diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2016-10-26 23:54:08 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2016-10-26 23:54:08 +0200 |
| commit | 2409369d3a665f2b8e0b7333f4c2286a61614179 (patch) | |
| tree | 218a40a7fb824e3d88e77007263e786a539d5ce6 | |
| parent | 8f38147e145c66ebd27f5d9fcc6f00172c25872f (diff) | |
Complete pkgdown conf, rerun with current master branch
40 files changed, 462 insertions, 354 deletions
diff --git a/_pkgdown.yml b/_pkgdown.yml index 6552d156..cdd8994a 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -1,7 +1,7 @@ title: mkin template: - bootswatch: cerulean + bootswatch: spacelab reference: - title: Main functions @@ -11,22 +11,50 @@ reference: - mkinfit - mmkin - title: Show results - contents: Functions working with mkinfit objects + desc: Functions working with mkinfit objects + contents: - plot.mkinfit - summary.mkinfit - mkinresplot - mkinparplot - endpoints - mkinerrmin - -navbar: - title: mkin - type: default - left: - - text: Home - href: index.html - - text: Reference - href: reference/index.html - right: - - icon: fa-github fa-lg - href: https://github.com/jranke/mkin + - title: Work with mmkin objects + desc: Functions working with aggregated results + contents: + - "[.mmkin" + - plot.mmkin + - title: Datasets and known results + contents: + - FOCUS_2006_datasets + - FOCUS_2006_SFO_ref_A_to_F + - FOCUS_2006_FOMC_ref_A_to_F + - FOCUS_2006_HS_ref_A_to_F + - FOCUS_2006_DFOP_ref_A_to_B + - mccall81_245T + - schaefer07_complex_case + - synthetic_data_for_UBA_2014 + - title: Helper functions + contents: + - mkin_wide_to_long + - mkin_long_to_wide + - mkinsub + - mkinds, print.mkinds + - print.mkinmod + - mkinpredict + - transform_odeparms + - ilr + - geometric_mean + - title: Analytical solutions + desc: Parent only model solutions + contents: + - SFO.solution, + - FOMC.solution + - DFOP.solution + - SFORB.solution + - HS.solution + - IORE.solution + - title: Deprecated functions + desc: Functions that have been superseeded + contents: + - mkinplot diff --git a/docs/index.html b/docs/index.html index 180fe5f9..04f10ed8 100644 --- a/docs/index.html +++ b/docs/index.html @@ -16,18 +16,15 @@ </div> <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"><li> - <a href="index.html">Home</a> + <a href="reference/index.html">Reference</a> </li> <li> - <a href="reference/index.html">Reference</a> + <a href="articles/index.html">Articles</a> </li> - </ul><ul class="nav navbar-nav navbar-right"><li> - <a href="https://github.com/jranke/mkin"> - <span class="fa fa-github fa-lg"></span> - - </a> +<li> + <a href="news/index.html">News</a> </li> - </ul></div><!--/.nav-collapse --> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html index 5c90809c..3b8e0e03 100644 --- a/docs/reference/DFOP.solution.html +++ b/docs/reference/DFOP.solution.html @@ -50,20 +50,18 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="../index.html">Home</a> + <a href="../reference/index.html">Reference</a> </li> <li> - <a href="../reference/index.html">Reference</a> + <a href="../articles/index.html">Articles</a> +</li> +<li> + <a href="../news/index.html">News</a> </li> </ul> <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin"> - <span class="fa fa-github fa-lg"></span> - - </a> -</li> + </ul> </div><!--/.nav-collapse --> </div><!--/.container --> diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index ee86854a..4ea16d10 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -49,20 +49,18 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="../index.html">Home</a> + <a href="../reference/index.html">Reference</a> </li> <li> - <a href="../reference/index.html">Reference</a> + <a href="../articles/index.html">Articles</a> +</li> +<li> + <a href="../news/index.html">News</a> </li> </ul> <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin"> - <span class="fa fa-github fa-lg"></span> - - </a> -</li> + </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -195,7 +193,7 @@ #> #> $time #> user system elapsed -#> 0.268 0.000 0.264 +#> 0.26 0.00 0.26 #> #> $mkinmod #> <mkinmod> model generated with @@ -381,7 +379,7 @@ #> } #> return(mC) #> } -#> <environment: 0x49c37f0> +#> <environment: 0x5421f48> #> #> $cost_notrans #> function (P) @@ -403,7 +401,7 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x49c37f0> +#> <environment: 0x5421f48> #> #> $hessian_notrans #> parent_0 alpha beta @@ -469,7 +467,7 @@ #> 99.66619 #> #> $date -#> [1] "Wed Oct 26 23:16:41 2016" +#> [1] "Wed Oct 26 23:50:33 2016" #> #> attr(,"class") #> [1] "mkinfit" "modFit" @@ -550,7 +548,7 @@ #> #> $time #> user system elapsed -#> 0.072 0.004 0.074 +#> 0.068 0.000 0.070 #> #> $mkinmod #> <mkinmod> model generated with @@ -737,7 +735,7 @@ #> } #> return(mC) #> } -#> <environment: 0x4ae0880> +#> <environment: 0x2b30d68> #> #> $cost_notrans #> function (P) @@ -759,7 +757,7 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x4ae0880> +#> <environment: 