ddtlcm0.2.1 package

Compute divergence function

Compute divergence function

Add a leaf branch to an existing tree tree_old

Add a leaf branch to an existing tree tree_old to make a multichotomus...

Functions to simulate trees and node parameters from a DDT process. Ad...

Add a singular root node to an existing nonsingular tree

Attach a subtree to a given DDT at a randomly selected location

Compute information criteria for the DDT-LCM model

Create a tree-structured covariance matrix from a given tree

ddtlcm: Latent Class Analysis with Dirichlet Diffusion Tree Process Pr...

MH-within-Gibbs sampler to sample from the full posterior distribution...

Sample divergence time on an edge uv previously traversed by m(v) data...

Efficiently sample multivariate normal using precision matrix from $x ...

Compute normalized probabilities: exp(x_i) / sum_j exp(x_j)

The expit function

Harmonic series

Initialize the MH-within-Gibbs algorithm for DDT-LCM

Estimate an initial binary tree on latent classes using hclust()

Estimate an initial response profile from latent class model using poL...

Provide a random initial response profile based on latent class mode

Compute factor in the exponent of the divergence time distribution

Numerically accurately compute f(x) = log(x / (1/x)).

The logistic function

Calculate loglikelihood of a DDT, including the tree structure and nod...

Calculate loglikelihood of the DDT-LCM

Compute loglikelihood of divergence times for a(t) = c/(1-t)

Compute loglikelihood of divergence times for a(t) = c/(1-t)^2

Calculate loglikelihood of the latent class model, conditional on tree...

Compute log likelihood of parameters

Compute loglikelihood of the tree topology

Create trace plots of DDT-LCM parameters

Plot the MAP tree and class profiles of summarized DDT-LCM results

Plot the MAP tree and class profiles (bar plot) of summarized DDT-LCM ...

Plot the MAP tree and class profiles (heatmap) of summarized DDT-LCM r...

Prediction of class memberships from posterior predictive distribution...

Prediction of class memberships from posterior summaries

Print out setup of a ddt_lcm model

Print out summary of a ddt_lcm model

Calculate proposal likelihood

Suppress print from cat()

Metropolis-Hasting algorithm for sampling tree topology and branch len...

Attach a subtree to a given DDT at a randomly selected location

Sample divergence function parameter c for a(t) = c / (1-t) through Gi...

Sample divergence function parameter c for a(t) = c / (1-t)^2 through ...

Sample individual class assignments Z_i, i = 1, ..., N

Sample the leaf locations and Polya-Gamma auxilliary variables

Sample item group-specific variances through Gibbs sampler

Sample a new tree topology using Metropolis-Hastings through randomly ...

Simulate a tree from a DDT process. Only the tree topology and branch ...

Simulate multivariate binary responses from a latent class model given...

Simulate multivariate binary responses from a latent class model

Simulate node parameters along a given tree.

Summarize the output of a ddt_lcm model

Compute WAIC