From 6211f3ef4995657798686d8d4ab43ed9406e8a08 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 12 May 2020 16:34:00 +0200 Subject: Update vignettes and docs --- docs/reference/AIC.mmkin.html | 2 +- docs/reference/CAKE_export.html | 49 +++++----- docs/reference/DFOP.solution.html | 2 +- docs/reference/Extract.mmkin.html | 60 +++++++------ docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html | 48 +++++----- docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html | 48 +++++----- docs/reference/FOCUS_2006_HS_ref_A_to_F.html | 48 +++++----- docs/reference/FOCUS_2006_SFO_ref_A_to_F.html | 48 +++++----- docs/reference/FOCUS_2006_datasets.html | 48 +++++----- docs/reference/FOMC.solution.html | 2 +- docs/reference/HS.solution.html | 2 +- docs/reference/IORE.solution.html | 2 +- docs/reference/NAFTA_SOP_2015.html | 50 ++++++----- docs/reference/NAFTA_SOP_Attachment.html | 52 ++++++----- docs/reference/SFO.solution.html | 2 +- docs/reference/SFORB.solution.html | 2 +- docs/reference/aw.html | 48 +++++----- docs/reference/confint.mkinfit.html | 6 +- docs/reference/create_deg_func.html | 10 +-- docs/reference/experimental_data_for_UBA-1.png | Bin 92900 -> 107146 bytes docs/reference/experimental_data_for_UBA.html | 50 ++++++----- docs/reference/get_deg_func.html | 2 +- docs/reference/ilr.html | 2 +- docs/reference/loftest-3.png | Bin 65397 -> 78761 bytes docs/reference/loftest-4.png | Bin 64457 -> 76899 bytes docs/reference/loftest-5.png | Bin 63057 -> 75806 bytes docs/reference/loftest.html | 49 +++++----- docs/reference/logLik.mkinfit.html | 2 +- docs/reference/lrtest.mkinfit.html | 48 +++++----- docs/reference/max_twa_parent.html | 2 +- docs/reference/mkin_long_to_wide.html | 50 ++++++----- docs/reference/mkin_wide_to_long.html | 50 ++++++----- docs/reference/mkinds.html | 2 +- docs/reference/mkinerrmin.html | 50 ++++++----- docs/reference/mkinerrplot.html | 2 +- docs/reference/mkinfit.html | 26 +++--- docs/reference/mkinmod.html | 4 +- docs/reference/mkinparplot.html | 2 +- docs/reference/mkinplot.html | 49 +++++----- docs/reference/mkinpredict.html | 6 +- docs/reference/mkinresplot.html | 2 +- docs/reference/mkinsub.html | 50 ++++++----- docs/reference/mmkin.html | 6 +- docs/reference/nafta.html | 2 +- docs/reference/nlme.html | 2 +- docs/reference/nlme.mmkin.html | 4 +- docs/reference/nobs.mkinfit.html | 47 +++++----- docs/reference/parms.html | 48 +++++----- docs/reference/plot.mkinfit.html | 2 +- docs/reference/plot.mmkin.html | 2 +- docs/reference/plot.nafta.html | 52 +++++------ docs/reference/plot.nlme.mmkin.html | 2 +- docs/reference/print.mkinds.html | 46 +++++----- docs/reference/print.mkinmod.html | 47 +++++----- docs/reference/reexports.html | 47 +++++----- docs/reference/residuals.mkinfit.html | 47 +++++----- docs/reference/schaefer07_complex_case-1.png | Bin 55626 -> 67740 bytes docs/reference/schaefer07_complex_case.html | 63 ++++++------- docs/reference/sigma_twocomp.html | 2 +- docs/reference/summary.mkinfit.html | 10 +-- docs/reference/synthetic_data_for_UBA_2014-1.png | Bin 62550 -> 70430 bytes docs/reference/synthetic_data_for_UBA_2014.html | 93 ++++++++++--------- docs/reference/test_data_from_UBA_2014-1.png | Bin 52908 -> 59294 bytes docs/reference/test_data_from_UBA_2014-2.png | Bin 68111 -> 78194 bytes docs/reference/test_data_from_UBA_2014.html | 109 +++++++++++------------ docs/reference/transform_odeparms.html | 2 +- docs/reference/update.mkinfit.html | 49 +++++----- 67 files changed, 882 insertions(+), 777 deletions(-) (limited to 'docs/reference') diff --git a/docs/reference/AIC.mmkin.html b/docs/reference/AIC.mmkin.html index b91d40e3..3f474d56 100644 --- a/docs/reference/AIC.mmkin.html +++ b/docs/reference/AIC.mmkin.html @@ -73,7 +73,7 @@ same dataset." /> mkin - 0.9.50.1 + 0.9.50.2 diff --git a/docs/reference/CAKE_export.html b/docs/reference/CAKE_export.html index a4161abc..4e456651 100644 --- a/docs/reference/CAKE_export.html +++ b/docs/reference/CAKE_export.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -38,7 +42,6 @@ - @@ -56,7 +59,7 @@ specified as well." /> - +
@@ -114,7 +117,12 @@ specified as well." />
@@ -129,7 +137,7 @@ specified as well." />

Export a list of datasets format to a CAKE study file

- + Source: R/CAKE_export.R
@@ -221,15 +229,10 @@ compatible with CAKE.

The function is called for its side effect.

- @@ -240,7 +243,7 @@ compatible with CAKE.

-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 1.5.1.

diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html index e0094738..3c1fff89 100644 --- a/docs/reference/DFOP.solution.html +++ b/docs/reference/DFOP.solution.html @@ -73,7 +73,7 @@ two exponential decline functions." /> mkin - 0.9.50.1 + 0.9.50.2 diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 7273b5de..b7e8427e 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -37,7 +41,6 @@ - @@ -55,7 +58,7 @@ - +
@@ -113,7 +116,12 @@
@@ -128,7 +136,7 @@

Subsetting method for mmkin objects

- + Source: R/mmkin.R
@@ -176,16 +184,16 @@ either a list of mkinfit objects or a single mkinfit object.

cores = 1, quiet = TRUE) fits["FOMC", ]
#> dataset #> model B C -#> FOMC List,41 List,41 +#> FOMC List,39 List,39 #> attr(,"class") #> [1] "mmkin"
fits[, "B"]
#> dataset #> model B -#> SFO List,41 -#> FOMC List,41 +#> SFO List,39 +#> FOMC List,39 #> attr(,"class") #> [1] "mmkin"
fits["SFO", "B"]
#> dataset #> model B -#> SFO List,41 +#> SFO List,39 #> attr(,"class") #> [1] "mmkin"
head( @@ -206,23 +214,17 @@ either a list of mkinfit objects or a single mkinfit object.

#> #> $evaluations #> function gradient -#> 25 72 +#> 25 78 #> #> $message #> [1] "both X-convergence and relative convergence (5)" #>
- @@ -233,7 +235,7 @@ either a list of mkinfit objects or a single mkinfit object.

-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 1.5.1.

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 83d624bb..b2292604 100644 --- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html +++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -41,7 +45,6 @@ generated with different software packages. Taken directly from FOCUS (2006). The results from fitting the data with the Topfit software was removed, as the initial concentration of the parent compound was fixed to a value of 100 in this fit." /> - @@ -59,7 +62,7 @@ in this fit." /> - +
@@ -117,7 +120,12 @@ in this fit." />
@@ -149,7 +157,7 @@ in this fit.

Format

-

A data frame containing the following variables.

+

A data frame containing the following variables.

package

a factor giving the name of the software package

M0

The fitted initial concentration of the parent compound

f

The fitted f parameter

@@ -172,14 +180,10 @@ in this fit.

Examples

data(FOCUS_2006_DFOP_ref_A_to_B)
- @@ -190,7 +194,7 @@ in this fit.

-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 1.5.1.

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 75a0da96..71cfb721 100644 --- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -41,7 +45,6 @@ generated with different software packages. Taken directly from FOCUS (2006). The results from fitting the data with the Topfit software was removed, as the initial concentration of the parent compound was fixed to a value of 100 in this fit." /> - @@ -59,7 +62,7 @@ in this fit." /> - +
@@ -117,7 +120,12 @@ in this fit." />
@@ -149,7 +157,7 @@ in this fit.

