From 2c848eb02075d1cc2abcc9bc258630a04f51949d Mon Sep 17 00:00:00 2001 From: "Matthew L. Fidler" Date: Tue, 12 Dec 2023 11:26:45 -0600 Subject: [PATCH] Version bump --- DESCRIPTION | 5 +++-- NEWS.md | 2 +- R/pknca.R | 21 ++++++++++++--------- man/as.nlmixr2.Rd | 6 +++--- man/bblDatToMonolix.Rd | 25 +++++++++++++------------ man/getStandardColNames.Rd | 4 ++-- man/modelUnitConversion.Rd | 6 +++--- man/monolixControl.Rd | 10 +++++----- man/nlmixr2Est.pknca.Rd | 27 +++++++++++++-------------- man/nonmemControl.Rd | 6 +++--- man/pkncaControl.Rd | 2 +- man/simplifyUnit.Rd | 4 ++-- 12 files changed, 61 insertions(+), 57 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index c1238d1c..f375a378 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: babelmixr2 Type: Package Title: Use 'nlmixr2' to Interact with Open Source and Commercial Software -Version: 0.1.1.9000 +Version: 0.1.2 Authors@R: c(person("Matthew","Fidler", role = c("aut", "cre"), email = "matt.fidler@novartis.com", comment=c(ORCID="0000-0001-8538-6691")), person("Bill", "Denney", email="wdenney@humanpredictions.com", role="aut", comment=c(ORCID="0000-0002-5759-428X")), person("Nook", "Fulloption", role="ctb", comment="goldfish art")) @@ -35,12 +35,13 @@ Imports: digest, lotri, nlmixr2est (>= 2.1.6), - nonmem2rx (> 0.1.2), + nonmem2rx (>= 0.1.3), methods, qs, rex, rxode2 RoxygenNote: 7.2.3 +Roxygen: list(markdown = TRUE) Config/testthat/edition: 3 LinkingTo: Rcpp, rxode2, RcppArmadillo, RcppEigen, rxode2parse diff --git a/NEWS.md b/NEWS.md index 4c97701a..9ae51423 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# babelmixr2 (development version) +# babelmixr2 0.1.2 * Handle algebraic `mu` expressions diff --git a/R/pknca.R b/R/pknca.R index 22c98df4..ef3161b9 100644 --- a/R/pknca.R +++ b/R/pknca.R @@ -2,17 +2,20 @@ #' #' @details Parameters are estimated as follows: #' -#' \itemize{ -#' \item{ka}{4 half-lives to Tmax but not higher than 3: \code{log(2)/(tmax/4)}} -#' \item{vc}{Inverse of dose-normalized Cmax} -#' \item{cl}{Estimated as the median clearance} -#' \item{vp,vp2}{2- and 4-fold the \code{vc}, respectively by default, +#' +#' - \code{ka} 4 half-lives to Tmax but not higher than 3: \code{log(2)/(tmax/4)} +#' +#' - \code{vc} Inverse of dose-normalized Cmax +#' +#' - \code{cl} Estimated as the median clearance +#' +#' - \code{vp,vp2}2- and 4-fold the \code{vc}, respectively by default, #' controlled by the \code{vpMult} and \code{vp2Mult} arguments to -#' \code{pkncaControl}} -#' \item{q,q2}{0.5- and 0.25-fold the \code{cl}, respectively by default, +#' \code{pkncaControl} +#' +#' - \code{q,q2} 0.5- and 0.25-fold the \code{cl}, respectively by default, #' controlled by the \code{qMult} and \code{q2Mult} arguments to -#' \code{pkncaControl}} -#' } +#' \code{pkncaControl} #' #' The bounds for the parameter estimates are set to 10% of the first percentile #' and 10 times the 99th percentile. (For ka, the lower bound is set to the diff --git a/man/as.nlmixr2.Rd b/man/as.nlmixr2.Rd index aa81e18c..cdcc3568 100644 --- a/man/as.nlmixr2.Rd +++ b/man/as.nlmixr2.Rd @@ -24,10 +24,10 @@ as.nlmixr( \item{...}{Other arguments} -\item{table}{is the `nlmixr2est::tableControl()` options} +\item{table}{is the \code{nlmixr2est::tableControl()} options} -\item{rxControl}{is the `rxode2::rxControl()` options, which is -generally needed for how `addl` doses are handled in the +\item{rxControl}{is the \code{rxode2::rxControl()} options, which is +generally needed for how \code{addl} doses are handled in the translation} } \value{ diff --git a/man/bblDatToMonolix.Rd b/man/bblDatToMonolix.Rd index 1ecb729b..2bd0420d 100644 --- a/man/bblDatToMonolix.Rd +++ b/man/bblDatToMonolix.Rd @@ -59,24 +59,25 @@ there are additional columns to keep.} \item{rxControl}{is the rxode2 control options; This is to figure out how to handle the addl dosing information.} -\item{env}{When `NULL` (default) nothing is done. When an -environment, the function `nlmixr2est::.foceiPreProcessData(data, -env, model, rxControl)` is called on the provided environment.} +\item{env}{When \code{NULL} (default) nothing is done. When an +environment, the function \code{nlmixr2est::.foceiPreProcessData(data, env, model, rxControl)} is called on the provided environment.