0x2b30d68> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -822,7 +820,7 @@ #> 99.17407 #> #> $date -#> [1] "Wed Oct 26 23:16:41 2016" +#> [1] "Wed Oct 26 23:50:32 2016" #> #> attr(,"class") #> [1] "mkinfit" "modFit" @@ -899,7 +897,7 @@ #> #> $time #> user system elapsed -#> 0.072 0.004 0.074 +#> 0.068 0.000 0.070 #> #> $mkinmod #> <mkinmod> model generated with @@ -1086,7 +1084,7 @@ #> } #> return(mC) #> } -#> <environment: 0x4ae0880> +#> <environment: 0x2b30d68> #> #> $cost_notrans #> function (P) @@ -1108,7 +1106,7 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x4ae0880> +#> <environment: 0x2b30d68> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -1171,7 +1169,7 @@ #> 99.17407 #> #> $date -#> [1] "Wed Oct 26 23:16:41 2016" +#> [1] "Wed Oct 26 23:50:32 2016" #> #> attr(,"class") #> [1] "mkinfit" "modFit" diff --git a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html index 61871ba9..6f071674 100644 --- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html +++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html @@ -50,20 +50,18 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="../index.html">Home</a> + <a href="../reference/index.html">Reference</a> </li> <li> - <a href="../reference/index.html">Reference</a> + <a href="../articles/index.html">Articles</a> +</li> +<li> + <a href="../news/index.html">News</a> </li> </ul> <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin"> - <span class="fa fa-github fa-lg"></span> - - </a> -</li> + </ul> </div><!--/.nav-collapse --> </div><!--/.container --> diff --git a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html index 4fdb5f45..d721b2d9 100644 --- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html @@ -50,20 +50,18 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="../index.html">Home</a> + <a href="../reference/index.html">Reference</a> </li> <li> - <a href="../reference/index.html">Reference</a> + <a href="../articles/index.html">Articles</a> +</li> +<li> + <a href="../news/index.html">News</a> </li> </ul> <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin"> - <span class="fa fa-github fa-lg"></span> - - </a> -</li> + </ul> </div><!--/.nav-collapse --> </div><!--/.container --> diff --git a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html index d9e43f4a..11fcea7c 100644 --- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html @@ -50,20 +50,18 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="../index.html">Home</a> + <a href="../reference/index.html">Reference</a> </li> <li> - <a href="../reference/index.html">Reference</a> + <a href="../articles/index.html">Articles</a> +</li> +<li> + <a href="../news/index.html">News</a> </li> </ul> <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin"> - <span class="fa fa-github fa-lg"></span> - - </a> -</li> + </ul> </div><!--/.nav-collapse --> </div><!--/.container --> diff --git a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html index 68475b64..17c34f0f 100644 --- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html @@ -50,20 +50,18 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="../index.html">Home</a> + <a href="../reference/index.html">Reference</a> </li> <li> - <a href="../reference/index.html">Reference</a> + <a href="../articles/index.html">Articles</a> +</li> +<li> + <a href="../news/index.html">News</a> </li> </ul> <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin"> - <span class="fa fa-github fa-lg"></span> - - </a> -</li> + </ul> </div><!--/.nav-collapse --> </div><!--/.container --> diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html index 6221f53f..c5bdae8b 100644 --- a/docs/reference/FOCUS_2006_datasets.html +++ b/docs/reference/FOCUS_2006_datasets.html @@ -50,20 +50,18 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="../index.html">Home</a> + <a href="../reference/index.html">Reference</a> </li> <li> - <a href="../reference/index.html">Reference</a> + <a href="../articles/index.html">Articles</a> +</li> +<li> + <a href="../news/index.html">News</a> </li> </ul> <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin"> - <span class="fa fa-github fa-lg"></span> - - </a> -</li> + </ul> </div><!--/.nav-collapse --> </div><!--/.container --> diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html index 99d95fcb..a2e84ce0 100644 --- a/docs/reference/FOMC.solution.html +++ b/docs/reference/FOMC.solution.html @@ -49,20 +49,18 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="../index.html">Home</a> + <a href="../reference/index.html">Reference</a> </li> <li> - <a href="../reference/index.html">Reference</a> + <a href="../articles/index.html">Articles</a> +</li> +<li> + <a href="../news/index.html">News</a> </li> </ul> <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin"> - <span class="fa fa-github fa-lg"></span> - - </a> -</li> + </ul> </div><!--/.nav-collapse --> </div><!