From f39815aa87272849f8e0c808099c4cee780c2a81 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 3 Nov 2016 14:33:05 +0100 Subject: Static documentation rebuilt by pkgdown::build_site() Using pkgdown with PR hadley/pkgdown#212 --- DESCRIPTION | 3 +- README.md | 4 +- _pkgdown.yml | 7 +- docs/articles/FOCUS_D.html | 25 ++-- .../data_df09328a15a9c09625fe6f7d481671d8.RData | Bin 0 -> 3177 bytes .../html/data_df09328a15a9c09625fe6f7d481671d8.rdb | 0 .../html/data_df09328a15a9c09625fe6f7d481671d8.rdx | Bin 0 -> 113 bytes .../fit_449df36a8c1e5c902ad4f45fc76df647.RData | Bin 0 -> 2735 bytes .../html/fit_449df36a8c1e5c902ad4f45fc76df647.rdb | Bin 0 -> 100333 bytes .../html/fit_449df36a8c1e5c902ad4f45fc76df647.rdx | Bin 0 -> 168 bytes .../model_911bdb95adf8c19a8e50c4150b20f2fc.RData | Bin 0 -> 2935 bytes .../model_911bdb95adf8c19a8e50c4150b20f2fc.rdb | Bin 0 -> 1775 bytes .../model_911bdb95adf8c19a8e50c4150b20f2fc.rdx | Bin 0 -> 147 bytes .../plot_2_3aa531f4c45b3e89e3259e0bb1cf7cf7.RData | 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docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdx create mode 100644 docs/authors.html create mode 100644 test.R diff --git a/DESCRIPTION b/DESCRIPTION index db72a3bd..1a29ec35 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -25,5 +25,4 @@ LazyData: yes Encoding: UTF-8 VignetteBuilder: knitr BugReports: http://github.com/jranke/mkin/issues -URL: http://kinfit.r-forge.r-project.org/mkin_static - http://github.com/jranke/mkin +URL: http://github.com/jranke/mkin diff --git a/README.md b/README.md index 1ab3f07d..4372be93 100644 --- a/README.md +++ b/README.md @@ -36,8 +36,8 @@ at the package vignettes ## Documentation -The [HTML documentation](http://kinfit.r-forge.r-project.org/mkin_static) is -maintained at the R-Forge project site. +The [HTML documentation](http://jranke.github.io/mkin) is +maintained at the github project site. ## Features diff --git a/_pkgdown.yml b/_pkgdown.yml index cdd8994a..a46bc34f 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -34,6 +34,8 @@ reference: - mccall81_245T - schaefer07_complex_case - synthetic_data_for_UBA_2014 + - mkinds + - print.mkinds - title: Helper functions contents: - mkin_wide_to_long @@ -48,12 +50,15 @@ reference: - title: Analytical solutions desc: Parent only model solutions contents: - - SFO.solution, + - SFO.solution - FOMC.solution - DFOP.solution - SFORB.solution - HS.solution - IORE.solution + - title: Generate synthetic datasets + contents: + - add_err - title: Deprecated functions desc: Functions that have been superseeded contents: diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index df259e21..726c8378 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -16,13 +16,16 @@ @@ -105,16 +108,16 @@ 
fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)

A plot of the fit including a residual plot for both observed variables is obtained using the plot method for mkinfit objects.

plot(fit, show_residuals = TRUE)
-

+

Confidence intervals for the parameter estimates are obtained using the mkinparplot function.

mkinparplot(fit)
-

+

A comprehensive report of the results is obtained using the summary method for mkinfit objects.

summary(fit)
## mkin version:    0.9.44.9000 
-## R version:       3.3.1 
-## Date of fit:     Wed Oct 26 23:18:10 2016 
-## Date of summary: Wed Oct 26 23:18:10 2016 
+## R version:       3.3.2 
+## Date of fit:     Wed Nov  2 16:25:22 2016 
+## Date of summary: Wed Nov  2 16:25:22 2016 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent - k_parent_m1 * parent
@@ -122,7 +125,7 @@
 ## 
 ## Model predictions using solution type deSolve 
 ## 
-## Fitted with method Port using 153 model solutions performed in 0.628 s
+## Fitted with method Port using 153 model solutions performed in 0.665 s
 ## 
 ## Weighting: none
 ## 
@@ -243,7 +246,7 @@
 
 
       
smb.2["median"]/smb.2["deSolve, compiled", "median"]
##   median
 ## 1     NA
 ## 2     NA
autoplot(mb.2)

-

Here we get a performance benefit of a factor of 10.1 using the version of the differential equation model compiled from C code!

