From 04ce0434ec3e57ec629df6f983e4b50bb7ba8d20 Mon Sep 17 00:00:00 2001 From: levenc Date: Sat, 3 Sep 2022 22:35:11 +0200 Subject: [PATCH] spellcheck and missing tags --- R/dosing_optim.R | 1 - R/posologyr.R | 1 + docs/news/index.html | 6 +-- docs/pkgdown.yml | 2 +- docs/reference/poso_inter_cmin.html | 5 +-- man/poso_inter_cmin.Rd | 2 - man/posologyr.Rd | 58 ----------------------------- 7 files changed, 6 insertions(+), 69 deletions(-) delete mode 100644 man/posologyr.Rd diff --git a/R/dosing_optim.R b/R/dosing_optim.R index b6d3e87..dd3d386 100644 --- a/R/dosing_optim.R +++ b/R/dosing_optim.R @@ -644,7 +644,6 @@ poso_dose_conc <- function(dat=NULL,prior_model=NULL,time_c,target_conc, #' @param indiv_param Optional. A set of individual parameters : THETA, #' estimates of ETA, and covariates. #' -#' @return A numeric #' #' @return A list containing the following components: #' \describe{ diff --git a/R/posologyr.R b/R/posologyr.R index fc71e76..d454867 100644 --- a/R/posologyr.R +++ b/R/posologyr.R @@ -63,6 +63,7 @@ #' } #' #' @keywords internal +#' @noRd posologyr <- function(prior_model=NULL,dat=NULL,nocb=FALSE){ validate_priormod(prior_model) diff --git a/docs/news/index.html b/docs/news/index.html index 481f925..0b41c2a 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -71,7 +71,7 @@

posologyr v1.0

Breaking changes

  • -posologyr() is now an internal function, all exported functions take patient data and a prior model as input parameters
    • +posologyr() is now an internal function, all exported functions take patient data and a prior model as input parameters
  • The adaptive MAP forecasting option is removed
@@ -82,7 +82,7 @@

Additional features

Internal changes

  • RxODE import is updated to rxode2
    • -
  • All tests are updated to take into account the internalization of the posologyr() function
    • +
  • All tests are updated to take into account the internalization of the posologyr() function

Bug fixes

@@ -108,7 +108,7 @@

posologyr v0.2
  • poso_dose_conc() is the new name of poso_dose_ctime().
  • Issues #5 and #6 are fixed: poso_time_cmin(), poso_dose_auc(), poso_dose_conc(), and poso_inter_cmin() now work with prior and posterior distributions of ETA, and not only with point estimates (such as the MAP).
    • -
  • A new nocb parameter is added to posologyr(). The interpolation method for time-varying covariates can be either last observation carried forward (locf, the RxODE default), or next observation carried backward (nocb, the NONMEM default).
    • +
  • A new nocb parameter is added to posologyr(). The interpolation method for time-varying covariates can be either last observation carried forward (locf, the RxODE default), or next observation carried backward (nocb, the NONMEM default).
  • vignette("uncertainty_estimates") is removed.
  • The built-in models are removed.
    • diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 17aa4b0..b80949c 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -6,5 +6,5 @@ articles: case_study_vancomycin: case_study_vancomycin.html patient_data_input: patient_data_input.html posologyr_user_defined_models: posologyr_user_defined_models.html -last_built: 2022-08-27T18:45Z +last_built: 2022-09-03T20:33Z diff --git a/docs/reference/poso_inter_cmin.html b/docs/reference/poso_inter_cmin.html index a6c6652..9127b16 100644 --- a/docs/reference/poso_inter_cmin.html +++ b/docs/reference/poso_inter_cmin.html @@ -168,9 +168,6 @@

    Arguments

    Value

    -

    A numeric

    - -

    A list containing the following components:

    interval

    Numeric. An inter-dose interval to reach the target trough concentration before each dosing of a multiple dose regimen.

    @@ -249,7 +246,7 @@

    Examples

    #> #> $indiv_param #> THETA_Cl THETA_Vc THETA_Ka ETA_Cl ETA_Vc ETA_Ka -#> 1 4 70 1 0.6019036 -0.4291734 0.1278478 +#> 1 4 70 1 0.6019037 -0.4291733 0.1278479 #>
    diff --git a/man/poso_inter_cmin.Rd b/man/poso_inter_cmin.Rd index 4e8c424..24001dc 100644 --- a/man/poso_inter_cmin.Rd +++ b/man/poso_inter_cmin.Rd @@ -63,8 +63,6 @@ administrations.} estimates of ETA, and covariates.} } \value{ -A numeric - A list containing the following components: \describe{ \item{interval}{Numeric. An inter-dose interval to reach the target trough diff --git a/man/posologyr.Rd b/man/posologyr.Rd deleted file mode 100644 index cfc7fb7..0000000 --- a/man/posologyr.Rd +++ /dev/null @@ -1,58 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/posologyr.R -\name{posologyr} -\alias{posologyr} -\title{Creates a posologyr list from a prior model and an individual event -record} -\usage{ -posologyr(prior_model = NULL, dat = NULL, nocb = FALSE) -} -\arguments{ -\item{prior_model}{A \code{posologyr} prior population pharmacokinetics -model, a list of six objects.} - -\item{dat}{Dataframe. An individual subject dataset following the -structure of NONMEM/rxode2 event records.} - -\item{nocb}{A boolean. for time-varying covariates: the next observation -carried backward (nocb) interpolation style, similar to NONMEM. If -\code{FALSE}, the last observation carried forward (locf) style will be used. -Defaults to \code{FALSE}. - -\code{posologyr} will check the validity of the compiled rxode2 -model. If \code{prior_model$ppk_model$isValid()} returns \code{FALSE}, -\code{posologyr} will call \code{\link[rxode2]{rxode2}} -to recompile the model before solving it using \code{prior_model} -and \code{dat}.} -} -\value{ -A list of eight objects: the posologyr prior population -pharmacokinetics model given as \code{prior_model} parameter (6 objects), -the individual event record (\code{tdm_data}) given as \code{dat} parameter, -and the solved model (\code{solved_ppk_model}). -\describe{ -\item{ppk_model}{A rxode2 model implementing the structural -population pharmacokinetics model with the individual model -(i.e. the model of inter-individual variability) and the -covariates} -\item{error_model}{A function of the residual error model} -\item{theta}{A named vector of the population estimates of the -fixed effects parameters (called THETAs, following NONMEM -terminology)} -\item{omega}{A named square variance-covariance matrix of the -population parameters inter-individual variability} -\item{covariates}{A character vector of the covariates of -the model} -\item{sigma}{The estimates of the parameters of the residual error model} -\item{tdm_data}{A dataframe. The individual subject dataset -given as \code{dat} parameter} -\item{solved_ppk_model}{An \code{\link[rxode2]{rxSolve}} solve object, -created with \code{prior_ppk_model} and using \code{dat} as the event record.} -} -} -\description{ -Creates a list for a \code{posologyr} prior model, an individual event -record, and an \code{\link[rxode2]{rxSolve}} solve object, -created from the prior ppk model and the individual event record. -} -\keyword{internal}