From 9ae42bd20bc2543a94cf1581ba9820c2f9e3afbd Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 20 Apr 2023 19:53:28 +0200 Subject: Fix and rebuild documentation, see NEWS I had to fix the two pathway vignettes, as they did not work with the released version any more. So they and the multistart vignette which got some small fixes as well were rebuilt. Complete rebuild of the online docs with the released version. The documentation of the 'hierarchial_kinetics' format had to be fixed as well. --- docs/reference/AIC.mmkin.html | 35 +- docs/reference/CAKE_export.html | 35 +- docs/reference/D24_2014.html | 35 +- docs/reference/DFOP.solution-1.png | Bin 31230 -> 31964 bytes docs/reference/DFOP.solution.html | 35 +- docs/reference/Extract.mmkin.html | 35 +- docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html | 35 +- docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html | 35 +- docs/reference/FOCUS_2006_HS_ref_A_to_F.html | 35 +- docs/reference/FOCUS_2006_SFO_ref_A_to_F.html | 35 +- docs/reference/FOCUS_2006_datasets.html | 35 +- docs/reference/FOMC.solution-1.png | Bin 29016 -> 29520 bytes docs/reference/FOMC.solution.html | 35 +- docs/reference/HS.solution-1.png | Bin 29376 -> 29572 bytes docs/reference/HS.solution.html | 35 +- docs/reference/IORE.solution-1.png | Bin 30069 -> 30800 bytes docs/reference/IORE.solution.html | 37 +- docs/reference/NAFTA_SOP_2015-1.png | Bin 63022 -> 63875 bytes 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35 +- docs/reference/aw.html | 35 +- docs/reference/confint.mkinfit.html | 39 +- docs/reference/create_deg_func.html | 43 +- docs/reference/dimethenamid_2018-1.png | Bin 251312 -> 253269 bytes docs/reference/dimethenamid_2018.html | 85 +++- docs/reference/ds_mixed-1.png | Bin 219939 -> 219137 bytes docs/reference/ds_mixed.html | 35 +- docs/reference/endpoints.html | 48 +- docs/reference/experimental_data_for_UBA-1.png | Bin 102904 -> 103470 bytes docs/reference/experimental_data_for_UBA.html | 35 +- docs/reference/f_time_norm_focus.html | 35 +- docs/reference/focus_soil_moisture.html | 35 +- docs/reference/get_deg_func.html | 35 +- docs/reference/hierarchical_kinetics.html | 197 ++++++++ docs/reference/illparms.html | 50 +- docs/reference/ilr.html | 35 +- docs/reference/index.html | 45 +- docs/reference/intervals.saem.mmkin.html | 35 +- docs/reference/llhist.html | 35 +- docs/reference/loftest-1.png | Bin 40003 -> 40983 bytes docs/reference/loftest-2.png | Bin 39622 -> 40501 bytes 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docs/reference/mkin_wide_to_long.html | 35 +- docs/reference/mkinds.html | 35 +- docs/reference/mkindsg.html | 35 +- docs/reference/mkinerrmin.html | 35 +- docs/reference/mkinerrplot-1.png | Bin 41273 -> 41525 bytes docs/reference/mkinerrplot.html | 35 +- docs/reference/mkinfit-1.png | Bin 66250 -> 65332 bytes docs/reference/mkinfit.html | 61 ++- docs/reference/mkinmod.html | 48 +- docs/reference/mkinparplot-1.png | Bin 25998 -> 26970 bytes docs/reference/mkinparplot.html | 35 +- docs/reference/mkinplot.html | 35 +- docs/reference/mkinpredict.html | 84 ++-- docs/reference/mkinresplot-1.png | Bin 23910 -> 23996 bytes docs/reference/mkinresplot.html | 35 +- docs/reference/mmkin-1.png | Bin 111900 -> 111798 bytes docs/reference/mmkin-2.png | Bin 108747 -> 108900 bytes docs/reference/mmkin-3.png | Bin 96798 -> 97013 bytes docs/reference/mmkin-4.png | Bin 67454 -> 67638 bytes docs/reference/mmkin-5.png | Bin 65333 -> 65329 bytes docs/reference/mmkin.html | 61 ++- 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docs/reference/test_data_from_UBA_2014-2.png | Bin 72597 -> 73864 bytes docs/reference/test_data_from_UBA_2014.html | 35 +- docs/reference/transform_odeparms.html | 35 +- docs/reference/update.mkinfit-1.png | Bin 42522 -> 44071 bytes docs/reference/update.mkinfit-2.png | Bin 43527 -> 43998 bytes docs/reference/update.mkinfit.html | 35 +- 161 files changed, 3207 insertions(+), 1139 deletions(-) create mode 100644 docs/reference/hierarchical_kinetics.html create mode 100644 docs/reference/mhmkin-1.png create mode 100644 docs/reference/mhmkin-2.png create mode 100644 docs/reference/summary_listing.html (limited to 'docs/reference') diff --git a/docs/reference/AIC.mmkin.html b/docs/reference/AIC.mmkin.html index 48e3b7e2..a53a2735 100644 --- a/docs/reference/AIC.mmkin.html +++ b/docs/reference/AIC.mmkin.html @@ -18,13 +18,13 @@ same dataset."> + + +
+
+ + + +
+
+
+

