diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2017-03-15 09:46:01 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2017-03-15 09:46:01 +0100 |
| commit | 4a048d8f6f70029141ffe4b6630c5eff4ba672f0 (patch) | |
| tree | b0fb102dc7cf95adfbcc994bd14348f8e9deefb5 /docs/reference | |
| parent | 30a648c8159af5fa927c2f0efa394b5d5dcfd342 (diff) | |
Static documentation except articles rebuilt by pkgdown
Diffstat (limited to 'docs/reference')
29 files changed, 238 insertions, 113 deletions
diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html index ed30ee50..bad6dd57 100644 --- a/docs/reference/DFOP.solution.html +++ b/docs/reference/DFOP.solution.html @@ -6,7 +6,8 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>Double First-Order in Parallel kinetics — DFOP.solution • mkin</title> +<title> + — DFOP.solution • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -72,6 +73,9 @@ </li> </ul> </li> +<li> + <a href="../news/index.html">News</a> +</li> </ul> <ul class="nav navbar-nav navbar-right"> @@ -92,7 +96,8 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1>Double First-Order in Parallel kinetics</h1> + <h1> +</h1> </div> diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 4ef3bb00..0131342a 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -72,6 +72,9 @@ </li> </ul> </li> +<li> + <a href="../news/index.html">News</a> +</li> </ul> <ul class="nav navbar-nav navbar-right"> @@ -239,7 +242,7 @@ #> #> $time #> user system elapsed -#> 0.064 0.000 0.065 +#> 0.068 0.000 0.066 #> #> $mkinmod #> <mkinmod> model generated with @@ -428,7 +431,7 @@ #> } #> return(mC) #> } -#> <environment: 0x5ce33e0> +#> <environment: 0x3b9eeb8> #> #> $cost_notrans #> function (P) @@ -450,7 +453,7 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x5ce33e0> +#> <environment: 0x3b9eeb8> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -513,7 +516,7 @@ #> 99.17407 #> #> $date -#> [1] "Thu Dec 8 07:56:34 2016" +#> [1] "Wed Mar 15 09:44:44 2017" #> #> 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 df8280d7..fff99b6c 100644 --- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html +++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html @@ -6,7 +6,8 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>Results of fitting the DFOP model to Datasets A to B of FOCUS (2006) — FOCUS_2006_DFOP_ref_A_to_B • mkin</title> +<title> + — FOCUS_2006_DFOP_ref_A_to_B • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -72,6 +73,9 @@ </li> </ul> </li> +<li> + <a href="../news/index.html">News</a> +</li> </ul> <ul class="nav navbar-nav navbar-right"> @@ -92,7 +96,8 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1>Results of fitting the DFOP model to Datasets A to B of FOCUS (2006)</h1> + <h1> +</h1> </div> 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 6132388f..5c9feb23 100644 --- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html @@ -6,7 +6,8 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>Results of fitting the FOMC model to Datasets A to F of FOCUS (2006) — FOCUS_2006_FOMC_ref_A_to_F • mkin</title> +<title> + — FOCUS_2006_FOMC_ref_A_to_F • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -72,6 +73,9 @@ </li> </ul> </li> +<li> + <a href="../news/index.html">News</a> +</li> </ul> <ul class="nav navbar-nav navbar-right"> @@ -92,7 +96,8 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1>Results of fitting the FOMC model to Datasets A to F of FOCUS (2006)</h1> + <h1> +</h1> </div> 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 86b071cf..8ccbd86a 100644 --- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html @@ -6,7 +6,8 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>Results of fitting the HS model to Datasets A to F of FOCUS (2006) — FOCUS_2006_HS_ref_A_to_F • mkin</title> +<title> + — FOCUS_2006_HS_ref_A_to_F • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -72,6 +73,9 @@ </li> </ul> </li> +<li> + <a href="../news/index.html">News</a> +</li> </ul> <ul class="nav navbar-nav navbar-right"> @@ -92,7 +96,8 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1>Results of fitting the HS model to Datasets A to F of FOCUS (2006)</h1> + <h1> +</h1> </div> 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 b2d199d3..263b9b31 100644 --- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html @@ -6,7 +6,8 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>Results of fitting the SFO model to Datasets A to F of FOCUS (2006) — FOCUS_2006_SFO_ref_A_to_F • mkin</title> +<title> + — FOCUS_2006_SFO_ref_A_to_F • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -72,6 +73,9 @@ </li> </ul> </li> +<li> + <a href="../news/index.html">News</a> +</li> </ul> <ul class="nav navbar-nav navbar-right"> @@ -92,7 +96,8 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1>Results of fitting the SFO model to Datasets A to F of FOCUS (2006)</h1> + <h1> +</h1> </div> diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html index cde972b7..71dbe761 100644 --- a/docs/reference/FOCUS_2006_datasets.html +++ b/docs/reference/FOCUS_2006_datasets.html @@ -6,7 +6,8 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>Datasets A to F from the FOCUS Kinetics report from 2006 — FOCUS_2006_datasets • mkin</title> +<title> + — FOCUS_2006_datasets • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -72,6 +73,9 @@ </li> </ul> </li> +<li> + <a href="../news/index.html">News</a> +</li> </ul> <ul class="nav navbar-nav navbar-right"> @@ -92,7 +96,8 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1>Datasets A to F from the FOCUS Kinetics report from 2006</h1> + <h1> +</h1> </div> diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html index 932935b4..8d0ed869 100644 --- a/docs/reference/FOMC.solution.html +++ b/docs/reference/FOMC.solution.html @@ -6,7 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>First-Order Multi-Compartment kinetics — FOMC.solution • mkin</title> +<title> First-Order Multi-Compartment kinetics — FOMC.solution • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -72,6 +72,9 @@ </li> </ul> </li> +<li> + <a href="../news/index.html">News</a> +</li> </ul> <ul class="nav navbar-nav navbar-right"> @@ -92,7 +95,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1>First-Order Multi-Compartment kinetics</h1> + <h1> First-Order Multi-Compartment kinetics </h1> </div> diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html index 2d0b6e4f..b8e6f524 100644 --- a/docs/reference/HS.solution.html +++ b/docs/reference/HS.solution.html @@ -6,7 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>Hockey-Stick kinetics — HS.solution • mkin</title> +<title> Hockey-Stick kinetics — HS.solution • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -72,6 +72,9 @@ </li> </ul> </li> +<li> + <a href="../news/index.html">News</a> +</li> </ul> <ul class="nav navbar-nav navbar-right"> @@ -92,7 +95,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1>Hockey-Stick kinetics</h1> + <h1> Hockey-Stick kinetics </h1> </div> diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html index 35e01039..8caef574 100644 --- a/docs/reference/IORE.solution.html +++ b/docs/reference/IORE.solution.html @@ -6,7 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>Indeterminate order rate equation kinetics — IORE.solution • mkin</title> +<title> Indeterminate order rate equation kinetics — IORE.solution • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -72,6 +72,9 @@ </li> </ul> </li> +<li> + <a href="../news/index.html">News</a> +</li> </ul> <ul class="nav navbar-nav navbar-right"> @@ -92,7 +95,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1>Indeterminate order rate equation kinetics</h1> + <h1> Indeterminate order rate equation kinetics </h1> </div> diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html index 3fa6d1d4..e2c93102 100644 --- a/docs/reference/SFO.solution.html +++ b/docs/reference/SFO.solution.html @@ -6,7 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>Single First-Order kinetics — SFO.solution • mkin</title> +<title> Single First-Order kinetics — SFO.solution • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -72,6 +72,9 @@ </li> </ul> </li> +<li> + <a href="../news/index.html">News</a> +</li> </ul> <ul class="nav navbar-nav navbar-right"> @@ -92,7 +95,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1>Single First-Order kinetics</h1> + <h1> Single First-Order kinetics </h1> </div> diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html index d4661cfd..4a73ba9e 100644 --- a/docs/reference/SFORB.solution.html +++ b/docs/reference/SFORB.solution.html @@ -6,7 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>Single First-Order Reversible Binding kinetics — SFORB.solution • mkin</title> +<title> Single First-Order Reversible Binding kinetics — SFORB.solution • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -72,6 +72,9 @@ </li> </ul> </li> +<li> + <a href="../news/index.html">News</a> +</li> </ul> <ul class="nav