From f39815aa87272849f8e0c808099c4cee780c2a81 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 3 Nov 2016 14:33:05 +0100 Subject: Static documentation rebuilt by pkgdown::build_site() Using pkgdown with PR hadley/pkgdown#212 --- docs/reference/DFOP.solution.html | 14 ++- docs/reference/Extract.mmkin.html | 50 ++++---- docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html | 14 ++- docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html | 14 ++- docs/reference/FOCUS_2006_HS_ref_A_to_F.html | 14 ++- docs/reference/FOCUS_2006_SFO_ref_A_to_F.html | 14 ++- docs/reference/FOCUS_2006_datasets.html | 17 +-- docs/reference/FOMC.solution.html | 14 ++- docs/reference/HS.solution.html | 14 ++- docs/reference/IORE.solution.html | 20 ++-- docs/reference/SFO.solution.html | 14 ++- docs/reference/SFORB.solution.html | 14 ++- docs/reference/add_err.html | 16 +-- docs/reference/endpoints.html | 11 +- docs/reference/geometric_mean.html | 19 ++- docs/reference/ilr.html | 39 +++--- docs/reference/index.html | 159 +++++++++++++------------ docs/reference/mccall81_245T.html | 27 +++-- docs/reference/mkin_long_to_wide.html | 17 +-- docs/reference/mkin_wide_to_long.html | 17 +-- docs/reference/mkinds.html | 14 ++- docs/reference/mkinerrmin.html | 24 ++-- docs/reference/mkinfit.html | 40 +++---- docs/reference/mkinmod.html | 16 +-- docs/reference/mkinparplot.html | 16 +-- docs/reference/mkinplot.html | 13 +- docs/reference/mkinpredict.html | 64 ++++------ docs/reference/mkinresplot.html | 18 +-- docs/reference/mkinsub.html | 20 ++-- docs/reference/mmkin.html | 14 ++- docs/reference/plot.mkinfit.html | 16 +-- docs/reference/plot.mmkin.html | 16 +-- docs/reference/print.mkinds.html | 9 +- docs/reference/print.mkinmod.html | 9 +- docs/reference/schaefer07_complex_case.html | 16 +-- docs/reference/summary.mkinfit.html | 25 ++-- docs/reference/synthetic_data_for_UBA.html | 14 ++- docs/reference/transform_odeparms.html | 39 +++--- 38 files changed, 473 insertions(+), 428 deletions(-) (limited to 'docs/reference') diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html index 3b8e0e03..e05cdc29 100644 --- a/docs/reference/DFOP.solution.html +++ b/docs/reference/DFOP.solution.html @@ -61,7 +61,12 @@ @@ -113,10 +118,7 @@ http://focus.jrc.ec.europa.eu/dk

-

- - Examples -

+

Examples

  plot(function(x) DFOP.solution(x, 100, 5, 0.5, 0.3), 0, 4, ylim=c(0,100))
@@ -102,10 +107,7 @@

An object of class mmkin.

