From 517d9378284bb4341c1bbce6716b89b341c8b61e Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 4 Nov 2016 17:11:50 +0100 Subject: Rebuild docs with updated PR for pkgdown --- docs/reference/DFOP.solution.html | 13 +++++++---- docs/reference/Extract.mmkin.html | 31 ++++++++++++++----------- docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html | 13 +++++++---- docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html | 13 +++++++---- docs/reference/FOCUS_2006_HS_ref_A_to_F.html | 13 +++++++---- docs/reference/FOCUS_2006_SFO_ref_A_to_F.html | 13 +++++++---- docs/reference/FOCUS_2006_datasets.html | 13 +++++++---- docs/reference/FOMC.solution.html | 11 ++++++--- docs/reference/HS.solution.html | 11 ++++++--- docs/reference/IORE.solution.html | 11 ++++++--- docs/reference/SFO.solution.html | 11 ++++++--- docs/reference/SFORB.solution.html | 11 ++++++--- docs/reference/add_err.html | 13 +++++++---- docs/reference/endpoints.html | 13 +++++++---- docs/reference/geometric_mean.html | 11 ++++++--- docs/reference/ilr.html | 13 +++++++---- docs/reference/index.html | 7 +++++- docs/reference/mccall81_245T.html | 19 ++++++++------- docs/reference/mkin_long_to_wide.html | 13 +++++++---- docs/reference/mkin_wide_to_long.html | 13 +++++++---- docs/reference/mkinds.html | 7 +++++- docs/reference/mkinerrmin.html | 13 +++++++---- docs/reference/mkinfit.html | 19 ++++++++------- docs/reference/mkinmod.html | 13 +++++++---- docs/reference/mkinparplot.html | 15 ++++++++---- docs/reference/mkinplot.html | 13 +++++++---- docs/reference/mkinpredict.html | 17 ++++++++------ docs/reference/mkinresplot.html | 13 +++++++---- docs/reference/mkinsub.html | 13 +++++++---- docs/reference/mmkin.html | 13 +++++++---- docs/reference/plot.mkinfit.html | 13 +++++++---- docs/reference/plot.mmkin.html | 13 +++++++---- docs/reference/print.mkinds.html | 13 +++++++---- docs/reference/print.mkinmod.html | 13 +++++++---- docs/reference/schaefer07_complex_case.html | 13 +++++++---- docs/reference/summary.mkinfit.html | 17 ++++++++------ docs/reference/synthetic_data_for_UBA.html | 13 +++++++---- docs/reference/transform_odeparms.html | 19 ++++++++------- docs/reference/unknown-10.png | Bin 18197 -> 0 bytes docs/reference/unknown-2.png | Bin 10552 -> 0 bytes docs/reference/unknown-4.png | Bin 10559 -> 0 bytes docs/reference/unknown-6.png | Bin 7945 -> 0 bytes docs/reference/unknown-8.png | Bin 13728 -> 0 bytes 43 files changed, 325 insertions(+), 191 deletions(-) delete mode 100644 docs/reference/unknown-10.png delete mode 100644 docs/reference/unknown-2.png delete mode 100644 docs/reference/unknown-4.png delete mode 100644 docs/reference/unknown-6.png delete mode 100644 docs/reference/unknown-8.png (limited to 'docs/reference') diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html index 7d036804..c0690f41 100644 --- a/docs/reference/DFOP.solution.html +++ b/docs/reference/DFOP.solution.html @@ -6,8 +6,7 @@ - - — DFOP.solution • mkin +Double First-Order in Parallel kinetics — DFOP.solution • mkin @@ -61,7 +60,12 @@ @@ -73,8 +77,7 @@
-