Hierarchical kinetics template

+ Source: R/hierarchical_kinetics.R + +
+ +
+

R markdown format for setting up hierarchical kinetics based on a template +provided with the mkin package. This format is based on rmarkdown::pdf_document. +Chunk options are adapted. Echoing R code from code chunks and caching are +turned on per default. character for prepending output from code chunks is +set to the empty string, code tidying is off, figure alignment defaults to +centering, and positioning of figures is set to "H", which means that +figures will not move around in the document, but stay where the user +includes them.

+
+ +
+ 
hierarchical_kinetics(..., keep_tex = FALSE)
+
+ +
+

Arguments

+
...
+

Arguments to rmarkdown::pdf_document

+ + +
keep_tex
+

Keep the intermediate tex file used in the conversion to PDF

+ +
+
+

Value

+ + +

R Markdown output format to pass to +render

+ + +
+
+

Details

+

The latter feature (positioning the figures with "H") depends on the LaTeX +package 'float'. In addition, the LaTeX package 'listing' is used in the +template for showing model fit summaries in the Appendix. This means that +the LaTeX packages 'float' and 'listing' need to be installed in the TeX +distribution used.

+

On Windows, the easiest way to achieve this (if no TeX distribution +is present before) is to install the 'tinytex' R package, to run +'tinytex::install_tinytex()' to get the basic tiny Tex distribution, +and then to run 'tinytex::tlmgr_install(c("float", "listing"))'.

+
+ +
+

Examples

+ 

+# \dontrun{
+library(rmarkdown)
+# The following is now commented out after the relase of v1.2.3 for the generation
+# of online docs, as the command creates a directory and opens an editor
+#draft("example_analysis.rmd", template = "hierarchical_kinetics", package = "mkin")
+# }
+
+
+
+
+ +
+ + +
+

Developed by Johannes Ranke.

+
+ +
+

Site built with pkgdown 2.0.7.

+
+ +
+ + + + + + + + diff --git a/docs/reference/illparms.html b/docs/reference/illparms.html index 52f130e6..f0829482 100644 --- a/docs/reference/illparms.html +++ b/docs/reference/illparms.html @@ -21,13 +21,13 @@ without parameter transformations is used."> + + +
+
+ + + +
+
+
+

Display the output of a summary function according to the output format

+ Source: R/summary_listing.R + +
+ +
+

This function is intended for use in a R markdown code chunk with the chunk +option results = "asis".

+
+ +
+ 
summary_listing(object, caption = NULL, label = NULL, clearpage = TRUE)
+
+tex_listing(object, caption = NULL, label = NULL, clearpage = TRUE)
+
+html_listing(object, caption = NULL)
+
+ +
+

Arguments

+
object
+

The object for which the summary is to be listed

+ + +
caption
+

An optional caption

+ + +
label
+

An optional label, ignored in html output

+ + +
clearpage
+

Should a new page be started after the listing? Ignored in html output

+ +
+ +
+ +
+ + +
+

Developed by Johannes Ranke.

+
+ +
+

Site built with pkgdown 2.0.7.

+
+ +
+ + + + + + + + diff --git a/docs/reference/synthetic_data_for_UBA_2014-1.png b/docs/reference/synthetic_data_for_UBA_2014-1.png index 132380a8..11eae1f9 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 c00d1b55..cd2338eb 100644 --- a/docs/reference/synthetic_data_for_UBA_2014.html +++ b/docs/reference/synthetic_data_for_UBA_2014.html @@ -32,13 +32,13 @@ Compare also the code in the example section to see the degradation models."> mkin - 1.2.0 + 1.2.3 diff --git a/docs/reference/test_data_from_UBA_2014-1.png b/docs/reference/test_data_from_UBA_2014-1.png index e4fc2a4c..a007a102 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 4ce36561..f460ac83 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 a76f23ab..e57141ec 100644 --- a/docs/reference/test_data_from_UBA_2014.html +++ b/docs/reference/test_data_from_UBA_2014.html @@ -18,13 +18,13 @@ mkin - 1.2.0 + 1.2.3
-

Site built with pkgdown 2.0.6.

+

Site built with pkgdown 2.0.7.

diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index 66e94941..2845c6c1 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -22,13 +22,13 @@ the ilr transformation is used.">