-

- - Examples -

+

Examples

  # Only use one core, to pass R CMD check --as-cran
   fits <- mmkin(c("SFO", "FOMC"), list(B = FOCUS_2006_B, C = FOCUS_2006_C),
                 cores = 1, quiet = TRUE)
@@ -113,14 +115,12 @@
 #> model  B       C      
 #>   FOMC List,42 List,42
 #> attr(,"class")
-#> [1] "mmkin"
-#> 
  fits[, "B"]
#>       dataset
+#> [1] "mmkin"
  fits[, "B"]
#>       dataset
 #> model  B      
 #>   SFO  List,42
 #>   FOMC List,42
 #> attr(,"class")
-#> [1] "mmkin"
-#> 
  fits[, "B", drop = TRUE]$FOMC
#> $par
+#> [1] "mmkin"
  fits[, "B", drop = TRUE]$FOMC
#> $par
 #>  parent_0 log_alpha  log_beta 
 #> 99.666193  2.549849  5.050586 
 #> 
@@ -193,7 +193,7 @@
 #> 
 #> $time
 #>    user  system elapsed 
-#>    0.26    0.00    0.26 
+#>   0.256   0.000   0.256 
 #> 
 #> $mkinmod
 #> <mkinmod> model generated with
@@ -379,7 +379,7 @@
 #>     }
 #>     return(mC)
 #> }
-#> <environment: 0x5421f48>
+#> <environment: 0x5b47f50>
 #> 
 #> $cost_notrans
 #> function (P) 
@@ -401,7 +401,7 @@
 #>         scaleVar = scaleVar)
 #>     return(mC)
 #> }
-#> <environment: 0x5421f48>
+#> <environment: 0x5b47f50>
 #> 
 #> $hessian_notrans
 #>            parent_0     alpha       beta
@@ -467,16 +467,14 @@
 #> 99.66619 
 #> 
 #> $date
-#> [1] "Wed Oct 26 23:50:33 2016"
+#> [1] "Thu Nov  3 17:46:18 2016"
 #> 
 #> attr(,"class")
-#> [1] "mkinfit" "modFit" 
-#> 
  fits["SFO", "B"]
#>      dataset
+#> [1] "mkinfit" "modFit" 
  fits["SFO", "B"]
#>      dataset
 #> model B      
 #>   SFO List,42
 #> attr(,"class")
-#> [1] "mmkin"
-#> 
  fits[["SFO", "B"]] # This is equivalent to
#> $par
+#> [1] "mmkin"
  fits[["SFO", "B"]] # This is equivalent to
#> $par
 #>          parent_0 log_k_parent_sink 
 #>         99.174072         -2.549028 
 #> 
@@ -735,7 +733,7 @@
 #>     }
 #>     return(mC)
 #> }
-#> <environment: 0x2b30d68>
+#> <environment: 0x46881c0>
 #> 
 #> $cost_notrans
 #> function (P) 
@@ -757,7 +755,7 @@
 #>         scaleVar = scaleVar)
 #>     return(mC)
 #> }
-#> <environment: 0x2b30d68>
+#> <environment: 0x46881c0>
 #> 
 #> $hessian_notrans
 #>                   parent_0 k_parent_sink
@@ -820,11 +818,10 @@
 #> 99.17407 
 #> 
 #> $date
-#> [1] "Wed Oct 26 23:50:32 2016"
+#> [1] "Thu Nov  3 17:46:18 2016"
 #> 
 #> attr(,"class")
-#> [1] "mkinfit" "modFit" 
-#> 
  fits["SFO", "B", drop = TRUE]
#> [[1]]
+#> [1] "mkinfit" "modFit" 
  fits["SFO", "B", drop = TRUE]
#> [[1]]
 #> $par
 #>          parent_0 log_k_parent_sink 
 #>         99.174072         -2.549028 
@@ -1084,7 +1081,7 @@
 #>     }
 #>     return(mC)
 #> }
-#> <environment: 0x2b30d68>
+#> <environment: 0x46881c0>
 #> 
 #> $cost_notrans
 #> function (P) 
@@ -1106,7 +1103,7 @@
 #>         scaleVar = scaleVar)
 #>     return(mC)
 #> }
-#> <environment: 0x2b30d68>
+#> <environment: 0x46881c0>
 #> 
 #> $hessian_notrans
 #>                   parent_0 k_parent_sink
@@ -1169,11 +1166,10 @@
 #> 99.17407 
 #> 
 #> $date
-#> [1] "Wed Oct 26 23:50:32 2016"
+#> [1] "Thu Nov  3 17:46:18 2016"
 #> 
 #> attr(,"class")
 #> [1] "mkinfit" "modFit" 
-#> 
 #>
@@ -110,10 +115,7 @@ in this fit.

