diff options
Diffstat (limited to 'R/saemix.R')
| -rw-r--r-- | R/saemix.R | 37 |
1 files changed, 31 insertions, 6 deletions
@@ -1,8 +1,8 @@ #' Fit nonlinear mixed models with SAEM #' #' This function uses [saemix::saemix()] as a backend for fitting nonlinear mixed -#' effects models created from [mmkin] row objects using the stochastic approximation -#' to the expectation maximisation algorithm (SAEM). +#' effects models created from [mmkin] row objects using the Stochastic Approximation +#' Expectation Maximisation algorithm (SAEM). #' #' An mmkin row object is essentially a list of mkinfit objects that have been #' obtained by fitting the same model to a list of datasets using [mkinfit]. @@ -23,7 +23,9 @@ #' @param control Passed to [saemix::saemix] #' @param \dots Further parameters passed to [saemix::saemixData] #' and [saemix::saemixModel]. -#' @return An [saemix::SaemixObject]. +#' @return An S3 object of class 'saem.mmkin', containing the fitted +#' [saemix::SaemixObject] as a list component named 'so'. +#' @seealso [summary.saem.mmkin] #' @examples #' \dontrun{ #' ds <- lapply(experimental_data_for_UBA_2019[6:10], @@ -57,7 +59,7 @@ #' # Using a single core, the following takes about 6 minutes, using 10 cores #' # it is slower instead of faster #' f_saem_des <- saem(f_mmkin_des, cores = 1) -#' compare.saemix(list(f_saemix$so, f_saemix_des$so)) +#' compare.saemix(list(f_saem$so, f_saem_des$so)) #' } #' @export saem <- function(object, control, ...) UseMethod("saem") @@ -79,18 +81,40 @@ saem.mmkin <- function(object, tmp <- tempfile() grDevices::png(tmp) } - f_saemix <- saemix::saemix(m_saemix, d_saemix, control) + fit_time <- system.time({ + f_saemix <- saemix::saemix(m_saemix, d_saemix, control) + f_saemix <- saemix::saemix.predict(f_saemix) + }) if (suppressPlot) { grDevices::dev.off() unlink(tmp) } + transparms_optim = f_saemix@results@fixed.effects + names(transparms_optim) = f_saemix@results@name.fixed + bparms_optim <- backtransform_odeparms(transparms_optim, + object[[1]]$mkinmod, + object[[1]]$transform_rates, + object[[1]]$transform_fractions) + result <- list( mkinmod = object[[1]]$mkinmod, mmkin = object, solution_type = object[[1]]$solution_type, transform_rates = object[[1]]$transform_rates, transform_fractions = object[[1]]$transform_fractions, - so = f_saemix) + so = f_saemix, + time = fit_time, + mean_dp_start = attr(m_saemix, "mean_dp_start"), + bparms.optim = bparms_optim, + bparms.fixed = object[[1]]$bparms.fixed, + data = nlme_data(object), + err_mod = object[[1]]$err_mod, + date.fit = date(), + saemixversion = as.character(utils::packageVersion("saemix")), + mkinversion = as.character(utils::packageVersion("mkin")), + Rversion = paste(R.version$major, R.version$minor, sep=".") + ) + class(result) <- "saem.mmkin" return(result) } @@ -256,6 +280,7 @@ saemix_model <- function(object, cores = 1, verbose = FALSE, ...) { error.init = error.init, verbose = verbose ) + attr(res, "mean_dp_start") <- degparms_optim return(res) } |