ushr (version 0.2.3)

get_optim_fit_triphasic: Fit triphasic model to data using optim

Description

This function uses optim to fit the triphasic model to data from a given subject

Usage

get_optim_fit_triphasic(initial_params, param_names, free_param_index,
  data, forward_param_transform_fn = forward_param_transform_fn,
  inv_param_transform_fn = inv_param_transform_fn, searchmethod)

Arguments

initial_params

named vector of the initial parameter guess.

param_names

names of parameter vector.

free_param_index

logical vector indicating whether the parameters A, delta, A_b, delta_b, B, gamma are to be recovered. This should be c(TRUE, TRUE, TRUE, TRUE, TRUE, TRUE) for the triphasic model.

data

dataframe with columns for the subject's viral load measurements ('vl'), and timing of sampling ('time')

forward_param_transform_fn

list of transformation functions to be used when fitting the model in optim. Defaults to log transformations for all parameters (to allow unconstrained optimization).

inv_param_transform_fn

list of transformation functions to be used when back-transforming the transformed parameters. Should be the inverse of the forward transformation functions. Defaults to exponential.

searchmethod

optimization algorithm to be used in optim. Defaults to Nelder-Mead.