From af2e1540cdad2fd00bb6216a38a754ff748629ad Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 25 Oct 2019 02:10:08 +0200 Subject: Static documentation rebuilt by pkgdown --- docs/reference/mkinpredict.html | 107 +++++++++++++++++++++++----------------- 1 file changed, 62 insertions(+), 45 deletions(-) (limited to 'docs/reference/mkinpredict.html') diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 5faff3c7..f7d543ad 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -8,11 +8,13 @@ Produce predictions from a kinetic model using specific parameters — mkinpredict • mkin + + @@ -32,15 +34,16 @@ - + +kinetic model as specified by mkinmod, using a specific set of +kinetic parameters and initial values for the state variables." /> + @@ -111,7 +114,6 @@ News - @@ -133,89 +135,105 @@
-

This function produces a time series for all the observed variables in a - kinetic model as specified by mkinmod, using a specific set of - kinetic parameters and initial values for the state variables.

- +kinetic model as specified by mkinmod, using a specific set of +kinetic parameters and initial values for the state variables.

mkinpredict(x, odeparms, odeini, outtimes = seq(0, 120, by = 0.1),
-    solution_type = "deSolve", use_compiled = "auto", method.ode = "lsoda",
-    atol = 1e-08, rtol = 1e-10, map_output = TRUE, ...)
- + solution_type = "deSolve", use_compiled = "auto", + method.ode = "lsoda", atol = 1e-08, rtol = 1e-10, + map_output = TRUE, ...) + +# S3 method for mkinmod +mkinpredict(x, odeparms = c(k_parent_sink = 0.1), + odeini = c(parent = 100), outtimes = seq(0, 120, by = 0.1), + solution_type = "deSolve", use_compiled = "auto", + method.ode = "lsoda", atol = 1e-08, rtol = 1e-10, + map_output = TRUE, ...) + +# S3 method for mkinfit +mkinpredict(x, odeparms = x$bparms.ode, + odeini = x$bparms.state, outtimes = seq(0, 120, by = 0.1), + solution_type = "deSolve", use_compiled = "auto", + method.ode = "lsoda", atol = 1e-08, rtol = 1e-10, + map_output = TRUE, ...) +

Arguments

+fit as fitted by mkinfit. In the latter case, the fitted +parameters are used for the prediction.

- + - + - + - + - - + + - - + + - + - + - + - +
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

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.
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.
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.
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.

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.
use_compiled

If set to FALSE, no compiled version of the mkinmod - model is used, even if is present.

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.
atol

Absolute error tolerance, passed to ode. Default is 1e-8, - lower than in lsoda.

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.

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).

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.

Further arguments passed to the ode solver in case such a +solver is used.
- +

Value

A matrix in the same format as the output of ode.

-

Examples

- 
  SFO <- mkinmod(degradinol = mkinsub("SFO"))
+    

+  SFO <- mkinmod(degradinol = mkinsub("SFO"))
   # Compare solution types
   mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
         solution_type = "analytical")
#>    time  degradinol
@@ -342,7 +360,7 @@
                 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 verstrichen 
-#>       0.022       0.000       0.021 

+#>       0.021       0.000       0.021 

   # \dontrun{
     # Predict from a fitted model
     f <- mkinfit(SFO_SFO, FOCUS_2006_C)
#> Ordinary least squares optimisation
#> Sum of squared residuals at call 1: 552.5739
@@ -380,15 +398,14 @@
 #> 4  0.3 75.25515 3.399419
 #> 5  0.4 72.98675 4.441969
 #> 6  0.5 70.78673 5.441679
  # }
+