From a52d76a13f36c112e27383af1cac3f98b1bbed0a Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Mon, 9 Nov 2020 11:59:16 +0100
Subject: object$mmkin_orig -> object$mmkin

---
 R/nlme.mmkin.R         |  6 +++---
 R/plot.nlme.mmkin.R    | 10 ++++------
 R/summary.nlme.mmkin.R |  6 +++---
 3 files changed, 10 insertions(+), 12 deletions(-)

diff --git a/R/nlme.mmkin.R b/R/nlme.mmkin.R
index af92e8a1..ca849b85 100644
--- a/R/nlme.mmkin.R
+++ b/R/nlme.mmkin.R
@@ -183,7 +183,7 @@ nlme.mmkin <- function(model, data = sys.frame(sys.parent()),
 
   val$mkinmod <- model[[1]]$mkinmod
   val$data <- thisCall[["data"]]
-  val$mmkin_orig <- model
+  val$mmkin <- model
   val$mean_dp_start <- mean_dp_start
   val$transform_rates <- model[[1]]$transform_rates
   val$transform_fractions <- model[[1]]$transform_fractions
@@ -211,7 +211,7 @@ print.nlme.mmkin <- function(x, ...) {
   cat( "Kinetic nonlinear mixed-effects model fit by " )
   cat( if(x$method == "REML") "REML\n" else "maximum likelihood\n")
   cat("\nStructural model:\n")
-  diffs <- x$mmkin_orig[[1]]$mkinmod$diffs
+  diffs <- x$mmkin[[1]]$mkinmod$diffs
   nice_diffs <- gsub("^(d.*) =", "\\1/dt =", diffs)
   writeLines(strwrap(nice_diffs, exdent = 11))
   cat("\nData:\n")
@@ -239,7 +239,7 @@ print.nlme.mmkin <- function(x, ...) {
 #' @param ... Update specifications passed to update.nlme
 update.nlme.mmkin <- function(object, ...) {
   res <- NextMethod()
-  res$mmkin_orig <- object$mmkin_orig
+  res$mmkin <- object$mmkin
   class(res) <- c("nlme.mmkin", "nlme", "lme")
   return(res)
 }
diff --git a/R/plot.nlme.mmkin.R b/R/plot.nlme.mmkin.R
index 05a17a22..4228b18a 100644
--- a/R/plot.nlme.mmkin.R
+++ b/R/plot.nlme.mmkin.R
@@ -13,8 +13,6 @@ if(getRversion() >= '2.15.1') utils::globalVariables("ds")
 #' @param ymax Vector of maximum y axis values
 #' @param ncol.legend Number of columns to use in the legend
 #' @param nrow.legend Number of rows to use in the legend
-#' @param \dots Further arguments passed to \code{\link{plot.mkinfit}} and
-#'   \code{\link{mkinresplot}}.
 #' @param resplot Should the residuals plotted against time or against
 #'   predicted values?
 #' @param col_ds Colors used for plotting the observed data and the
@@ -41,7 +39,7 @@ if(getRversion() >= '2.15.1') utils::globalVariables("ds")
 #' plot(f_nlme)
 #' }
 #' @export
-plot.nlme.mmkin <- function(x, i = 1:ncol(x$mmkin_orig),
+plot.nlme.mmkin <- function(x, i = 1:ncol(x$mmkin),
   obs_vars = names(x$mkinmod$map),
   standardized = TRUE,
   xlab = "Time",
@@ -55,13 +53,13 @@ plot.nlme.mmkin <- function(x, i = 1:ncol(x$mmkin_orig),
   pch_ds = 1:length(i),
   col_ds = pch_ds + 1,
   lty_ds = col_ds,
-  frame = TRUE, ...)
+  frame = TRUE)
 {
 
   oldpar <- par(no.readonly = TRUE)
 
-  fit_1 = x$mmkin_orig[[1]]
-  ds_names <- colnames(x$mmkin_orig)
+  fit_1 = x$mmkin[[1]]
+  ds_names <- colnames(x$mmkin)
 
   degparms_optim <- coefficients(x)
   degparms_optim_names <- names(degparms_optim)
diff --git a/R/summary.nlme.mmkin.R b/R/summary.nlme.mmkin.R
index d930f845..ad730f9a 100644
--- a/R/summary.nlme.mmkin.R
+++ b/R/summary.nlme.mmkin.R
@@ -122,8 +122,8 @@ summary.nlme.mmkin <- function(object, data = FALSE, verbose = FALSE, distimes =
 
   object$date.summary = date()
   object$use_of_ff = object$mkinmod$use_of_ff
-  object$error_model_algorithm = object$mmkin_orig[[1]]$error_model_algorithm
-  err_mod = object$mmkin_orig[[1]]$err_mod
+  object$error_model_algorithm = object$mmkin[[1]]$error_model_algorithm
+  err_mod = object$mmkin[[1]]$err_mod
 
   object$diffs <- object$mkinmod$diffs
   object$print_data <- data
@@ -139,7 +139,7 @@ summary.nlme.mmkin <- function(object, data = FALSE, verbose = FALSE, distimes =
   object$data[["standardized"]] <- residuals(object, type = "pearson")
   object$verbose <- verbose
 
-  object$fixed <- object$mmkin_orig[[1]]$fixed
+  object$fixed <- object$mmkin[[1]]$fixed
   object$AIC = AIC(object)
   object$BIC = BIC(object)
   object$logLik = logLik(object)
-- 
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