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Diffstat (limited to 'R/saemix.R')
-rw-r--r-- | R/saemix.R | 118 |
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diff --git a/R/saemix.R b/R/saemix.R new file mode 100644 index 00000000..d3af8b43 --- /dev/null +++ b/R/saemix.R @@ -0,0 +1,118 @@ +#' Create saemix models from mmkin row objects +#' +#' This function sets up a nonlinear mixed effects model for an mmkin row +#' object for use with the saemix package. 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. +#' +#' @param object An mmkin row object containing several fits of the same model to different datasets +#' @rdname saemix +#' @examples +#' ds <- lapply(experimental_data_for_UBA_2019[6:10], +#' function(x) subset(x$data[c("name", "time", "value")])) +#' names(ds) <- paste("Dataset", 6:10) +#' sfo_sfo <- mkinmod(parent = mkinsub("SFO", "A1"), +#' A1 = mkinsub("SFO")) +#' f_mmkin <- mmkin(list("SFO-SFO" = sfo_sfo), ds, quiet = TRUE, cores = 5) +#' \dontrun{ +#' if (require(saemix)) { +#' m_saemix <- saemix_model(f_mmkin) +#' d_saemix <- saemix_data(f_mmkin) +#' saemix_options <- list(seed = 123456, save = FALSE, save.graphs = FALSE) +#' saemix(m_saemix, d_saemix, saemix_options) +#' } +#' } +#' @return An [saemix::SaemixModel] object. +#' @export +saemix_model <- function(object) { + if (nrow(object) > 1) stop("Only row objects allowed") + + mkin_model <- object[[1]]$mkinmod + analytical <- is.function(mkin_model$deg_func) + + degparms_optim <- mean_degparms(object) + psi0 <- matrix(degparms_optim, nrow = 1) + colnames(psi0) <- names(degparms_optim) + + degparms_fixed <- object[[1]]$bparms.fixed + + odeini_optim_parm_names <- grep('_0$', names(degparms_optim), value = TRUE) + odeini_fixed_parm_names <- grep('_0$', names(degparms_fixed), value = TRUE) + + odeparms_fixed_names <- setdiff(names(degparms_fixed), odeini_fixed_parm_names) + odeparms_fixed <- degparms_fixed[odeparms_fixed_names] + + odeini_fixed <- degparms_fixed[odeini_fixed_parm_names] + names(odeini_fixed) <- gsub('_0$', '', odeini_fixed_parm_names) + + model_function <- function(psi, id, xidep) { + + uid <- unique(id) + + res_list <- parallel::mclapply(uid, function(i) { + transparms_optim <- psi[i, ] + names(transparms_optim) <- names(degparms_optim) + + odeini_optim <- transparms_optim[odeini_optim_parm_names] + names(odeini_optim) <- gsub('_0$', '', odeini_optim_parm_names) + + odeini <- c(odeini_optim, odeini_fixed)[names(mkin_model$diffs)] + + ode_transparms_optim_names <- setdiff(names(transparms_optim), odeini_optim_parm_names) + odeparms_optim <- backtransform_odeparms(transparms_optim[ode_transparms_optim_names], mkin_model, + transform_rates = object[[1]]$transform_rates, + transform_fractions = object[[1]]$transform_fractions) + odeparms <- c(odeparms_optim, odeparms_fixed) + + xidep_i <- subset(xidep, id == i) + + if (analytical) { + out_values <- mkin_model$deg_func(xidep_i, odeini, odeparms) + } else { + + i_time <- xidep_i$time + i_name <- xidep_i$name + + out_wide <- mkinpredict(mkin_model, + odeparms = odeparms, odeini = odeini, + solution_type = object[[1]]$solution_type, + outtimes = sort(unique(i_time))) + + out_index <- cbind(as.character(i_time), as.character(i_name)) + out_values <- out_wide[out_index] + } + return(out_values) + }, mc.cores = 15) + res <- unlist(res_list) + return(res) + } + + res <- saemixModel(model_function, psi0, + "Mixed model generated from mmkin object", + transform.par = rep(0, length(degparms_optim))) + return(res) +} + +#' @rdname saemix +#' @param \dots Further parameters passed to [saemix::saemixData] +#' @return An [saemix::SaemixData] object. +#' @export +saemix_data <- function(object, ...) { + if (nrow(object) > 1) stop("Only row objects allowed") + ds_names <- colnames(object) + + ds_list <- lapply(object, function(x) x$data[c("time", "variable", "observed")]) + names(ds_list) <- ds_names + ds_saemix_all <- purrr::map_dfr(ds_list, function(x) x, .id = "ds") + ds_saemix <- data.frame(ds = ds_saemix_all$ds, + name = as.character(ds_saemix_all$variable), + time = ds_saemix_all$time, + value = ds_saemix_all$observed, + stringsAsFactors = FALSE) + + res <- saemixData(ds_saemix, + name.group = "ds", + name.predictors = c("time", "name"), + name.response = "value", ...) + return(res) +} |