From 4f62f39b8979cb3a5c52d65d425e530dc0770665 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <johannes.ranke@jrwb.de>
Date: Sun, 16 Feb 2025 17:27:18 +0100
Subject: Fix solution type "deSolve" for a special case

The special case occurs if not observed data for time zero
are available. Fixes #16. Write NEWS and update docs.

A lot of html was regenerated, because I had checked out
the main branch in between, which made pkgdown believe that
I have changed the help files.
---
 docs/dev/articles/prebuilt/2022_cyan_pathway.html | 71 +++++++++++------------
 1 file changed, 34 insertions(+), 37 deletions(-)

(limited to 'docs/dev/articles/prebuilt/2022_cyan_pathway.html')

diff --git a/docs/dev/articles/prebuilt/2022_cyan_pathway.html b/docs/dev/articles/prebuilt/2022_cyan_pathway.html
index b93e5e7e..0a37915d 100644
--- a/docs/dev/articles/prebuilt/2022_cyan_pathway.html
+++ b/docs/dev/articles/prebuilt/2022_cyan_pathway.html
@@ -85,7 +85,7 @@
 Ranke</h4>
             
             <h4 data-toc-skip class="date">Last change on 13 February
-2023, last compiled on 14 Februar 2025</h4>
+2023, last compiled on 16 Februar 2025</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/prebuilt/2022_cyan_pathway.rmd" class="external-link"><code>vignettes/prebuilt/2022_cyan_pathway.rmd</code></a></small>
       <div class="d-none name"><code>2022_cyan_pathway.rmd</code></div>
@@ -2254,7 +2254,7 @@ saemix version used for fitting:      3.3
 mkin version used for pre-fitting:  1.2.10 
 R version used for fitting:         4.4.2 
 Date of fit:     Fri Feb 14 07:42:26 2025 
-Date of summary: Fri Feb 14 08:12:55 2025 
+Date of summary: Sun Feb 16 17:03:40 2025 
 
 Equations:
 d_cyan/dt = - k_cyan * cyan
@@ -2382,7 +2382,7 @@ saemix version used for fitting:      3.3
 mkin version used for pre-fitting:  1.2.10 
 R version used for fitting:         4.4.2 
 Date of fit:     Fri Feb 14 07:42:06 2025 
-Date of summary: Fri Feb 14 08:12:55 2025 
+Date of summary: Sun Feb 16 17:03:40 2025 
 
 Equations:
 d_cyan/dt = - k_cyan * cyan
@@ -2512,7 +2512,7 @@ saemix version used for fitting:      3.3
 mkin version used for pre-fitting:  1.2.10 
 R version used for fitting:         4.4.2 
 Date of fit:     Fri Feb 14 07:42:57 2025 
-Date of summary: Fri Feb 14 08:12:55 2025 
+Date of summary: Sun Feb 16 17:03:40 2025 
 
 Equations:
 d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan
@@ -2657,7 +2657,7 @@ saemix version used for fitting:      3.3
 mkin version used for pre-fitting:  1.2.10 
 R version used for fitting:         4.4.2 
 Date of fit:     Fri Feb 14 07:42:50 2025 
-Date of summary: Fri Feb 14 08:12:55 2025 
+Date of summary: Sun Feb 16 17:03:40 2025 
 
 Equations:
 d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan
@@ -2795,7 +2795,7 @@ saemix version used for fitting:      3.3
 mkin version used for pre-fitting:  1.2.10 
 R version used for fitting:         4.4.2 
 Date of fit:     Fri Feb 14 07:43:33 2025 
-Date of summary: Fri Feb 14 08:12:55 2025 
+Date of summary: Sun Feb 16 17:03:40 2025 
 
 Equations:
 d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -2941,7 +2941,7 @@ saemix version used for fitting:      3.3
 mkin version used for pre-fitting:  1.2.10 
 R version used for fitting:         4.4.2 
 Date of fit:     Fri Feb 14 07:46:07 2025 
-Date of summary: Fri Feb 14 08:12:55 2025 
+Date of summary: Sun Feb 16 17:03:40 2025 
 
 Equations:
 d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -3087,7 +3087,7 @@ saemix version used for fitting:      3.3
 mkin version used for pre-fitting:  1.2.10 
 R version used for fitting:         4.4.2 
 Date of fit:     Fri Feb 14 07:43:36 2025 
-Date of summary: Fri Feb 14 08:12:55 2025 
+Date of summary: Sun Feb 16 17:03:40 2025 
 