-

+

Double First-Order in Parallel kinetics

diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index cfe6329b..ad4614fb 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -60,7 +60,12 @@
@@ -188,7 +193,7 @@ #> #> $time #> user system elapsed -#> 0.316 0.000 0.317 +#> 0.264 0.000 0.262 #> #> $mkinmod #> <mkinmod> model generated with @@ -374,7 +379,7 @@ #> } #> return(mC) #> } -#> <environment: 0x5d4a3b0> +#> <environment: 0x50d32d0> #> #> $cost_notrans #> function (P) @@ -396,7 +401,7 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x5d4a3b0> +#> <environment: 0x50d32d0> #> #> $hessian_notrans #> parent_0 alpha beta @@ -462,7 +467,7 @@ #> 99.66619 #> #> $date -#> [1] "Fri Nov 4 15:36:31 2016" +#> [1] "Fri Nov 4 17:08:52 2016" #> #> attr(,"class") #> [1] "mkinfit" "modFit"
fits["SFO", "B"]
#> dataset @@ -541,7 +546,7 @@ #> #> $time #> user system elapsed -#> 0.076 0.000 0.077 +#> 0.068 0.000 0.067 #> #> $mkinmod #> <mkinmod> model generated with @@ -728,7 +733,7 @@ #> } #> return(mC) #> } -#> <environment: 0x5d98970> +#> <environment: 0x4f17408> #> #> $cost_notrans #> function (P) @@ -750,7 +755,7 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x5d98970> +#> <environment: 0x4f17408> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -813,7 +818,7 @@ #> 99.17407 #> #> $date -#> [1] "Fri Nov 4 15:36:30 2016" +#> [1] "Fri Nov 4 17:08:51 2016" #> #> attr(,"class") #> [1] "mkinfit" "modFit"
fits["SFO", "B", drop = TRUE]
#> [[1]] @@ -889,7 +894,7 @@ #> #> $time #> user system elapsed -#> 0.076 0.000 0.077 +#> 0.068 0.000 0.067 #> #> $mkinmod #> <mkinmod> model generated with @@ -1076,7 +1081,7 @@ #> } #> return(mC) #> } -#> <environment: 0x5d98970> +#> <environment: 0x4f17408> #> #> $cost_notrans #> function (P) @@ -1098,7 +1103,7 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x5d98970> +#> <environment: 0x4f17408> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -1161,7 +1166,7 @@ #> 99.17407 #> #> $date -#> [1] "Fri Nov 4 15:36:30 2016" +#> [1] "Fri Nov 4 17:08:51 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 97af2f9c..13dfa186 100644 --- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html +++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html @@ -6,8 +6,7 @@ - - — FOCUS_2006_DFOP_ref_A_to_B • mkin +Results of fitting the DFOP model to Datasets A to B of FOCUS (2006) — FOCUS_2006_DFOP_ref_A_to_B • mkin @@ -61,7 +60,12 @@
@@ -73,8 +77,7 @@
-

-

+

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

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 1487e2c9..5b36ac74 100644 --- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html @@ -6,8 +6,7 @@ - - — FOCUS_2006_FOMC_ref_A_to_F • mkin +Results of fitting the FOMC model to Datasets A to F of FOCUS (2006) — FOCUS_2006_FOMC_ref_A_to_F • mkin @@ -61,7 +60,12 @@
@@ -73,8 +77,7 @@
-

-

+

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

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 4571c175..446ce4d7 100644 --- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html @@ -6,8 +6,7 @@ - - — FOCUS_2006_HS_ref_A_to_F • mkin +Results of fitting the HS model to Datasets A to F of FOCUS (2006) — FOCUS_2006_HS_ref_A_to_F • mkin @@ -61,7 +60,12 @@
@@ -73,8 +77,7 @@
-

-

+

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

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 7003fa0e..db462f10 100644 --- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html @@ -6,8 +6,7 @@ - - — FOCUS_2006_SFO_ref_A_to_F • mkin +Results of fitting the SFO model to Datasets A to F of FOCUS (2006) — FOCUS_2006_SFO_ref_A_to_F • mkin @@ -61,7 +60,12 @@
@@ -73,8 +77,7 @@
-

