From 09f4f904af23a34d68d5d78482a5b9e12d9a9494 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 4 Nov 2016 15:38:09 +0100 Subject: Static documentation rebuilt by pkgdown::build_site() With updated pkgdown with my PR --- docs/reference/DFOP.solution.html | 7 +----- docs/reference/Extract.mmkin.html | 31 ++++++++++------------- docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html | 7 +----- docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html | 7 +----- docs/reference/FOCUS_2006_HS_ref_A_to_F.html | 7 +----- docs/reference/FOCUS_2006_SFO_ref_A_to_F.html | 7 +----- docs/reference/FOCUS_2006_datasets.html | 7 +----- docs/reference/FOMC.solution.html | 7 +----- docs/reference/HS.solution.html | 7 +----- docs/reference/IORE.solution.html | 7 +----- docs/reference/SFO.solution.html | 7 +----- docs/reference/SFORB.solution.html | 7 +----- docs/reference/add_err.html | 7 +----- docs/reference/endpoints.html | 9 ++----- docs/reference/geometric_mean.html | 7 +----- docs/reference/ilr.html | 7 +----- docs/reference/index.html | 34 ++++++++++++++++++++------ docs/reference/mccall81_245T.html | 13 +++------- docs/reference/mkin_long_to_wide.html | 7 +----- docs/reference/mkin_wide_to_long.html | 7 +----- docs/reference/mkinds.html | 7 +----- docs/reference/mkinerrmin.html | 9 ++----- docs/reference/mkinfit.html | 21 ++++++---------- docs/reference/mkinmod.html | 7 +----- docs/reference/mkinparplot.html | 7 +----- docs/reference/mkinplot.html | 11 +++------ docs/reference/mkinpredict.html | 13 +++------- docs/reference/mkinresplot.html | 9 ++----- docs/reference/mkinsub.html | 7 +----- docs/reference/mmkin.html | 7 +----- docs/reference/plot.mkinfit.html | 7 +----- docs/reference/plot.mmkin.html | 9 ++----- docs/reference/print.mkinds.html | 7 +----- docs/reference/print.mkinmod.html | 7 +----- docs/reference/schaefer07_complex_case.html | 7 +----- docs/reference/summary.mkinfit.html | 13 +++------- docs/reference/synthetic_data_for_UBA.html | 7 +----- docs/reference/transform_odeparms.html | 19 ++++++-------- 38 files changed, 104 insertions(+), 269 deletions(-) (limited to 'docs/reference') diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html index e05cdc29..7d036804 100644 --- a/docs/reference/DFOP.solution.html +++ b/docs/reference/DFOP.solution.html @@ -61,12 +61,7 @@ diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index fe39ce6e..cfe6329b 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -60,12 +60,7 @@ @@ -193,7 +188,7 @@ #> #> $time #> user system elapsed -#> 0.256 0.000 0.256 +#> 0.316 0.000 0.317 #> #> $mkinmod #> <mkinmod> model generated with @@ -379,7 +374,7 @@ #> } #> return(mC) #> } -#> <environment: 0x5b47f50> +#> <environment: 0x5d4a3b0> #> #> $cost_notrans #> function (P) @@ -401,7 +396,7 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x5b47f50> +#> <environment: 0x5d4a3b0> #> #> $hessian_notrans #> parent_0 alpha beta @@ -467,7 +462,7 @@ #> 99.66619 #> #> $date -#> [1] "Thu Nov 3 17:46:18 2016" +#> [1] "Fri Nov 4 15:36:31 2016" #> #> attr(,"class") #> [1] "mkinfit" "modFit"
fits["SFO", "B"]
