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-rw-r--r--R/plot.mixed.mmkin.R8
-rw-r--r--R/saem.R31
-rw-r--r--R/summary.saem.mmkin.R9
3 files changed, 26 insertions, 22 deletions
diff --git a/R/plot.mixed.mmkin.R b/R/plot.mixed.mmkin.R
index 0d6b15c0..d8a1c2ac 100644
--- a/R/plot.mixed.mmkin.R
+++ b/R/plot.mixed.mmkin.R
@@ -75,8 +75,8 @@ plot.mixed.mmkin <- function(x,
rownames(degparms_optim) <- ds_names
degparms_optim_names <- setdiff(names(fit_1$par), names(fit_1$errparms))
colnames(degparms_optim) <- degparms_optim_names
- residual_type = ifelse(standardized, "iwres", "ires")
- residuals <- x$so@results@predictions[[residual_type]]
+ residual_type = ifelse(standardized, "residual", "standardized")
+ residuals <- x$data[[residual_type]]
degparms_pop <- x$so@results@fixed.effects
names(degparms_pop) <- degparms_optim_names
}
@@ -95,9 +95,7 @@ plot.mixed.mmkin <- function(x,
odeini_names <- grep("_0$", degparms_all_names, value = TRUE)
odeparms_names <- setdiff(degparms_all_names, odeini_names)
- residual_type = ifelse(standardized, "iwres", "ires")
-
- observed <- cbind(x$data,
+ observed <- cbind(x$data[c("ds", "name", "time", "value")],
residual = residuals)
solution_type = fit_1$solution_type
diff --git a/R/saem.R b/R/saem.R
index 377da903..18152baf 100644
--- a/R/saem.R
+++ b/R/saem.R
@@ -63,7 +63,7 @@
#' dfop_sfo <- mkinmod(parent = mkinsub("DFOP", "A1"),
#' A1 = mkinsub("SFO"))
#' # The following fit uses analytical solutions for SFO-SFO and DFOP-SFO,
-#' # and compiled ODEs for FOMC, both are fast
+#' # and compiled ODEs for FOMC that are much slower
#' f_mmkin <- mmkin(list(
#' "SFO-SFO" = sfo_sfo, "FOMC-SFO" = fomc_sfo, "DFOP-SFO" = dfop_sfo),
#' ds, quiet = TRUE)
@@ -75,11 +75,12 @@
#' # We can use print, plot and summary methods to check the results
#' print(f_saem_dfop_sfo)
#' plot(f_saem_dfop_sfo)
-#' summary(f_saem_dfop_sfo, data = FALSE)
+#' summary(f_saem_dfop_sfo, data = TRUE)
#'
#' # Using a single core, the following takes about 6 minutes as we do not have an
#' # analytical solution. Using 10 cores it is slower instead of faster
-#' #f_saem_fomc <- saem(f_mmkin["FOMC-SFO", ], cores = 1)
+#' f_saem_fomc <- saem(f_mmkin["FOMC-SFO", ], cores = 1)
+#' plot(f_saem_fomc)
#' }
#' @export
saem <- function(object, control, ...) UseMethod("saem")
@@ -103,12 +104,6 @@ saem.mmkin <- function(object,
}
fit_time <- system.time({
utils::capture.output(f_saemix <- saemix::saemix(m_saemix, d_saemix, control), split = !quiet)
- f_pred <- try(saemix::saemix.predict(f_saemix), silent = TRUE)
- if (!inherits(f_pred, "try-error")) {
- f_saemix <- f_pred
- } else {
- warning("Creating predictions from the saemix model failed")
- }
})
if (suppressPlot) {
grDevices::dev.off()
@@ -121,6 +116,20 @@ saem.mmkin <- function(object,
object[[1]]$transform_rates,
object[[1]]$transform_fractions)
+ return_data <- nlme_data(object)
+
+ return_data$predicted <- f_saemix@model@model(
+ psi = saemix::psi(f_saemix),
+ id = as.numeric(return_data$ds),
+ xidep = return_data[c("time", "name")])
+
+ return_data <- transform(return_data,
+ residual = predicted - value,
+ std = sigma_twocomp(predicted,
+ f_saemix@results@respar[1], f_saemix@results@respar[2]))
+ return_data <- transform(return_data,
+ standardized = residual / std)
+
result <- list(
mkinmod = object[[1]]$mkinmod,
mmkin = object,
@@ -132,7 +141,7 @@ saem.mmkin <- function(object,
mean_dp_start = attr(m_saemix, "mean_dp_start"),
bparms.optim = bparms_optim,
bparms.fixed = object[[1]]$bparms.fixed,
- data = nlme_data(object),
+ data = return_data,
err_mod = object[[1]]$err_mod,
date.fit = date(),
saemixversion = as.character(utils::packageVersion("saemix")),
@@ -323,7 +332,7 @@ saemix_model <- function(object, cores = 1, verbose = FALSE, ...) {
uid <- unique(id)
res_list <- parallel::mclapply(uid, function(i) {
- transparms_optim <- psi[i, ]
+ transparms_optim <- as.numeric(psi[i, ])
names(transparms_optim) <- names(degparms_optim)
odeini_optim <- transparms_optim[odeini_optim_parm_names]
diff --git a/R/summary.saem.mmkin.R b/R/summary.saem.mmkin.R
index 536693a3..97f9f2da 100644
--- a/R/summary.saem.mmkin.R
+++ b/R/summary.saem.mmkin.R
@@ -151,14 +151,11 @@ summary.saem.mmkin <- function(object, data = FALSE, verbose = FALSE, distimes =
err_mod = object$mmkin_orig[[1]]$err_mod
object$diffs <- object$mkinmod$diffs
- object$print_data <- data
+ object$print_data <- data # boolean: Should we print the data?
so_pred <- object$so@results@predictions
- object$data[["observed"]] <- object$data[["value"]]
- object$data[["value"]] <- NULL
- object$data[["predicted"]] <- so_pred$ipred
- object$data[["residual"]] <- so_pred$ires
- object$data[["standardized"]] <- so_pred$iwres
+ names(object$data)[4] <- "observed" # rename value to observed
+
object$verbose <- verbose
object$fixed <- object$mmkin_orig[[1]]$fixed

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