From 2409369d3a665f2b8e0b7333f4c2286a61614179 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 26 Oct 2016 23:54:08 +0200 Subject: Complete pkgdown conf, rerun with current master branch --- _pkgdown.yml | 56 ++++++-- docs/index.html | 13 +- docs/reference/DFOP.solution.html | 14 +- docs/reference/Extract.mmkin.html | 38 +++--- 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 | 14 +- docs/reference/FOMC.solution.html | 14 +- docs/reference/HS.solution.html | 14 +- docs/reference/IORE.solution.html | 14 +- docs/reference/SFO.solution.html | 14 +- docs/reference/SFORB.solution.html | 14 +- docs/reference/add_err.html | 14 +- docs/reference/endpoints.html | 14 +- docs/reference/geometric_mean.html | 14 +- docs/reference/ilr.html | 14 +- docs/reference/index.html | 173 +++++++++++++++++++++++-- docs/reference/mccall81_245T.html | 20 ++- docs/reference/mkin_long_to_wide.html | 14 +- docs/reference/mkin_wide_to_long.html | 14 +- docs/reference/mkinds.html | 14 +- docs/reference/mkinerrmin.html | 14 +- docs/reference/mkinfit.html | 22 ++-- docs/reference/mkinmod.html | 14 +- docs/reference/mkinparplot.html | 14 +- docs/reference/mkinplot.html | 14 +- docs/reference/mkinpredict.html | 20 ++- docs/reference/mkinresplot.html | 14 +- docs/reference/mkinsub.html | 14 +- docs/reference/mmkin.html | 14 +- docs/reference/plot.mkinfit.html | 14 +- docs/reference/plot.mmkin.html | 14 +- docs/reference/print.mkinds.html | 14 +- docs/reference/print.mkinmod.html | 14 +- docs/reference/schaefer07_complex_case.html | 14 +- docs/reference/summary.mkinfit.html | 20 ++- docs/reference/synthetic_data_for_UBA.html | 14 +- docs/reference/transform_odeparms.html | 20 ++- 40 files changed, 462 insertions(+), 354 deletions(-) diff --git a/_pkgdown.yml b/_pkgdown.yml index 6552d156..cdd8994a 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -1,7 +1,7 @@ title: mkin template: - bootswatch: cerulean + bootswatch: spacelab reference: - title: Main functions @@ -11,22 +11,50 @@ reference: - mkinfit - mmkin - title: Show results - contents: Functions working with mkinfit objects + desc: Functions working with mkinfit objects + contents: - plot.mkinfit - summary.mkinfit - mkinresplot - mkinparplot - endpoints - mkinerrmin - -navbar: - title: mkin - type: default - left: - - text: Home - href: index.html - - text: Reference - href: reference/index.html - right: - - icon: fa-github fa-lg - href: https://github.com/jranke/mkin + - title: Work with mmkin objects + desc: Functions working with aggregated results + contents: + - "[.mmkin" + - plot.mmkin + - title: Datasets and known results + contents: + - FOCUS_2006_datasets + - FOCUS_2006_SFO_ref_A_to_F + - FOCUS_2006_FOMC_ref_A_to_F + - FOCUS_2006_HS_ref_A_to_F + - FOCUS_2006_DFOP_ref_A_to_B + - mccall81_245T + - schaefer07_complex_case + - synthetic_data_for_UBA_2014 + - title: Helper functions + contents: + - mkin_wide_to_long + - mkin_long_to_wide + - mkinsub + - mkinds, print.mkinds + - print.mkinmod + - mkinpredict + - transform_odeparms + - ilr + - geometric_mean + - title: Analytical solutions + desc: Parent only model solutions + contents: + - SFO.solution, + - FOMC.solution + - DFOP.solution + - SFORB.solution + - HS.solution + - IORE.solution + - title: Deprecated functions + desc: Functions that have been superseeded + contents: + - mkinplot diff --git a/docs/index.html b/docs/index.html index 180fe5f9..04f10ed8 100644 --- a/docs/index.html +++ b/docs/index.html @@ -16,18 +16,15 @@ + diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html index 5c90809c..3b8e0e03 100644 --- a/docs/reference/DFOP.solution.html +++ b/docs/reference/DFOP.solution.html @@ -50,20 +50,18 @@ diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index ee86854a..4ea16d10 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -49,20 +49,18 @@ @@ -195,7 +193,7 @@ #> #> $time #> user system elapsed -#> 0.268 0.000 0.264 +#> 0.26 0.00 0.26 #> #> $mkinmod #> <mkinmod> model generated with @@ -381,7 +379,7 @@ #> } #> return(mC) #> } -#> <environment: 0x49c37f0> +#> <environment: 0x5421f48> #> #> $cost_notrans #> function (P) @@ -403,7 +401,7 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x49c37f0> +#> <environment: 