Format

-

A data frame containing the following variables.

+

A data frame containing the following variables.

package

a factor giving the name of the software package

M0

The fitted initial concentration of the parent compound

alpha

The fitted alpha parameter

@@ -171,14 +179,10 @@ in this fit.

Examples

data(FOCUS_2006_FOMC_ref_A_to_F)
- @@ -189,7 +193,7 @@ in this fit.

-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 1.5.1.

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 d9d24bdf..21d778a8 100644 --- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -41,7 +45,6 @@ generated with different software packages. Taken directly from FOCUS (2006). The results from fitting the data with the Topfit software was removed, as the initial concentration of the parent compound was fixed to a value of 100 in this fit." /> - @@ -59,7 +62,7 @@ in this fit." /> - +
@@ -117,7 +120,12 @@ in this fit." />
@@ -149,7 +157,7 @@ in this fit.

Format

-

A data frame containing the following variables.

+

A data frame containing the following variables.

package

a factor giving the name of the software package

M0

The fitted initial concentration of the parent compound

tb

The fitted tb parameter

@@ -172,14 +180,10 @@ in this fit.

Examples

data(FOCUS_2006_HS_ref_A_to_F)
- @@ -190,7 +194,7 @@ in this fit.

-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 1.5.1.

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 8c0f5bc9..8d5a0c59 100644 --- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -41,7 +45,6 @@ generated with different software packages. Taken directly from FOCUS (2006). The results from fitting the data with the Topfit software was removed, as the initial concentration of the parent compound was fixed to a value of 100 in this fit." /> - @@ -59,7 +62,7 @@ in this fit." /> - +
@@ -117,7 +120,12 @@ in this fit." />
@@ -149,7 +157,7 @@ in this fit.

Format

-

A data frame containing the following variables.

+

A data frame containing the following variables.

package

a factor giving the name of the software package

M0

The fitted initial concentration of the parent compound

k

The fitted first-order degradation rate constant

@@ -170,14 +178,10 @@ in this fit.

Examples

data(FOCUS_2006_SFO_ref_A_to_F)
- @@ -188,7 +192,7 @@ in this fit.

-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 1.5.1.

diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html index 8ccf363e..51ea1ded 100644 --- a/docs/reference/FOCUS_2006_datasets.html +++ b/docs/reference/FOCUS_2006_datasets.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -37,7 +41,6 @@ - @@ -55,7 +58,7 @@ - +
@@ -113,7 +116,12 @@
@@ -146,7 +154,7 @@

Format

-

6 datasets with observations on the following variables.

+

6 datasets with observations on the following variables.

name

a factor containing the name of the observed variable

time

a numeric vector containing time points

value

a numeric vector containing concentrations in percent of applied radioactivity

@@ -173,14 +181,10 @@ #> 8 parent 91 3.9 #> 9 parent 119 0.6 - @@ -191,7 +195,7 @@
-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 1.5.1.

diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html index f8fbd2ba..a7236844 100644 --- a/docs/reference/FOMC.solution.html +++ b/docs/reference/FOMC.solution.html @@ -73,7 +73,7 @@ a decreasing rate constant." /> mkin - 0.9.50.1 + 0.9.50.2 diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html index 9404893c..2c4eebe3 100644 --- a/docs/reference/HS.solution.html +++ b/docs/reference/HS.solution.html @@ -73,7 +73,7 @@ between them." /> mkin - 0.9.50.1 + 0.9.50.2 diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html index 194d11aa..9c8df9b3 100644 --- a/docs/reference/IORE.solution.html +++ b/docs/reference/IORE.solution.html @@ -73,7 +73,7 @@ a concentration dependent rate constant." /> mkin - 0.9.50.1 + 0.9.50.2 diff --git a/docs/reference/NAFTA_SOP_2015.html b/docs/reference/NAFTA_SOP_2015.html index 5ad02bf9..97674400 100644 --- a/docs/reference/NAFTA_SOP_2015.html +++ b/docs/reference/NAFTA_SOP_2015.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -37,7 +41,6 @@ - @@ -55,7 +58,7 @@ - +
@@ -113,7 +116,12 @@
@@ -142,7 +150,7 @@

Format

-

2 datasets with observations on the following variables.

+

2 datasets with observations on the following variables.

name

a factor containing the name of the observed variable

time

a numeric vector containing time points

value

a numeric vector containing concentrations

@@ -198,16 +206,12 @@ #> DFOP 429 2380 841 #> #> Representative half-life: -#> [1] 841.41
plot(nafta_evaluation)
+#> [1] 841.41
plot(nafta_evaluation)
- @@ -218,7 +222,7 @@
-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 1.5.1.

diff --git a/docs/reference/NAFTA_SOP_Attachment.html b/docs/reference/NAFTA_SOP_Attachment.html index 110ccc86..99b9f8c3 100644 --- a/docs/reference/NAFTA_SOP_Attachment.html +++ b/docs/reference/NAFTA_SOP_Attachment.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -37,7 +41,6 @@ - @@ -55,7 +58,7 @@ - +
@@ -113,7 +116,12 @@
@@ -180,7 +188,7 @@ #> Estimate Pr(>t) Lower Upper #> parent_0 9.99e+01 1.41e-26 98.8116 101.0810 #> k1 2.67e-02 5.05e-06 0.0243 0.0295 -#> k2 2.86e-12 5.00e-01 0.0000 Inf +#> k2 2.17e-12 5.00e-01 0.0000 Inf #> g 6.47e-01 3.67e-06 0.6248 0.6677 #> sigma 1.27e+00 8.91e-06 0.8395 1.6929 #> @@ -189,19 +197,15 @@ #> DT50 DT90 DT50_rep #> SFO 67.7 2.25e+02 6.77e+01 #> IORE 58.2 1.07e+03 3.22e+02 -#> DFOP 55.5 4.42e+11 2.42e+11 +#> DFOP 55.5 5.83e+11 3.20e+11 #> #> Representative half-life: -#> [1] 321.51
plot(nafta_att_p5a)
+#> [1] 321.51
plot(nafta_att_p5a)
- @@ -212,7 +216,7 @@
-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 1.5.1.

diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html index b263f2f3..05332377 100644 --- a/docs/reference/SFO.solution.html +++ b/docs/reference/SFO.solution.html @@ -72,7 +72,7 @@ mkin - 0.9.50.1 + 0.9.50.2 diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html index 4ef85274..e4c84edd 100644 --- a/docs/reference/SFORB.solution.html +++ b/docs/reference/SFORB.solution.html @@ -76,7 +76,7 @@ and no substance in the bound fraction." /> mkin - 0.9.50.1 + 0.9.50.2 diff --git a/docs/reference/aw.html b/docs/reference/aw.html index 0b37847c..78f17958 100644 --- a/docs/reference/aw.html +++ b/docs/reference/aw.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -39,7 +43,6 @@ - @@ -57,7 +60,7 @@ by Burnham and Anderson (2004)." /> - +
@@ -115,7 +118,12 @@ by Burnham and Anderson (2004)." />
@@ -130,7 +138,7 @@ by Burnham and Anderson (2004)." />

Calculate Akaike weights for model averaging

- + Source: R/aw.R
@@ -181,14 +189,10 @@ Inference: Understanding AIC and BIC in Model Selection. aw(f)
#> [1] 0.4808722 0.1945539 0.3245740
sum(aw(f))
#> [1] 1
aw(f[c("SFO", "DFOP")])
#> [1] 0.5970258 0.4029742
# }
- @@ -199,7 +203,7 @@ Inference: Understanding AIC and BIC in Model Selection.
-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 1.5.1.

