diff options
Diffstat (limited to 'R/saem.R')
| -rw-r--r-- | R/saem.R | 32 |
1 files changed, 20 insertions, 12 deletions
@@ -239,10 +239,6 @@ print.saem.mmkin <- function(x, digits = max(3, getOption("digits") - 3), ...) { saemix_model <- function(object, solution_type = "auto", transformations = c("mkin", "saemix"), degparms_start = numeric(), test_log_parms = FALSE, conf.level = 0.6, verbose = FALSE, ...) { - if (packageVersion("saemix") < "3.0") { - stop("To use the interface to saemix, you need to install a version >= 3.0\n") - } - if (nrow(object) > 1) stop("Only row objects allowed") mkin_model <- object[[1]]$mkinmod @@ -444,9 +440,22 @@ saemix_model <- function(object, solution_type = "auto", transformations = c("mk solution_type = "analytical saemix" } else { + if (transformations == "saemix") { + stop("Using saemix transformations is only supported if an analytical solution is implemented for saemix") + } + if (solution_type == "auto") solution_type <- object[[1]]$solution_type + # Define some variables to avoid function calls in model function + transparms_optim_names <- names(degparms_optim) + odeini_optim_names <- gsub('_0$', '', odeini_optim_parm_names) + diff_names <- names(mkin_model$diffs) + ode_transparms_optim_names <- setdiff(transparms_optim_names, odeini_optim_parm_names) + transform_rates <- object[[1]]$transform_rates + transform_fractions <- object[[1]]$transform_fractions + + # Define the model function model_function <- function(psi, id, xidep) { uid <- unique(id) @@ -454,22 +463,21 @@ saemix_model <- function(object, solution_type = "auto", transformations = c("mk res_list <- lapply(uid, function(i) { transparms_optim <- as.numeric(psi[i, ]) # psi[i, ] is a dataframe when called in saemix.predict - names(transparms_optim) <- names(degparms_optim) + names(transparms_optim) <- transparms_optim_names odeini_optim <- transparms_optim[odeini_optim_parm_names] - names(odeini_optim) <- gsub('_0$', '', odeini_optim_parm_names) + names(odeini_optim) <- odeini_optim_names - odeini <- c(odeini_optim, odeini_fixed)[names(mkin_model$diffs)] + odeini <- c(odeini_optim, odeini_fixed)[diff_names] - 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) + transform_rates = transform_rates, + transform_fractions = transform_fractions) odeparms <- c(odeparms_optim, odeparms_fixed) - xidep_i <- subset(xidep, id == i) + xidep_i <- xidep[which(id == i), ] - if (solution_type == "analytical") { + if (solution_type[1] == "analytical") { out_values <- mkin_model$deg_func(xidep_i, odeini, odeparms) } else { |