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/index.html | 2 +- docs/reference/mkinpredict.html | 158 +++++++++++++++++++--------------------- docs/reference/nlme-1.png | Bin 78105 -> 76554 bytes docs/reference/nlme-2.png | Bin 90402 -> 88313 bytes docs/reference/nlme.html | 137 ++++++++++++++++------------------ 5 files changed, 135 insertions(+), 162 deletions(-) (limited to 'docs/reference') diff --git a/docs/reference/index.html b/docs/reference/index.html index 63e1e634..1448bbe6 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -722,7 +722,7 @@ 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.

-

- - + + diff --git a/docs/reference/nlme-1.png b/docs/reference/nlme-1.png index 9583da2a..ecb71d6c 100644 Binary files a/docs/reference/nlme-1.png and b/docs/reference/nlme-1.png differ diff --git a/docs/reference/nlme-2.png b/docs/reference/nlme-2.png index 02aa0573..e3a6e226 100644 Binary files a/docs/reference/nlme-2.png and b/docs/reference/nlme-2.png differ diff --git a/docs/reference/nlme.html b/docs/reference/nlme.html index d94e4bbe..0eaba377 100644 --- a/docs/reference/nlme.html +++ b/docs/reference/nlme.html @@ -1,80 +1,67 @@ -Helper functions to create nlme models from mmkin row objects — nlme_function • mkinHelper functions to create nlme models from mmkin row objects — nlme_function • mkin +datasets. They are used internally by the nlme.mmkin() method."> - -

- + +

@@ -95,18 +82,16 @@ datasets. They are used internally by the

nlme.m
 
     
     Arguments
-    object
+
+
+object
 An mmkin row object containing several fits of the same model to different datasets
 
 
     
     Value
-    
-
-A function that can be used with nlme
-
-
-A groupedData object
+    A function that can be used with nlme
+A nlme::groupedData object
     
     
     See also
@@ -156,28 +141,28 @@ datasets. They are used internally by the nlme.m
 #>   Model: value ~ nlme_f(name, time, parent_0, log_k_parent_sink) 
 #>   Data: grouped_data 
 #>        AIC      BIC    logLik
-#>   266.6428 275.8935 -128.3214
+#>   298.2781 307.7372 -144.1391
 #> 
 #> Random effects:
 #>  Formula: list(parent_0 ~ 1, log_k_parent_sink ~ 1)
 #>  Level: ds
 #>  Structure: Diagonal
-#>             parent_0 log_k_parent_sink Residual
-#> StdDev: 0.0003775775         0.7058039 3.065183
+#>          parent_0 log_k_parent_sink Residual
+#> StdDev: 0.9376498         0.7098079 3.835419
 #> 
 #> Fixed effects:  parent_0 + log_k_parent_sink ~ 1 
-#>                       Value Std.Error DF   t-value p-value
-#> parent_0          101.18323 0.7900461 43 128.07257       0
-#> log_k_parent_sink  -3.08708 0.4171755 43  -7.39995       0
+#>                       Value Std.Error DF  t-value p-value
+#> parent_0          101.76810 1.1445941 45 88.91196       0
+#> log_k_parent_sink  -3.05445 0.4195607 45 -7.28011       0
 #>  Correlation: 
 #>                   prnt_0
-#> log_k_parent_sink 0.031 
+#> log_k_parent_sink 0.034 
 #> 
 #> Standardized Within-Group Residuals:
 #>         Min          Q1         Med          Q3         Max 
-#> -2.38427070 -0.52059848  0.03593021  0.39987268  2.73188969 
+#> -2.61695902 -0.21869858  0.05745687  0.57209490  3.04575223 
 #> 
-#> Number of Observations: 47
+#> Number of Observations: 49
 #> Number of Groups: 3 
 plot(augPred(m_nlme, level = 0:1), layout = c(3, 1))
 
@@ -190,23 +175,23 @@ datasets. They are used internally by the nlme.m


-  On this page
+  On this page


 
 
     
-  
Developed by Johannes Ranke.
+  Developed by Johannes Ranke.
 
 
 
-  Site built with pkgdown 2.0.7.
+  Site built with pkgdown 2.1.1.


 
-  
 
-  
+
+
 
   
 
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