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 <= 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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