0x5421f48> #> #> $hessian_notrans #> parent_0 alpha beta @@ -469,7 +467,7 @@ #> 99.66619 #> #> $date -#> [1] "Wed Oct 26 23:16:41 2016" +#> [1] "Wed Oct 26 23:50:33 2016" #> #> attr(,"class") #> [1] "mkinfit" "modFit" @@ -550,7 +548,7 @@ #> #> $time #> user system elapsed -#> 0.072 0.004 0.074 +#> 0.068 0.000 0.070 #> #> $mkinmod #> <mkinmod> model generated with @@ -737,7 +735,7 @@ #> } #> return(mC) #> } -#> <environment: 0x4ae0880> +#> <environment: 0x2b30d68> #> #> $cost_notrans #> function (P) @@ -759,7 +757,7 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x4ae0880> +#> <environment: 0x2b30d68> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -822,7 +820,7 @@ #> 99.17407 #> #> $date -#> [1] "Wed Oct 26 23:16:41 2016" +#> [1] "Wed Oct 26 23:50:32 2016" #> #> attr(,"class") #> [1] "mkinfit" "modFit" @@ -899,7 +897,7 @@ #> #> $time #> user system elapsed -#> 0.072 0.004 0.074 +#> 0.068 0.000 0.070 #> #> $mkinmod #> <mkinmod> model generated with @@ -1086,7 +1084,7 @@ #> } #> return(mC) #> } -#> <environment: 0x4ae0880> +#> <environment: 0x2b30d68> #> #> $cost_notrans #> function (P) @@ -1108,7 +1106,7 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x4ae0880> +#> <environment: 0x2b30d68> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -1171,7 +1169,7 @@ #> 99.17407 #> #> $date -#> [1] "Wed Oct 26 23:16:41 2016" +#> [1] "Wed Oct 26 23:50:32 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 61871ba9..6f071674 100644 --- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html +++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html @@ -50,20 +50,18 @@ 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 4fdb5f45..d721b2d9 100644 --- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html @@ -50,20 +50,18 @@ 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 d9e43f4a..11fcea7c 100644 --- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html @@ -50,20 +50,18 @@ 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 68475b64..17c34f0f 100644 --- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html @@ -50,20 +50,18 @@ diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html index 6221f53f..c5bdae8b 100644 --- a/docs/reference/FOCUS_2006_datasets.html +++ b/docs/reference/FOCUS_2006_datasets.html @@ -50,20 +50,18 @@ diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html index 99d95fcb..a2e84ce0 100644 --- a/docs/reference/FOMC.solution.html +++ b/docs/reference/FOMC.solution.html @@ -49,20 +49,18 @@ diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html index 06c6e3c1..e41b7b6a 100644 --- a/docs/reference/HS.solution.html +++ b/docs/reference/HS.solution.html @@ -49,20 +49,18 @@ diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html index 58546489..c39e7818 100644 --- a/docs/reference/IORE.solution.html +++ b/docs/reference/IORE.solution.html @@ -49,20 +49,18 @@ diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html index b2d5526e..3ce813bf 100644 --- a/docs/reference/SFO.solution.html +++ b/docs/reference/SFO.solution.html @@ -49,20 +49,18 @@ diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html index 135edb51..942fa576 100644 --- a/docs/reference/SFORB.solution.html +++ b/docs/reference/SFORB.solution.html @@ -49,20 +49,18 @@ diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html index 9020a486..2500e092 100644 --- a/docs/reference/add_err.html +++ b/docs/reference/add_err.html @@ -50,20 +50,18 @@ diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html index 89e9cf52..73d7e746 100644 --- a/docs/reference/endpoints.html +++ b/docs/reference/endpoints.html @@ -50,20 +50,18 @@ diff --git a/docs/reference/geometric_mean.html b/docs/reference/geometric_mean.html index 793d893c..62a9163f 100644 --- a/docs/reference/geometric_mean.html +++ b/docs/reference/geometric_mean.html @@ -49,20 +49,18 @@ diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html index d249101d..82accca4 100644 --- a/docs/reference/ilr.html +++ b/docs/reference/ilr.html @@ -50,20 +50,18 @@ diff --git a/docs/reference/index.html b/docs/reference/index.html index 60d11171..6fcf39c8 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -49,20 +49,18 @@ @@ -98,8 +96,162 @@
  • mmkin

