From 5a21dc4016b0208264e22e6a7e36af62397c13b6 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 30 Jun 2022 10:29:05 +0200 Subject: Remove stray sentence from vignette, update docs --- docs/reference/Rplot001.png | Bin 27711 -> 1011 bytes docs/reference/Rplot002.png | Bin 59119 -> 17010 bytes docs/reference/Rplot003.png | Bin 59152 -> 48687 bytes docs/reference/Rplot004.png | Bin 60094 -> 58906 bytes docs/reference/Rplot005.png | Bin 19451 -> 22787 bytes docs/reference/create_deg_func.html | 8 ++++---- docs/reference/dimethenamid_2018-3.png | Bin 245058 -> 247960 bytes docs/reference/dimethenamid_2018.html | 8 ++++---- docs/reference/nlme.mmkin-1.png | Bin 124929 -> 124053 bytes docs/reference/nlme.mmkin-2.png | Bin 169786 -> 168550 bytes docs/reference/nlme.mmkin-3.png | Bin 173135 -> 172051 bytes docs/reference/plot.mkinfit.html | 5 ++++- docs/reference/saem-4.png | Bin 174097 -> 171244 bytes docs/reference/saem.html | 8 ++++---- docs/reference/summary.nlme.mmkin.html | 12 ++++++------ 15 files changed, 22 insertions(+), 19 deletions(-) (limited to 'docs/reference') diff --git a/docs/reference/Rplot001.png b/docs/reference/Rplot001.png index fa5f3834..17a35806 100644 Binary files a/docs/reference/Rplot001.png and b/docs/reference/Rplot001.png differ diff --git a/docs/reference/Rplot002.png b/docs/reference/Rplot002.png index 3caf465f..f06a860e 100644 Binary files a/docs/reference/Rplot002.png and b/docs/reference/Rplot002.png differ diff --git a/docs/reference/Rplot003.png b/docs/reference/Rplot003.png index 88ebd2d4..f8bf10bb 100644 Binary files a/docs/reference/Rplot003.png and b/docs/reference/Rplot003.png differ diff --git a/docs/reference/Rplot004.png b/docs/reference/Rplot004.png index 7e87d63d..12d337a4 100644 Binary files a/docs/reference/Rplot004.png and b/docs/reference/Rplot004.png differ diff --git a/docs/reference/Rplot005.png b/docs/reference/Rplot005.png index 76f25647..cb419daa 100644 Binary files a/docs/reference/Rplot005.png and b/docs/reference/Rplot005.png differ diff --git a/docs/reference/create_deg_func.html b/docs/reference/create_deg_func.html index 2516edff..1c70a094 100644 --- a/docs/reference/create_deg_func.html +++ b/docs/reference/create_deg_func.html @@ -120,8 +120,8 @@ replications = 2) #> Loading required package: rbenchmark #> test replications elapsed relative user.self sys.self user.child -#> 1 analytical 2 0.394 1.000 0.393 0 0 -#> 2 deSolve 2 0.678 1.721 0.677 0 0 +#> 1 analytical 2 0.401 1.00 0.401 0.000 0 +#> 2 deSolve 2 1.211 3.02 1.210 0.002 0 #> sys.child #> 1 0 #> 2 0 @@ -134,8 +134,8 @@ 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 0.829 1.000 0.829 0 0 -#> 2 deSolve 2 1.559 1.881 1.559 0 0 +#> 1 analytical 2 0.84 1.000 0.839 0.001 0 +#> 2 deSolve 2 3.19 3.798 3.188 0.001 0 #> sys.child #> 1 0 #> 2 0 diff --git a/docs/reference/dimethenamid_2018-3.png b/docs/reference/dimethenamid_2018-3.png index efb89bdb..7c876208 100644 Binary files a/docs/reference/dimethenamid_2018-3.png and b/docs/reference/dimethenamid_2018-3.png differ diff --git a/docs/reference/dimethenamid_2018.html b/docs/reference/dimethenamid_2018.html index d2ed8647..e913fa27 100644 --- a/docs/reference/dimethenamid_2018.html +++ b/docs/reference/dimethenamid_2018.html @@ -202,9 +202,9 @@ specific pieces of information in the comments.

summary(f_dmta_saem_tc) #> saemix version used for fitting: 3.0 #> mkin version used for pre-fitting: 1.1.0 -#> R version used for fitting: 4.1.3 -#> Date of fit: Sat Apr 9 18:03:34 2022 -#> Date of summary: Sat Apr 9 18:03:34 2022 +#> R version used for fitting: 4.2.1 +#> Date of fit: Thu Jun 30 10:21:01 2022 +#> Date of summary: Thu Jun 30 10:21:01 2022 #> #> Equations: #> d_DMTA/dt = - k_DMTA * DMTA @@ -217,7 +217,7 @@ specific pieces of information in the comments.

