diff options
| -rw-r--r-- | NAMESPACE | 2 | ||||
| -rw-r--r-- | R/multistart.R | 26 | ||||
| -rw-r--r-- | R/parms.mkinfit.R | 30 | ||||
| -rw-r--r-- | man/mkinfit.Rd | 4 | ||||
| -rw-r--r-- | man/multistart.Rd | 43 | ||||
| -rw-r--r-- | man/parms.Rd | 17 |
6 files changed, 99 insertions, 23 deletions
@@ -27,6 +27,7 @@ S3method(mhmkin,list) S3method(mixed,mmkin) S3method(mkinpredict,mkinfit) S3method(mkinpredict,mkinmod) +S3method(multistart,saem.mmkin) S3method(nlme,mmkin) S3method(nobs,mkinfit) S3method(parms,mkinfit) @@ -106,6 +107,7 @@ export(mkinpredict) export(mkinresplot) export(mkinsub) export(mmkin) +export(multistart) export(nafta) export(nlme) export(nlme_data) diff --git a/R/multistart.R b/R/multistart.R index db482cc4..819fcc1b 100644 --- a/R/multistart.R +++ b/R/multistart.R @@ -7,18 +7,38 @@ #' inspired by the article on practical identifiabiliy in the frame of nonlinear #' mixed-effects models by Duchesne et al (2021). #' +#' Currently, parallel execution of the fits is only supported using +#' [parallel::mclapply], i.e. not available on Windows. +#' +#' @param object The fit object to work with +#' @param n How many different combinations of starting parameters should be +#' used? +#' @param cores How many fits should be run in parallel? +#' @param \dots Passed to the update function. +#' @return A list of [saem.mmkin] objects, with class attributes +#' 'multistart.saem.mmkin' and 'multistart'. +#' #' @references Duchesne R, Guillemin A, Gandrillon O, Crauste F. Practical #' identifiability in the frame of nonlinear mixed effects models: the example #' of the in vitro erythropoiesis. BMC Bioinformatics. 2021 Oct 4;22(1):478. #' doi: 10.1186/s12859-021-04373-4. #' @export -multistart <- function(object, n = 50, ...) +multistart <- function(object, n = 50, cores = 1, ...) { UseMethod("multistart", object) } #' @rdname multistart #' @export -multistart.saem.mmkin <- function(object, n = 50, ...) { - +multistart.saem.mmkin <- function(object, n = 50, cores = 1, ...) { + start_parms <- apply( + parms(object$mmkin, errparms = FALSE), 1, + function(x) stats::runif(n, min(x), max(x)) + ) + + res <- parallel::mclapply(1:n, function(x) { + update(object, degparms_start = start_parms[x], ...) + }, mc.cores = cores) + class(res) <- c("multistart.saem.mmkin", "multistart") + return(res) } diff --git a/R/parms.mkinfit.R b/R/parms.mkinfit.R index a1f2d209..31ca05bc 100644 --- a/R/parms.mkinfit.R +++ b/R/parms.mkinfit.R @@ -8,9 +8,9 @@ #' [mkinfit()] objects and for [mmkin()] objects. #' @param \dots Not used #' @return For mkinfit objects, a numeric vector of fitted model parameters. -#' For mmkin row objects, a matrix with the parameters with a -#' row for each dataset. If the mmkin object has more than one row, a list of -#' such matrices is returned. +#' For mmkin row objects, a matrix with the parameters with a row for each +#' dataset. If the mmkin object has more than one row, a list of such matrices +#' is returned. #' @examples #' # mkinfit objects #' fit <- mkinfit("SFO", FOCUS_2006_C, quiet = TRUE) @@ -34,27 +34,35 @@ parms <- function(object, ...) UseMethod("parms", object) } -#' @param transformed Should the parameters be returned -#' as used internally during the optimisation? +#' @param transformed Should the parameters be returned as used internally +#' during the optimisation? +#' @param errparms Should the error model parameters be returned +#' in addition to the degradation parameters? #' @rdname parms #' @export -parms.mkinfit <- function(object, transformed = FALSE, ...) +parms.mkinfit <- function(object, transformed = FALSE, errparms = TRUE, ...) { - if (transformed) object$par - else c(object$bparms.optim, object$errparms) + res <- if (transformed) object$par + else c(object$bparms.optim, object$errparms) + if (!errparms) { + res[setdiff(names(res), names(object$errparms))] + } + else return(res) } #' @rdname parms #' @export -parms.mmkin <- function(object, transformed = FALSE, ...) +parms.mmkin <- function(object, transformed = FALSE, errparms = TRUE, ...) { if (nrow(object) == 1) { - res <- sapply(object, parms, transformed = transformed, ...) + res <- sapply(object, parms, transformed = transformed, + errparms = errparms, ...) colnames(res) <- colnames(object) } else { res <- list() for (i in 1:nrow(object)) { - res[[i]] <- parms(object[i, ], transformed = transformed, ...) + res[[i]] <- parms(object[i, ], transformed = transformed, + errparms = errparms, ...) } names(res) <- rownames(object) } diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd index f96b4d22..b5b24449 100644 --- a/man/mkinfit.Rd +++ b/man/mkinfit.Rd @@ -23,8 +23,8 @@ mkinfit( atol = 1e-08, rtol = 1e-10, error_model = c("const", "obs", "tc"), - error_model_algorithm = c("auto", "d_3", "direct", "twostep", "threestep", "fourstep", - "IRLS", "OLS"), + error_model_algorithm = c("auto", "d_3", "direct", "twostep", "threestep", + "fourstep", "IRLS", "OLS"), reweight.tol = 1e-08, reweight.max.iter = 10, trace_parms = FALSE, diff --git a/man/multistart.Rd b/man/multistart.Rd new file mode 100644 index 00000000..ff60b01d --- /dev/null +++ b/man/multistart.Rd @@ -0,0 +1,43 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/multistart.R +\name{multistart} +\alias{multistart} +\alias{multistart.saem.mmkin} +\title{Perform a hierarchical model fit with multiple starting values} +\usage{ +multistart(object, n = 50, cores = 1, ...) + +\method{multistart}{saem.mmkin}(object, n = 50, cores = 1, ...) +} +\arguments{ +\item{object}{The fit object to work with} + +\item{n}{How many different combinations of starting parameters should be +used?} + +\item{cores}{How many fits should be run in parallel?} + +\item{\dots}{Passed to the update function.} +} +\value{ +A list of \link{saem.mmkin} objects, with class attributes +'multistart.saem.mmkin' and 'multistart'. +} +\description{ +The purpose of this method is to check if a certain algorithm for fitting +nonlinear hierarchical models (also known as nonlinear mixed-effects models) +will reliably yield results that are sufficiently similar to each other, if +started with a certain range of reasonable starting parameters. It is +inspired by the article on practical identifiabiliy in the frame of nonlinear +mixed-effects models by Duchesne et al (2021). +} +\details{ +Currently, parallel execution of the fits is only supported using +\link[parallel:mclapply]{parallel::mclapply}, i.e. not available on Windows. +} +\references{ +Duchesne R, Guillemin A, Gandrillon O, Crauste F. Practical +identifiability in the frame of nonlinear mixed effects models: the example +of the in vitro erythropoiesis. BMC Bioinformatics. 2021 Oct 4;22(1):478. +doi: 10.1186/s12859-021-04373-4. +} diff --git a/man/parms.Rd b/man/parms.Rd index af92bd2a..293bdaab 100644 --- a/man/parms.Rd +++ b/man/parms.Rd @@ -8,9 +8,9 @@ \usage{ parms(object, ...) -\method{parms}{mkinfit}(object, transformed = FALSE, ...) +\method{parms}{mkinfit}(object, transformed = FALSE, errparms = TRUE, ...) -\method{parms}{mmkin}(object, transformed = FALSE, ...) +\method{parms}{mmkin}(object, transformed = FALSE, errparms = TRUE, ...) } \arguments{ \item{object}{A fitted model object. Methods are implemented for @@ -18,14 +18,17 @@ parms(object, ...) \item{\dots}{Not used} -\item{transformed}{Should the parameters be returned -as used internally during the optimisation?} +\item{transformed}{Should the parameters be returned as used internally +during the optimisation?} + +\item{errparms}{Should the error model parameters be returned +in addition to the degradation parameters?} } \value{ For mkinfit objects, a numeric vector of fitted model parameters. -For mmkin row objects, a matrix with the parameters with a -row for each dataset. If the mmkin object has more than one row, a list of -such matrices is returned. +For mmkin row objects, a matrix with the parameters with a row for each +dataset. If the mmkin object has more than one row, a list of such matrices +is returned. } \description{ This function always returns degradation model parameters as well as error |