Description Usage Arguments Value Examples
Fit a covariate latent variable model using coordinate ascent variational inference.
1 2 3 4 
y 
A NbyG (dynamic) input matrix 
x 
A NbyP (static) input matrix 
maxiter 
Maximum number of CAVI iterations 
elbo_tol 
The (percent) change in the ELBO below which it is considered converged 
thin 
The number of iterations to wait each time before recalculating the elbo 
verbose 
Print convergence messages 
z_init 
The initialisation of the latent trajectory. Should be one of

tau_q 
Hyperparameter tau_q 
tau_mu 
Hyperparameter tau_mu 
tau_c 
Hyperparameter tau_c 
a 
Hyperparameter a 
b 
Hyperparameter b 
tau_alpha 
Hyperparameter tau_alpha 
a_beta 
Hyperparameter a_beta 
b_beta 
Hyperparameter b_beta 
q 
Priors on the latent variables 
model_mu 
Logical  should a genespecific intercept term be modelled? 
scale_y 
Logical  should the expression matrix be centre scaled? 
A list whose entries correspond to the converged values of the variational parameters along with the ELBO.
1 2  sim < simulate_phenopath()
fit < clvm(sim$y, matrix(sim$x))

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