-

+

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

diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html index 83edd323..ffc7558e 100644 --- a/docs/reference/FOCUS_2006_datasets.html +++ b/docs/reference/FOCUS_2006_datasets.html @@ -6,8 +6,7 @@ - - — FOCUS_2006_datasets • mkin +Datasets A to F from the FOCUS Kinetics report from 2006 — FOCUS_2006_datasets • mkin @@ -61,7 +60,12 @@
@@ -73,8 +77,7 @@
-

-

+

Datasets A to F from the FOCUS Kinetics report from 2006

diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html index 83bca886..fdbf0d1f 100644 --- a/docs/reference/FOMC.solution.html +++ b/docs/reference/FOMC.solution.html @@ -6,7 +6,7 @@ - First-Order Multi-Compartment kinetics — FOMC.solution • mkin +First-Order Multi-Compartment kinetics — FOMC.solution • mkin @@ -60,7 +60,12 @@
@@ -72,7 +77,7 @@
-

First-Order Multi-Compartment kinetics

+

First-Order Multi-Compartment kinetics

diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html index 13db29aa..fbe0b590 100644 --- a/docs/reference/HS.solution.html +++ b/docs/reference/HS.solution.html @@ -6,7 +6,7 @@ - Hockey-Stick kinetics — HS.solution • mkin +Hockey-Stick kinetics — HS.solution • mkin @@ -60,7 +60,12 @@
@@ -72,7 +77,7 @@
-

Hockey-Stick kinetics

+

Hockey-Stick kinetics

diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html index 56c2b48e..553c38b0 100644 --- a/docs/reference/IORE.solution.html +++ b/docs/reference/IORE.solution.html @@ -6,7 +6,7 @@ - Indeterminate order rate equation kinetics — IORE.solution • mkin +Indeterminate order rate equation kinetics — IORE.solution • mkin @@ -60,7 +60,12 @@
@@ -72,7 +77,7 @@
-

Indeterminate order rate equation kinetics

+

Indeterminate order rate equation kinetics

diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html index 8ff5b5ba..2ead8f24 100644 --- a/docs/reference/SFO.solution.html +++ b/docs/reference/SFO.solution.html @@ -6,7 +6,7 @@ - Single First-Order kinetics — SFO.solution • mkin +Single First-Order kinetics — SFO.solution • mkin @@ -60,7 +60,12 @@
@@ -72,7 +77,7 @@
-

Single First-Order kinetics

+

Single First-Order kinetics

diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html index 43b6028a..be425d83 100644 --- a/docs/reference/SFORB.solution.html +++ b/docs/reference/SFORB.solution.html @@ -6,7 +6,7 @@ - Single First-Order Reversible Binding kinetics — SFORB.solution • mkin +Single First-Order Reversible Binding kinetics — SFORB.solution • mkin @@ -60,7 +60,12 @@
@@ -72,7 +77,7 @@
-

Single First-Order Reversible Binding kinetics

+

Single First-Order Reversible Binding kinetics

diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html index 8e491bc9..0a126c5c 100644 --- a/docs/reference/add_err.html +++ b/docs/reference/add_err.html @@ -6,8 +6,7 @@ - - — add_err • mkin +Add normally distributed errors to simulated kinetic degradation data — add_err • mkin @@ -61,7 +60,12 @@
@@ -73,8 +77,7 @@
-

-

+

Add normally distributed errors to simulated kinetic degradation data

diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html index a3716060..44a8f4c4 100644 --- a/docs/reference/endpoints.html +++ b/docs/reference/endpoints.html @@ -6,8 +6,7 @@ - - — endpoints • mkin +Function to calculate endpoints for further use from kinetic models fitted with mkinfit — endpoints • mkin @@ -61,7 +60,12 @@
@@ -73,8 +77,7 @@
-

-

+

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

diff --git a/docs/reference/geometric_mean.html b/docs/reference/geometric_mean.html index 633e0865..97352ff8 100644 --- a/docs/reference/geometric_mean.html +++ b/docs/reference/geometric_mean.html @@ -6,7 +6,7 @@ - Calculate the geometric mean — geometric_mean • mkin +Calculate the geometric mean — geometric_mean • mkin @@ -60,7 +60,12 @@
@@ -72,7 +77,7 @@
-

