Skip to content

feat: Upgrade to PMcore 0.29 #388

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Closed
Siel wants to merge 1 commit into from
Closed

feat: Upgrade to PMcore 0.29 #388

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
16 changes: 8 additions & 8 deletions Cargo.lock
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

28 changes: 18 additions & 10 deletions R/PM_model.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -252,17 +252,20 @@ PM_model <- R6::R6Class(
#' - `dx[i]` for the change in amount with respect to time (i.e., \eqn{dx/dt}),
#' where `i` is the compartment number,
#' - `x[i]` for the compartment amount, where `i` is the compartment number.
#' - `rateiv[j]` for the infusion rate of input `j`, where `j` is the input number
#' in the data corresponding to doses for that input.
#' - Bolus doses are indicated by `DUR = 0` for dose events in the
#' data. Currently only one bolus input is allowed, which goes into compartment 1
#' and is not modifiable. It does not appear in the differential equations.
#' - `rateiv[j]` or `R[j]` for the infusion rate of input `j`, where `j` is
#' the input number in the data. An infusion may be a standalone additive term
#' or one exact product with a scale, such as `R[1] * iv_scale`. The scale is
#' evaluated continuously in the differential equation.
#' - `B[j]` or `bolus[j]` for a bolus input. A bolus may be a standalone
#' additive term or one exact product with a scale, such as `B[1] * v`.
#' The scale is applied to the bolus dose and does not affect an infusion with
#' the same input number.
#'
#' For example,
#' ```
#' eqn = function() {
#' dx[1] = -ka * x[1]
#' dx[2] = rateiv[1] + ka * x[1] - ke * x[2]
#' dx[1] = B[1] * fa1 - ka * x[1]
#' dx[2] = rateiv[1] * iv_scale + ka * x[1] - ke * x[2]
#' }
#' ```
#' * **Additional equations** in R code can be defined in this block, which are similar to
Expand All @@ -286,7 +289,8 @@ PM_model <- R6::R6Class(
#' As for `eqn`, additional equations in R code can be defined in this block,
#' but will only be available within the `lag` block.
#' @param fa A function defining the bioavailability (fraction absorbed) equations,
#' similar to `lag`.
#' similar to `lag`. The `lag` and `fa` blocks also apply to analytical bolus
#' models; they are not valid for analytical infusion-only models.
#'
#' Example:
#' ```
Expand All @@ -308,7 +312,8 @@ PM_model <- R6::R6Class(
#' This sets the initial amount of drug in compartment 2 to the value
#' of a covariate `init2` multiplied by the volume of the compartment,
#' `V`, assuming `V` is either a primary parameter or defined in the
#' `sec` block.
#' `sec` block. Initial conditions are evaluated before the first event of
#' every occasion, including occasions started by an `EVID = 4` row.
#'
#' As for `eqn`, additional equations in R code can be defined in this block,
#' but will only be available within the `ini` block.
Expand Down Expand Up @@ -471,7 +476,10 @@ PM_model <- R6::R6Class(
}
})
self$arg_list$x <- NULL
self$dsl <- x$dsl
# `dsl` is rendered from `arg_list`, so it is never inherited. A
# PM_model saved before a DSL change would otherwise replay stale
# source instead of rendering the model it defines.
self$dsl <- NULL
} else {
cli::cli_abort(c(
"x" = "Non supported input for {.arg x}: {typeof(x)}",
Expand Down
Loading
Loading