likelihood_pos_R: Likelihood for using proportion detectable only (R version)

In jameshay218/virosolver: Infer epidemic dynamics using viral load data

Likelihood for using proportion detectable only (R version)

Description

This function is written in R. It returns the likelihood of observing a particular set of Ct values conditional on the underlying model parameters using only the proportion of Ct samples that are detectable.Despite being slower than the corresponding likelihood function written in C, it more closely matches the written equations in the paper and is retained for didactic purposes.

Usage

likelihood_pos_R(obs_dat, ages, pars, prob_infection)

Arguments

obs_dat	Tibble of observed data. Contains two columns, t for time of sample collection and ct for the Ct values.
ages	Vector of times since infection.
pars	Model parameters.
prob_infection	Probability of infection.

Value

Returns the likelihood.

Author(s)

James Hay, [e-mail]

See Also

Other likelihood functions: likelihood_R(), likelihood_cpp_wrapper(), likelihood_detectable(), p_a(), prob_detectable_curve(), prop_detectable_single(), prop_detectable()

jameshay218/virosolver documentation built on April 17, 2025, 2:57 p.m.