Various improvements, the most prominent being the addition of the

test dataset from the original KinGUI Piacenza paper.



git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@10 edb9625f-4e0d-4859-8d74-9fd3b1da38cb

2 files changed, 25 insertions, 13 deletions

diff --git a/R/mkin_wide_to_long.R b/R/mkin_wide_to_long.R
index 6db2f33..21ab77b 100644
--- a/R/mkin_wide_to_long.R
+++ b/R/mkin_wide_to_long.R
@@ -1,9 +1,9 @@
 mkin_wide_to_long <- function(wide_data, time = "t")

 {

   colnames <- names(wide_data)

+  if (!(time %in% colnames)) stop("The data in wide format have to contain a variable named ", time, ".")

   vars <- subset(colnames, colnames != time)

   n <- length(colnames) - 1

-  if (!(time %in% colnames)) stop("The data in wide format have to contain a variable named ", time, ".")

   long_data <- data.frame(

     name = rep(vars, each = length(wide_data[[time]])),

     time = rep(wide_data[[time]], n),

diff --git a/R/mkinfit.R b/R/mkinfit.R
index c149027..9e872fc 100644
--- a/R/mkinfit.R
+++ b/R/mkinfit.R
@@ -1,6 +1,7 @@
 mkinfit <- function(mkinmod, observed,

   parms.ini = rep(0.1, length(mkinmod$parms)),

   state.ini = c(100, rep(0, length(mkinmod$diffs) - 1)), 

+  lower = 0, upper = Inf,

   fixed_parms = NULL,

   fixed_initials = names(mkinmod$diffs)[-1],

   plot = FALSE, quiet = FALSE,

@@ -58,11 +59,7 @@ mkinfit <- function(mkinmod, observed,
 

     odeparms <- c(P[(length(state.ini.optim) + 1):length(P)], parms.fixed)

 

-    # Get more timepoints if plotting is desired

-    if(plot) {

-      outtimes = unique(sort(c(observed$time, 

-        seq(min(observed$time), max(observed$time), length.out=100))))

-    } else outtimes = unique(observed$time)

+    outtimes = unique(observed$time)

 

     # Solve the ode

     out <- ode(

@@ -70,7 +67,7 @@ mkinfit <- function(mkinmod, observed,
       times = outtimes,

       func = mkindiff, 

       parms = odeparms)

-     

+

   

     # Output transformation for models with unobserved compartments like SFORB

     out_transformed <- data.frame(time = out[,"time"])

@@ -81,7 +78,7 @@ mkinfit <- function(mkinmod, observed,
         out_transformed[var] <- rowSums(out[, mkinmod$map[[var]]])

       }

     }    

-    assign("out_predicted", subset(out_transformed, time %in% observed$time), inherits=TRUE)

+    assign("out_predicted", out_transformed, inherits=TRUE)

 

     mC <- modCost(out_transformed, observed, y = "value",

       err = err, weight = weight, scaleVar = scaleVar)

@@ -90,8 +87,23 @@ mkinfit <- function(mkinmod, observed,
     if (mC$model < cost.old) {

       if(!quiet) cat("Model cost at call ", calls, ": ", mC$model, "\n")

 

-      # Plot the data and the current model output if requested

+      # Plot the data and current model output if requested

       if(plot) {

+        outtimes_plot = seq(min(observed$time), max(observed$time), length.out=100)

+        out_plot <- ode(

+          y = odeini,

+          times = outtimes_plot,

+          func = mkindiff, 

+          parms = odeparms)

+        out_transformed_plot <- data.frame(time = out_plot[,"time"])

+        for (var in names(mkinmod$map)) {

+          if(length(mkinmod$map[[var]]) == 1) {

+            out_transformed_plot[var] <- out_plot[, var]

+          } else {

+            out_transformed_plot[var] <- rowSums(out_plot[, mkinmod$map[[var]]])

+          }

+        }    

+

         plot(0, type="n", 

           xlim = range(observed$time), ylim = range(observed$value, na.rm=TRUE),

           xlab = "Time", ylab = "Observed")

@@ -101,7 +113,7 @@ mkinfit <- function(mkinmod, observed,
           points(subset(observed, name == obs_var, c(time, value)), 

             pch = pch_obs[obs_var], col = col_obs[obs_var])

         }

-        matlines(out_transformed$time, out_transformed[-1])

+        matlines(out_transformed_plot$time, out_transformed_plot[-1])

         legend("topright", inset=c(0.05, 0.05), legend=obs_vars, 

           col=col_obs, pch=pch_obs, lty=1:length(pch_obs))

       }

@@ -110,7 +122,7 @@ mkinfit <- function(mkinmod, observed,
     }

     return(mC)

   }

-  fit <- modFit(cost, c(state.ini.optim, parms.optim), ...)

+  fit <- modFit(cost, c(state.ini.optim, parms.optim), lower = lower, upper = upper, ...)

 

   # We need the function for plotting

   fit$mkindiff <- mkindiff

@@ -125,8 +137,8 @@ mkinfit <- function(mkinmod, observed,
   # Collect initial parameter values in two dataframes

   fit$start <- data.frame(initial = c(state.ini.optim, parms.optim))

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

-  if (exists("lower")) fit$start$lower <- lower

-  if (exists("upper")) fit$start$upper <- upper

+  fit$start$lower <- lower

+  fit$start$upper <- upper

 

   fit$fixed <- data.frame(

     value = c(state.ini.fixed, parms.fixed))