diff --git a/docs/reference/confint.mkinfit.html b/docs/reference/confint.mkinfit.html index 7658a572..190494bc 100644 --- a/docs/reference/confint.mkinfit.html +++ b/docs/reference/confint.mkinfit.html @@ -79,7 +79,7 @@ method of Venzon and Moolgavkar (1988)." /> mkin - 0.9.50.1 + 0.9.50.2 @@ -271,12 +271,12 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, use_of_ff = "max", quiet = TRUE) f_d_1 <- mkinfit(SFO_SFO, subset(FOCUS_2006_D, value != 0), quiet = TRUE) system.time(ci_profile <- confint(f_d_1, method = "profile", cores = 1, quiet = TRUE))
#> User System verstrichen -#> 3.362 0.000 3.364
# Using more cores does not save much time here, as parent_0 takes up most of the time +#> 3.410 0.000 3.412
# Using more cores does not save much time here, as parent_0 takes up most of the time # If we additionally exclude parent_0 (the confidence of which is often of # minor interest), we get a nice performance improvement from about 50 # seconds to about 12 seconds if we use at least four cores system.time(ci_profile_no_parent_0 <- confint(f_d_1, method = "profile", - c("k_parent_sink", "k_parent_m1", "k_m1_sink", "sigma"), cores = n_cores))
#> Profiling the likelihood
#> Warning: scheduled cores 1, 2, 3 encountered errors in user code, all values of the jobs will be affected
#> Error in dimnames(x) <- dn: Länge von 'dimnames' [2] ungleich der Arrayausdehnung
#> Timing stopped at: 0.011 0.045 0.201
ci_profile
#> 2.5% 97.5% + c("k_parent_sink", "k_parent_m1", "k_m1_sink", "sigma"), cores = n_cores))
#> Profiling the likelihood
#> Warning: scheduled cores 1, 2, 3 encountered errors in user code, all values of the jobs will be affected
#> Error in dimnames(x) <- dn: Länge von 'dimnames' [2] ungleich der Arrayausdehnung
#> Timing stopped at: 0.008 0.044 0.201
ci_profile
#> 2.5% 97.5% #> parent_0 96.456003640 1.027703e+02 #> k_parent 0.090911032 1.071578e-01 #> k_m1 0.003892605 6.702778e-03 diff --git a/docs/reference/create_deg_func.html b/docs/reference/create_deg_func.html index 6d05e811..1a6da920 100644 --- a/docs/reference/create_deg_func.html +++ b/docs/reference/create_deg_func.html @@ -72,7 +72,7 @@ mkin - 0.9.50 + 0.9.50.2
@@ -176,8 +176,8 @@ analytical = mkinfit(SFO_SFO, FOCUS_D, solution_type = "analytical", quiet = TRUE), deSolve = mkinfit(SFO_SFO, FOCUS_D, solution_type = "deSolve", quiet = TRUE), replications = 2)
#> Lade nötiges Paket: rbenchmark
#> test replications elapsed relative user.self sys.self user.child -#> 1 analytical 2 0.395 1.000 0.393 0.002 0 -#> 2 deSolve 2 0.693 1.754 0.692 0.000 0 +#> 1 analytical 2 0.410 1.000 0.410 0.000 0 +#> 2 deSolve 2 0.704 1.717 0.703 0.001 0 #> sys.child #> 1 0 #> 2 0
DFOP_SFO <- mkinmod( @@ -186,8 +186,8 @@ analytical = mkinfit(DFOP_SFO, FOCUS_D, solution_type = "analytical", quiet = TRUE), deSolve = mkinfit(DFOP_SFO, FOCUS_D, solution_type = "deSolve", quiet = TRUE), replications = 2)
#> test replications elapsed relative user.self sys.self user.child -#> 1 analytical 2 0.870 1.000 0.870 0 0 -#> 2 deSolve 2 1.678 1.929 1.677 0 0 +#> 1 analytical 2 0.894 1.000 0.894 0.000 0 +#> 2 deSolve 2 1.717 1.921 1.716 0.001 0 #> sys.child #> 1 0 #> 2 0
# } diff --git a/docs/reference/experimental_data_for_UBA-1.png b/docs/reference/experimental_data_for_UBA-1.png index d3880fea..6c225daa 100644 Binary files a/docs/reference/experimental_data_for_UBA-1.png and b/docs/reference/experimental_data_for_UBA-1.png differ diff --git a/docs/reference/experimental_data_for_UBA.html b/docs/reference/experimental_data_for_UBA.html index 18e11261..b9670390 100644 --- a/docs/reference/experimental_data_for_UBA.html +++ b/docs/reference/experimental_data_for_UBA.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -65,7 +69,6 @@ Dataset 11 is from the Renewal Assessment Report (RAR) for 2,4-D to one half of the LOD reported to be 1% AR. Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl (United Kingdom, 2014, p. 81)." /> - @@ -83,7 +86,7 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl - +
@@ -141,7 +144,12 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl
@@ -198,7 +206,7 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl

Format

A list containing twelve datasets as an R6 class defined by mkinds, - each containing, among others, the following components

+ each containing, among others, the following components

title

The name of the dataset, e.g. Soil 1

data

A data frame with the data in the form expected by mkinfit

@@ -257,17 +265,13 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl f_1_2_tc <- mmkin(list("DFOP-SFO-SFO" = dfop_sfo_sfo), d_1_2, error_model = "tc") -plot(f_1_2_tc, resplot = "errmod")
+plot(f_1_2_tc, resplot = "errmod")
# }
- @@ -278,7 +282,7 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl
-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 1.5.1.

diff --git a/docs/reference/get_deg_func.html b/docs/reference/get_deg_func.html index 598a25c0..812b25d7 100644 --- a/docs/reference/get_deg_func.html +++ b/docs/reference/get_deg_func.html @@ -72,7 +72,7 @@ mkin - 0.9.50.1 + 0.9.50.2 diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html index 8410e499..30be0a73 100644 --- a/docs/reference/ilr.html +++ b/docs/reference/ilr.html @@ -73,7 +73,7 @@ transformations." /> mkin - 0.9.50.1 + 0.9.50.2 diff --git a/docs/reference/loftest-3.png b/docs/reference/loftest-3.png index ecc4c3ee..39fca72d 100644 Binary files a/docs/reference/loftest-3.png and b/docs/reference/loftest-3.png differ diff --git a/docs/reference/loftest-4.png b/docs/reference/loftest-4.png index da86d97f..e2b8ac5c 100644 Binary files a/docs/reference/loftest-4.png and b/docs/reference/loftest-4.png differ diff --git a/docs/reference/loftest-5.png b/docs/reference/loftest-5.png index 54b176e7..a4d9fd48 100644 Binary files a/docs/reference/loftest-5.png and b/docs/reference/loftest-5.png differ diff --git a/docs/reference/loftest.html b/docs/reference/loftest.html index 7d4df9f5..bc9ec146 100644 --- a/docs/reference/loftest.html +++ b/docs/reference/loftest.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -40,7 +44,6 @@ objects. It fits an anova model to the data contained in the object and compares the likelihoods using the likelihood ratio test lrtest.default from the lmtest package." /> - @@ -58,7 +61,7 @@ lrtest.default from the lmtest package." /> - +
@@ -116,7 +119,12 @@ lrtest.default from the lmtest package." />
@@ -131,7 +139,7 @@ lrtest.default from the lmtest package." />

Lack-of-fit test for models fitted to data with replicates

- + Source: R/loftest.R
@@ -309,15 +317,10 @@ of replicate samples.

#>
# }
- @@ -328,7 +331,7 @@ of replicate samples.

-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 1.5.1.

diff --git a/docs/reference/logLik.mkinfit.html b/docs/reference/logLik.mkinfit.html index 8e33c28f..22561d8a 100644 --- a/docs/reference/logLik.mkinfit.html +++ b/docs/reference/logLik.mkinfit.html @@ -76,7 +76,7 @@ the error model." /> mkin - 0.9.50.1 + 0.9.50.2 diff --git a/docs/reference/lrtest.mkinfit.html b/docs/reference/lrtest.mkinfit.html index 6861b747..433b0a8b 100644 --- a/docs/reference/lrtest.mkinfit.html +++ b/docs/reference/lrtest.mkinfit.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -41,7 +45,6 @@ mkinfit objects are given as arguments, it is checked if they have been fitted to the same data. It is the responsibility of the user to make sure that the models are nested, i.e. one of them has less degrees of freedom and can be expressed by fixing the parameters of the other." /> - @@ -59,7 +62,7 @@ and can be expressed by fixing the parameters of the other." /> - +
@@ -117,7 +120,12 @@ and can be expressed by fixing the parameters of the other." />
@@ -132,7 +140,7 @@ and can be expressed by fixing the parameters of the other." />

Likelihood ratio test for mkinfit models

- + Source: R/lrtest.mkinfit.R
@@ -225,14 +233,10 @@ lower number of fitted parameters (null hypothesis).

#> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
# }
- @@ -243,7 +247,7 @@ lower number of fitted parameters (null hypothesis).

-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 1.5.1.

diff --git a/docs/reference/max_twa_parent.html b/docs/reference/max_twa_parent.html index b8ce5397..ada54cba 100644 --- a/docs/reference/max_twa_parent.html +++ b/docs/reference/max_twa_parent.html @@ -78,7 +78,7 @@ soil section of the FOCUS guidance." /> mkin - 0.9.50.1 + 0.9.50.2 diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html index bb7c263a..7f3e7949 100644 --- a/docs/reference/mkin_long_to_wide.html +++ b/docs/reference/mkin_long_to_wide.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -39,7 +43,6 @@ - @@ -57,7 +60,7 @@ variable and several dependent variables as columns." /> - +
@@ -115,7 +118,12 @@ variable and several dependent variables as columns." />
@@ -130,7 +138,7 @@ variable and several dependent variables as columns." />

Convert a dataframe from long to wide format

- + Source: R/mkin_long_to_wide.R
@@ -193,16 +201,10 @@ observed values called "value".

#> 22 120 NA 33.31
- @@ -213,7 +215,7 @@ observed values called "value".

-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 1.5.1.

diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html index 523d45e1..a232688c 100644 --- a/docs/reference/mkin_wide_to_long.html +++ b/docs/reference/mkin_wide_to_long.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -39,7 +43,6 @@ - @@ -57,7 +60,7 @@ mkinfit." /> - +
@@ -115,7 +118,12 @@ mkinfit." />
@@ -130,7 +138,7 @@ mkinfit." />

Convert a dataframe with observations over time into long format

- + Source: R/mkin_wide_to_long.R
@@ -173,16 +181,10 @@ column of observed values.

#> 6 y 3 5
- @@ -193,7 +195,7 @@ column of observed values.

-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 1.5.1.

diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html index 778c5132..2e52a95d 100644 --- a/docs/reference/mkinds.html +++ b/docs/reference/mkinds.html @@ -75,7 +75,7 @@ provided by this package come as mkinds objects nevertheless." /> mkin - 0.9.49.11 + 0.9.50.2 diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html index 1a31bc60..10daee93 100644 --- a/docs/reference/mkinerrmin.html +++ b/docs/reference/mkinerrmin.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -38,7 +42,6 @@ - @@ -56,7 +59,7 @@ the chi-squared test as defined in the FOCUS kinetics report from 2006." /> - +
@@ -114,7 +117,12 @@ the chi-squared test as defined in the FOCUS kinetics report from 2006." />
@@ -129,7 +137,7 @@ the chi-squared test as defined in the FOCUS kinetics report from 2006." />

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

- + Source: R/mkinerrmin.R
@@ -193,16 +201,10 @@ Document Reference Sanco/10058/2005 version 2.0, 434 pp,
- @@ -213,7 +215,7 @@ Document Reference Sanco/10058/2005 version 2.0, 434 pp,
-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 1.5.1.

diff --git a/docs/reference/mkinerrplot.html b/docs/reference/mkinerrplot.html index 7e5a00f2..c2be5abf 100644 --- a/docs/reference/mkinerrplot.html +++ b/docs/reference/mkinerrplot.html @@ -76,7 +76,7 @@ using the argument show_errplot = TRUE." /> mkin - 0.9.50.1 + 0.9.50.2 diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 5d8dd81c..54ca377f 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -422,8 +422,8 @@ Degradation Data. Environments 6(12) 124 fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE) summary(fit)
#> mkin version used for fitting: 0.9.50.2 #> R version used for fitting: 4.0.0 -#> Date of fit: Tue May 12 10:55:39 2020 -#> Date of summary: Tue May 12 10:55:39 2020 +#> Date of fit: Tue May 12 15:29:48 2020 +#> Date of summary: Tue May 12 15:29:48 2020 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent @@ -507,7 +507,7 @@ Degradation Data. Environments 6(12) 124 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 -#> 0.408 0.001 0.410
parms(fit)
#> parent_0 k_parent k_m1 f_parent_to_m1 sigma +#> 0.417 0.000 0.417
parms(fit)
#> parent_0 k_parent k_m1 f_parent_to_m1 sigma #> 99.598483222 0.098697734 0.005260651 0.514475962 3.125503875
endpoints(fit)
#> $ff #> parent_m1 parent_sink #> 0.514476 0.485524 @@ -597,7 +597,7 @@ Degradation Data. Environments 6(12) 124 #> Sum of squared residuals at call 166: 371.2134 #> Sum of squared residuals at call 168: 371.2134 #> Negative log-likelihood at call 178: 97.22429
#> Optimisation successfully terminated.
#> User System verstrichen -#> 0.353 0.000 0.352
parms(fit.deSolve)
#> parent_0 k_parent k_m1 f_parent_to_m1 sigma +#> 0.363 0.001 0.364
parms(fit.deSolve)
#> parent_0 k_parent k_m1 f_parent_to_m1 sigma #> 99.598480759 0.098697739 0.005260651 0.514475958 3.125503874
endpoints(fit.deSolve)
#> $ff #> parent_m1 parent_sink #> 0.514476 0.485524 @@ -631,8 +631,8 @@ Degradation Data. Environments 6(12) 124 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: 0.9.50.2 #> R version used for fitting: 4.0.0 -#> Date of fit: Tue May 12 10:55:44 2020 -#> Date of summary: Tue May 12 10:55:44 2020 +#> Date of fit: Tue May 12 15:29:53 2020 +#> Date of summary: Tue May 12 15:29:53 2020 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -640,7 +640,7 @@ Degradation Data. Environments 6(12) 124 #> #> Model predictions using solution type analytical #> -#> Fitted using 421 model solutions performed in 0.147 s +#> Fitted using 421 model solutions performed in 0.13 s #> #> Error model: Constant variance #> @@ -753,8 +753,8 @@ Degradation Data. Environments 6(12) 124 #> 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: 0.9.50.2 #> R version used for fitting: 4.0.0 -#> Date of fit: Tue May 12 10:55:44 2020 -#> Date of summary: Tue May 12 10:55:44 2020 +#> Date of fit: Tue May 12 15:29:53 2020 +#> Date of summary: Tue May 12 15:29:53 2020 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -762,7 +762,7 @@ Degradation Data. Environments 6(12) 124 #> #> Model predictions using solution type analytical #> -#> Fitted using 978 model solutions performed in 0.334 s +#> Fitted using 978 model solutions performed in 0.337 s #> #> Error model: Variance unique to each observed variable #> @@ -890,8 +890,8 @@ Degradation Data. Environments 6(12) 124 #> 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: 0.9.50.2 #> R version used for fitting: 4.0.0 -#> Date of fit: Tue May 12 10:55:45 2020 -#> Date of summary: Tue May 12 10:55:45 2020 +#> Date of fit: Tue May 12 15:29:54 2020 +#> Date of summary: Tue May 12 15:29:54 2020 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -899,7 +899,7 @@ Degradation Data. Environments 6(12) 124 #> #> Model predictions using solution type analytical #> -#> Fitted using 1875 model solutions performed in 0.643 s +#> Fitted using 1875 model solutions performed in 0.645 s #> #> Error model: Two-component variance function #> diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index 1c97048e..79b21d33 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -75,7 +75,7 @@ list of lists can be given in the speclist argument." /> mkin - 0.9.50.1 + 0.9.50.2
@@ -255,7 +255,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media

SFO_SFO <- mkinmod( parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"), verbose = TRUE)
#> Compilation argument: -#> /usr/lib/R/bin/R CMD SHLIB file15d32c282a7d.c 2> file15d32c282a7d.c.err.txt +#> /usr/lib/R/bin/R CMD SHLIB file61b4ce789c7.c 2> file61b4ce789c7.c.err.txt #> Program source: #> 1: #include <R.h> #> 2: diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html index dfe695d0..4ff4970e 100644 --- a/docs/reference/mkinparplot.html +++ b/docs/reference/mkinparplot.html @@ -73,7 +73,7 @@ mkinfit." /> mkin - 0.9.50.1 + 0.9.50.2
diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html index d078e239..166e6b1a 100644 --- a/docs/reference/mkinplot.html +++ b/docs/reference/mkinplot.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -38,7 +42,6 @@ - @@ -56,7 +59,7 @@ plot.mkinfit." /> - +
@@ -114,7 +117,12 @@ plot.mkinfit." />
@@ -129,7 +137,7 @@ plot.mkinfit." />

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

- + Source: R/plot.mkinfit.R
@@ -158,15 +166,10 @@ plot.mkinfit." />

The function is called for its side effect.