--/.container --> diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html index 06c6e3c1..e41b7b6a 100644 --- a/docs/reference/HS.solution.html +++ b/docs/reference/HS.solution.html @@ -49,20 +49,18 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="../index.html">Home</a> + <a href="../reference/index.html">Reference</a> </li> <li> - <a href="../reference/index.html">Reference</a> + <a href="../articles/index.html">Articles</a> +</li> +<li> + <a href="../news/index.html">News</a> </li> </ul> <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin"> - <span class="fa fa-github fa-lg"></span> - - </a> -</li> + </ul> </div><!--/.nav-collapse --> </div><!--/.container --> diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html index 58546489..c39e7818 100644 --- a/docs/reference/IORE.solution.html +++ b/docs/reference/IORE.solution.html @@ -49,20 +49,18 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="../index.html">Home</a> + <a href="../reference/index.html">Reference</a> </li> <li> - <a href="../reference/index.html">Reference</a> + <a href="../articles/index.html">Articles</a> +</li> +<li> + <a href="../news/index.html">News</a> </li> </ul> <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin"> - <span class="fa fa-github fa-lg"></span> - - </a> -</li> + </ul> </div><!--/.nav-collapse --> </div><!--/.container --> diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html index b2d5526e..3ce813bf 100644 --- a/docs/reference/SFO.solution.html +++ b/docs/reference/SFO.solution.html @@ -49,20 +49,18 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="../index.html">Home</a> + <a href="../reference/index.html">Reference</a> </li> <li> - <a href="../reference/index.html">Reference</a> + <a href="../articles/index.html">Articles</a> +</li> +<li> + <a href="../news/index.html">News</a> </li> </ul> <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin"> - <span class="fa fa-github fa-lg"></span> - - </a> -</li> + </ul> </div><!--/.nav-collapse --> </div><!--/.container --> diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html index 135edb51..942fa576 100644 --- a/docs/reference/SFORB.solution.html +++ b/docs/reference/SFORB.solution.html @@ -49,20 +49,18 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="../index.html">Home</a> + <a href="../reference/index.html">Reference</a> </li> <li> - <a href="../reference/index.html">Reference</a> + <a href="../articles/index.html">Articles</a> +</li> +<li> + <a href="../news/index.html">News</a> </li> </ul> <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin"> - <span class="fa fa-github fa-lg"></span> - - </a> -</li> + </ul> </div><!--/.nav-collapse --> </div><!--/.container --> diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html index 9020a486..2500e092 100644 --- a/docs/reference/add_err.html +++ b/docs/reference/add_err.html @@ -50,20 +50,18 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="../index.html">Home</a> + <a href="../reference/index.html">Reference</a> </li> <li> - <a href="../reference/index.html">Reference</a> + <a href="../articles/index.html">Articles</a> +</li> +<li> + <a href="../news/index.html">News</a> </li> </ul> <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin"> - <span class="fa fa-github fa-lg"></span> - - </a> -</li> + </ul> </div><!--/.nav-collapse --> </div><!--/.container --> diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html index 89e9cf52..73d7e746 100644 --- a/docs/reference/endpoints.html +++ b/docs/reference/endpoints.html @@ -50,20 +50,18 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="../index.html">Home</a> + <a href="../reference/index.html">Reference</a> </li> <li> - <a href="../reference/index.html">Reference</a> + <a href="../articles/index.html">Articles</a> +</li> +<li> + <a href="../news/index.html">News</a> </li> </ul> <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin"> - <span class="fa fa-github fa-lg"></span> - - </a> -</li> + </ul> </div><!--/.nav-collapse --> </div><!--/.container --> diff --git a/docs/reference/geometric_mean.html b/docs/reference/geometric_mean.html index 793d893c..62a9163f 100644 --- a/docs/reference/geometric_mean.html +++ b/docs/reference/geometric_mean.html @@ -49,20 +49,18 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="../index.html">Home</a> + <a href="../reference/index.html">Reference</a> </li> <li> - <a href="../reference/index.html">Reference</a> + <a href="../articles/index.html">Articles</a> +</li> +<li> + <a href="../news/index.html">News</a> </li> </ul> <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin"> - <span class="fa fa-github fa-lg"></span> - - </a> -</li> + </ul> </div><!--/.nav-collapse --> </div><!--/.container --> diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html index d249101d..82accca4 100644 --- a/docs/reference/ilr.html +++ b/docs/reference/ilr.html @@ -50,20 +50,18 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="../index.html">Home</a> + <a href="../reference/index.html">Reference</a> </li> <li> - <a href="../reference/index.html">Reference</a> + <a href="../articles/index.html">Articles</a> +</li> +<li> + <a href="../news/index.html">News</a> </li> </ul> <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin"> - <span class="fa fa-github fa-lg"></span> - - </a> -</li> + </ul> </div><!