get_optim_fit {ushr}

Fit model to data using optim

Description

This function uses optim to fit either the biphasic or single phase model to data from a given subject

Usage

get_optim_fit(initial_params, param_names, free_param_index, data,
  model_list = "four",
  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, B, gamma are to be recovered. This should be c(TRUE, TRUE, TRUE, TRUE) for the biphasic model and c(FALSE, FALSE, TRUE, TRUE) for the single phase model.

data

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

model_list

character indicating which model is begin fit. Can be either 'four' for the biphasic model, or 'two' for the single phase model. Defaults to 'four'.

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.