From 4e37669ac2ad3b3138480c3209f414101469fac7 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 11 Jan 2021 12:59:50 +0100 Subject: Rebuild docs --- R/mkinfit.R | 2 +- build.log | 4 ++- docs/dev/news/index.html | 26 ++++++++++++----- docs/dev/pkgdown.yml | 2 +- docs/dev/reference/D24_2014.html | 32 +++++++++++---------- docs/dev/reference/Rplot001.png | Bin 19395 -> 1011 bytes docs/dev/reference/mccall81_245T.html | 4 +-- docs/dev/reference/mkinfit.html | 23 +++++++-------- docs/dev/reference/saem.html | 43 ++++++++++++++++------------- docs/dev/reference/summary.saem.mmkin.html | 20 +++++++------- man/mccall81_245T.Rd | 2 +- man/mkinfit.Rd | 2 +- man/saem.Rd | 8 +++--- man/summary.saem.mmkin.Rd | 2 +- 14 files changed, 97 insertions(+), 73 deletions(-) diff --git a/R/mkinfit.R b/R/mkinfit.R index c659e446..d7de718b 100644 --- a/R/mkinfit.R +++ b/R/mkinfit.R @@ -169,7 +169,7 @@ utils::globalVariables(c("name", "time", "value")) #' #' Ranke J and Meinecke S (2019) Error Models for the Kinetic Evaluation of Chemical #' Degradation Data. *Environments* 6(12) 124 -#' [doi:10.3390/environments6120124](https://doi.org/10.3390/environments6120124). +#' \doi{10.3390/environments6120124}. #' @examples #' #' # Use shorthand notation for parent only degradation diff --git a/build.log b/build.log index d101d06b..6d426c06 100644 --- a/build.log +++ b/build.log @@ -1,9 +1,11 @@ * checking for file ‘./DESCRIPTION’ ... OK * preparing ‘mkin’: * checking DESCRIPTION meta-information ... OK -* installing the package to build vignettes +* installing the package to process help pages +* saving partial Rd database * creating vignettes ... OK * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories +Removed empty directory ‘mkin/tests/testthat/_snaps’ * building ‘mkin_0.9.50.4.tar.gz’ diff --git a/docs/dev/news/index.html b/docs/dev/news/index.html index e21de4c2..c3597efe 100644 --- a/docs/dev/news/index.html +++ b/docs/dev/news/index.html @@ -145,20 +145,32 @@

mkin 0.9.50.4 (unreleased) Unreleased

+
+

+General new features

+
+
+

+Mixed-effects models

+ +

diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml index 85a358df..3591cac8 100644 --- a/docs/dev/pkgdown.yml +++ b/docs/dev/pkgdown.yml @@ -10,7 +10,7 @@ articles: web_only/NAFTA_examples: NAFTA_examples.html web_only/benchmarks: benchmarks.html web_only/compiled_models: compiled_models.html -last_built: 2020-12-21T04:57Z +last_built: 2021-01-11T11:41Z urls: reference: https://pkgdown.jrwb.de/mkin/reference article: https://pkgdown.jrwb.de/mkin/articles diff --git a/docs/dev/reference/D24_2014.html b/docs/dev/reference/D24_2014.html index 8160316f..2498c58e 100644 --- a/docs/dev/reference/D24_2014.html +++ b/docs/dev/reference/D24_2014.html @@ -183,22 +183,25 @@ specific pieces of information in the comments.

print(D24_2014)
 
#> <mkindsg> holding 5 mkinds objects
 #> Title $title:  Aerobic soil degradation data on 2,4-D from the EU assessment in 2014 
-#> Occurrene of observed compounds $observed_n:
+#> Occurrence of observed compounds $observed_n:
 #> D24 DCP DCA 
 #>   5   4   4 
+#> Time normalisation factors $f_time_norm:
+#> [1] 1.6062378 0.7118732 0.7156063 0.7156063 0.8977124
 #> Meta information $meta:
-#>                       study usda_soil_type study_moisture_ref_type rel_moisture
-#> 1                Cohen 1991      Silt loam                    <NA>           NA
-#> 2 Liu and Adelfinskaya 2011      Silt loam                     pF1          0.5
-#> 3 Liu and Adelfinskaya 2011           Loam                     pF1          0.5
-#> 4 Liu and Adelfinskaya 2011           Loam                     pF1          0.5
-#> 5 Liu and Adelfinskaya 2011     Loamy sand                     pF1          0.5
-#>   temperature
-#> 1          25
-#> 2          20
-#> 3          20
-#> 4          20
-#> 5          20
print(D24_2014$ds[[1]], data = TRUE)
+#>                                 study usda_soil_type study_moisture_ref_type
+#> Mississippi                Cohen 1991      Silt loam                    <NA>
+#> Fayette     Liu and Adelfinskaya 2011      Silt loam                     pF1
+#> RefSol 03-G Liu and Adelfinskaya 2011           Loam                     pF1
+#> Site E1     Liu and Adelfinskaya 2011           Loam                     pF1
+#> Site I2     Liu and Adelfinskaya 2011     Loamy sand                     pF1
+#>             rel_moisture temperature
+#> Mississippi           NA          25
+#> Fayette              0.5          20
+#> RefSol 03-G          0.5          20
+#> Site E1              0.5          20
+#> Site I2              0.5          20
# \dontrun{
+print(D24_2014$ds[[1]], data = TRUE)
 
#> <mkinds> with $title:  Mississippi 
 #> Observed compounds $observed:  D24 
 #> Sampling times $sampling_times:
@@ -256,7 +259,8 @@ specific pieces of information in the comments.

 #> d_DCP/dt = + f_D24_to_DCP * ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
 #>            exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2
 #>            * time))) * D24 - k_DCP * DCP
-#> d_DCA/dt = + f_DCP_to_DCA * k_DCP * DCP - k_DCA * DCA
+#> d_DCA/dt = + f_DCP_to_DCA * k_DCP * DCP - k_DCA * DCA

# } +