--/.nav-collapse --> </div><!--/.container --> diff --git a/docs/reference/index.html b/docs/reference/index.html index 60d11171..6fcf39c8 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -49,20 +49,18 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="../index.html">Home</a> + <a href="../reference/index.html">Reference</a> </li> <li> - <a href="../reference/index.html">Reference</a> + <a href="../articles/index.html">Articles</a> +</li> +<li> + <a href="../news/index.html">News</a> </li> </ul> <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin"> - <span class="fa fa-github fa-lg"></span> - - </a> -</li> + </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -98,8 +96,162 @@ <li><code><a href="mmkin.html">mmkin</a></code></li> </ul> <h2 id="section-show-results" class="hasAnchor"><a href="#section-show-results" class="anchor"></a>Show results</h2> + <p class="section-desc"><p>Functions working with mkinfit objects</p></p> + + <p><a href="endpoints.html"> +</a></p> + <ul> + <li><code><a href="endpoints.html">endpoints</a></code></li> + </ul> + <p><a href="mkinerrmin.html"> +</a></p> + <ul> + <li><code><a href="mkinerrmin.html">mkinerrmin</a></code></li> + </ul> + <p><a href="mkinparplot.html"> +</a></p> + <ul> + <li><code><a href="mkinparplot.html">mkinparplot</a></code></li> + </ul> + <p><a href="mkinresplot.html"> +</a></p> + <ul> + <li><code><a href="mkinresplot.html">mkinresplot</a></code></li> + </ul> + <p><a href="plot.mkinfit.html"> +</a></p> + <ul> + <li><code><a href="plot.mkinfit.html">plot.mkinfit</a></code></li><li><code><a href="plot.mkinfit.html">plot_sep</a></code></li> + </ul> + <p><a href="summary.mkinfit.html"> +</a></p> + <ul> + <li><code><a href="summary.mkinfit.html">summary.mkinfit</a></code></li><li><code><a href="summary.mkinfit.html">print.summary.mkinfit</a></code></li> + </ul> + <h2 id="section-work-with-mmkin-objects" class="hasAnchor"><a href="#section-work-with-mmkin-objects" class="anchor"></a>Work with mmkin objects</h2> + <p class="section-desc"><p>Functions working with aggregated results</p></p> + + <p><a href="Extract.mmkin.html">Subsetting method for mmkin objects</a></p> + <ul> + <li><code><a href="Extract.mmkin.html">[.mmkin</a></code></li> + </ul> + <p><a href="plot.mmkin.html"> +</a></p> + <ul> + <li><code><a href="plot.mmkin.html">plot.mmkin</a></code></li> + </ul> + <h2 id="section-datasets-and-known-results" class="hasAnchor"><a href="#section-datasets-and-known-results" class="anchor"></a>Datasets and known results</h2> <p class="section-desc"></p> + <p><a href="FOCUS_2006_DFOP_ref_A_to_B.html"> +</a></p> + <ul> + <li><code><a href="FOCUS_2006_DFOP_ref_A_to_B.html">FOCUS_2006_DFOP_ref_A_to_B</a></code></li> + </ul> + <p><a href="FOCUS_2006_FOMC_ref_A_to_F.html"> +</a></p> + <ul> + <li><code><a href="FOCUS_2006_FOMC_ref_A_to_F.html">FOCUS_2006_FOMC_ref_A_to_F</a></code></li> + </ul> + <p><a href="FOCUS_2006_HS_ref_A_to_F.html"> +</a></p> + <ul> + <li><code><a href="FOCUS_2006_HS_ref_A_to_F.html">FOCUS_2006_HS_ref_A_to_F</a></code></li> + </ul> + <p><a href="FOCUS_2006_SFO_ref_A_to_F.html"> +</a></p> + <ul> + <li><code><a href="FOCUS_2006_SFO_ref_A_to_F.html">FOCUS_2006_SFO_ref_A_to_F</a></code></li> + </ul> + <p><a href="mccall81_245T.html"> +</a></p> + <ul> + <li><code><a href="mccall81_245T.html">mccall81_245T</a></code></li> + </ul> + <p><a href="schaefer07_complex_case.html"> +</a></p> + <ul> + <li><code><a href="schaefer07_complex_case.html">schaefer07_complex_case</a></code></li><li><code><a href="schaefer07_complex_case.html">schaefer07_complex_results</a></code></li> + </ul> + <p><a href="synthetic_data_for_UBA.html"> +</a></p> + <ul> + <li><code><a href="synthetic_data_for_UBA.html">synthetic_data_for_UBA_2014</a></code></li> + </ul> + <h2 id="section-helper-functions" class="hasAnchor"><a href="#section-helper-functions" class="anchor"></a>Helper functions</h2> + <p class="section-desc"></p> + + <p><a href="geometric_mean.html"> Calculate the geometric mean </a></p> + <ul> + <li><code><a href="geometric_mean.html">geometric_mean</a></code></li> + </ul> + <p><a href="ilr.html"> +</a></p> + <ul> + <li><code><a href="ilr.html">ilr</a></code></li><li><code><a href="ilr.html">invilr</a></code></li> + </ul> + <p><a href="mkin_long_to_wide.html"> +</a></p> + <ul> + <li><code><a href="mkin_long_to_wide.html">mkin_long_to_wide</a></code></li> + </ul> + <p><a href="mkinpredict.html"> +</a></p> + <ul> + <li><code><a href="mkinpredict.html">mkinpredict</a></code></li> + </ul> + <p><a href="mkinsub.html"> +</a></p> + <ul> + <li><code><a href="mkinsub.html">mkinsub</a></code></li> + </ul> + <p><a href="mkin_wide_to_long.html"> +</a></p> + <ul> + <li><code><a