Calculate the geometric mean

+

Calculate the geometric mean

diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html index 955b5c58..95fed72e 100644 --- a/docs/reference/ilr.html +++ b/docs/reference/ilr.html @@ -6,8 +6,7 @@ - - — ilr • mkin +Function to perform isometric log-ratio transformation — ilr • mkin @@ -61,7 +60,12 @@
@@ -73,8 +77,7 @@
-

-

+

Function to perform isometric log-ratio transformation

diff --git a/docs/reference/index.html b/docs/reference/index.html index b7d59a21..32455baa 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -60,7 +60,12 @@
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index d32acb5b..6eb4741b 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -6,8 +6,7 @@ - - — mccall81_245T • mkin +Datasets on aerobic soil metabolism of 2,4,5-T in six soils — mccall81_245T • mkin @@ -61,7 +60,12 @@ @@ -73,8 +77,7 @@
-

-

+

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

@@ -119,8 +122,8 @@ fixed_parms = "k_phenol_sink", quiet = TRUE) summary(fit.2, data = FALSE)
#> mkin version: 0.9.44.9000 #> R version: 3.3.2 -#> Date of fit: Fri Nov 4 15:36:38 2016 -#> Date of summary: Fri Nov 4 15:36:38 2016 +#> Date of fit: Fri Nov 4 17:08:59 2016 +#> Date of summary: Fri Nov 4 17:08:59 2016 #> #> Equations: #> d_T245 = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -130,7 +133,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 246 model solutions performed in 1.886 s +#> Fitted with method Port using 246 model solutions performed in 1.497 s #> #> Weighting: none #> diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html index 21a8a8f8..fa131a6d 100644 --- a/docs/reference/mkin_long_to_wide.html +++ b/docs/reference/mkin_long_to_wide.html @@ -6,8 +6,7 @@ - - — mkin_long_to_wide • mkin +Convert a dataframe from long to wide format — mkin_long_to_wide • mkin @@ -61,7 +60,12 @@
@@ -73,8 +77,7 @@
-

-

+

Convert a dataframe from long to wide format

diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html index fe6e47e4..077c0b7d 100644 --- a/docs/reference/mkin_wide_to_long.html +++ b/docs/reference/mkin_wide_to_long.html @@ -6,8 +6,7 @@ - - — mkin_wide_to_long • mkin +Convert a dataframe with observations over time into long format — mkin_wide_to_long • mkin @@ -61,7 +60,12 @@
@@ -73,8 +77,7 @@
-

-

+

Convert a dataframe with observations over time into long format

diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html index f5dd4c88..522aab33 100644 --- a/docs/reference/mkinds.html +++ b/docs/reference/mkinds.html @@ -60,7 +60,12 @@
diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html index 8d420165..d212e3b2 100644 --- a/docs/reference/mkinerrmin.html +++ b/docs/reference/mkinerrmin.html @@ -6,8 +6,7 @@ - - — mkinerrmin • mkin +Calculate the minimum error to assume in order to pass the variance test — mkinerrmin • mkin @@ -61,7 +60,12 @@ @@ -73,8 +77,7 @@
-

-

+

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

diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index b298d90a..93185eff 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -6,8 +6,7 @@ - - — mkinfit • mkin +Fit a kinetic model to data with one or more state variables — mkinfit • mkin @@ -61,7 +60,12 @@
@@ -73,8 +77,7 @@
-

-

+

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

@@ -356,8 +359,8 @@ fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE) summary(fit)
#> mkin version: 0.9.44.9000 #> R version: 3.3.2 -#> Date of fit: Fri Nov 4 15:36:41 2016 -#> Date of summary: Fri Nov 4 15:36:41 2016 +#> Date of fit: Fri Nov 4 17:09:01 2016 +#> Date of summary: Fri Nov 4 17:09:01 2016 #> #> Equations: #> d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent @@ -433,7 +436,7 @@ 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 -#> 1.244 1.208 0.933
coef(fit)
#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 1.256 1.216 0.946
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 7dba1b6d..f328c34a 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -6,8 +6,7 @@ - - — mkinmod • mkin +Function to set up a kinetic model with one or more state variables — mkinmod • mkin @@ -61,7 +60,12 @@
@@ -73,8 +77,7 @@
-