 Equations:
 d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound *
@@ -3252,7 +3252,7 @@ saemix version used for fitting:      3.3
 mkin version used for pre-fitting:  1.2.10 
 R version used for fitting:         4.4.2 
 Date of fit:     Fri Feb 14 07:46:14 2025 
-Date of summary: Fri Feb 14 08:12:55 2025 
+Date of summary: Sun Feb 16 17:03:40 2025 
 
 Equations:
 d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound *
@@ -3417,7 +3417,7 @@ saemix version used for fitting:      3.3
 mkin version used for pre-fitting:  1.2.10 
 R version used for fitting:         4.4.2 
 Date of fit:     Fri Feb 14 07:43:42 2025 
-Date of summary: Fri Feb 14 08:12:55 2025 
+Date of summary: Sun Feb 16 17:03:40 2025 
 
 Equations:
 d_cyan/dt = - ifelse(time &lt;= tb, k1, k2) * cyan
@@ -3563,7 +3563,7 @@ saemix version used for fitting:      3.3
 mkin version used for pre-fitting:  1.2.10 
 R version used for fitting:         4.4.2 
 Date of fit:     Fri Feb 14 07:54:36 2025 
-Date of summary: Fri Feb 14 08:12:55 2025 
+Date of summary: Sun Feb 16 17:03:40 2025 
 
 Equations:
 d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan
@@ -3729,7 +3729,7 @@ saemix version used for fitting:      3.3
 mkin version used for pre-fitting:  1.2.10 
 R version used for fitting:         4.4.2 
 Date of fit:     Fri Feb 14 07:55:32 2025 
-Date of summary: Fri Feb 14 08:12:55 2025 
+Date of summary: Sun Feb 16 17:03:40 2025 
 
 Equations:
 d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -3920,7 +3920,7 @@ saemix version used for fitting:      3.3
 mkin version used for pre-fitting:  1.2.10 
 R version used for fitting:         4.4.2 
 Date of fit:     Fri Feb 14 07:57:56 2025 
-Date of summary: Fri Feb 14 08:12:55 2025 
+Date of summary: Sun Feb 16 17:03:40 2025 
 
 Equations:
 d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -4111,7 +4111,7 @@ saemix version used for fitting:      3.3
 mkin version used for pre-fitting:  1.2.10 
 R version used for fitting:         4.4.2 
 Date of fit:     Fri Feb 14 07:55:26 2025 
-Date of summary: Fri Feb 14 08:12:55 2025 
+Date of summary: Sun Feb 16 17:03:40 2025 
 
 Equations:
 d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound *
@@ -4307,7 +4307,7 @@ saemix version used for fitting:      3.3
 mkin version used for pre-fitting:  1.2.10 
 R version used for fitting:         4.4.2 
 Date of fit:     Fri Feb 14 07:58:06 2025 
-Date of summary: Fri Feb 14 08:12:55 2025 
+Date of summary: Sun Feb 16 17:03:40 2025 
 
 Equations:
 d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound *
@@ -4508,7 +4508,7 @@ saemix version used for fitting:      3.3
 mkin version used for pre-fitting:  1.2.10 
 R version used for fitting:         4.4.2 
 Date of fit:     Fri Feb 14 08:11:01 2025 
-Date of summary: Fri Feb 14 08:12:55 2025 
+Date of summary: Sun Feb 16 17:03:41 2025 
 
 Equations:
 d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan
@@ -4651,7 +4651,7 @@ saemix version used for fitting:      3.3
 mkin version used for pre-fitting:  1.2.10 
 R version used for fitting:         4.4.2 
 Date of fit:     Fri Feb 14 08:12:27 2025 
-Date of summary: Fri Feb 14 08:12:55 2025 
+Date of summary: Sun Feb 16 17:03:41 2025 
 
 Equations:
 d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -4817,7 +4817,7 @@ saemix version used for fitting:      3.3
 mkin version used for pre-fitting:  1.2.10 
 R version used for fitting:         4.4.2 
 Date of fit:     Fri Feb 14 08:12:54 2025 
-Date of summary: Fri Feb 14 08:12:55 2025 
+Date of summary: Sun Feb 16 17:03:41 2025 
 
