Produce predictions from a kinetic model using specific parameters

From 328d1173db2395c1a5705b5f0980e2956db8be1f Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 13 Feb 2025 12:43:29 +0100 Subject: Update wordlist, bump date and simplify DESCRIPTION Also, the R-Universe URL that the badge points to is updated --- docs/reference/mkinpredict.html | 158 +++++++++++++++++++--------------------- 1 file changed, 73 insertions(+), 85 deletions(-) (limited to 'docs/reference/mkinpredict.html') diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 860c7cfc..13f42da0 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -1,78 +1,65 @@ -Produce predictions from a kinetic model using specific parameters — mkinpredict • mkinProduce predictions from a kinetic model using specific parameters — mkinpredict • mkin +kinetic parameters and initial values for the state variables."> - -

- + +

@@ -87,7 +74,7 @@ kinetic parameters and initial values for the state variables.

Usage

mkinpredict(x, odeparms, odeini, outtimes, ...)
 
-# S3 method for mkinmod
+# S3 method for class 'mkinmod'
 mkinpredict(
   x,
   odeparms = c(k_parent_sink = 0.1),
@@ -105,7 +92,7 @@ kinetic parameters and initial values for the state variables.
   ...
 )
 
-# S3 method for mkinfit
+# S3 method for class 'mkinfit'
 mkinpredict(
   x,
   odeparms = x$bparms.ode,
@@ -123,35 +110,37 @@ kinetic parameters and initial values for the state variables.
 
     
     Arguments
-    x
+
+
+x
 A kinetic model as produced by mkinmod, or a kinetic fit as
 fitted by mkinfit. In the latter case, the fitted parameters are used for
 the prediction.
 
 
-odeparms
+odeparms
 A numeric vector specifying the parameters used in the
 kinetic model, which is generally defined as a set of ordinary differential
 equations.
 
 
-odeini
+odeini
 A numeric vector 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.
 
 
-outtimes
+outtimes
 A numeric vector specifying the time points for which model
 predictions should be generated.
 
 
-...
+...
 Further arguments passed to the ode solver in case such a
 solver is used.
 
 
-solution_type
+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
@@ -160,50 +149,48 @@ ODE models, but not applicable to some models, e.g. using FOMC for the
 parent compound.
 
 
-use_compiled
+use_compiled
 If set to FALSE, no compiled version of the
 mkinmod model is used, even if is present.
 
 
-use_symbols
+use_symbols
 If set to TRUE (default), symbol info present in
 the mkinmod object is used if available for accessing compiled code
 
 
-method.ode
-The solution method passed via mkinpredict to ode] in
+
method.ode
+The solution method passed via mkinpredict to deSolve::ode() in
 case the solution type is "deSolve" and we are not using compiled code.
 When using compiled code, only lsoda is supported.
 
 
-atol
+atol
 Absolute error tolerance, passed to the ode solver.
 
 
-rtol
+rtol
 Absolute error tolerance, passed to the ode solver.
 
 
-maxsteps
+maxsteps
 Maximum number of steps, passed to the ode solver.
 
 
-map_output
+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). Setting this to FALSE has no effect for analytical solutions,
 as these always return mapped output.
 
 
-na_stop
-Should it be an error if ode returns NaN values
+na_stop
+Should it be an error if deSolve::ode() returns NaN values
 
 
     
     Value
-    
-
-A matrix with the numeric solution in wide format
+    A matrix with the numeric solution in wide format
     
     
     Author
@@ -365,11 +352,12 @@ as these always return mapped output.
       c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),
       solution_type = "analytical", use_compiled = FALSE)[201,])
 }
+#> Loading required package: rbenchmark
 #>               test relative elapsed
-#> 4       analytical        1   0.001
-#> 2 deSolve_compiled        2   0.002
-#> 1            eigen        8   0.008
-#> 3          deSolve       64   0.064
+#> 2 deSolve_compiled      1.0   0.002
+#> 1            eigen      3.5   0.007
+#> 4       analytical      4.0   0.008
+#> 3          deSolve     31.5   0.063
 
 # \dontrun{
   # Predict from a fitted model
@@ -381,23 +369,23 @@ as these always return mapped output.

-

- - + + -- cgit v1.2.1