-

+

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

diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html index 923abc6d..764f1ab4 100644 --- a/docs/reference/mkinparplot.html +++ b/docs/reference/mkinparplot.html @@ -6,8 +6,8 @@ - - — mkinparplot • mkin +Function to plot the confidence intervals obtained using + list(list("mkinfit")) — mkinparplot • mkin @@ -61,7 +61,12 @@
@@ -73,8 +78,8 @@
-

-

+

Function to plot the confidence intervals obtained using + list(list("mkinfit"))

diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html index 5fe94a8a..921affdc 100644 --- a/docs/reference/mkinplot.html +++ b/docs/reference/mkinplot.html @@ -6,8 +6,7 @@ - - — mkinplot • mkin +Plot the observed data and the fitted model of an mkinfit object — mkinplot • mkin @@ -61,7 +60,12 @@
@@ -73,8 +77,7 @@
-

-

+

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

diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index f7eb950a..9f00dab7 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -6,8 +6,7 @@ - - — mkinpredict • mkin +Produce predictions from a kinetic model using specific parameters — mkinpredict • mkin @@ -61,7 +60,12 @@
@@ -73,8 +77,7 @@
-

-

+

Produce predictions from a kinetic model using specific parameters

@@ -272,7 +275,7 @@ 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 -#> 0.008 0.024 0.005
system.time( +#> 0.004 0.028 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 @@ -282,7 +285,7 @@ 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 0.037
+#> 0.052 0.000 0.052
@@ -73,8 +77,7 @@
-

-

+

Function to plot residuals stored in an mkin object

diff --git a/docs/reference/mkinsub.html b/docs/reference/mkinsub.html index 8424eaab..8bb2ce1c 100644 --- a/docs/reference/mkinsub.html +++ b/docs/reference/mkinsub.html @@ -6,8 +6,7 @@ - - — mkinsub • mkin +Function to set up a kinetic submodel for one state variable — mkinsub • mkin @@ -61,7 +60,12 @@
@@ -73,8 +77,7 @@
-

-

+

Function to set up a kinetic submodel for one state variable

diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index 5613a720..a21a980b 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -6,8 +6,7 @@ - - — mmkin • mkin +Fit one or more kinetic models with one or more state variables to one or more datasets — mmkin • mkin @@ -61,7 +60,12 @@
@@ -73,8 +77,7 @@
-

-

+

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

diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html index e7158180..52db9bc6 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -6,8 +6,7 @@ - - — plot.mkinfit • mkin +Plot the observed data and the fitted model of an mkinfit object — plot.mkinfit • mkin @@ -61,7 +60,12 @@
@@ -73,8 +77,7 @@
-

-

+

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

diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html index ef5c04b7..eac31273 100644 --- a/docs/reference/plot.mmkin.html +++ b/docs/reference/plot.mmkin.html @@ -6,8 +6,7 @@ - - — plot.mmkin • mkin +Plot model fits (observed and fitted) and the residuals for a row or column of an mmkin object — plot.mmkin • mkin @@ -61,7 +60,12 @@
@@ -73,8 +77,7 @@
-

-

+

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

diff --git a/docs/reference/print.mkinds.html b/docs/reference/print.mkinds.html index c578f4ee..9057114d 100644 --- a/docs/reference/print.mkinds.html +++ b/docs/reference/print.mkinds.html @@ -6,8 +6,7 @@ - - — print.mkinds • mkin +Print mkinds objects — print.mkinds • mkin @@ -61,7 +60,12 @@
@@ -73,8 +77,7 @@
-

-

+

Print mkinds objects

diff --git a/docs/reference/print.mkinmod.html b/docs/reference/print.mkinmod.html index 3f653971..2034ea10 100644 --- a/docs/reference/print.mkinmod.html +++ b/docs/reference/print.mkinmod.html @@ -6,8 +6,7 @@ - - — print.mkinmod • mkin +Print mkinmod objects — print.mkinmod • mkin @@ -61,7 +60,12 @@
@@ -73,8 +77,7 @@
-