} } \value{ -With the function `bblDatToMonolix()` return a list with: - - Monolix compatible dataset ($monolix) - - Monolix ADM information ($adm) +With the function \code{bblDatToMonolix()} return a list with: +\itemize{ +\item Monolix compatible dataset ($monolix) +\item Monolix ADM information ($adm) +} -With the function `nlmixrDataToNonmem()` return a dataset that is +With the function \code{nlmixrDataToNonmem()} return a dataset that is compatible with NONMEM. -With the function `nlmixrDataToMrgsolve()` return a dataset that is -compatible with `mrgsolve`. Unlike NONMEM, it supports replacement -events with `evid=8` (note with `rxode2` replacement `evid` is `5`). +With the function \code{nlmixrDataToMrgsolve()} return a dataset that is +compatible with \code{mrgsolve}. Unlike NONMEM, it supports replacement +events with \code{evid=8} (note with \code{rxode2} replacement \code{evid} is \code{5}). -With the function `nlmixrDataToRxode()` this will normalize the -dataset to use newer `evid` definitions that are closer to NONMEM +With the function \code{nlmixrDataToRxode()} this will normalize the +dataset to use newer \code{evid} definitions that are closer to NONMEM instead of any classic definitions that are used at a lower level } \description{ diff --git a/man/getStandardColNames.Rd b/man/getStandardColNames.Rd index 5c5d7e87..f77949f6 100644 --- a/man/getStandardColNames.Rd +++ b/man/getStandardColNames.Rd @@ -11,8 +11,8 @@ getStandardColNames(data) } \value{ A named character vector where the names are the standardized names - and the values are either the name of the column from the data or \code{NA} - if the column is not present in the data. +and the values are either the name of the column from the data or \code{NA} +if the column is not present in the data. } \description{ Determine standardized rxode2 column names from data diff --git a/man/modelUnitConversion.Rd b/man/modelUnitConversion.Rd index 2afeb8f9..b78a6cc6 100644 --- a/man/modelUnitConversion.Rd +++ b/man/modelUnitConversion.Rd @@ -18,9 +18,9 @@ modelUnitConversion( } \value{ A list with names for the units associated with each parameter - ("amtu", "clearanceu", "volumeu", "timeu", "dvu") and the numeric value to - multiply the modeled estimate (for example, \code{cp}) so that the model is - consistent with the data units. +("amtu", "clearanceu", "volumeu", "timeu", "dvu") and the numeric value to +multiply the modeled estimate (for example, \code{cp}) so that the model is +consistent with the data units. } \description{ Unit conversion for pharmacokinetic models diff --git a/man/monolixControl.Rd b/man/monolixControl.Rd index b0ce449d..854e5cde 100644 --- a/man/monolixControl.Rd +++ b/man/monolixControl.Rd @@ -48,11 +48,11 @@ fim.} The combined1 error type can be described by the following equation: - y = f + (a + b*f^c)*err + \deqn{y = f + (a + b\times f^c) \times \varepsilon}{y = f + (a + b*f^c)*err} The combined2 error model can be described by the following equation: - y = f + sqrt(a^2 + b^2*(f^c)^2)*err + \deqn{y = f + \sqrt{a^2 + b^2\times f^{2\times c}} \times \varepsilon}{y = f + sqrt(a^2 + b^2*(f^c)^2)*err} Where: @@ -70,7 +70,7 @@ The combined2 error model can be described by the following equation: phase auto-stop of SAEM (default 250)} \item{smoothingAutoStop}{Boolean indicating if the smoothing should -automatically stop (default `FALSE`)} +automatically stop (default \code{FALSE})} \item{burnInIterations}{Number of burn in iterations} @@ -86,7 +86,7 @@ iterations} exploratory phase (default 200)} \item{exploratoryAlpha}{Convergence memory in the exploratory phase -(only used when `exploratoryAutoStop` is `TRUE`)} +(only used when \code{exploratoryAutoStop} is \code{TRUE})} \item{omegaTau}{Proportional rate on variance for simulated annealing} @@ -131,7 +131,7 @@ If not specified, then it matches the significant digits in the be used for the monolix runs} \item{modelName}{Model name used to generate the NONMEM output. If -`NULL` try to infer from the model name (could be `x` if not +\code{NULL} try to infer from the model name (could be \code{x} if not clear). Otherwise use this character for outputs.