#> dataset @@ -546,7 +541,7 @@ #> #> $time #> user system elapsed -#> 0.068 0.000 0.070 +#> 0.076 0.000 0.077 #> #> $mkinmod #> <mkinmod> model generated with @@ -733,7 +728,7 @@ #> } #> return(mC) #> } -#> <environment: 0x46881c0> +#> <environment: 0x5d98970> #> #> $cost_notrans #> function (P) @@ -755,7 +750,7 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x46881c0> +#> <environment: 0x5d98970> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -818,7 +813,7 @@ #> 99.17407 #> #> $date -#> [1] "Thu Nov 3 17:46:18 2016" +#> [1] "Fri Nov 4 15:36:30 2016" #> #> attr(,"class") #> [1] "mkinfit" "modFit"
fits["SFO", "B", drop = TRUE]
#> [[1]] @@ -894,7 +889,7 @@ #> #> $time #> user system elapsed -#> 0.068 0.000 0.070 +#> 0.076 0.000 0.077 #> #> $mkinmod #> <mkinmod> model generated with @@ -1081,7 +1076,7 @@ #> } #> return(mC) #> } -#> <environment: 0x46881c0> +#> <environment: 0x5d98970> #> #> $cost_notrans #> function (P) @@ -1103,7 +1098,7 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x46881c0> +#> <environment: 0x5d98970> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -1166,7 +1161,7 @@ #> 99.17407 #> #> $date -#> [1] "Thu Nov 3 17:46:18 2016" +#> [1] "Fri Nov 4 15:36:30 2016" #> #> attr(,"class") #> [1] "mkinfit" "modFit" diff --git a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html index 9f098ff3..97af2f9c 100644 --- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html +++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html @@ -61,12 +61,7 @@
diff --git a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html index e45463ba..1487e2c9 100644 --- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html @@ -61,12 +61,7 @@ diff --git a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html index 247c3e00..4571c175 100644 --- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html @@ -61,12 +61,7 @@ diff --git a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html index 006a3876..7003fa0e 100644 --- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html @@ -61,12 +61,7 @@ diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html index c2501a7f..83edd323 100644 --- a/docs/reference/FOCUS_2006_datasets.html +++ b/docs/reference/FOCUS_2006_datasets.html @@ -61,12 +61,7 @@ diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html index 1fbf7741..83bca886 100644 --- a/docs/reference/FOMC.solution.html +++ b/docs/reference/FOMC.solution.html @@ -60,12 +60,7 @@ diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html index 2cecda28..13db29aa 100644 --- a/docs/reference/HS.solution.html +++ b/docs/reference/HS.solution.html @@ -60,12 +60,7 @@ diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html index 68b7be44..56c2b48e 100644 --- a/docs/reference/IORE.solution.html +++ b/docs/reference/IORE.solution.html @@ -60,12 +60,7 @@ diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html index 51c35eee..8ff5b5ba 100644 --- a/docs/reference/SFO.solution.html +++ b/docs/reference/SFO.solution.html @@ -60,12 +60,7 @@ diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html index 2f7dcb5d..43b6028a 100644 --- a/docs/reference/SFORB.solution.html +++ b/docs/reference/SFORB.solution.html @@ -60,12 +60,7 @@ diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html index 82a0b039..8e491bc9 100644 --- a/docs/reference/add_err.html +++ b/docs/reference/add_err.html @@ -61,12 +61,7 @@ diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html index 6ff7ac36..a3716060 100644 --- a/docs/reference/endpoints.html +++ b/docs/reference/endpoints.html @@ -61,12 +61,7 @@ @@ -101,7 +96,7 @@ with the advantage that the SFORB model can also be used for metabolites.

