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initial attempt (updates for neutropenia model) #90

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initial attempt (updates for neutropenia model) #90

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18 changes: 13 additions & 5 deletions R/get_var_y.R
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Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,8 @@
#' @param in_parallel run simulations in parallel?
#' @param n_cores if run in parallel, on how many cores?
#' @param return_all return object with all relevant information?
#' @param exclude_parameters Vector of parameters to exclude from variability
#' calculation, implemented for "delta" method only.
#' @param ... passed on to `sim_ode()`
#'
#' @export
Expand All @@ -47,6 +49,7 @@ get_var_y <- function(
in_parallel = FALSE,
n_cores = 3,
return_all = FALSE,
exclude_parameters = NULL,
...) {
if(method == "sim" && is.null(n_ind)) {
stop("Please specify number of individuals when using simulation method!")
Expand Down Expand Up @@ -93,6 +96,11 @@ get_var_y <- function(
}
if(auc) y <- diff(y)
nams <- names(parameters_est)
if (!is.null(exclude_parameters)) {
ind <- which(!nams %in% exclude_parameters)
nams <- setdiff(nams, exclude_parameters)
omega_full <- omega_full[ind,ind]
}
jac <- c()
if(!(method %in% c("delta", "sim"))) {
stop("Requested method not recognized!")
Expand All @@ -101,10 +109,10 @@ get_var_y <- function(
v <- list()
qnt <- list()
if(method == "delta") {
sim_func <- function(i, ...) {
sim_func <- function(par, ...) {
par_tmp <- parameters
dP <- rel_delta * par_tmp[[nams[i]]]
par_tmp[[nams[i]]] <- par_tmp[[nams[i]]] + dP
dP <- rel_delta * par_tmp[[par]]
par_tmp[[par]] <- par_tmp[[par]] + dP
res_dP <- PKPDsim::sim_ode(
ode = model,
regimen = regimen,
Expand Down Expand Up @@ -132,9 +140,9 @@ get_var_y <- function(
}
# running in parallel is actually not faster for most simple models. Only for models with larger number of parameters.
if(in_parallel) {
jac <- matrix(unlist(parallel::mclapply(seq(along = nams), sim_func, mc.cores = n_cores, ...)), nrow = ifelse(auc, 1, length(t_obs)))
jac <- matrix(unlist(parallel::mclapply(nams, sim_func, mc.cores = n_cores, ...)), nrow = ifelse(auc, 1, length(t_obs)))
} else {
jac <- matrix(unlist(lapply(seq(along = nams), sim_func, ...)), nrow = ifelse(auc, 1, length(t_obs)))
jac <- matrix(unlist(lapply(nams, sim_func, ...)), nrow = ifelse(auc, 1, length(t_obs)))
}
for(i in seq(types)) {
type <- types[i]
Expand Down
4 changes: 4 additions & 0 deletions man/get_var_y.Rd
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25 changes: 25 additions & 0 deletions tests/testthat/test_get_var_y.R
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Original file line number Diff line number Diff line change
Expand Up @@ -164,3 +164,28 @@ test_that("One compartment with MM kinetics", {
expect_equal(round(v1$regular, 3), c(0.120, 4.206))

})

test_that("delta method, exclude a parameter", {
skip_on_cran()
v_delta_with <- get_var_y(
model = mod_1cmt_iv,
parameters = par,
t_obs = t_obs,
regimen = reg,
omega = omega,
method = "delta"
)
v_delta_without <- get_var_y(
model = mod_1cmt_iv,
parameters = par,
t_obs = t_obs,
regimen = reg,
omega = omega,
method = "delta",
exclude_parameters = "V"
)

expect_true(all(v_delta_with$regular > v_delta_without$regular))
expect_true(all(v_delta_with$log > v_delta_without$log))
expect_equal(round(v_delta_without$regular, 3), c(0.055, 0.240))
})
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