From ccc70e82af4ba435f0a71ba1ae4e0e92045c3852 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 5 May 2017 12:46:31 +0200 Subject: Static docs except articles rebuilt with current pkgdown --- docs/reference/mkinpredict.html | 140 +++++++++++++++++++++------------------- 1 file changed, 72 insertions(+), 68 deletions(-) (limited to 'docs/reference/mkinpredict.html') diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 2348d40e..327a7d8d 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -6,8 +6,7 @@ - - — mkinpredict • mkin +Produce predictions from a kinetic model using specific parameters — mkinpredict • mkin @@ -26,12 +25,14 @@ - + + + @@ -71,6 +72,9 @@
  • Performance benefit by using compiled model definitions in mkin
    • +
  • + Calculation of time weighted average concentrations with mkin +
  • @@ -96,8 +100,7 @@
    -

    -

    +

    Produce predictions from a kinetic model using specific parameters

    @@ -106,71 +109,72 @@ kinetic parameters and initial values for the state variables.

    - 
    mkinpredict(mkinmod, odeparms, odeini, outtimes, solution_type = "deSolve",
+    
    mkinpredict(mkinmod, odeparms, odeini, outtimes, solution_type = "deSolve",
               use_compiled = "auto", method.ode = "lsoda", atol = 1e-08, rtol = 1e-10,
         map_output = TRUE, ...)
    
     
     
     Arguments
    
-    
    
-      
    mkinmod
    
-      
    
-    A kinetic model as produced by mkinmod.
-  
    
-      
    odeparms
    
-      
    
-    A numeric vector specifying the parameters used in the kinetic model, which
-    is generally defined as a set of ordinary differential equations.
-  
    
-      
    odeini
    
-      
    
-    A numeric vectory containing the initial values of the state variables of
+    
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
    mkinmod
    A kinetic model as produced by mkinmod.
    odeparms
    A numeric vector specifying the parameters used in the kinetic model, which
+    is generally defined as a set of ordinary differential equations.
    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.
-  
-      
    outtimes
    
-      
    
-    A numeric vector specifying the time points for which model predictions
-    should be generated.
-  
    
-      
    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 not applicable to some models e.g.
-    using FOMC for the parent compound.
-  
    
-      
    method.ode
    
-      
    
-    The solution method passed via mkinpredict to
-    ode in case the solution type is "deSolve". The default
-    "lsoda" is performant, but sometimes fails to converge.
-  
    
-      
    use_compiled
    
-      
    
-    If set to FALSE, no compiled version of the mkinmod
-    model is used, even if is present.
-  
    
-      
    atol
    
-      
    
-    Absolute error tolerance, passed to ode. Default is 1e-8,
-    lower than in lsoda.
-  
    
-      
    rtol
    
-      
    
-    Absolute error tolerance, passed to ode. Default is 1e-10,
-    much lower than in lsoda.
-  
    
-      
    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).
-  
    
-      
    …
    
-      
    
-    Further arguments passed to the ode solver in case such a solver is used.
-  
    
-    
+    variables, for example in the case of the SFORB model.
    outtimes
    A numeric vector specifying the time points for which model predictions
+    should be generated.
    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 not applicable to some models e.g.
+    using FOMC for the parent compound.
    method.ode
    The solution method passed via mkinpredict to
+    ode in case the solution type is "deSolve". The default
+    "lsoda" is performant, but sometimes fails to converge.
    use_compiled
    If set to FALSE, no compiled version of the mkinmod
+    model is used, even if is present.
    atol
    Absolute error tolerance, passed to ode. Default is 1e-8,
+    lower than in lsoda.
    rtol
    Absolute error tolerance, passed to ode. Default is 1e-10,
+    much lower than in lsoda.
    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).
    …
    Further arguments passed to the ode solver in case such a solver is used.
    
     
     
    Value
    
 
@@ -295,17 +299,17 @@
                 c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),
                 solution_type = "eigen")[201,]))
    #> time parent m1 #> 201 20 4.978707 27.46227
    #> user system elapsed -#> 0.016 0.016 0.004
    system.time( +#> 0.004 0.000 0.004
    system.time( print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01), c(parent = 100, m1 = 0), seq(0, 20, by = 0.1), solution_type = "deSolve")[201,]))
    #> time parent m1 #> 201 20 4.978707 27.46227
    #> user system elapsed -#> 0.016 0.004 0.002
    system.time( +#> 0.004 0.000 0.002
    system.time( print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01), c(parent = 100, m1 = 0), seq(0, 20, by = 0.1), solution_type = "deSolve", use_compiled = FALSE)[201,]))
    #> time parent m1 #> 201 20 4.978707 27.46227
    #> user system elapsed -#> 0.032 0.000 0.034
    +#> 0.032 0.000 0.033