Note

-

The function is used internally by summary.mkinfit.

+

The function is used internally by summary.mkinfit.

Value

diff --git a/docs/reference/geometric_mean.html b/docs/reference/geometric_mean.html index a4b661e2..633e0865 100644 --- a/docs/reference/geometric_mean.html +++ b/docs/reference/geometric_mean.html @@ -60,12 +60,7 @@ diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html index d2551059..955b5c58 100644 --- a/docs/reference/ilr.html +++ b/docs/reference/ilr.html @@ -61,12 +61,7 @@ diff --git a/docs/reference/index.html b/docs/reference/index.html index 23eb608b..b7d59a21 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -60,12 +60,7 @@ @@ -115,7 +110,7 @@

Function to plot the confidence intervals obtained using - mkinfit

+ list(list("mkinfit"))

@@ -124,6 +119,16 @@ + +

Plot the observed data and the fitted model of an mkinfit object

+ + +

Summary method for class "mkinfit"

+

Work with mmkin objects

Functions working with aggregated results

@@ -176,6 +181,11 @@
  • print.mkinds
    • +

    Metabolism data set used for checking the software quality of KinGUI

    + +

    Synthetic datasets for one parent compound with two metabolites

    +

    Function to perform isometric log-ratio transformation

    + +

    Convert a dataframe from long to wide format

    @@ -124,8 +119,8 @@ fixed_parms = "k_phenol_sink", quiet = TRUE) summary(fit.2, data = FALSE)
    #> mkin version: 0.9.44.9000 #> R version: 3.3.2 -#> Date of fit: Thu Nov 3 17:46:24 2016 -#> Date of summary: Thu Nov 3 17:46:24 2016 +#> Date of fit: Fri Nov 4 15:36:38 2016 +#> Date of summary: Fri Nov 4 15:36:38 2016 #> #> Equations: #> d_T245 = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -135,7 +130,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 246 model solutions performed in 1.662 s +#> Fitted with method Port using 246 model solutions performed in 1.886 s #> #> Weighting: none #> diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html index 0385ccbb..21a8a8f8 100644 --- a/docs/reference/mkin_long_to_wide.html +++ b/docs/reference/mkin_long_to_wide.html @@ -61,12 +61,7 @@
    diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html index 965262ce..fe6e47e4 100644 --- a/docs/reference/mkin_wide_to_long.html +++ b/docs/reference/mkin_wide_to_long.html @@ -61,12 +61,7 @@ diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html index 522aab33..f5dd4c88 100644 --- a/docs/reference/mkinds.html +++ b/docs/reference/mkinds.html @@ -60,12 +60,7 @@ diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html index 4e1be39c..8d420165 100644 --- a/docs/reference/mkinerrmin.html +++ b/docs/reference/mkinerrmin.html @@ -61,12 +61,7 @@ @@ -110,7 +105,7 @@ as defined in the FOCUS kinetics report from 2006.

    Details

    -

    This function is used internally by summary.mkinfit.

    +

    This function is used internally by summary.mkinfit.

    References

    diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 867fb9ff..b298d90a 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -61,12 +61,7 @@ @@ -256,7 +251,7 @@ to do transformations. If TRUE, the g parameter of the DFOP and HS models are also transformed, as they can also be seen as compositional data. The transformation used for these transformations is the - ilr transformation. + ilr transformation.
    plot
    @@ -332,11 +327,11 @@

    Value

    A list with "mkinfit" and "modFit" in the class attribute. - A summary can be obtained by summary.mkinfit.

    + A summary can be obtained by summary.mkinfit.

    See also

    -

    Plotting methods plot.mkinfit and +

    Plotting methods plot.mkinfit and mkinparplot.

    Fitting of several models to several datasets in a single call to mmkin.

    @@ -361,15 +356,15 @@ fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE) summary(fit)
    #> mkin version: 0.9.44.9000 #> R version: 3.3.2 -#> Date of fit: Thu Nov 3 17:46:27 2016 -#> Date of summary: Thu Nov 3 17:46:27 2016 +#> Date of fit: Fri Nov 4 15:36:41 2016 +#> Date of summary: Fri Nov 4 15:36:41 2016 #> #> Equations: #> d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent #> #> Model predictions using solution type analytical #> -#> Fitted with method Port using 64 model solutions performed in 0.147 s +#> Fitted with method Port using 64 model solutions performed in 0.156 s #> #> Weighting: none #> @@ -438,7 +433,7 @@ 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)))
    #> user system elapsed -#> 1.204 1.244 0.932
    coef(fit)
    #> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 1.244 1.208 0.933
    coef(fit)
    #> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink #> 99.59848 -3.03822 -2.98030 -5.24750
    endpoints(fit)
    #> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index bdfd0e09..7dba1b6d 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -61,12 +61,7 @@
    diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html index f8151c16..923abc6d 100644 --- a/docs/reference/mkinparplot.html +++ b/docs/reference/mkinparplot.html @@ -61,12 +61,7 @@ diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html index 9ed92dd0..5fe94a8a 100644 --- a/docs/reference/mkinplot.html +++ b/docs/reference/mkinplot.html @@ -61,12 +61,7 @@ @@ -83,7 +78,7 @@ -

    Deprecated function. It now only calls the plot method plot.mkinfit.

    +

    Deprecated function. It now only calls the plot method plot.mkinfit.

    mkinplot(fit, ...)
    @@ -96,7 +91,7 @@
    &#8230;
    - further arguments passed to plot.mkinfit. + further arguments passed to plot.mkinfit.
    diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 57bb747c..f7eb950a 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -61,12 +61,7 @@ @@ -277,17 +272,17 @@ 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 -#> 0.004 0.024 0.004
    system.time( +#> 0.008 0.024 0.005
    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 -#> 0.004 0.016 0.003
    system.time( +#> 0.000 0.020 0.003
    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 -#> 0.036 0.000 0.033
    +#> 0.036 0.000 0.037 @@ -85,7 +80,7 @@

    This function plots the residuals for the specified subset of the observed variables from an mkinfit object. A combined plot of the fitted - model and the residuals can be obtained using plot.mkinfit + model and the residuals can be obtained using plot.mkinfit using the argument show_residuals = TRUE.