#> #> Model predictions using solution type deSolve #> -#> Fitted in 787.836 s +#> Fitted in 1845.619 s #> Using 300, 100 iterations and 9 chains #> #> Variance model: Two-component variance function diff --git a/docs/reference/nlme.mmkin-1.png b/docs/reference/nlme.mmkin-1.png index d93b0950..45e4eebe 100644 Binary files a/docs/reference/nlme.mmkin-1.png and b/docs/reference/nlme.mmkin-1.png differ diff --git a/docs/reference/nlme.mmkin-2.png b/docs/reference/nlme.mmkin-2.png index 5afccfbb..b9a68e92 100644 Binary files a/docs/reference/nlme.mmkin-2.png and b/docs/reference/nlme.mmkin-2.png differ diff --git a/docs/reference/nlme.mmkin-3.png b/docs/reference/nlme.mmkin-3.png index bf3aac6c..2a724bed 100644 Binary files a/docs/reference/nlme.mmkin-3.png and b/docs/reference/nlme.mmkin-3.png differ diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html index 4c2ff570..b74d1e7b 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -155,7 +155,8 @@ variables in the model.

xlim

Plot range in x direction.

ylim
-

Plot range in y direction.

+

Plot range in y direction. If given as a list, plot ranges +for the different plot rows can be given for row layout.

col_obs

Colors used for plotting the observed data and the corresponding model prediction lines.

@@ -237,7 +238,9 @@ latex is being used for the formatting of the chi2 error level, if m1 = mkinsub("SFO", full = "Metabolite M1" )) #> Temporary DLL for differentials generated and loaded fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE) +#> Warning: Observations with value of zero were removed from the data fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE, error_model = "tc") +#> Warning: Observations with value of zero were removed from the data plot(fit) plot_res(fit) diff --git a/docs/reference/saem-4.png b/docs/reference/saem-4.png index 5f65ba2e..bb775c25 100644 Binary files a/docs/reference/saem-4.png and b/docs/reference/saem-4.png differ diff --git a/docs/reference/saem.html b/docs/reference/saem.html index cc597665..f9e6565f 100644 --- a/docs/reference/saem.html +++ b/docs/reference/saem.html @@ -303,9 +303,9 @@ using mmkin.

summary(f_saem_dfop_sfo, data = TRUE) #> saemix version used for fitting: 3.0 #> mkin version used for pre-fitting: 1.1.0 -#> R version used for fitting: 4.1.2 -#> Date of fit: Mon Mar 7 13:15:26 2022 -#> Date of summary: Mon Mar 7 13:15:26 2022 +#> R version used for fitting: 4.2.1 +#> Date of fit: Thu Jun 30 10:23:53 2022 +#> Date of summary: Thu Jun 30 10:23:53 2022 #> #> Equations: #> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -320,7 +320,7 @@ using mmkin.

#> #> Model predictions using solution type analytical #> -#> Fitted in 8.741 s +#> Fitted in 8.85 s #> Using 300, 100 iterations and 10 chains #> #> Variance model: Constant variance diff --git a/docs/reference/summary.nlme.mmkin.html b/docs/reference/summary.nlme.mmkin.html index 3f98bec7..4879269e 100644 --- a/docs/reference/summary.nlme.mmkin.html +++ b/docs/reference/summary.nlme.mmkin.html @@ -96,7 +96,7 @@ endpoints such as formation fractions and DT50 values. Optionally 
# S3 method for nlme.mmkin
-summary(
+summary(
   object,
   data = FALSE,
   verbose = FALSE,
@@ -201,12 +201,12 @@ José Pinheiro and Douglas Bates for the components inherited from nlme

 #> iteration limit reached without convergence (10)
 f_nlme <- nlme(f_mmkin)
 #> Warning: Iteration 4, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)
-summary(f_nlme, data = TRUE)
+summary(f_nlme, data = TRUE)
 #> nlme version used for fitting:      3.1.155 
 #> mkin version used for pre-fitting:  1.1.0 
-#> R version used for fitting:         4.1.3 
-#> Date of fit:     Mon Mar 14 08:58:29 2022 
-#> Date of summary: Mon Mar 14 08:58:29 2022 
+#> R version used for fitting:         4.2.1 
+#> Date of fit:     Thu Jun 30 10:23:57 2022 
+#> Date of summary: Thu Jun 30 10:23:57 2022 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -216,7 +216,7 @@ José Pinheiro and Douglas Bates for the components inherited from nlme

 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted in 0.527 s using 4 iterations
+#> Fitted in 0.538 s using 4 iterations
 #> 
 #> Variance model: Two-component variance function 
 #> 
-- 
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