- @@ -177,7 +180,7 @@ plot.mkinfit." />
-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 1.5.1.

diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 3035e03e..89f48a09 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -396,11 +396,11 @@ solver is used.

c(k_parent = 0.15, f_parent_to_m1 = 0.5, k_m1 = 0.01), c(parent = 100, m1 = 0), seq(0, 20, by = 0.1), solution_type = "analytical", use_compiled = FALSE)[201,]) -}
#> Lade nötiges Paket: rbenchmark
#> test relative elapsed +}
#> test relative elapsed +#> 2 deSolve_compiled 1.0 0.005 #> 4 analytical 1.0 0.005 -#> 2 deSolve_compiled 1.2 0.006 #> 1 eigen 4.0 0.020 -#> 3 deSolve 43.8 0.219
+#> 3 deSolve 43.6 0.218
# \dontrun{ # Predict from a fitted model f <- mkinfit(SFO_SFO, FOCUS_2006_C, quiet = TRUE) diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html index cd6bf4a1..82afe2e2 100644 --- a/docs/reference/mkinresplot.html +++ b/docs/reference/mkinresplot.html @@ -75,7 +75,7 @@ argument show_residuals = TRUE." /> mkin - 0.9.50.1 + 0.9.50.2
diff --git a/docs/reference/mkinsub.html b/docs/reference/mkinsub.html index b3be7c2c..ac1220e0 100644 --- a/docs/reference/mkinsub.html +++ b/docs/reference/mkinsub.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -38,7 +42,6 @@ - @@ -56,7 +59,7 @@ mkinmod." /> - +
@@ -114,7 +117,12 @@ mkinmod." />
@@ -129,7 +137,7 @@ mkinmod." />

Function to set up a kinetic submodel for one state variable

- + Source: R/mkinsub.R
@@ -188,16 +196,10 @@ results on other operating systems or system configurations.

m1 = mkinsub("SFO", full_name = "Metabolite M1"))
#> Successfully compiled differential equation model from auto-generated C code.
# }
- @@ -208,7 +210,7 @@ results on other operating systems or system configurations.

-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 1.5.1.

diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index db359f48..3be3b4b9 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -75,7 +75,7 @@ datasets specified in its first two arguments." /> mkin - 0.9.50.1 + 0.9.50.2 @@ -216,8 +216,8 @@ plotting.

time_1 <- system.time(fits.4 <- mmkin(models, datasets, cores = 1, quiet = TRUE))
#> Warning: Optimisation did not converge: #> false convergence (8)
time_default
#> User System verstrichen -#> 4.370 0.401 1.265
time_1
#> User System verstrichen -#> 5.000 0.008 5.011
+#> 4.520 0.374 1.284
time_1
#> User System verstrichen +#> 5.076 0.004 5.083
endpoints(fits.0[["SFO_lin", 2]])
#> $ff #> parent_M1 parent_sink M1_M2 M1_sink #> 0.7340478 0.2659522 0.7505691 0.2494309 diff --git a/docs/reference/nafta.html b/docs/reference/nafta.html index 02c44737..34cce546 100644 --- a/docs/reference/nafta.html +++ b/docs/reference/nafta.html @@ -76,7 +76,7 @@ order of increasing model complexity, i.e. SFO, then IORE, and finally DFOP." /> mkin - 0.9.50.1 + 0.9.50.2
diff --git a/docs/reference/nlme.html b/docs/reference/nlme.html index 78489ee7..8ef7e7c9 100644 --- a/docs/reference/nlme.html +++ b/docs/reference/nlme.html @@ -75,7 +75,7 @@ datasets." /> mkin - 0.9.50.1 + 0.9.50.2 diff --git a/docs/reference/nlme.mmkin.html b/docs/reference/nlme.mmkin.html index 4e5a86cb..928ee378 100644 --- a/docs/reference/nlme.mmkin.html +++ b/docs/reference/nlme.mmkin.html @@ -74,7 +74,7 @@ have been obtained by fitting the same model to a list of datasets." /> mkin - 0.9.50.1 + 0.9.50.2 @@ -181,7 +181,7 @@ have been obtained by fitting the same model to a list of datasets.

data -

Should the data be printed?

+

Ignored, data are taken from the mmkin model

fixed diff --git a/docs/reference/nobs.mkinfit.html b/docs/reference/nobs.mkinfit.html index 1bd97732..55eb6a3f 100644 --- a/docs/reference/nobs.mkinfit.html +++ b/docs/reference/nobs.mkinfit.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -37,7 +41,6 @@ - @@ -55,7 +58,7 @@ - +
@@ -113,7 +116,12 @@
@@ -128,7 +136,7 @@

Number of observations on which an mkinfit object was fitted

- + Source: R/nobs.mkinfit.R
@@ -157,13 +165,10 @@

The number of rows in the data included in the mkinfit object

- @@ -174,7 +179,7 @@
-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 1.5.1.

diff --git a/docs/reference/parms.html b/docs/reference/parms.html index 2162fdc0..f62b3898 100644 --- a/docs/reference/parms.html +++ b/docs/reference/parms.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -39,7 +43,6 @@ - @@ -57,7 +60,7 @@ considering the error structure that was assumed for the fit." /> - +
@@ -115,7 +118,12 @@ considering the error structure that was assumed for the fit." />
@@ -130,7 +138,7 @@ considering the error structure that was assumed for the fit." />

Extract model parameters from mkinfit models

- + Source: R/parms.mkinfit.R
@@ -184,14 +192,10 @@ as used internally during the optimisation?

#> 82.4921598 0.3060633 4.6730124
parms(fit, transformed = TRUE)
#> parent_0 log_k_parent_sink sigma #> 82.492160 -1.183963 4.673012
- @@ -202,7 +206,7 @@ as used internally during the optimisation?

-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 1.5.1.

diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html index 284c30a6..f78ccf73 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -74,7 +74,7 @@ observed data together with the solution of the fitted model." /> mkin - 0.9.50.1 + 0.9.50.2 diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html index 4b893032..6c9f2449 100644 --- a/docs/reference/plot.mmkin.html +++ b/docs/reference/plot.mmkin.html @@ -76,7 +76,7 @@ the fit of at least one model to the same dataset is shown." /> mkin - 0.9.50.1 + 0.9.50.2 diff --git a/docs/reference/plot.nafta.html b/docs/reference/plot.nafta.html index 294a79a4..17a80aa2 100644 --- a/docs/reference/plot.nafta.html +++ b/docs/reference/plot.nafta.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -38,7 +42,6 @@ - @@ -56,7 +59,7 @@ function (SFO, then IORE, then DFOP)." /> - +
@@ -114,7 +117,12 @@ function (SFO, then IORE, then DFOP)." />
@@ -129,7 +137,7 @@ function (SFO, then IORE, then DFOP)." />

Plot the results of the three models used in the NAFTA scheme.

- + Source: R/nafta.R
@@ -139,7 +147,7 @@ function (SFO, then IORE, then DFOP).

# S3 method for nafta
-plot(x, legend = FALSE, main = "auto", ...)
+plot(x, legend = FALSE, main = "auto", ...)

Arguments

@@ -170,16 +178,10 @@ function (SFO, then IORE, then DFOP).

Calls plot.mmkin.

- @@ -190,7 +192,7 @@ function (SFO, then IORE, then DFOP).