 Equations:
 d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -4983,7 +4983,7 @@ saemix version used for fitting:      3.3
 mkin version used for pre-fitting:  1.2.10 
 R version used for fitting:         4.4.2 
 Date of fit:     Fri Feb 14 08:12:32 2025 
-Date of summary: Fri Feb 14 08:12:55 2025 
+Date of summary: Sun Feb 16 17:03:41 2025 
 
 Equations:
 d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound *
@@ -5154,7 +5154,7 @@ saemix version used for fitting:      3.3
 mkin version used for pre-fitting:  1.2.10 
 R version used for fitting:         4.4.2 
 Date of fit:     Fri Feb 14 08:12:36 2025 
-Date of summary: Fri Feb 14 08:12:55 2025 
+Date of summary: Sun Feb 16 17:03:41 2025 
 
 Equations:
 d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound *
@@ -5345,25 +5345,22 @@ attached base packages:
 [8] base     
 
 other attached packages:
-[1] rmarkdown_2.29  nvimcom_0.9-167 saemix_3.3      npde_3.5       
-[5] knitr_1.49      mkin_1.2.10    
+[1] saemix_3.3  npde_3.5    knitr_1.49  mkin_1.2.10
 
 loaded via a namespace (and not attached):
- [1] sass_0.4.9        utf8_1.2.4        generics_0.1.3    lattice_0.22-6   
- [5] digest_0.6.37     magrittr_2.0.3    evaluate_1.0.1    grid_4.4.2       
- [9] fastmap_1.2.0     cellranger_1.1.0  jsonlite_1.8.9    processx_3.8.4   
-[13] pkgbuild_1.4.5    deSolve_1.40      mclust_6.1.1      ps_1.8.1         
-[17] gridExtra_2.3     fansi_1.0.6       scales_1.3.0      codetools_0.2-20 
-[21] textshaping_0.4.1 jquerylib_0.1.4   cli_3.6.3         rlang_1.1.4      
-[25] munsell_0.5.1     cachem_1.1.0      yaml_2.3.10       inline_0.3.20    
-[29] tools_4.4.2       dplyr_1.1.4       colorspace_2.1-1  ggplot2_3.5.1    
-[33] vctrs_0.6.5       R6_2.5.1          zoo_1.8-12        lifecycle_1.0.4  
-[37] fs_1.6.5          htmlwidgets_1.6.4 MASS_7.3-61       ragg_1.3.3       
-[41] callr_3.7.6       pkgconfig_2.0.3   desc_1.4.3        pkgdown_2.1.1    
-[45] pillar_1.9.0      bslib_0.8.0       gtable_0.3.6      glue_1.8.0       
-[49] systemfonts_1.1.0 xfun_0.49         tibble_3.2.1      lmtest_0.9-40    
-[53] tidyselect_1.2.1  htmltools_0.5.8.1 nlme_3.1-166      compiler_4.4.2   
-[57] readxl_1.4.3     </code></pre>
+ [1] gtable_0.3.6      jsonlite_1.8.9    dplyr_1.1.4       compiler_4.4.2   
+ [5] tidyselect_1.2.1  gridExtra_2.3     jquerylib_0.1.4   systemfonts_1.1.0
+ [9] scales_1.3.0      textshaping_0.4.1 yaml_2.3.10       fastmap_1.2.0    
+[13] lattice_0.22-6    ggplot2_3.5.1     R6_2.5.1          generics_0.1.3   
+[17] lmtest_0.9-40     MASS_7.3-61       htmlwidgets_1.6.4 tibble_3.2.1     
+[21] desc_1.4.3        munsell_0.5.1     bslib_0.8.0       pillar_1.9.0     
+[25] rlang_1.1.4       utf8_1.2.4        inline_0.3.20     cachem_1.1.0     
+[29] xfun_0.49         fs_1.6.5          sass_0.4.9        cli_3.6.3        
+[33] pkgdown_2.1.1     magrittr_2.0.3    digest_0.6.37     grid_4.4.2       
+[37] mclust_6.1.1      lifecycle_1.0.4   nlme_3.1-166      vctrs_0.6.5      
+[41] evaluate_1.0.1    glue_1.8.0        ragg_1.3.3        zoo_1.8-12       
+[45] fansi_1.0.6       colorspace_2.1-1  rmarkdown_2.29    pkgconfig_2.0.3  
+[49] tools_4.4.2       htmltools_0.5.8.1</code></pre>
 </div>
 <div class="section level3">
 <h3 id="hardware-info">Hardware info<a class="anchor" aria-label="anchor" href="#hardware-info"></a>
-- 
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