From 01284e456dc6df8e064a7a42f194fcd81d9ce7a1 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 12 May 2020 10:58:25 +0200 Subject: Improve documentation, now using a spell checker --- docs/reference/mkinfit.html | 42 +++++++++++++++++++++--------------------- 1 file changed, 21 insertions(+), 21 deletions(-) (limited to 'docs/reference/mkinfit.html') diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index ceac59bf..5d8dd81c 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -42,7 +42,7 @@ mkin - 0.9.50.1 + 0.9.50.2 @@ -149,7 +149,7 @@ likelihood function." />

This function maximises the likelihood of the observed data using the Port algorithm nlminb, and the specified initial or fixed -parameters and starting values. In each step of the optimsation, the +parameters and starting values. In each step of the optimisation, the kinetic model is solved using the function mkinpredict. The parameters of the selected error model are fitted simultaneously with the degradation model parameters, as both of them are arguments of the @@ -420,17 +420,17 @@ Degradation Data. Environments 6(12) 124 


 # Use shorthand notation for parent only degradation
 fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
-summary(fit)
#> mkin version used for fitting:    0.9.50.1 
+summary(fit)
#> mkin version used for fitting:    0.9.50.2 
 #> R version used for fitting:       4.0.0 
-#> Date of fit:     Tue May 12 08:36:07 2020 
-#> Date of summary: Tue May 12 08:36:07 2020 
+#> Date of fit:     Tue May 12 10:55:39 2020 
+#> Date of summary: Tue May 12 10:55:39 2020 
 #> 
 #> Equations:
 #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted using 222 model solutions performed in 0.047 s
+#> Fitted using 222 model solutions performed in 0.043 s
 #> 
 #> Error model: Constant variance 
 #> 
@@ -507,7 +507,7 @@ Degradation Data. Environments 6(12) 124
   m1 = mkinsub("SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
# Fit the model to the FOCUS example dataset D using defaults
 print(system.time(fit <- mkinfit(SFO_SFO, FOCUS_2006_D,
                            solution_type = "eigen", quiet = TRUE)))
#> Warning: Observations with value of zero were removed from the data
#>        User      System verstrichen 
-#>       0.408       0.008       0.416 
parms(fit)
#>       parent_0       k_parent           k_m1 f_parent_to_m1          sigma 
+#>       0.408       0.001       0.410 
parms(fit)
#>       parent_0       k_parent           k_m1 f_parent_to_m1          sigma 
 #>   99.598483222    0.098697734    0.005260651    0.514475962    3.125503875 
endpoints(fit)
#> $ff
 #>   parent_m1 parent_sink 
 #>    0.514476    0.485524 
@@ -597,7 +597,7 @@ Degradation Data. Environments 6(12) 124
 #> Sum of squared residuals at call 166: 371.2134
 #> Sum of squared residuals at call 168: 371.2134
 #> Negative log-likelihood at call 178: 97.22429
#> Optimisation successfully terminated.
#>        User      System verstrichen 
-#>       0.350       0.001       0.351 
parms(fit.deSolve)
#>       parent_0       k_parent           k_m1 f_parent_to_m1          sigma 
+#>       0.353       0.000       0.352 
parms(fit.deSolve)
#>       parent_0       k_parent           k_m1 f_parent_to_m1          sigma 
 #>   99.598480759    0.098697739    0.005260651    0.514475958    3.125503874 
endpoints(fit.deSolve)
#> $ff
 #>   parent_m1 parent_sink 
 #>    0.514476    0.485524 
@@ -629,10 +629,10 @@ Degradation Data. Environments 6(12) 124
 # \dontrun{
 # Weighted fits, including IRLS (error_model = "obs")
 SFO_SFO.ff <- mkinmod(parent = mkinsub("SFO", "m1"),
-                      m1 = mkinsub("SFO"), use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.
f.noweight <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.noweight)
#> mkin version used for fitting:    0.9.50.1 
+                      m1 = mkinsub("SFO"), use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.
f.noweight <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.noweight)
#> mkin version used for fitting:    0.9.50.2 
 #> R version used for fitting:       4.0.0 
-#> Date of fit:     Tue May 12 08:36:12 2020 
-#> Date of summary: Tue May 12 08:36:12 2020 
+#> Date of fit:     Tue May 12 10:55:44 2020 
+#> Date of summary: Tue May 12 10:55:44 2020 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -640,7 +640,7 @@ Degradation Data. Environments 6(12) 124
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted using 421 model solutions performed in 0.146 s
+#> Fitted using 421 model solutions performed in 0.147 s
 #> 
 #> Error model: Constant variance 
 #> 
@@ -751,10 +751,10 @@ Degradation Data. Environments 6(12) 124
 #>   100       m1    31.04  31.98163 -9.416e-01
 #>   100       m1    33.13  31.98163  1.148e+00
 #>   120       m1    25.15  28.78984 -3.640e+00
-#>   120       m1    33.31  28.78984  4.520e+00
f.obs <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, error_model = "obs", quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.obs)
#> mkin version used for fitting:    0.9.50.1 
+#>   120       m1    33.31  28.78984  4.520e+00
f.obs <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, error_model = "obs", quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.obs)
#> mkin version used for fitting:    0.9.50.2 
 #> R version used for fitting:       4.0.0 
-#> Date of fit:     Tue May 12 08:36:13 2020 
-#> Date of summary: Tue May 12 08:36:13 2020 
+#> Date of fit:     Tue May 12 10:55:44 2020 
+#> Date of summary: Tue May 12 10:55:44 2020 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -762,7 +762,7 @@ Degradation Data. Environments 6(12) 124
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted using 978 model solutions performed in 0.337 s
+#> Fitted using 978 model solutions performed in 0.334 s
 #> 
 #> Error model: Variance unique to each observed variable 
 #> 
@@ -888,10 +888,10 @@ Degradation Data. Environments 6(12) 124
 #>   100       m1    31.04  31.98773 -9.477e-01
 #>   100       m1    33.13  31.98773  1.142e+00
 #>   120       m1    25.15  28.80429 -3.654e+00
-#>   120       m1    33.31  28.80429  4.506e+00
f.tc <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, error_model = "tc", quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.tc)
#> mkin version used for fitting:    0.9.50.1 
+#>   120       m1    33.31  28.80429  4.506e+00
f.tc <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, error_model = "tc", quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.tc)
#> mkin version used for fitting:    0.9.50.2 
 #> R version used for fitting:       4.0.0 
-#> Date of fit:     Tue May 12 08:36:14 2020 
-#> Date of summary: Tue May 12 08:36:14 2020 
+#> Date of fit:     Tue May 12 10:55:45 2020 
+#> Date of summary: Tue May 12 10:55:45 2020 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -899,7 +899,7 @@ Degradation Data. Environments 6(12) 124
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted using 1875 model solutions performed in 0.647 s
+#> Fitted using 1875 model solutions performed in 0.643 s
 #> 
 #> Error model: Two-component variance function 
 #> 
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