href="mkin_wide_to_long.html">mkin_wide_to_long</a></code></li> + </ul> + <p><a href="print.mkinmod.html"> +</a></p> + <ul> + <li><code><a href="print.mkinmod.html">print.mkinmod</a></code></li> + </ul> + <p><a href="transform_odeparms.html"> +</a></p> + <ul> + <li><code><a href="transform_odeparms.html">transform_odeparms</a></code></li><li><code><a href="transform_odeparms.html">backtransform_odeparms</a></code></li> + </ul> + <h2 id="section-analytical-solutions" class="hasAnchor"><a href="#section-analytical-solutions" class="anchor"></a>Analytical solutions</h2> + <p class="section-desc"><p>Parent only model solutions</p></p> + + <p><a href="DFOP.solution.html"> +</a></p> + <ul> + <li><code><a href="DFOP.solution.html">DFOP.solution</a></code></li> + </ul> + <p><a href="FOMC.solution.html"> First-Order Multi-Compartment kinetics </a></p> + <ul> + <li><code><a href="FOMC.solution.html">FOMC.solution</a></code></li> + </ul> + <p><a href="HS.solution.html"> Hockey-Stick kinetics </a></p> + <ul> + <li><code><a href="HS.solution.html">HS.solution</a></code></li> + </ul> + <p><a href="IORE.solution.html"> Indeterminate order rate equation kinetics </a></p> + <ul> + <li><code><a href="IORE.solution.html">IORE.solution</a></code></li> + </ul> + <p><a href="SFORB.solution.html"> Single First-Order Reversible Binding kinetics </a></p> + <ul> + <li><code><a href="SFORB.solution.html">SFORB.solution</a></code></li> + </ul> + <h2 id="section-deprecated-functions" class="hasAnchor"><a href="#section-deprecated-functions" class="anchor"></a>Deprecated functions</h2> + <p class="section-desc"><p>Functions that have been superseeded</p></p> + + <p><a href="mkinplot.html"> +</a></p> + <ul> + <li><code><a href="mkinplot.html">mkinplot</a></code></li> + </ul> </div> </div> @@ -109,6 +261,11 @@ <ul class="nav nav-pills nav-stacked"> <li><a href="#section-main-functions">Main functions</a></li> <li><a href="#section-show-results">Show results</a></li> + <li><a href="#section-work-with-mmkin-objects">Work with mmkin objects</a></li> + <li><a href="#section-datasets-and-known-results">Datasets and known results</a></li> + <li><a href="#section-helper-functions">Helper functions</a></li> + <li><a href="#section-analytical-solutions">Analytical solutions</a></li> + <li><a href="#section-deprecated-functions">Deprecated functions</a></li> </ul> </div> </div> diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 7a96be3b..74b9c088 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -50,20 +50,18 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="../index.html">Home</a> + <a href="../reference/index.html">Reference</a> </li> <li> - <a href="../reference/index.html">Reference</a> + <a href="../articles/index.html">Articles</a> +</li> +<li> + <a href="../news/index.html">News</a> </li> </ul> <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin"> - <span class="fa fa-github fa-lg"></span> - - </a> -</li> + </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -124,8 +122,8 @@ <span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='st'>"k_phenol_sink"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>summary</span>(<span class='no'>fit.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> mkin version: 0.9.44.9000 #> R version: 3.3.1 -#> Date of fit: Wed Oct 26 23:16:47 2016 -#> Date of summary: Wed Oct 26 23:16:47 2016 +#> Date of fit: Wed Oct 26 23:50:40 2016 +#> Date of summary: Wed Oct 26 23:50:40 2016 #> #> Equations: #> d_T245 = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -135,7 +133,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 246 model solutions performed in 1.487 s +#> Fitted with method Port using 246 model solutions performed in 1.43 s #> #> Weighting: none #> diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html index d8b616c2..cc50bf7d 100644 --- a/docs/reference/mkin_long_to_wide.html +++ b/docs/reference/mkin_long_to_wide.html @@ -50,20 +50,18 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="../index.html">Home</a> + <a href="../reference/index.html">Reference</a> </li> <li> - <a href="../reference/index.html">Reference</a> + <a href="../articles/index.html">Articles</a> +</li> +<li> + <a href="../news/index.html">News</a> </li> </ul> <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin"> - <span class="fa fa-github fa-lg"></span> - - </a> -</li> + </ul> </div><!--/.nav-collapse --> </div><!--/.container --> diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html index 31207861..bce6d6a4 100644 --- a/docs/reference/mkin_wide_to_long.html +++ b/docs/reference/mkin_wide_to_long.html @@ -50,20 +50,18 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="../index.html">Home</a> + <a href="../reference/index.html">Reference</a> </li> <li> - <a href="../reference/index.html">Reference</a> + <a href="../articles/index.html">Articles</a> +</li> +<li> + <a href="../news/index.html">News</a> </li> </ul> <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin"> - <span class="fa fa-github fa-lg"></span> - - </a> -</li> + </ul> </div><!