http://focus.jrc.ec.europa.eu/dk

-

- - Examples -

+

Examples

data(FOCUS_2006_DFOP_ref_A_to_B)
@@ -109,10 +114,7 @@ in this fit.

http://focus.jrc.ec.europa.eu/dk

-

- - Examples -

+

Examples

data(FOCUS_2006_FOMC_ref_A_to_F)
@@ -110,10 +115,7 @@ in this fit.

http://focus.jrc.ec.europa.eu/dk

-

- - Examples -

+

Examples

data(FOCUS_2006_HS_ref_A_to_F)
@@ -108,10 +113,7 @@ in this fit.

http://focus.jrc.ec.europa.eu/dk

-

- - Examples -

+

Examples

data(FOCUS_2006_SFO_ref_A_to_F)
@@ -101,10 +106,7 @@ http://focus.jrc.ec.europa.eu/dk

-

- - Examples -

+

Examples

FOCUS_2006_C
#>     name time value
 #> 1 parent    0  85.1
 #> 2 parent    1  57.9
@@ -114,8 +116,7 @@
 #> 6 parent   28   6.6
 #> 7 parent   63   4.0
 #> 8 parent   91   3.9
-#> 9 parent  119   0.6
-#>
+#> 9 parent 119 0.6 @@ -125,10 +130,7 @@ Technology 24, 1032-1038

-

- - Examples -

+

Examples

  plot(function(x) FOMC.solution(x, 100, 10, 2), 0, 2, ylim = c(0, 100))
@@ -111,10 +116,7 @@ http://focus.jrc.ec.europa.eu/dk

-

- - Examples -

+

Examples

  plot(function(x) HS.solution(x, 100, 2, 0.3, 0.5), 0, 2, ylim=c(0,100))
@@ -112,10 +117,7 @@ Media

-

- - Examples -

+

Examples

  plot(function(x) IORE.solution(x, 100, 0.2, 1.3), 0, 2,
                                        ylim = c(0, 100))
  fit.fomc <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
   fit.iore <- mkinfit("IORE", FOCUS_2006_C, quiet = TRUE)
@@ -125,13 +127,11 @@
                    row.names = paste("model par", 1:3)))
#>             coef.fit.fomc. coef.fit.iore. coef.fit.iore.deS.
 #> model par 1    85.87489063      85.874891          85.874890
 #> model par 2     0.05192238      -4.826631          -4.826631
-#> model par 3     0.65096665       1.949403           1.949403
-#> 
  print(rbind(fomc = endpoints(fit.fomc)$distimes, iore = endpoints(fit.iore)$distimes,
+#> model par 3     0.65096665       1.949403           1.949403
  print(rbind(fomc = endpoints(fit.fomc)$distimes, iore = endpoints(fit.iore)$distimes,
               iore.deS = endpoints(fit.iore)$distimes))
#>              DT50    DT90 DT50back
 #> fomc     1.785233 15.1479 4.559973
 #> iore     1.785233 15.1479 4.559973
-#> iore.deS 1.785233 15.1479 4.559973
-#>
+#> iore.deS 1.785233 15.1479 4.559973 @@ -104,10 +109,7 @@ http://focus.jrc.ec.europa.eu/dk

-

- - Examples -

+

Examples

  ## Not run: plot(function(x) SFO.solution(x, 100, 3), 0, 2)
@@ -113,10 +118,7 @@ http://focus.jrc.ec.europa.eu/dk

-

- - Examples -

+

Examples

  ## Not run: plot(function(x) SFORB.solution(x, 100, 0.5, 2, 3), 0, 2)
@@ -135,13 +140,10 @@ http://chem.uft.uni-bremen.de/ranke/posters/piacenza_2015.pdf

-

- - Examples -

+

Examples

# The kinetic model
 m_SFO_SFO <- mkinmod(parent = mkinsub("SFO", "M1"),
-                     M1 = mkinsub("SFO"), use_of_ff = "max")
Successfully compiled differential equation model from auto-generated C code.