-

+

Print mkinmod objects

diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html index c63ba490..e2f845d9 100644 --- a/docs/reference/schaefer07_complex_case.html +++ b/docs/reference/schaefer07_complex_case.html @@ -6,8 +6,7 @@ - - — schaefer07_complex_case • mkin +Metabolism data set used for checking the software quality of KinGUI — schaefer07_complex_case • mkin @@ -61,7 +60,12 @@
@@ -73,8 +77,7 @@
-

-

+

Metabolism data set used for checking the software quality of KinGUI

diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index 241964a7..f67bc1d1 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -6,8 +6,7 @@ - - — summary.mkinfit • mkin +Summary method for class "mkinfit" — summary.mkinfit • mkin @@ -61,7 +60,12 @@
@@ -73,8 +77,7 @@
-

-

+

Summary method for class "mkinfit"

@@ -139,8 +142,8 @@

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:     Fri Nov  4 15:36:49 2016 
-#> Date of summary: Fri Nov  4 15:36:49 2016 
+#> Date of fit:     Fri Nov  4 17:09:10 2016 
+#> Date of summary: Fri Nov  4 17:09:10 2016 
 #> 
 #> Equations:
 #> d_parent = - k_parent_sink * parent
diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html
index 333b3dbf..c6f29582 100644
--- a/docs/reference/synthetic_data_for_UBA.html
+++ b/docs/reference/synthetic_data_for_UBA.html
@@ -6,8 +6,7 @@
 
 
 
-
- — synthetic_data_for_UBA_2014 • mkin
+Synthetic datasets for one parent compound with two metabolites — synthetic_data_for_UBA_2014 • mkin
 
 
 
@@ -61,7 +60,12 @@
@@ -73,8 +77,7 @@
-

-

+

Synthetic datasets for one parent compound with two metabolites

diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index 5ee1e9cc..60208ff4 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -6,8 +6,7 @@ - - — transform_odeparms • mkin +Functions to transform and backtransform kinetic parameters for fitting — transform_odeparms • mkin @@ -61,7 +60,12 @@
@@ -73,8 +77,7 @@
-

-

+

Functions to transform and backtransform kinetic parameters for fitting

@@ -146,8 +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: 3.3.2 -#> Date of fit: Fri Nov 4 15:36:50 2016 -#> Date of summary: Fri Nov 4 15:36:50 2016 +#> Date of fit: Fri Nov 4 17:09:11 2016 +#> Date of summary: Fri Nov 4 17:09:11 2016 #> #> Equations: #> d_parent = - k_parent_sink * parent - k_parent_m1 * parent @@ -155,7 +158,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 153 model solutions performed in 0.663 s +#> Fitted with method Port using 153 model solutions performed in 0.638 s #> #> Weighting: none #> diff --git a/docs/reference/unknown-10.png b/docs/reference/unknown-10.png deleted file mode 100644 index 09bb687c..00000000 Binary files a/docs/reference/unknown-10.png and /dev/null differ diff --git a/docs/reference/unknown-2.png b/docs/reference/unknown-2.png deleted file mode 100644 index a26e413f..00000000 Binary files a/docs/reference/unknown-2.png and /dev/null differ diff --git a/docs/reference/unknown-4.png b/docs/reference/unknown-4.png deleted file mode 100644 index f23ed172..00000000 Binary files a/docs/reference/unknown-4.png and /dev/null differ diff --git a/docs/reference/unknown-6.png b/docs/reference/unknown-6.png deleted file mode 100644 index dc24d92f..00000000 Binary files a/docs/reference/unknown-6.png and /dev/null differ diff --git a/docs/reference/unknown-8.png b/docs/reference/unknown-8.png deleted file mode 100644 index e4ab674a..00000000 Binary files a/docs/reference/unknown-8.png and /dev/null differ -- cgit v1.2.1