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authorJohannes Ranke <jranke@uni-bremen.de>2020-11-09 11:59:16 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2020-11-09 11:59:16 +0100
commita52d76a13f36c112e27383af1cac3f98b1bbed0a (patch)
tree18f61d83823fad7ae67d1ada1975d4e1d7781dfc
parent8ba0bc6f52183ad97377e4d13d082be13b0383bd (diff)
object$mmkin_orig -> object$mmkin
-rw-r--r--R/nlme.mmkin.R6
-rw-r--r--R/plot.nlme.mmkin.R10
-rw-r--r--R/summary.nlme.mmkin.R6
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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