--/.nav-collapse --> </div><!--/.container --> diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html index 45cc315f..e5d99fd5 100644 --- a/docs/reference/mkinds.html +++ b/docs/reference/mkinds.html @@ -49,20 +49,18 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="../index.html">Home</a> + <a href="../reference/index.html">Reference</a> </li> <li> - <a href="../reference/index.html">Reference</a> + <a href="../articles/index.html">Articles</a> +</li> +<li> + <a href="../news/index.html">News</a> </li> </ul> <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin"> - <span class="fa fa-github fa-lg"></span> - - </a> -</li> + </ul> </div><!--/.nav-collapse --> </div><!--/.container --> diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html index 2e1833da..5b437b08 100644 --- a/docs/reference/mkinerrmin.html +++ b/docs/reference/mkinerrmin.html @@ -50,20 +50,18 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="../index.html">Home</a> + <a href="../reference/index.html">Reference</a> </li> <li> - <a href="../reference/index.html">Reference</a> + <a href="../articles/index.html">Articles</a> +</li> +<li> + <a href="../news/index.html">News</a> </li> </ul> <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin"> - <span class="fa fa-github fa-lg"></span> - - </a> -</li> + </ul> </div><!--/.nav-collapse --> </div><!--/.container --> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 3c9bd05c..6bfb9352 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -50,20 +50,18 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="../index.html">Home</a> + <a href="../reference/index.html">Reference</a> </li> <li> - <a href="../reference/index.html">Reference</a> + <a href="../articles/index.html">Articles</a> +</li> +<li> + <a href="../news/index.html">News</a> </li> </ul> <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin"> - <span class="fa fa-github fa-lg"></span> - - </a> -</li> + </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -361,15 +359,15 @@ <span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>summary</span>(<span class='no'>fit</span>)</div><div class='output co'>#> mkin version: 0.9.44.9000 #> R version: 3.3.1 -#> Date of fit: Wed Oct 26 23:16:49 2016 -#> Date of summary: Wed Oct 26 23:16:49 2016 +#> Date of fit: Wed Oct 26 23:50:42 2016 +#> Date of summary: Wed Oct 26 23:50:42 2016 #> #> Equations: #> d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent #> #> Model predictions using solution type analytical #> -#> Fitted with method Port using 64 model solutions performed in 0.148 s +#> Fitted with method Port using 64 model solutions performed in 0.168 s #> #> Weighting: none #> @@ -439,7 +437,7 @@ <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span> <span class='fu'>print</span>(<span class='fu'>system.time</span>(<span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)))</div><div class='output co'>#> user system elapsed -#> 1.224 1.196 0.913 +#> 1.272 1.204 0.943 #> </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit</span>)</div><div class='output co'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink #> 99.59848 -3.03822 -2.98030 -5.24750 #> </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> $ff diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index 53c87e92..40381656 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -50,20 +50,18 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="../index.html">Home</a> + <a href="../reference/index.html">Reference</a> </li> <li> - <a href="../reference/index.html">Reference</a> + <a href="../articles/index.html">Articles</a> +</li> +<li> + <a href="../news/index.html">News</a> </li> </ul> <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin"> - <span class="fa fa-github fa-lg"></span> - - </a> -</li> + </ul> </div><!--/.nav-collapse --> </div><!--/.container --> diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html index 6d4f2cfd..dff30930 100644 --- a/docs/reference/mkinparplot.html +++ b/docs/reference/mkinparplot.html @@ -50,20 +50,18 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="../index.html">Home</a> + <a href="../reference/index.html">Reference</a> </li> <li> - <a href="../reference/index.html">Reference</a> + <a href="../articles/index.html">Articles</a> +</li> +<li> + <a href="../news/index.html">News</a> </li> </ul> <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin"> - <span class="fa fa-github fa-lg"></span> - - </a> -</li> + </ul> </div><!--/.nav-collapse --> </div><!--/.container --> diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html index 925a6683..d3f0c1f6 100644 --- a/docs/reference/mkinplot.html +++ b/docs/reference/mkinplot.html @@ -50,20 +50,18 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="../index.html">Home</a> + <a href="../reference/index.html">Reference</a> </li> <li> - <a href="../reference/index.html">Reference</a> + <a href="../articles/index.html">Articles</a> +</li> +<li> + <a href="../news/index.html">News</a> </li> </ul> <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin"> - <span class="fa fa-github fa-lg"></span> - - </a> -</li> + </ul> </div><!