    • Show results

    +

    Functions working with mkinfit objects

    + +

    +

    + +

    +

    + +

    +

    + +

    +

    + +

    +

    + +

    +

    + +

    Work with mmkin objects

    +

    Functions working with aggregated results

    + +

    Subsetting method for mmkin objects

    + +

    +

    + +

    Datasets and known results

    +

    +

    + +

    +

    + +

    +

    + +

    +

    + +

    +

    + +

    +

    + +

    +

    + +

    Helper functions

    +

    + +

    Calculate the geometric mean

    + +

    +

    + +

    +

    + +

    +

    + +

    +

    + +

    +

    + +

    +

    + +

    +

    + +

    Analytical solutions

    +

    Parent only model solutions

    + +

    +

    + +

    First-Order Multi-Compartment kinetics

    + +

    Hockey-Stick kinetics

    + +

    Indeterminate order rate equation kinetics

    + +

    Single First-Order Reversible Binding kinetics

    + +

    Deprecated functions

    +

    Functions that have been superseeded

    + +

    +

    + @@ -109,6 +261,11 @@ diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 7a96be3b..74b9c088 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -50,20 +50,18 @@ @@ -124,8 +122,8 @@ fixed_parms = "k_phenol_sink", quiet = TRUE) summary(fit.2, data = FALSE)
    #> mkin version: 0.9.44.9000 #> R version: 3.3.1 -#> Date of fit: Wed Oct 26 23:16:47 2016 -#> Date of summary: Wed Oct 26 23:16:47 2016 +#> Date of fit: Wed Oct 26 23:50:40 2016 +#> Date of summary: Wed Oct 26 23:50:40 2016 #> #> Equations: #> d_T245 = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -135,7 +133,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 246 model solutions performed in 1.487 s +#> Fitted with method Port using 246 model solutions performed in 1.43 s #> #> Weighting: none #> diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html index d8b616c2..cc50bf7d 100644 --- a/docs/reference/mkin_long_to_wide.html +++ b/docs/reference/mkin_long_to_wide.html @@ -50,20 +50,18 @@
    diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html index 31207861..bce6d6a4 100644 --- a/docs/reference/mkin_wide_to_long.html +++ b/docs/reference/mkin_wide_to_long.html @@ -50,20 +50,18 @@ diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html index 45cc315f..e5d99fd5 100644 --- a/docs/reference/mkinds.html +++ b/docs/reference/mkinds.html @@ -49,20 +49,18 @@ diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html index 2e1833da..5b437b08 100644 --- a/docs/reference/mkinerrmin.html +++ b/docs/reference/mkinerrmin.html @@ -50,20 +50,18 @@ diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 3c9bd05c..6bfb9352 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -50,20 +50,18 @@ @@ -361,15 +359,15 @@ fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE) summary(fit)
    #> mkin version: 0.9.44.9000 #> R version: 3.3.1 -#> Date of fit: Wed Oct 26 23:16:49 2016 -#> Date of summary: Wed Oct 26 23:16:49 2016 +#> Date of fit: Wed Oct 26 23:50:42 2016 +#> Date of summary: Wed Oct 26 23:50:42 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 0.148 s +#> Fitted with method Port using 64 model solutions performed in 0.168 s #> #> Weighting: none #> @@ -439,7 +437,7 @@ 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 -#> 1.224 1.196 0.913 +#> 1.272 1.204 0.943 #>
    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 diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index 53c87e92..40381656 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -50,20 +50,18 @@
    diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html index 6d4f2cfd..dff30930 100644 --- a/docs/reference/mkinparplot.html +++ b/docs/reference/mkinparplot.html @@ -50,20 +50,18 @@ diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html index 925a6683..d3f0c1f6 100644 --- a/docs/reference/mkinplot.html +++ b/docs/reference/mkinplot.html @@ -50,20 +50,18 @@ diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index cf04c6b6..31556527 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -50,20 +50,18 @@ @@ -288,21 +286,21 @@ solution_type = "eigen")[201,]))
    #> time parent m1 #> 201 20 4.978707 27.46227 #>
    #> user system elapsed -#> 0.008 0.024 0.004 +#> 0.028 0.004 0.004 #>
    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 -#> 0.000 0.020 0.002 +#> 0.016 0.004 0.002 #>
    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 0.035 +#> 0.052 0.000 0.052 #>
    diff --git a/docs/reference/mkinsub.html b/docs/reference/mkinsub.html index 2432e981..89387468 100644 --- a/docs/reference/mkinsub.html +++ b/docs/reference/mkinsub.html @@ -50,20 +50,18 @@ diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index 0ad3321c..a6e74b8a 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -50,20 +50,18 @@ diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html index 631ea429..4eb7369a 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -50,20 +50,18 @@ diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html index 44ae760f..e0a20f3d 100644 --- a/docs/reference/plot.mmkin.html +++ b/docs/reference/plot.mmkin.html @@ -50,20 +50,18 @@ diff --git a/docs/reference/print.mkinds.html b/docs/reference/print.mkinds.html index c4bc08d5..a586a103 100644 --- a/docs/reference/print.mkinds.html +++ b/docs/reference/print.mkinds.html @@ -50,20 +50,18 @@ diff --git a/docs/reference/print.mkinmod.html b/docs/reference/print.mkinmod.html index edc9cde7..73bfd60e 100644 --- a/docs/reference/print.mkinmod.html +++ b/docs/reference/print.mkinmod.html @@ -50,20 +50,18 @@ diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html index 1cd71697..4714747a 100644 --- a/docs/reference/schaefer07_complex_case.html +++ b/docs/reference/schaefer07_complex_case.html @@ -50,20 +50,18 @@ diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index 1e1a0e2f..b88a5469 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -50,20 +50,18 @@ @@ -144,15 +142,15 @@ 
      summary(mkinfit(mkinmod(parent = list(type = "SFO")), FOCUS_2006_A, quiet = TRUE))
    #> mkin version:    0.9.44.9000 
 #> R version:       3.3.1 
-#> Date of fit:     Wed Oct 26 23:16:57 2016 
-#> Date of summary: Wed Oct 26 23:16:57 2016 
+#> Date of fit:     Wed Oct 26 23:50:50 2016 
+#> Date of summary: Wed Oct 26 23:50:50 2016 
 #> 
 #> Equations:
 #> d_parent = - k_parent_sink * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted with method Port using 35 model solutions performed in 0.089 s
+#> Fitted with method Port using 35 model solutions performed in 0.083 s
 #> 
 #> Weighting: none
 #> 
diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html
index b45c07fc..45d5f53a 100644
--- a/docs/reference/synthetic_data_for_UBA.html
+++ b/docs/reference/synthetic_data_for_UBA.html
@@ -50,20 +50,18 @@
     
   
    
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index a07be0a0..ab5ce062 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -50,20 +50,18 @@
     
   
@@ -151,8 +149,8 @@
 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:       3.3.1 
-#> Date of fit:     Wed Oct 26 23:16:59 2016 
-#> Date of summary: Wed Oct 26 23:16:59 2016 
+#> Date of fit:     Wed Oct 26 23:50:51 2016 
+#> Date of summary: Wed Oct 26 23:50:51 2016 
 #> 
 #> Equations:
 #> d_parent = - k_parent_sink * parent - k_parent_m1 * parent
@@ -160,7 +158,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 153 model solutions performed in 0.721 s
+#> Fitted with method Port using 153 model solutions performed in 0.629 s
 #> 
 #> Weighting: none
 #> 
-- 
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