- Completion of the multicompartment part of the mkin examples vignette

- Fix to chi2 error level calculation by correctly returning backtransformed
  parameters as bparms.optim and bparms.fixed
- Adaptations of unit tests, summary and plot functions



git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@67 edb9625f-4e0d-4859-8d74-9fd3b1da38cb

4 files changed, 17 insertions, 14 deletions

diff --git a/R/endpoints.R b/R/endpoints.R
index 98e290d..163dc8d 100644
--- a/R/endpoints.R
+++ b/R/endpoints.R
@@ -3,7 +3,7 @@ endpoints <- function(fit, pseudoDT50 = FALSE) {
   # fractions and SFORB eigenvalues from optimised parameters

   ep <- list()

   obs_vars <- fit$obs_vars

-  parms.all <- fit$parms.all

+  parms.all <- fit$bparms.ode

   ep$distimes <- data.frame(DT50 = rep(NA, length(obs_vars)), 

 			    DT90 = rep(NA, length(obs_vars)), 

     row.names = obs_vars)

diff --git a/R/mkinerrmin.R b/R/mkinerrmin.R
index 49538e3..8b1e9b2 100644
--- a/R/mkinerrmin.R
+++ b/R/mkinerrmin.R
@@ -20,7 +20,7 @@
 utils::globalVariables(c("name"))

 mkinerrmin <- function(fit, alpha = 0.05)

 {

-  parms.optim <- fit$parms.all

+  parms.optim <- fit$par

   kinerrmin <- function(errdata, n.parms) {

     means.mean <- mean(errdata$value_mean, na.rm=TRUE)

     df = length(errdata$value_mean) - n.parms

diff --git a/R/mkinfit.R b/R/mkinfit.R
index e084cf1..3ca3899 100644
--- a/R/mkinfit.R
+++ b/R/mkinfit.R
@@ -191,7 +191,9 @@ mkinfit <- function(mkinmod, observed,
     value = c(state.ini.fixed, parms.fixed))

   fit$fixed$type = c(rep("state", length(state.ini.fixed)), rep("deparm", length(parms.fixed)))

 

-  parms.all = backtransform_odeparms(c(fit$par, parms.fixed), mod_vars)

+  bparms.optim = backtransform_odeparms(fit$par, mod_vars)

+  bparms.fixed = backtransform_odeparms(c(state.ini.fixed, parms.fixed), mod_vars)

+  bparms.all = c(bparms.optim, bparms.fixed)

 

   # Collect observed, predicted and residuals

   data <- merge(fit$observed, fit$predicted, by = c("time", "name"))

@@ -201,8 +203,10 @@ mkinfit <- function(mkinmod, observed,
   fit$data <- data[order(data$variable, data$time), ]

   fit$atol <- atol

   fit$rtol <- rtol

-  fit$parms.all <- parms.all # Return all backtransformed parameters for summary

-  fit$odeparms.final <- parms.all[mkinmod$parms] # Return ode parameters for further fitting

+  # Return all backtransformed parameters for summary

+  fit$bparms.optim <- bparms.optim 

+  fit$bparms.fixed <- bparms.fixed

+  fit$bparms.ode <- bparms.all[mkinmod$parms] # Return ode parameters for further fitting

   fit$date <- date()

 

   class(fit) <- c("mkinfit", "modFit") 

@@ -231,7 +235,7 @@ summary.mkinfit <- function(object, data = TRUE, distimes = TRUE, ...) {
   param <- cbind(param, se)

   dimnames(param) <- list(pnames, c("Estimate", "Std. Error"))

 

-  bparam <- as.matrix(object$parms.all)

+  bparam <- as.matrix(object$bparms.optim)

   dimnames(bparam) <- list(pnames, c("Estimate"))

 

   ans <- list(

@@ -259,9 +263,9 @@ summary.mkinfit <- function(object, data = TRUE, distimes = TRUE, ...) {
 

   ans$errmin <- mkinerrmin(object, alpha = 0.05)

 

-  ans$parms.all <- object$parms.all

+  ans$bparms.ode <- object$bparms.ode

   ep <- endpoints(object)

-  if (!is.null(ep$ff))

+  if (length(ep$ff) != 0)

     ans$ff <- ep$ff

   if(distimes) ans$distimes <- ep$distimes

   if(length(ep$SFORB) != 0) ans$SFORB <- ep$SFORB

@@ -305,19 +309,19 @@ print.summary.mkinfit <- function(x, digits = max(3, getOption("digits") - 3), .
   if(printdistimes){

     cat("\nEstimated disappearance times:\n")

     print(x$distimes, digits=digits,...)

-  }    

+  }

 

   printff <- !is.null(x$ff)

   if(printff & x$use_of_ff == "min"){

     cat("\nEstimated formation fractions:\n")

     print(data.frame(ff = x$ff), digits=digits,...)

-  }    

+  }

 

   printSFORB <- !is.null(x$SFORB)

   if(printSFORB){

     cat("\nEstimated Eigenvalues of SFORB model(s):\n")

     print(x$SFORB, digits=digits,...)

-  }    

+  }

 

   printcor <- is.numeric(x$cov.unscaled)

   if (printcor){

diff --git a/R/plot.mkinfit.R b/R/plot.mkinfit.R
index fc8ecf7..59ef861 100644
--- a/R/plot.mkinfit.R
+++ b/R/plot.mkinfit.R
@@ -30,9 +30,8 @@ plot.mkinfit <- function(x, fit = x,
   add = FALSE, legend = !add, ...)
 {
   solution_type = fit$solution_type
-  fixed <- fit$fixed$value
-  names(fixed) <- rownames(fit$fixed)
-  parms.all <- c(fit$parms.all, fixed)
+  parms.all <- c(fit$bparms.optim, fit$bparms.fixed)
+
   ininames <- c(
     rownames(subset(fit$start, type == "state")),
     rownames(subset(fit$fixed, type == "state")))