--/.nav-collapse --> </div><!--/.container --> diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index cf04c6b6..31556527 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -50,20 +50,18 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="../index.html">Home</a> + <a href="../reference/index.html">Reference</a> </li> <li> - <a href="../reference/index.html">Reference</a> + <a href="../articles/index.html">Articles</a> +</li> +<li> + <a href="../news/index.html">News</a> </li> </ul> <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin"> - <span class="fa fa-github fa-lg"></span> - - </a> -</li> + </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -288,21 +286,21 @@ <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#> time parent m1 #> 201 20 4.978707 27.46227 #> </div><div class='output co'>#> user system elapsed -#> 0.008 0.024 0.004 +#> 0.028 0.004 0.004 #> </div><div class='input'> <span class='fu'>system.time</span>( <span class='fu'>print</span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>), <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#> time parent m1 #> 201 20 4.978707 27.46227 #> </div><div class='output co'>#> user system elapsed -#> 0.000 0.020 0.002 +#> 0.016 0.004 0.002 #> </div><div class='input'> <span class='fu'>system.time</span>( <span class='fu'>print</span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>), <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#> time parent m1 #> 201 20 4.978707 27.46227 #> </div><div class='output co'>#> user system elapsed -#> 0.036 0.000 0.035 +#> 0.052 0.000 0.052 #> </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html index f16dee5d..d8c84191 100644 --- a/docs/reference/mkinresplot.html +++ b/docs/reference/mkinresplot.html @@ -50,20 +50,18 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="../index.html">Home</a> + <a href="../reference/index.html">Reference</a> </li> <li> - <a href="../reference/index.html">Reference</a> + <a href="../articles/index.html">Articles</a> +</li> +<li> + <a href="../news/index.html">News</a> </li> </ul> <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin"> - <span class="fa fa-github fa-lg"></span> - - </a> -</li> + </ul> </div><!--/.nav-collapse --> </div><!--/.container --> diff --git a/docs/reference/mkinsub.html b/docs/reference/mkinsub.html index 2432e981..89387468 100644 --- a/docs/reference/mkinsub.html +++ b/docs/reference/mkinsub.html @@ -50,20 +50,18 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="../index.html">Home</a> + <a href="../reference/index.html">Reference</a> </li> <li> - <a href="../reference/index.html">Reference</a> + <a 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</ul> </div><!--/.nav-collapse --> </div><!--/.container --> diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html index 631ea429..4eb7369a 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -50,20 +50,18 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="../index.html">Home</a> + <a href="../reference/index.html">Reference</a> </li> <li> - <a href="../reference/index.html">Reference</a> + <a href="../articles/index.html">Articles</a> +</li> +<li> + <a href="../news/index.html">News</a> </li> </ul> <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin"> - <span class="fa fa-github fa-lg"></span> - - </a> -</li> + </ul> </div><!--/.nav-collapse --> </div><!--/.container --> diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html index 44ae760f..e0a20f3d 100644 --- a/docs/reference/plot.mmkin.html +++ b/docs/reference/plot.mmkin.html @@ -50,20 +50,18 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="../index.html">Home</a> + <a href="../reference/index.html">Reference</a> </li> <li> - <a href="../reference/index.html">Reference</a> + <a href="../articles/index.html">Articles</a> +</li> +<li> + <a href="../news/index.html">News</a> </li> </ul> <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin"> - <span class="fa fa-github fa-lg"></span> - - </a> -</li> + </ul> </div><!--/.nav-collapse --> </div><!--/.container --> diff --git a/docs/reference/print.mkinds.html b/docs/reference/print.mkinds.html index c4bc08d5..a586a103 100644 --- a/docs/reference/print.mkinds.html +++ b/docs/reference/print.mkinds.html @@ -50,20 +50,18 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="../index.html">Home</a> + <a href="../reference/index.html">Reference</a> </li> <li> - <a href="../reference/index.html">Reference</a> + <a href="../articles/index.html">Articles</a> +</li> +<li> + <a href="../news/index.html">News</a> </li> </ul> <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin"> - <span class="fa fa-github fa-lg"></span> - - </a> -</li> + </ul> </div><!