    diff --git a/docs/reference/mkinsub.html b/docs/reference/mkinsub.html index 86374e4b..8424eaab 100644 --- a/docs/reference/mkinsub.html +++ b/docs/reference/mkinsub.html @@ -61,12 +61,7 @@ diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index 21461986..5613a720 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -61,12 +61,7 @@ diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html index 61a597e7..e7158180 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -61,12 +61,7 @@ diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html index b107ca70..ef5c04b7 100644 --- a/docs/reference/plot.mmkin.html +++ b/docs/reference/plot.mmkin.html @@ -61,12 +61,7 @@ @@ -124,7 +119,7 @@
    &#8230;
    - Further arguments passed to plot.mkinfit and mkinresplot. + Further arguments passed to plot.mkinfit and mkinresplot.
    diff --git a/docs/reference/print.mkinds.html b/docs/reference/print.mkinds.html index 9bd088b1..c578f4ee 100644 --- a/docs/reference/print.mkinds.html +++ b/docs/reference/print.mkinds.html @@ -61,12 +61,7 @@ diff --git a/docs/reference/print.mkinmod.html b/docs/reference/print.mkinmod.html index 11b96036..3f653971 100644 --- a/docs/reference/print.mkinmod.html +++ b/docs/reference/print.mkinmod.html @@ -61,12 +61,7 @@ diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html index 526dde10..c63ba490 100644 --- a/docs/reference/schaefer07_complex_case.html +++ b/docs/reference/schaefer07_complex_case.html @@ -61,12 +61,7 @@ diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index 46d078bf..241964a7 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -61,12 +61,7 @@ @@ -144,15 +139,15 @@

    Examples

      summary(mkinfit(mkinmod(parent = list(type = "SFO")), FOCUS_2006_A, quiet = TRUE))
    #> mkin version:    0.9.44.9000 
 #> R version:       3.3.2 
-#> Date of fit:     Thu Nov  3 17:46:35 2016 
-#> Date of summary: Thu Nov  3 17:46:35 2016 
+#> Date of fit:     Fri Nov  4 15:36:49 2016 
+#> Date of summary: Fri Nov  4 15:36:49 2016 
 #> 
 #> Equations:
 #> d_parent = - k_parent_sink * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted with method Port using 35 model solutions performed in 0.08 s
+#> Fitted with method Port using 35 model solutions performed in 0.086 s
 #> 
 #> Weighting: none
 #> 
diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html
index a46a5781..333b3dbf 100644
--- a/docs/reference/synthetic_data_for_UBA.html
+++ b/docs/reference/synthetic_data_for_UBA.html
@@ -61,12 +61,7 @@
       
       
       
     
    
   
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index ccd56ca4..5ee1e9cc 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -61,12 +61,7 @@
       
       
       
     
   
@@ -88,7 +83,7 @@
   constants and other paramters that can only take on positive values, a
   simple log transformation is used. For compositional parameters, such as
   the formations fractions that should always sum up to 1 and can not be
-  negative, the ilr transformation is used.
    
+  negative, the ilr transformation is used.
    
 
     
    The transformation of sets of formation fractions is fragile, as it supposes
   the same ordering of the components in forward and backward transformation.
@@ -114,7 +109,7 @@
       
    
     The kinetic model of class mkinmod, containing the names of
     the model variables that are needed for grouping the formation fractions
-    before ilr transformation, the parameter names and 
+    before ilr transformation, the parameter names and 
     the information if the pathway to sink is included in the model. 
   
    
       
    transform_rates
    
@@ -133,7 +128,7 @@
     assumption of normal distribution of the estimator. The default (TRUE) is 
     to do transformations. The g parameter of the DFOP and HS models are also 
     transformed, as they can also be seen as compositional data. The
-    transformation used for these transformations is the ilr
+    transformation used for these transformations is the ilr
     transformation.
   
     
@@ -151,8 +146,8 @@
 fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
 summary(fit, data=FALSE) # See transformed and backtransformed parameters
    #> mkin version:    0.9.44.9000 
 #> R version:       3.3.2 
-#> Date of fit:     Thu Nov  3 17:46:36 2016 
-#> Date of summary: Thu Nov  3 17:46:36 2016 
+#> Date of fit:     Fri Nov  4 15:36:50 2016 
+#> Date of summary: Fri Nov  4 15:36:50 2016 
 #> 
 #> Equations:
 #> d_parent = - k_parent_sink * parent - k_parent_m1 * parent
@@ -160,7 +155,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 153 model solutions performed in 0.657 s
+#> Fitted with method Port using 153 model solutions performed in 0.663 s
 #> 
 #> Weighting: none
 #> 
-- 
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