} \item{muRefCovAlg}{This controls if algebraic expressions that can diff --git a/man/nlmixr2Est.pknca.Rd b/man/nlmixr2Est.pknca.Rd index 4c316879..491de2c9 100644 --- a/man/nlmixr2Est.pknca.Rd +++ b/man/nlmixr2Est.pknca.Rd @@ -22,30 +22,29 @@ flexibility but not currently used inside nlmixr} } \value{ A model with updated starting parameters. In the model a new element - named "nca" will be available which includes the PKNCA results used for the - calculation. +named "nca" will be available which includes the PKNCA results used for the +calculation. } \description{ Estimate starting parameters using PKNCA } \details{ Parameters are estimated as follows: - \itemize{ -\item{ka}{4 half-lives to Tmax but not higher than 3: \code{log(2)/(tmax/4)}} -\item{vc}{Inverse of dose-normalized Cmax} -\item{cl}{Estimated as the median clearance} -\item{vp,vp2}{2- and 4-fold the \code{vc}, respectively by default, - controlled by the \code{vpMult} and \code{vp2Mult} arguments to - \code{pkncaControl}} -\item{q,q2}{0.5- and 0.25-fold the \code{cl}, respectively by default, - controlled by the \code{qMult} and \code{q2Mult} arguments to - \code{pkncaControl}} +\item \code{ka} 4 half-lives to Tmax but not higher than 3: \code{log(2)/(tmax/4)} +\item \code{vc} Inverse of dose-normalized Cmax +\item \code{cl} Estimated as the median clearance +\item \code{vp,vp2}2- and 4-fold the \code{vc}, respectively by default, +controlled by the \code{vpMult} and \code{vp2Mult} arguments to +\code{pkncaControl} +\item \code{q,q2} 0.5- and 0.25-fold the \code{cl}, respectively by default, +controlled by the \code{qMult} and \code{q2Mult} arguments to +\code{pkncaControl} } -The bounds for the parameter estimates are set to 10% of the first percentile +The bounds for the parameter estimates are set to 10\% of the first percentile and 10 times the 99th percentile. (For ka, the lower bound is set to the -lower of 10% of the first percentile or 0.03 and the upper bound is not +lower of 10\% of the first percentile or 0.03 and the upper bound is not modified from 10 times the 99th percentile.) Parameter estimation methods may be changed in a future version. diff --git a/man/nonmemControl.Rd b/man/nonmemControl.Rd index 9be55309..8aeb196b 100644 --- a/man/nonmemControl.Rd +++ b/man/nonmemControl.Rd @@ -115,10 +115,10 @@ due to an apparent failed optimization} \item{mapinter}{is the MAPINTER parameter for the IMP method} -\item{noabort}{Add the `NOABORT` option for `$EST`} +\item{noabort}{Add the \code{NOABORT} option for \verb{$EST}} \item{modelName}{Model name used to generate the NONMEM output. If -`NULL` try to infer from the model name (could be `x` if not +\code{NULL} try to infer from the model name (could be \code{x} if not clear). Otherwise use this character for outputs.} \item{muRefCovAlg}{This controls if algebraic expressions that can @@ -144,7 +144,7 @@ automatic \code{rxControl} generation.} } \value{ babelmixr2 control option for generating NONMEM control stream and - reading it back into `babelmixr2`/`nlmixr2` +reading it back into \code{babelmixr2}/\code{nlmixr2} } \description{ NONMEM estimation control diff --git a/man/pkncaControl.Rd b/man/pkncaControl.Rd index 1fc48fdf..cbf1dcea 100644 --- a/man/pkncaControl.Rd +++ b/man/pkncaControl.Rd @@ -49,7 +49,7 @@ when a subset of the original data are informative for NCA.} bypass automatic calculations. At least the following parameters must be calculated in the NCA: tmax, cmax.dn, cl.last} -\item{rxControl}{Control options sent to `rxode2::rxControl()`} +\item{rxControl}{Control options sent to \code{rxode2::rxControl()}} } \value{ A list of parameters diff --git a/man/simplifyUnit.Rd b/man/simplifyUnit.Rd index f2a92f42..e450945a 100644 --- a/man/simplifyUnit.Rd +++ b/man/simplifyUnit.Rd @@ -14,14 +14,14 @@ is the whole unit specification)} } \value{ The units specified with units that are in both the numerator and - denominator cancelled. +denominator cancelled. } \description{ Simplify units by removing repeated units from the numerator and denominator } \details{ \code{NA} or \code{""} for \code{numerator} and \code{denominator} - are considered unitless. +are considered unitless. } \examples{ simplifyUnit("kg", "kg/mL")