--/.nav-collapse --> </div><!--/.container --> diff --git a/docs/reference/print.mkinmod.html b/docs/reference/print.mkinmod.html index edc9cde7..73bfd60e 100644 --- a/docs/reference/print.mkinmod.html +++ b/docs/reference/print.mkinmod.html @@ -50,20 +50,18 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="../index.html">Home</a> + <a href="../reference/index.html">Reference</a> </li> <li> - <a href="../reference/index.html">Reference</a> + <a href="../articles/index.html">Articles</a> +</li> +<li> + <a href="../news/index.html">News</a> </li> </ul> <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin"> - <span class="fa fa-github fa-lg"></span> - - </a> -</li> + </ul> </div><!--/.nav-collapse --> </div><!--/.container --> diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html index 1cd71697..4714747a 100644 --- a/docs/reference/schaefer07_complex_case.html +++ b/docs/reference/schaefer07_complex_case.html @@ -50,20 +50,18 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="../index.html">Home</a> + <a href="../reference/index.html">Reference</a> </li> <li> - <a href="../reference/index.html">Reference</a> + <a href="../articles/index.html">Articles</a> +</li> +<li> + <a href="../news/index.html">News</a> </li> </ul> <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin"> - <span class="fa fa-github fa-lg"></span> - - </a> -</li> + </ul> </div><!--/.nav-collapse --> </div><!--/.container --> diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index 1e1a0e2f..b88a5469 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -50,20 +50,18 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="../index.html">Home</a> + <a href="../reference/index.html">Reference</a> </li> <li> - <a href="../reference/index.html">Reference</a> + <a href="../articles/index.html">Articles</a> +</li> +<li> + <a href="../news/index.html">News</a> </li> </ul> <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin"> - <span class="fa fa-github fa-lg"></span> - - </a> -</li> + </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -144,15 +142,15 @@ </h2> <pre class="examples"><div class='input'> <span class='fu'>summary</span>(<span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>)), <span class='no'>FOCUS_2006_A</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#> mkin version: 0.9.44.9000 #> R version: 3.3.1 -#> Date of fit: Wed Oct 26 23:16:57 2016 -#> Date of summary: Wed Oct 26 23:16:57 2016 +#> Date of fit: Wed Oct 26 23:50:50 2016 +#> Date of summary: Wed Oct 26 23:50:50 2016 #> #> Equations: #> d_parent = - k_parent_sink * parent #> #> Model predictions using solution type analytical #> -#> Fitted with method Port using 35 model solutions performed in 0.089 s +#> Fitted with method Port using 35 model solutions performed in 0.083 s #> #> Weighting: none #> diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html index b45c07fc..45d5f53a 100644 --- a/docs/reference/synthetic_data_for_UBA.html +++ b/docs/reference/synthetic_data_for_UBA.html @@ -50,20 +50,18 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="../index.html">Home</a> + <a href="../reference/index.html">Reference</a> </li> <li> - <a href="../reference/index.html">Reference</a> + <a href="../articles/index.html">Articles</a> +</li> +<li> + <a href="../news/index.html">News</a> </li> </ul> <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin"> - <span class="fa fa-github fa-lg"></span> - - </a> -</li> + </ul> </div><!--/.nav-collapse --> </div><!--/.container --> diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index a07be0a0..ab5ce062 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -50,20 +50,18 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="../index.html">Home</a> + <a href="../reference/index.html">Reference</a> </li> <li> - <a href="../reference/index.html">Reference</a> + <a href="../articles/index.html">Articles</a> +</li> +<li> + <a href="../news/index.html">News</a> </li> </ul> <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin"> - <span class="fa fa-github fa-lg"></span> - - </a> -</li> + </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -151,8 +149,8 @@ <span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>summary</span>(<span class='no'>fit</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>) <span class='co'># See transformed and backtransformed parameters</span></div><div class='output co'>#> mkin version: 0.9.44.9000 #> R version: 3.3.1 -#> Date of fit: Wed Oct 26 23:16:59 2016 -#> Date of summary: Wed Oct 26 23:16:59 2016 +#> Date of fit: Wed Oct 26 23:50:51 2016 +#> Date of summary: Wed Oct 26 23:50:51 2016 #> #> Equations: #> d_parent = - k_parent_sink * parent - k_parent_m1 * parent @@ -160,7 +158,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 153 model solutions performed in 0.721 s +#> Fitted with method Port using 153 model solutions performed in 0.629 s #> #> Weighting: none #> |