-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 1.5.1.

diff --git a/docs/reference/plot.nlme.mmkin.html b/docs/reference/plot.nlme.mmkin.html index 9c85fbf0..17ec06cf 100644 --- a/docs/reference/plot.nlme.mmkin.html +++ b/docs/reference/plot.nlme.mmkin.html @@ -72,7 +72,7 @@ mkin - 0.9.50.1 + 0.9.50.2 diff --git a/docs/reference/print.mkinds.html b/docs/reference/print.mkinds.html index 824d961b..af85c78f 100644 --- a/docs/reference/print.mkinds.html +++ b/docs/reference/print.mkinds.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -37,7 +41,6 @@ - @@ -55,7 +58,7 @@ - +
@@ -113,7 +116,12 @@
@@ -128,7 +136,7 @@

Print mkinds objects

- + Source: R/mkinds.R
@@ -154,12 +162,10 @@
- @@ -170,7 +176,7 @@
-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 1.5.1.

diff --git a/docs/reference/print.mkinmod.html b/docs/reference/print.mkinmod.html index 03e73e29..6622decf 100644 --- a/docs/reference/print.mkinmod.html +++ b/docs/reference/print.mkinmod.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -38,7 +42,6 @@ - @@ -56,7 +59,7 @@ components." /> - +
@@ -114,7 +117,12 @@ components." />
@@ -129,7 +137,7 @@ components." />

Print mkinmod objects

- + Source: R/mkinmod.R
@@ -177,13 +185,10 @@ components.

#> d_M2/dt = + f_M1_to_M2 * k_M1 * M1 - k_M2 * M2
- @@ -194,7 +199,7 @@ components.

-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 1.5.1.

diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html index 90cbec1a..8a886c63 100644 --- a/docs/reference/reexports.html +++ b/docs/reference/reexports.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,6 @@ below to see their documentation. lmtestlrtest " /> - @@ -60,7 +63,7 @@ below to see their documentation. - +
@@ -118,7 +121,12 @@ below to see their documentation.
@@ -133,14 +141,14 @@ below to see their documentation.

Objects exported from other packages

- + Source: R/lrtest.mkinfit.R

These objects are imported from other packages. Follow the links below to see their documentation.

-
+
lmtest

lrtest

@@ -150,11 +158,10 @@ below to see their documentation.

- @@ -165,7 +172,7 @@ below to see their documentation.

-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 1.5.1.

diff --git a/docs/reference/residuals.mkinfit.html b/docs/reference/residuals.mkinfit.html index 96b02908..0933cd7b 100644 --- a/docs/reference/residuals.mkinfit.html +++ b/docs/reference/residuals.mkinfit.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -37,7 +41,6 @@ - @@ -55,7 +58,7 @@ - +
@@ -113,7 +116,12 @@
@@ -128,7 +136,7 @@

Extract residuals from an mkinfit model

- + Source: R/residuals.mkinfit.R
@@ -164,13 +172,10 @@ standard deviation obtained from the fitted error model?

#> [7] -0.03269102 1.45347805 -0.88423710
residuals(f, standardized = TRUE)
#> [1] 0.13969820 -0.19981894 -0.22048777 1.05407086 -0.12434027 -1.33869248 #> [7] -0.04695387 2.08761953 -1.27002305
- @@ -181,7 +186,7 @@ standard deviation obtained from the fitted error model?

-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 1.5.1.

diff --git a/docs/reference/schaefer07_complex_case-1.png b/docs/reference/schaefer07_complex_case-1.png index 34356613..40a1ed45 100644 Binary files a/docs/reference/schaefer07_complex_case-1.png and b/docs/reference/schaefer07_complex_case-1.png differ diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html index 27b19430..dcecc9b5 100644 --- a/docs/reference/schaefer07_complex_case.html +++ b/docs/reference/schaefer07_complex_case.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -39,7 +43,6 @@ - @@ -57,7 +60,7 @@ - +
@@ -115,7 +118,12 @@
@@ -145,7 +153,7 @@

Format

-

The data set is a data frame with 8 observations on the following 6 variables.

+

The data set is a data frame with 8 observations on the following 6 variables.

time

a numeric vector

parent

a numeric vector

A1

a numeric vector

@@ -170,20 +178,17 @@ C1 = list(type = "SFO"), A2 = list(type = "SFO"), use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.
# \dontrun{ fit <- mkinfit(model, data, quiet = TRUE) - plot(fit)
endpoints(fit)
#> $ff + plot(fit)
endpoints(fit)
#> $ff #> parent_A1 parent_B1 parent_C1 parent_sink A1_A2 A1_sink -#> 0.3809619 0.1954667 0.4235714 0.0000000 0.4479620 0.5520380 -#> -#> $SFORB -#> logical(0) +#> 0.3809618 0.1954667 0.4235715 0.0000000 0.4479625 0.5520375 #> #> $distimes #> DT50 DT90 #> parent 13.95078 46.34350 -#> A1 49.75344 165.27737 -#> B1 37.26907 123.80517 -#> C1 11.23131 37.30960 -#> A2 28.50627 94.69577 +#> A1 49.75346 165.27741 +#> B1 37.26904 123.80508 +#> C1 11.23130 37.30958 +#> A2 28.50628 94.69580 #>
# } # Compare with the results obtained in the original publication print(schaefer07_complex_results)
#> compound parameter KinGUI ModelMaker deviation @@ -202,14 +207,10 @@ #> 13 metabolite A2 degradation rate 0.0245 0.0244 0.4 #> 14 metabolite A2 DT50 28.2400 28.4500 0.7
- @@ -220,7 +221,7 @@
-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 1.5.1.

diff --git a/docs/reference/sigma_twocomp.html b/docs/reference/sigma_twocomp.html index 76e2eb8f..1e1f5798 100644 --- a/docs/reference/sigma_twocomp.html +++ b/docs/reference/sigma_twocomp.html @@ -73,7 +73,7 @@ dependence of the measured value \(y\):" /> mkin - 0.9.50.1 + 0.9.50.2 diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index 84e65787..55ce22cf 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -76,7 +76,7 @@ values." /> mkin - 0.9.50.1 + 0.9.50.2 @@ -229,17 +229,17 @@ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,

Examples


-  summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
#> mkin version used for fitting:    0.9.50.1 
+  summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
#> mkin version used for fitting:    0.9.50.2 
 #> R version used for fitting:       4.0.0 
-#> Date of fit:     Tue May 12 08:07:03 2020 
-#> Date of summary: Tue May 12 08:07:03 2020 
+#> Date of fit:     Tue May 12 15:31:20 2020 
+#> Date of summary: Tue May 12 15:31:20 2020 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted using 131 model solutions performed in 0.026 s
+#> Fitted using 131 model solutions performed in 0.027 s
 #> 
 #> Error model: Constant variance 
 #> 
diff --git a/docs/reference/synthetic_data_for_UBA_2014-1.png b/docs/reference/synthetic_data_for_UBA_2014-1.png
index 201ef0fd..02976ced 100644
Binary files a/docs/reference/synthetic_data_for_UBA_2014-1.png and b/docs/reference/synthetic_data_for_UBA_2014-1.png differ
diff --git a/docs/reference/synthetic_data_for_UBA_2014.html b/docs/reference/synthetic_data_for_UBA_2014.html
index 6ac7403a..17d2f973 100644
--- a/docs/reference/synthetic_data_for_UBA_2014.html
+++ b/docs/reference/synthetic_data_for_UBA_2014.html
@@ -10,23 +10,27 @@
 
 
 
-
+
 
 
-
+
 
-
+
+
+
+
+
 
 
-
-
+
+
 
 
-
+
 
 
-
-
+
+
 
 
 
@@ -52,7 +56,6 @@ Initial concentrations for metabolites and all values where adding the variance
 As an example, the first dataset has the title SFO_lin_a and is based on the SFO model
  with two sequential metabolites (linear pathway), with added variance component 'a'.
 Compare also the code in the example section to see the degradation models." />
-
 
 
 
@@ -70,7 +73,7 @@ Compare also the code in the example section to see the degradation models." />
 
   
 
-  
+  
     

       

       
 
@@ -128,7 +131,12 @@ Compare also the code in the example section to see the degradation models." />
 
       
       
       
     

@@ -172,7 +180,7 @@ Compare also the code in the example section to see the degradation models." />
     
Format

 
     
A list containing twelve datasets as an R6 class defined by mkinds,
-  each containing, among others, the following components