+                     M1 = mkinsub("SFO"), use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.

 # Generate a prediction for a specific set of parameters
 sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
 
@@ -200,7 +202,7 @@
 
       

       

-  
Developed by Johannes Ranke, Eurofins Regulatory AG.

+  
Developed by Johannes Ranke.

 

 
 

diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html
index 73d7e746..6ff7ac36 100644
--- a/docs/reference/endpoints.html
+++ b/docs/reference/endpoints.html
@@ -61,7 +61,12 @@
       
       
       
     

   

@@ -96,7 +101,7 @@ 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

 
@@ -123,7 +128,7 @@ with the advantage that the SFORB model can also be used for metabolites.

 
       

       

-  
Developed by Johannes Ranke, Eurofins Regulatory AG.

+  
Developed by Johannes Ranke.

 

 
 

diff --git a/docs/reference/geometric_mean.html b/docs/reference/geometric_mean.html
index 62a9163f..a4b661e2 100644
--- a/docs/reference/geometric_mean.html
+++ b/docs/reference/geometric_mean.html
@@ -60,7 +60,12 @@
       
       
       
     

   
@@ -94,14 +99,8 @@
     
The geometric mean.

     
 
-    

-      
-      Examples
-    

-    
  geometric_mean(c(1,3, 9))
#> [1] 3
-#> 
  geometric_mean(c(1,3, NA))
#> [1] NA
-#> 
  geometric_mean(c(1,3, NA), na.rm = TRUE)
#> [1] 1.732051
-#> 

+    
Examples

+    
  geometric_mean(c(1,3, 9))
#> [1] 3
  geometric_mean(c(1,3, NA))
#> [1] NA
  geometric_mean(c(1,3, NA), na.rm = TRUE)
#> [1] 1.732051

   
   
@@ -107,31 +112,17 @@
     
Another implementation can be found in R package robCompositions.

     
 
-    

-      
-      Examples
-    

+    
Examples

     
# Order matters
-ilr(c(0.1, 1, 10))
#> [1] -1.628174 -2.820079
-#> 
ilr(c(10, 1, 0.1))
#> [1] 1.628174 2.820079
-#> 
# Equal entries give ilr transformations with zeros as elements
-ilr(c(3, 3, 3))
#> [1] 0 0
-#> 
# Almost equal entries give small numbers
-ilr(c(0.3, 0.4, 0.3))
#> [1] -0.2034219  0.1174457
-#> 
# Only the ratio between the numbers counts, not their sum
-invilr(ilr(c(0.7, 0.29, 0.01)))
#> [1] 0.70 0.29 0.01
-#> 
invilr(ilr(2.1 * c(0.7, 0.29, 0.01)))
#> [1] 0.70 0.29 0.01
-#> 
# Inverse transformation of larger numbers gives unequal elements
-invilr(-10)
#> [1] 7.213536e-07 9.999993e-01
-#> 
invilr(c(-10, 0))
#> [1] 7.207415e-07 9.991507e-01 8.486044e-04
-#> 
# The sum of the elements of the inverse ilr is 1
-sum(invilr(c(-10, 0)))
#> [1] 1
-#> 
# This is why we do not need all elements of the inverse transformation to go back:
+ilr(c(0.1, 1, 10))
#> [1] -1.628174 -2.820079
ilr(c(10, 1, 0.1))
#> [1] 1.628174 2.820079
# Equal entries give ilr transformations with zeros as elements
+ilr(c(3, 3, 3))
#> [1] 0 0
# Almost equal entries give small numbers
+ilr(c(0.3, 0.4, 0.3))
#> [1] -0.2034219  0.1174457
# Only the ratio between the numbers counts, not their sum
+invilr(ilr(c(0.7, 0.29, 0.01)))
#> [1] 0.70 0.29 0.01
invilr(ilr(2.1 * c(0.7, 0.29, 0.01)))
#> [1] 0.70 0.29 0.01
# Inverse transformation of larger numbers gives unequal elements
+invilr(-10)
#> [1] 7.213536e-07 9.999993e-01
invilr(c(-10, 0))
#> [1] 7.207415e-07 9.991507e-01 8.486044e-04
# The sum of the elements of the inverse ilr is 1
+sum(invilr(c(-10, 0)))
#> [1] 1
# This is why we do not need all elements of the inverse transformation to go back:
 a <- c(0.1, 0.3, 0.5)
 b <- invilr(a)
-length(b) # Four elements
#> [1] 4
-#> 
ilr(c(b[1:3], 1 - sum(b[1:3]))) # Gives c(0.1, 0.3, 0.5)
#> [1] 0.1 0.3 0.5
-#> 

