- Formatting improvement of mkinmod

- Small fix in mkinplot

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@45 edb9625f-4e0d-4859-8d74-9fd3b1da38cb

2 files changed, 19 insertions, 18 deletions

diff --git a/R/mkinmod.R b/R/mkinmod.R
index c7f11d96..1a1c55c2 100644
--- a/R/mkinmod.R
+++ b/R/mkinmod.R
@@ -1,6 +1,6 @@
 # $Id$

 

-# Copyright (C) 2010-2012 Johannes Ranke#{{{

+# Copyright (C) 2010-2012 Johannes Ranke {{{

 # Contact: jranke@uni-bremen.de

 

 # This file is part of the R package mkin

@@ -16,7 +16,7 @@
 # details.

 

 # You should have received a copy of the GNU General Public License along with

-# this program. If not, see <http://www.gnu.org/licenses/>#}}}

+# this program. If not, see <http://www.gnu.org/licenses/> }}}

 

 mkinmod <- function(..., use_of_ff = "min")

 {

@@ -47,11 +47,11 @@ mkinmod <- function(..., use_of_ff = "min")
     } else message <- "ok"

   } else mat = TRUE#}}}

 

-  # Establish list of differential equations as well as map from observed#{{{

+  # Establish list of differential equations as well as map from observed {{{

   # compartments to differential equations

   for (varname in obs_vars)

   {

-    # Check the type component of the compartment specification#{{{

+    # Check the type component of the compartment specification {{{

     if(is.null(spec[[varname]]$type)) stop(

       "Every part of the model specification must be a list containing a type component")

     if(!spec[[varname]]$type %in% c("SFO", "FOMC", "DFOP", "HS", "SFORB")) stop(

@@ -59,8 +59,8 @@ mkinmod <- function(..., use_of_ff = "min")
     if(spec[[varname]]$type %in% c("FOMC", "DFOP", "HS") & match(varname, obs_vars) != 1) {

         stop(paste("Types FOMC, DFOP and HS are only implemented for the first compartment,", 

                    "which is assumed to be the source compartment"))

-    }#}}}

-    # New (sub)compartments (boxes) needed for the model type#{{{

+    } #}}}

+    # New (sub)compartments (boxes) needed for the model type {{{

     new_boxes <- switch(spec[[varname]]$type,

       SFO = varname,

       FOMC = varname,

@@ -69,22 +69,23 @@ mkinmod <- function(..., use_of_ff = "min")
       SFORB = paste(varname, c("free", "bound"), sep="_")

     )

     map[[varname]] <- new_boxes

-    names(map[[varname]]) <- rep(spec[[varname]]$type, length(new_boxes))#}}}

-    # Start a new differential equation for each new box#{{{

+    names(map[[varname]]) <- rep(spec[[varname]]$type, length(new_boxes)) #}}}

+    # Start a new differential equation for each new box {{{

     new_diffs <- paste("d_", new_boxes, " =", sep="")

     names(new_diffs) <- new_boxes

-    diffs <- c(diffs, new_diffs)#}}}

-  }#}}}

+    diffs <- c(diffs, new_diffs) #}}}

+  } #}}}

 

-  # Create content of differential equations and build parameter list#{{{

+  # Create content of differential equations and build parameter list {{{

   for (varname in obs_vars)

   {

     # Get the name of the box(es) we are working on for the decline term(s)

     box_1 = map[[varname]][[1]] # This is the only box unless type is SFORB

     if(spec[[varname]]$type %in% c("SFO", "SFORB")) { # {{{ Add SFO or SFORB decline term

       if (use_of_ff == "min") { # Minimum use of formation fractions

-        # Turn on sink if this is not explicitly excluded by the user by specifying sink=FALSE

-        if(is.null(spec[[varname]]$sink)) spec[[varname]]$sink <- TRUE

+	# Turn on sink if this is not explicitly excluded by the user by

+	# specifying sink=FALSE

+	if(is.null(spec[[varname]]$sink)) spec[[varname]]$sink <- TRUE

 

         if(spec[[varname]]$sink) {

           # If sink is required, add first-order sink term

@@ -170,7 +171,7 @@ mkinmod <- function(..., use_of_ff = "min")
         }

       }

     } #}}}

-  }#}}}

+  } #}}}

 

   model <- list(diffs = diffs, parms = parms, map = map, use_of_ff = use_of_ff)

 

diff --git a/R/mkinplot.R b/R/mkinplot.R
index 789a6f98..7641d262 100644
--- a/R/mkinplot.R
+++ b/R/mkinplot.R
@@ -24,15 +24,15 @@ mkinplot <- function(fit, xlab = "Time", ylab = "Observed", xlim = range(fit$dat
   plot(0, type="n", 
     xlim = xlim, ylim = ylim,
     xlab = xlab, ylab = ylab, ...)
-  col_obs <- pch_obs <- 1:length(fit$mkinmod$map)
-  names(col_obs) <- names(pch_obs) <- names(fit$mkinmod$map)
+  col_obs <- pch_obs <- lty_obs <- 1:length(fit$mkinmod$map)
+  names(col_obs) <- names(pch_obs) <- names(lty_obs) <- names(fit$mkinmod$map)
   for (obs_var in names(fit$mkinmod$map)) {
     points(subset(fit$data, variable == obs_var, c(time, observed)), 
-    pch = pch_obs[obs_var], col = col_obs[obs_var])
+      pch = pch_obs[obs_var], col = col_obs[obs_var])
   }
   matlines(out$time, out[-1])
   if (legend == TRUE) {
     legend("topright", inset=c(0.05, 0.05), legend=names(fit$mkinmod$map),
-      col=col_obs, pch=pch_obs, lty=1:length(pch_obs))
+      col=col_obs, pch=pch_obs, lty=lty_obs)
   }
 }