create a phylogenetic comparative model object |
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Quadratic polynomial parameters A, b, C, d, E, f for each node |
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Map a parametrization to its original form. |
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Check if the PCMBase version correpsonds to a dev release |
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A fixed palette of n colors |
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Conditional distribution of a daughter node given its parent node |
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Conditional distribution of a daughter node given its parent node |
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Variance-covariance matrix of an OU process with optional measurement error and jump at the start |
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Create a likelhood function of a numerical vector parameter |
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Generate a default object of a given PCM model type or parameter type |
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Human friendly description of a PCM |
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Describe the parameters of a PCM |
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Fix a parameter in a PCM model |
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Generate possible parameterizations for a given type of model |
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Get a vector of all parameters (real and discrete) describing a model on a tree including the numerical parameters of each model regime, the integer ids of the spliting nodes defining the regimes on the tree and the integer ids of the model classes associated with each regime. |
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Meta-information about a tree associated with a PCM |
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Likelihood of a multivariate Gaussian phylogenetic comparative model with non-interacting lineages |
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Specify the parameterizations for each parameter of a model |
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Quadratic polynomial parameters L, m, r |
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#' Regimes in a model #' @param model a PCM object #' @param tree a phylo object or NULL. If the regimes in the model are integers and tree is not NULL, #' then these integers are used as indexes in PCMTreeUniqueRegimes(tree). Default NULL. #' @return a character or an integer vector giving the regime names of the models #' @export PCMRegimes <- function(model, tree = NULL, preorder = if(is.null(tree)) NULL else PCMTreePreorder(tree)) UseMethod("PCMRegimes", model) |
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Expected mean vector at each tip conditioned on a trait-value vector at the root |
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Calculate the mean at time t, given X0, under a PCM model |
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Get a list of PCM models currently implemented |
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Number of regimes in a model |
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Number of traits modeled by a PCM |
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Global options for the PCMBase package |
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Create a function of time that calculates (1-exp(-lambda_ij*time))/lambda_ij for every element lambda_ij of the input matrix Lambda_ij. |
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Eigen-decomposition of a matrix H |
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Sums of pairs of elements in a vector |
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Module PCMParam |
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Count the number of free parameters associated with a PCM or a PCM-parameter |
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Get a vector of the variable numeric parameters in a model |
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Load (or store) a PCM parameter from (or to) a vector of the variable parameters in a model. |
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The lower limit for a given model or parameter type |
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Generate a random parameter vector for a model using uniform distribution between its lower and upper bounds. |
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Set model parameters from a named list |
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Parameter types |
The upper limit for a given model or parameter type |
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Parent S3 classes for a model class |
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Extract error information from a formatted error message. |
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A 2D Gaussian distribution density grid in the form of a ggplot object |
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A 2D sample from Gaussian distribution |
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Beautiful model description based on plotmath |
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Scatter plot of 2-dimensional data |
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Determine which traits are present (active) on each node of the tree |
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Regimes in a model |
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Simulation of a phylogenetic comparative model on a tree |
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Parameter specification of PCM model |
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Cartesian product of possible parameterizations for the different parameters of a model |
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Drop a clade from a phylogenetic tree |
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A data.table of the tips with their assigned regime |
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A matrix with the begin and end time from the root for each edge in tree |
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Perfrorm nested extractions or drops of clades from a tree |
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Prune the tree leaving one tip for each regime |
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Extract a clade from phylogenetic tree |
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The length of the branch leading to a node |
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A vector of the daughter nodes for a given parent node id in a tree |
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Get a vector of the tip and node labels in a tree |
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The parent node id of a daughter node in a tree |
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Get the regime of the branch leading to a node or a tip |
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Get the starting branch' nodes for each regime on a tree |
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Get the tips belonging to a regime tree |
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Insert singleton nodes on chosen edges |
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Jumps in modeled traits associated with branches in a tree |
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A list of all possible partitions of a tree with a number of splitting nodes |
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A list of the descendants for each node in a tree |
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A list of the path to the root from each node in a tree |
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Find the crossing points of an epoch-time with each lineage of a tree |
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Find the middle point of each branch longer than a threshold |
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Get the node numbers associated with tip- or node-labels in a tree |
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Regimes associated with branches in a tree |
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Which nodes in a tree belong to the same regime? |
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Which tips in a tree belong to the same regime? |
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Find the nearest node to a given time from the root (epoch) on each lineage crossing this epoch |
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Calculate the time from the root to each node of the tree |
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Number of all nodes in a tree |
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Wrapper for length(tree$tip.label) |
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Number of unique regimes on a tree |
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Plot a tree with regimes |
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Post-order tree traversal |
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Pre-order tree traversal |
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Set a default edge.regime member ot the passed tree object |
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Set tip and internal node labels in a tree |
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Assign regimes on a tree given a set of starting branches |
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Slit a tree at a given internal node into a clade rooted at this node and the remaining tree after dropping this clade |
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A matrix (table) of ancestors/descendants for each node in a tree |
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A character representation of a phylo object. |
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Unique regimes on a tree in the order of occurrence from the root to the tips (preorder) |
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Unfix a parameter in a PCM model |
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Expected variance-covariance matrix for each couple of tips (i,j) |
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Calculate the variance covariance k x k matrix at time t, under a PCM model |
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White Gaussian PCM ignoring phylogenetic history |
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Check if an object is a `MixedGaussian` PCM |
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Check if an object is a PCM. |