+length(b) # Four elements
#> [1] 4
ilr(c(b[1:3], 1 - sum(b[1:3]))) # Gives c(0.1, 0.3, 0.5)
#> [1] 0.1 0.3 0.5
@@ -80,175 +85,180 @@

Main functions

Essential functionality

-

-

+ +

Fit a kinetic model to data with one or more state variables

-

-

+ +

Function to set up a kinetic model with one or more state variables

-

-

+ +

Fit one or more kinetic models with one or more state variables to one or more datasets

Show results

Functions working with mkinfit objects

-

-

+ +

Function to calculate endpoints for further use from kinetic models fitted with mkinfit

-

-

+ +

Calculate the minimum error to assume in order to pass the variance test

-

-

+ +

Function to plot the confidence intervals obtained using + mkinfit

-

-

+ +

Function to plot residuals stored in an mkin object

-

-

- -

-

-

Work with mmkin objects

Functions working with aggregated results

+

Subsetting method for mmkin objects

-

-

+ +

Plot model fits (observed and fitted) and the residuals for a row or column of an mmkin object

Datasets and known results

-

-

+ +

Results of fitting the DFOP model to Datasets A to B of FOCUS (2006)

-

-

+ +

Results of fitting the FOMC model to Datasets A to F of FOCUS (2006)

-

-

+ +

Results of fitting the HS model to Datasets A to F of FOCUS (2006)

-

-

+ +

Results of fitting the SFO model to Datasets A to F of FOCUS (2006)

-

-

+ +

Datasets on aerobic soil metabolism of 2,4,5-T in six soils

-

-

+ +

A dataset class for mkin

-

-

+ +

Print mkinds objects

+ + +

Synthetic datasets for one parent compound with two metabolites

Helper functions

-

Calculate the geometric mean

+ +

Calculate the geometric mean

-

-

+ +

Convert a dataframe from long to wide format

-

-

+ +

Convert a dataframe with observations over time into long format

-

-

+ +

Produce predictions from a kinetic model using specific parameters

-

-

+ +

Function to set up a kinetic submodel for one state variable

-

-

- -

-

+ +

Print mkinmod objects

-

-

-

Analytical solutions

Parent only model solutions

-

-

+ +

Double First-Order in Parallel kinetics

-

First-Order Multi-Compartment kinetics

+ +

First-Order Multi-Compartment kinetics

-

Hockey-Stick kinetics

+ +

Hockey-Stick kinetics

-

Indeterminate order rate equation kinetics

+ +

Indeterminate order rate equation kinetics

-

Single First-Order Reversible Binding kinetics

+ +

Single First-Order kinetics

+ + +

Single First-Order Reversible Binding kinetics

+

Generate synthetic datasets

+

+ + +

Add normally distributed errors to simulated kinetic degradation data

+

Deprecated functions

Functions that have been superseeded

-

-

+ +

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

@@ -265,6 +275,7 @@
  • Datasets and known results
  • Helper functions
  • Analytical solutions
    • +
  • Generate synthetic datasets
  • Deprecated functions
    • @@ -272,7 +283,7 @@