+  each containing, among others, the following components

     
title
The name of the dataset, e.g. SFO_lin_a

     
data
A data frame with the data in the form expected by mkinfit

   
@@ -280,10 +288,10 @@ Compare also the code in the example section to see the degradation models." />
 # the generation of the data
   fit <- mkinfit(m_synth_SFO_lin, synthetic_data_for_UBA_2014[[1]]$data,
                  quiet = TRUE)
-  plot_sep(fit)
  summary(fit)
#> mkin version used for fitting:    0.9.49.6 
-#> R version used for fitting:       3.6.1 
-#> Date of fit:     Fri Nov  1 10:10:17 2019 
-#> Date of summary: Fri Nov  1 10:10:17 2019 
+  plot_sep(fit)
  summary(fit)
#> mkin version used for fitting:    0.9.50.2 
+#> R version used for fitting:       4.0.0 
+#> Date of fit:     Tue May 12 15:31:29 2020 
+#> Date of summary: Tue May 12 15:31:29 2020 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -292,7 +300,7 @@ Compare also the code in the example section to see the degradation models." />
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted using 847 model solutions performed in 2.468 s
+#> Fitted using 819 model solutions performed in 0.619 s
 #> 
 #> Error model: Constant variance 
 #> 
@@ -321,6 +329,11 @@ Compare also the code in the example section to see the degradation models." />
 #> M1_0     0 state
 #> M2_0     0 state
 #> 
+#> Results:
+#> 
+#>        AIC      BIC    logLik
+#>   188.7274 200.3723 -87.36368
+#> 
 #> Optimised, transformed parameters with symmetric confidence intervals:
 #>                Estimate Std. Error   Lower    Upper
 #> parent_0       102.1000    1.57000 98.8600 105.3000
@@ -339,15 +352,15 @@ Compare also the code in the example section to see the degradation models." />
 #> log_k_M2        2.819e-02    7.166e-02 -3.929e-01  1.000e+00     -2.658e-01
 #> f_parent_ilr_1 -4.624e-01   -5.682e-01  7.478e-01 -2.658e-01      1.000e+00
 #> f_M1_ilr_1      1.614e-01    4.102e-01 -8.109e-01  5.419e-01     -8.605e-01
-#> sigma          -3.704e-09   -1.104e-08  5.922e-08 -3.673e-08      5.867e-08
+#> sigma           1.285e-07    1.054e-07 -1.671e-07  3.644e-08     -2.503e-07
 #>                f_M1_ilr_1      sigma
-#> parent_0        1.614e-01 -3.704e-09
-#> log_k_parent    4.102e-01 -1.104e-08
-#> log_k_M1       -8.109e-01  5.922e-08
-#> log_k_M2        5.419e-01 -3.673e-08
-#> f_parent_ilr_1 -8.605e-01  5.867e-08
-#> f_M1_ilr_1      1.000e+00 -8.075e-08
-#> sigma          -8.075e-08  1.000e+00
+#> parent_0        1.614e-01  1.285e-07
+#> log_k_parent    4.102e-01  1.054e-07
+#> log_k_M1       -8.109e-01 -1.671e-07
+#> log_k_M2        5.419e-01  3.644e-08
+#> f_parent_ilr_1 -8.605e-01 -2.503e-07
+#> f_M1_ilr_1      1.000e+00  2.636e-07
+#> sigma           2.636e-07  1.000e+00
 #> 
 #> Backtransformed parameters:
 #> Confidence intervals for internally transformed parameters are asymmetric.
@@ -384,8 +397,8 @@ Compare also the code in the example section to see the degradation models." />
 #> 
 #> Data:
 #>  time variable observed  predicted residual
-#>     0   parent    101.5  1.021e+02 -0.56248
-#>     0   parent    101.2  1.021e+02 -0.86248
+#>     0   parent    101.5  1.021e+02 -0.56249
+#>     0   parent    101.2  1.021e+02 -0.86249
 #>     1   parent     53.9  4.873e+01  5.17118
 #>     1   parent     47.5  4.873e+01 -1.22882
 #>     3   parent     10.4  1.111e+01 -0.70773
@@ -394,8 +407,8 @@ Compare also the code in the example section to see the degradation models." />
 #>     7   parent      0.3  5.772e-01 -0.27717
 #>    14   parent      3.5  3.264e-03  3.49674
 #>    28   parent      3.2  1.045e-07  3.20000
-#>    90   parent      0.6 -1.875e-11  0.60000
-#>   120   parent      3.5 -2.805e-11  3.50000
+#>    90   parent      0.6  9.531e-10  0.60000
+#>   120   parent      3.5 -5.940e-10  3.50000
 #>     1       M1     36.4  3.479e+01  1.61088
 #>     1       M1     37.4  3.479e+01  2.61088
 #>     3       M1     34.3  3.937e+01 -5.07027
@@ -405,9 +418,9 @@ Compare also the code in the example section to see the degradation models." />
 #>    14       M1      5.8  1.995e+00  3.80469
 #>    14       M1      1.2  1.995e+00 -0.79531
 #>    60       M1      0.5  2.111e-06  0.50000
-#>    90       M1      3.2  2.913e-10  3.20000
-#>   120       M1      1.5  3.625e-11  1.50000
-#>   120       M1      0.6  3.625e-11  0.60000
+#>    90       M1      3.2 -9.670e-10  3.20000
+#>   120       M1      1.5  7.670e-10  1.50000
+#>   120       M1      0.6  7.670e-10  0.60000
 #>     1       M2      4.8  4.455e+00  0.34517
 #>     3       M2     20.9  2.153e+01 -0.62527
 #>     3       M2     19.3  2.153e+01 -2.22527
@@ -425,14 +438,10 @@ Compare also the code in the example section to see the degradation models." />
 #>   120       M2      3.3  5.521e+00 -2.22107
# }
- @@ -443,7 +452,7 @@ Compare also the code in the example section to see the degradation models." />
-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 1.5.1.

diff --git a/docs/reference/test_data_from_UBA_2014-1.png b/docs/reference/test_data_from_UBA_2014-1.png index 51b38eda..431181cf 100644 Binary files a/docs/reference/test_data_from_UBA_2014-1.png and b/docs/reference/test_data_from_UBA_2014-1.png differ diff --git a/docs/reference/test_data_from_UBA_2014-2.png b/docs/reference/test_data_from_UBA_2014-2.png index a40f7553..4a064163 100644 Binary files a/docs/reference/test_data_from_UBA_2014-2.png and b/docs/reference/test_data_from_UBA_2014-2.png differ diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html index 0040c331..237149a5 100644 --- a/docs/reference/test_data_from_UBA_2014.html +++ b/docs/reference/test_data_from_UBA_2014.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -38,7 +42,6 @@ - @@ -56,7 +59,7 @@ - +
@@ -114,7 +117,12 @@
@@ -144,7 +152,7 @@

Format

A list containing three datasets as an R6 class defined by mkinds. - Each dataset has, among others, the following components

