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-rw-r--r--R/endpoints.R20
-rw-r--r--R/plot.mmkin.R6
2 files changed, 16 insertions, 10 deletions
diff --git a/R/endpoints.R b/R/endpoints.R
index 14beadea..f7ee483a 100644
--- a/R/endpoints.R
+++ b/R/endpoints.R
@@ -1,12 +1,12 @@
#' Function to calculate endpoints for further use from kinetic models fitted
#' with mkinfit
-#'
+#'
#' This function calculates DT50 and DT90 values as well as formation fractions
#' from kinetic models fitted with mkinfit. If the SFORB model was specified
#' for one of the parents or metabolites, the Eigenvalues are returned. These
#' are equivalent to the rate constantes of the DFOP model, but with the
#' advantage that the SFORB model can also be used for metabolites.
-#'
+#'
#' @param fit An object of class \code{\link{mkinfit}}.
#' @importFrom stats optimize
#' @return A list with the components mentioned above.
@@ -14,10 +14,10 @@
#' @author Johannes Ranke
#' @keywords manip
#' @examples
-#'
+#'
#' fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
-#' endpoints(fit)
-#'
+#' endpoints(fit)
+#'
#' @export
endpoints <- function(fit) {
# Calculate dissipation times DT50 and DT90 and formation
@@ -29,8 +29,9 @@ endpoints <- function(fit) {
parms.all <- c(fit$bparms.optim, fit$bparms.fixed)
ep$ff <- vector()
ep$SFORB <- vector()
- ep$distimes <- data.frame(DT50 = rep(NA, length(obs_vars)),
- DT90 = rep(NA, length(obs_vars)),
+ ep$distimes <- data.frame(
+ DT50 = rep(NA, length(obs_vars)),
+ DT90 = rep(NA, length(obs_vars)),
row.names = obs_vars)
for (obs_var in obs_vars) {
type = names(fit$mkinmod$map[[obs_var]])[1]
@@ -41,8 +42,8 @@ endpoints <- function(fit) {
f_values = parms.all[f_names]
f_to_sink = 1 - sum(f_values)
names(f_to_sink) = ifelse(type == "SFORB",
- paste(obs_var, "free", "sink", sep = "_"),
- paste(obs_var, "sink", sep = "_"))
+ paste(obs_var, "free", "sink", sep = "_"),
+ paste(obs_var, "sink", sep = "_"))
for (f_name in f_names) {
ep$ff[[sub("f_", "", sub("_to_", "_", f_name))]] = f_values[[f_name]]
}
@@ -195,5 +196,6 @@ endpoints <- function(fit) {
}
ep$distimes[obs_var, c("DT50", "DT90")] = c(DT50, DT90)
}
+ if (length(ep$SFORB) == 0) ep$SFORB <- NULL
return(ep)
}
diff --git a/R/plot.mmkin.R b/R/plot.mmkin.R
index 182e74ca..15ea86eb 100644
--- a/R/plot.mmkin.R
+++ b/R/plot.mmkin.R
@@ -15,6 +15,9 @@
#' @param resplot Should the residuals plotted against time, using
#' \code{\link{mkinresplot}}, or as squared residuals against predicted
#' values, with the error model, using \code{\link{mkinerrplot}}.
+#' @param standardized Should the residuals be standardized? This option
+#' is passed to \code{\link{mkinresplot}}, it only takes effect if
+#' `resplot = "time"`.
#' @param show_errmin Should the chi2 error level be shown on top of the plots
#' to the left?
#' @param errmin_var The variable for which the FOCUS chi2 error value should
@@ -51,6 +54,7 @@
#' @export
plot.mmkin <- function(x, main = "auto", legends = 1,
resplot = c("time", "errmod"),
+ standardized = FALSE,
show_errmin = TRUE,
errmin_var = "All data", errmin_digits = 3,
cex = 0.7, rel.height.middle = 0.9,
@@ -136,7 +140,7 @@ plot.mmkin <- function(x, main = "auto", legends = 1,
}
if (resplot == "time") {
- mkinresplot(fit, legend = FALSE, ...)
+ mkinresplot(fit, legend = FALSE, standardized = standardized, ...)
} else {
mkinerrplot(fit, legend = FALSE, ...)
}

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