From 3a62211d9211cd0aedecec055226d66b55a17958 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 20 Apr 2020 18:52:52 +0200 Subject: Prepare release to address failed CRAN check --- docs/reference/mkinfit.html | 44 +++++++++++++++++++------------------------- 1 file changed, 19 insertions(+), 25 deletions(-) (limited to 'docs/reference/mkinfit.html') diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index ffc8d52b..09837505 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -75,7 +75,7 @@ likelihood function." /> mkin - 0.9.49.9 + 0.9.49.11 @@ -415,17 +415,17 @@ estimators.


 # Use shorthand notation for parent only degradation
 fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
-summary(fit)
#> mkin version used for fitting:    0.9.49.9 
+summary(fit)
#> mkin version used for fitting:    0.9.49.11 
 #> R version used for fitting:       3.6.3 
-#> Date of fit:     Mon Mar 30 21:41:20 2020 
-#> Date of summary: Mon Mar 30 21:41:20 2020 
+#> Date of fit:     Mon Apr 20 18:52:22 2020 
+#> Date of summary: Mon Apr 20 18:52:22 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 0.463 s
+#> Fitted using 222 model solutions performed in 0.473 s
 #> 
 #> Error model: Constant variance 
 #> 
@@ -497,13 +497,10 @@ estimators.

   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 
-#>       1.526       0.000       1.530 
coef(fit)
#> NULL
endpoints(fit)
#> $ff
+#>       1.465       0.003       1.474 
coef(fit)
#> NULL
endpoints(fit)
#> $ff
 #> parent_sink   parent_m1     m1_sink 
 #>    0.485524    0.514476    1.000000 
 #> 
-#> $SFORB
-#> logical(0)
-#> 
 #> $distimes
 #>              DT50      DT90
 #> parent   7.022929  23.32967
@@ -570,13 +567,10 @@ estimators.

 #> Sum of squared residuals at call 126: 371.2134
 #> Sum of squared residuals at call 135: 371.2134
 #> Negative log-likelihood at call 145: 97.22429
#> Optimisation successfully terminated.
#>        User      System verstrichen 
-#>       1.083       0.000       1.084 
coef(fit.deSolve)
#> NULL
endpoints(fit.deSolve)
#> $ff
+#>       1.052       0.000       1.068 
coef(fit.deSolve)
#> NULL
endpoints(fit.deSolve)
#> $ff
 #> parent_sink   parent_m1     m1_sink 
 #>    0.485524    0.514476    1.000000 
 #> 
-#> $SFORB
-#> logical(0)
-#> 
 #> $distimes
 #>              DT50      DT90
 #> parent   7.022929  23.32967
@@ -604,10 +598,10 @@ estimators.

 # \dontrun{
 # Weighted fits, including IRLS
 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:    0.9.49.9 
+                      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:    0.9.49.11 
 #> R version used for fitting:       3.6.3 
-#> Date of fit:     Mon Mar 30 21:41:36 2020 
-#> Date of summary: Mon Mar 30 21:41:36 2020 
+#> Date of fit:     Mon Apr 20 18:52:37 2020 
+#> Date of summary: Mon Apr 20 18:52:37 2020 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -615,7 +609,7 @@ estimators.

 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted using 422 model solutions performed in 1.144 s
+#> Fitted using 422 model solutions performed in 1.087 s
 #> 
 #> Error model: Constant variance 
 #> 
@@ -721,10 +715,10 @@ estimators.

 #>   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:    0.9.49.9 
+#>   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:    0.9.49.11 
 #> R version used for fitting:       3.6.3 
-#> Date of fit:     Mon Mar 30 21:41:39 2020 
-#> Date of summary: Mon Mar 30 21:41:39 2020 
+#> Date of fit:     Mon Apr 20 18:52:40 2020 
+#> Date of summary: Mon Apr 20 18:52:40 2020 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -732,7 +726,7 @@ estimators.

 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted using 979 model solutions performed in 2.576 s
+#> Fitted using 979 model solutions performed in 2.518 s
 #> 
 #> Error model: Variance unique to each observed variable 
 #> 
@@ -853,10 +847,10 @@ estimators.

 #>   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:    0.9.49.9 
+#>   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:    0.9.49.11 
 #> R version used for fitting:       3.6.3 
-#> Date of fit:     Mon Mar 30 21:41:50 2020 
-#> Date of summary: Mon Mar 30 21:41:50 2020 
+#> Date of fit:     Mon Apr 20 18:52:50 2020 
+#> Date of summary: Mon Apr 20 18:52:50 2020 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -864,7 +858,7 @@ estimators.

 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted using 2552 model solutions performed in 10.593 s
+#> Fitted using 2552 model solutions performed in 10.186 s
 #> 
 #> Error model: Two-component variance function 
 #> 
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