+ Each dataset has, among others, the following components

title

The name of the dataset, e.g. UBA_2014_WS_river

data

A data frame with the data in the form expected by mkinfit

@@ -165,23 +173,16 @@ # model). m_ws <- mkinmod(parent_w = mkinsub("SFO", "parent_s"), parent_s = mkinsub("SFO", "parent_w"))
#> Successfully compiled differential equation model from auto-generated C code.
f_river <- mkinfit(m_ws, test_data_from_UBA_2014[[1]]$data, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
plot_sep(f_river)
- summary(f_river)$bpar
#> Estimate se_notrans t value Pr(>t) -#> parent_w_0 9.598567e+01 2.12351789 4.520126e+01 9.476190e-18 -#> k_parent_w_sink 3.603743e-01 0.03149282 1.144306e+01 4.126593e-09 -#> k_parent_w_parent_s 6.031371e-02 0.01603582 3.761186e+00 9.436275e-04 -#> k_parent_s_sink 5.108964e-11 0.09482736 5.387647e-10 5.000000e-01 -#> k_parent_s_parent_w 7.419672e-02 0.10737376 6.910135e-01 2.500560e-01 -#> sigma 2.982879e+00 0.50545649 5.901356e+00 1.454535e-05 -#> Lower Upper -#> parent_w_0 91.48420503 100.4871438 -#> k_parent_w_sink 0.30668904 0.4234571 -#> k_parent_w_parent_s 0.03423904 0.1062455 -#> k_parent_s_sink 0.00000000 Inf -#> k_parent_s_parent_w 0.02289956 0.2404043 -#> sigma 2.00184022 3.9639169
mkinerrmin(f_river)
#> err.min n.optim df -#> All data 0.09246946 5 6 -#> parent_w 0.06377096 3 3 -#> parent_s 0.20882325 2 3
+ summary(f_river)$bpar
#> Warning: Could not calculate correlation; no covariance matrix
#> Estimate se_notrans t value Pr(>t) Lower Upper +#> parent_w_0 95.91998116 NA NA NA NA NA +#> k_parent_w 0.41145375 NA NA NA NA NA +#> k_parent_s 0.04663944 NA NA NA NA NA +#> f_parent_w_to_parent_s 0.12467894 NA NA NA NA NA +#> f_parent_s_to_parent_w 0.50000000 NA NA NA NA NA +#> sigma 3.13612618 NA NA NA NA NA
mkinerrmin(f_river)
#> err.min n.optim df +#> All data 0.1090929 5 6 +#> parent_w 0.0817436 3 3 +#> parent_s 0.1619965 2 3
# This is the evaluation used for the validation of software packages # in the expertise from 2014 m_soil <- mkinmod(parent = mkinsub("SFO", c("M1", "M2")), @@ -190,42 +191,38 @@ M3 = mkinsub("SFO"), use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.
f_soil <- mkinfit(m_soil, test_data_from_UBA_2014[[3]]$data, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
plot_sep(f_soil, lpos = c("topright", "topright", "topright", "bottomright"))
summary(f_soil)$bpar
#> Estimate se_notrans t value Pr(>t) Lower -#> parent_0 76.55425584 0.859186619 89.1008474 1.113866e-26 74.755959756 -#> k_parent 0.12081956 0.004601922 26.2541544 1.077373e-16 0.111561582 -#> k_M1 0.84258649 0.806231419 1.0450926 1.545475e-01 0.113839803 -#> k_M2 0.04210878 0.017083049 2.4649453 1.170195e-02 0.018013807 -#> k_M3 0.01122919 0.007245890 1.5497322 6.885127e-02 0.002909463 -#> f_parent_to_M1 0.32240199 0.240803555 1.3388589 9.820820e-02 NA -#> f_parent_to_M2 0.16099854 0.033691991 4.7785403 6.531224e-05 NA -#> f_M1_to_M3 0.27921501 0.269443514 1.0362655 1.565440e-01 0.022992937 -#> f_M2_to_M3 0.55641331 0.595125445 0.9349513 1.807725e-01 0.008003317 +#> parent_0 76.55425585 0.859186419 89.1008682 1.113862e-26 74.755958727 +#> k_parent 0.12081956 0.004601919 26.2541704 1.077361e-16 0.111561576 +#> k_M1 0.84258631 0.806165101 1.0451783 1.545282e-01 0.113778787 +#> k_M2 0.04210878 0.017083048 2.4649453 1.170195e-02 0.018013823 +#> k_M3 0.01122919 0.007245869 1.5497365 6.885076e-02 0.002909418 +#> f_parent_to_M1 0.32240194 0.240785506 1.3389591 9.819219e-02 NA +#> f_parent_to_M2 0.16099854 0.033691990 4.7785405 6.531222e-05 NA +#> f_M1_to_M3 0.27921506 0.269425556 1.0363347 1.565282e-01 0.022977927 +#> f_M2_to_M3 0.55641328 0.595121733 0.9349571 1.807710e-01 0.008002321 #> sigma 1.14005399 0.149696423 7.6157731 1.727024e-07 0.826735778 #> Upper -#> parent_0 78.35255192 +#> parent_0 78.35255298 #> k_parent 0.13084582 -#> k_M1 6.23641265 -#> k_M2 0.09843279 -#> k_M3 0.04333950 +#> k_M1 6.23975442 +#> k_M2 0.09843270 +#> k_M3 0.04334016 #> f_parent_to_M1 NA #> f_parent_to_M2 NA -#> f_M1_to_M3 0.86443083 -#> f_M2_to_M3 0.99489847 +#> f_M1_to_M3 0.86450919 +#> f_M2_to_M3 0.99489910 #> sigma 1.45337221
mkinerrmin(f_soil)
#> err.min n.optim df #> All data 0.09649963 9 20 #> parent 0.04721283 2 6 -#> M1 0.26551209 2 5 +#> M1 0.26551208 2 5 #> M2 0.20327575 2 5 -#> M3 0.05196549 3 4
# } +#> M3 0.05196550 3 4
# }
- @@ -236,7 +233,7 @@
-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 1.5.1.

diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index 185a8a64..61ed96d7 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -245,7 +245,7 @@ This is no problem for the internal use in mkinfit< #> sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.8549
# \dontrun{ # Compare to the version without transforming rate parameters -fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
#> Error in if (cost < cost.current) { assign("cost.current", cost, inherits = TRUE) if (!quiet) cat(ifelse(OLS, "Sum of squared residuals", "Negative log-likelihood"), " at call ", calls, ": ", cost.current, "\n", sep = "")}: Fehlender Wert, wo TRUE/FALSE nötig ist
#> Timing stopped at: 0.002 0 0.003
fit.2.s <- summary(fit.2)
#> Error in summary(fit.2): Objekt 'fit.2' nicht gefunden
print(fit.2.s$par, 3)
#> Error in print(fit.2.s$par, 3): Objekt 'fit.2.s' nicht gefunden
print(fit.2.s$bpar, 3)
#> Error in print(fit.2.s$bpar, 3): Objekt 'fit.2.s' nicht gefunden
# } +fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
#> Error in if (cost < cost.current) { assign("cost.current", cost, inherits = TRUE) if (!quiet) cat(ifelse(OLS, "Sum of squared residuals", "Negative log-likelihood"), " at call ", calls, ": ", cost.current, "\n", sep = "")}: Fehlender Wert, wo TRUE/FALSE nötig ist
#> Timing stopped at: 0.003 0 0.003
fit.2.s <- summary(fit.2)
#> Error in summary(fit.2): Objekt 'fit.2' nicht gefunden
print(fit.2.s$par, 3)
#> Error in print(fit.2.s$par, 3): Objekt 'fit.2.s' nicht gefunden
print(fit.2.s$bpar, 3)
#> Error in print(fit.2.s$bpar, 3): Objekt 'fit.2.s' nicht gefunden
# } initials <- fit$start$value names(initials) <- rownames(fit$start) diff --git a/docs/reference/update.mkinfit.html b/docs/reference/update.mkinfit.html index bb93a61e..f958fc14 100644 --- a/docs/reference/update.mkinfit.html +++ b/docs/reference/update.mkinfit.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -40,7 +44,6 @@ model parameters from the old fit are used as starting values for the updated fit. Values specified as 'parms.ini' and/or 'state.ini' will override these starting values." /> - @@ -58,7 +61,7 @@ override these starting values." /> - +
@@ -116,7 +119,12 @@ override these starting values." />
@@ -131,7 +139,7 @@ override these starting values." />

Update an mkinfit model with different arguments

- + Source: R/update.mkinfit.R
@@ -169,18 +177,15 @@ remove arguments given in the original call

# \dontrun{
 fit <- mkinfit("SFO", subset(FOCUS_2006_D, value != 0), quiet = TRUE)
 parms(fit)
#>      parent_0 k_parent_sink         sigma 
-#>   99.44423886    0.09793574    3.39632469 
plot_err(fit)
fit_2 <- update(fit, error_model = "tc")
+#>   99.44423885    0.09793574    3.39632469 
plot_err(fit)
fit_2 <- update(fit, error_model = "tc")
 parms(fit_2)
#>      parent_0 k_parent_sink     sigma_low      rsd_high 
 #>  1.008549e+02  1.005665e-01  3.752222e-03  6.763434e-02 
plot_err(fit_2)
# }
- @@ -191,7 +196,7 @@ remove arguments given in the original call

-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 1.5.1.

-- cgit v1.2.1