Some additions, fixes and formatting of the help files for mkinfit and mkinpredict.

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@110 edb9625f-4e0d-4859-8d74-9fd3b1da38cb

1 files changed, 22 insertions, 21 deletions

diff --git a/man/mkinpredict.Rd b/man/mkinpredict.Rd
index 9d181f5..afb57e0 100644
--- a/man/mkinpredict.Rd
+++ b/man/mkinpredict.Rd
@@ -4,9 +4,9 @@
   Produce predictions from a kinetic model using specifc parameters
 }
 \description{
-  This function produces a time series for all the observed variables in a kinetic model
-  as specified by \code{\link{mkinmod}}, using a specific set of kinetic parameters and
-  initial values for the state variables.
+  This function produces a time series for all the observed variables in a
+  kinetic model as specified by \code{\link{mkinmod}}, using a specific set of
+  kinetic parameters and initial values for the state variables.
 }
 \usage{
   mkinpredict(mkinmod, odeparms, odeini, outtimes, solution_type = "deSolve",
@@ -14,30 +14,31 @@
 }
 \arguments{
   \item{mkinmod}{
-  A kinetic model as produced by \code{\link{mkinmod}}.
+    A kinetic model as produced by \code{\link{mkinmod}}.
   }
   \item{odeparms}{
-  A numeric vector specifying the parameters used in the kinetic model, which is generally
-  defined as a set of ordinary differential equations.
+    A numeric vector specifying the parameters used in the kinetic model, which
+    is generally defined as a set of ordinary differential equations.
   }
   \item{odeini}{
-  A numeric vectory containing the initial values of the state variables of the model. Note
-  that the state variables can differ from the observed variables, for example in the case
-  of the SFORB model.
+    A numeric vectory containing the initial values of the state variables of
+    the model. Note that the state variables can differ from the observed
+    variables, for example in the case of the SFORB model.
   }
   \item{outtimes}{
-  A numeric vector specifying the time points for which model predictions should be 
-  generated.
+    A numeric vector specifying the time points for which model predictions
+    should be generated.
   }
   \item{solution_type}{
-  The method that should be used for producing the predictions. This should
-  generally be "analytical" if there is only one observed variable, and usually
-  "deSolve" in the case of several observed variables. The third possibility "eigen"
-  is faster but produces results that the author believes to be less accurate.
+    The method that should be used for producing the predictions. This should
+    generally be "analytical" if there is only one observed variable, and
+    usually "deSolve" in the case of several observed variables. The third
+    possibility "eigen" is faster but produces results that the author believes
+    to be less accurate.
   }
   \item{map_output}{
-  Boolean to specify if the output should list values for the observed variables (default)
-  or for all state variables (if set to FALSE). 
+    Boolean to specify if the output should list values for the observed
+    variables (default) or for all state variables (if set to FALSE). 
   }
   \item{atol}{
     Absolute error tolerance, passed to \code{\link{ode}}. Default is 1e-8,
@@ -70,10 +71,10 @@
 	      atol = 1e-20)[20,]
 
   # The integration method does not make a lot of difference
-  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, atol = 1e-20, 
-	      method = "ode45")[20,]
-  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, atol = 1e-20, 
-	      method = "rk4")[20,]
+  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, 
+	      atol = 1e-20, method = "ode45")[20,]
+  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, 
+	      atol = 1e-20, method = "rk4")[20,]
 
   # The number of output times used to make a lot of difference until the
   # default for atol was adjusted