+

Here we get a performance benefit of a factor of 10.4 using the version of the differential equation model compiled from C code!

This vignette was built with mkin 0.9.44.9000 on

-
## R version 3.3.1 (2016-06-21)
+
## R version 3.3.2 (2016-10-31)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
 ## Running under: Debian GNU/Linux 8 (jessie)

 
## CPU model: Intel(R) Core(TM) i7-4710MQ CPU @ 2.50GHz

@@ -144,7 +147,7 @@ smb.1["median"]/smb
-  
Developed by Johannes Ranke, Eurofins Regulatory AG.

+  
Developed by Johannes Ranke.

 
 
 

diff --git a/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png b/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png
index bba259d6..eec55773 100644
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diff --git a/docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.png b/docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.png
index 6b732075..b043c13b 100644
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diff --git a/docs/articles/index.html b/docs/articles/index.html
index 9994716d..cd6a7bea 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -49,16 +49,19 @@
+plot_sep(f_SFO_SFO_SFO, lpos = c("topright", "bottomright", "bottomright"))

@@ -169,7 +172,7 @@ f_SFO_SFO_SFO <- -

Developed by Johannes Ranke, Eurofins Regulatory AG.

+

Developed by Johannes Ranke.

diff --git a/docs/articles/mkin_cache/html/__packages b/docs/articles/mkin_cache/html/__packages index c8b1e877..03ece635 100644 --- a/docs/articles/mkin_cache/html/__packages +++ b/docs/articles/mkin_cache/html/__packages @@ -1,8 +1,13 @@ base +datasets +utils +grDevices +graphics +stats knitr minpack.lm rootSolve +methods inline +parallel mkin -microbenchmark -ggplot2 diff --git a/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.RData b/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.RData new file mode 100644 index 00000000..d11ccf31 Binary files /dev/null and b/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.RData differ diff --git a/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdb b/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdb new file mode 100644 index 00000000..5ac4f484 Binary files /dev/null and b/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdb differ diff --git a/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdx b/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdx new file mode 100644 index 00000000..8983f69e Binary files /dev/null and b/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdx differ diff --git a/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png b/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png index d34e3805..2e7e2244 100644 Binary files a/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png and b/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png differ diff --git a/docs/authors.html b/docs/authors.html new file mode 100644 index 00000000..fe3e6114 --- /dev/null +++ b/docs/authors.html @@ -0,0 +1,120 @@ + + + + + + + + +Authors • mkin + + + + + + + + + + + + + + + + + + + + + + + + +
+
+ + + +
+ +
+
+
+

Authors

+
+ +
    +
  • +

    Johannes Ranke. Author, maintainer, copyright holder. +

    +
    • +
  • +

    Katrin Lindenberger. Contributor. +

    +
    • +
  • +

    René Lehmann. Contributor. +

    +
    • +
  • +

    Eurofins Regulatory AG. Copyright holder. +

    +
    • +
+ +
+ +
+ + +
+
+

Developed by Johannes Ranke.

+
+ +
+

Site built with pkgdown.

+
+ +
+
+ + + diff --git a/docs/index.html b/docs/index.html index 04f10ed8..a3a0e46c 100644 --- a/docs/index.html +++ b/docs/index.html @@ -24,7 +24,13 @@
  • News
    • -
    + @@ -54,7 +60,7 @@

    Documentation

    -

    The HTML documentation is maintained at the R-Forge project site.

    +

    The HTML documentation is maintained at the github project site.

    @@ -102,25 +108,21 @@