navbar-nav navbar-right"> @@ -92,7 +95,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1>Single First-Order Reversible Binding kinetics</h1> + <h1> Single First-Order Reversible Binding kinetics </h1> </div> diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html index edced046..aab42f56 100644 --- a/docs/reference/add_err.html +++ b/docs/reference/add_err.html @@ -6,7 +6,8 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>Add normally distributed errors to simulated kinetic degradation data — add_err • mkin</title> +<title> + — add_err • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -72,6 +73,9 @@ </li> </ul> </li> +<li> + <a href="../news/index.html">News</a> +</li> </ul> <ul class="nav navbar-nav navbar-right"> @@ -92,7 +96,8 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1>Add normally distributed errors to simulated kinetic degradation data</h1> + <h1> +</h1> </div> diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html index 38a6a400..4145825a 100644 --- a/docs/reference/endpoints.html +++ b/docs/reference/endpoints.html @@ -6,7 +6,8 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>Function to calculate endpoints for further use from kinetic models fitted with mkinfit — endpoints • mkin</title> +<title> + — endpoints • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -72,6 +73,9 @@ </li> </ul> </li> +<li> + <a href="../news/index.html">News</a> +</li> </ul> <ul class="nav navbar-nav navbar-right"> @@ -92,7 +96,8 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1>Function to calculate endpoints for further use from kinetic models fitted with mkinfit</h1> + <h1> +</h1> </div> diff --git a/docs/reference/geometric_mean.html b/docs/reference/geometric_mean.html index 03b9f54b..828ec471 100644 --- a/docs/reference/geometric_mean.html +++ b/docs/reference/geometric_mean.html @@ -6,7 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>Calculate the geometric mean — geometric_mean • mkin</title> +<title> Calculate the geometric mean — geometric_mean • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -72,6 +72,9 @@ </li> </ul> </li> +<li> + <a href="../news/index.html">News</a> +</li> </ul> <ul class="nav navbar-nav navbar-right"> @@ -92,7 +95,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1>Calculate the geometric mean</h1> + <h1> Calculate the geometric mean </h1> </div> diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html index 85f203ed..4262fa81 100644 --- a/docs/reference/ilr.html +++ b/docs/reference/ilr.html @@ -6,7 +6,8 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>Function to perform isometric log-ratio transformation — ilr • mkin</title> +<title> + — ilr • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -72,6 +73,9 @@ </li> </ul> </li> +<li> + <a href="../news/index.html">News</a> +</li> </ul> <ul class="nav navbar-nav navbar-right"> @@ -92,7 +96,8 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1>Function to perform isometric log-ratio transformation</h1> + <h1> +</h1> </div> diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 123af096..4fa32b30 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -6,7 +6,8 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>Datasets on aerobic soil metabolism of 2,4,5-T in six soils — mccall81_245T • mkin</title> +<title> + — mccall81_245T • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -72,6 +73,9 @@ </li> </ul> </li> +<li> + <a href="../news/index.html">News</a> +</li> </ul> <ul class="nav navbar-nav navbar-right"> @@ -92,7 +96,8 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1>Datasets on aerobic soil metabolism of 2,4,5-T in six soils</h1> + <h1> +</h1> </div> @@ -128,10 +133,10 @@ <span class='kw'>phenol</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='kw'>to</span> <span class='kw'>=</span> <span class='st'>"anisole"</span>), <span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> <span class='no'>fit.1</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'>subset</span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Optimisation by method Port did not converge.</span> -#> <span class='warning'>Convergence code is 1</span></div><div class='input'> <span class='fu'>summary</span>(<span class='no'>fit.1</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: 3.3.2 -#> Date of fit: Thu Dec 8 07:56:42 2016 -#> Date of summary: Thu Dec 8 07:56:42 2016 +#> <span class='warning'>Convergence code is 1</span></div><div class='input'> <span class='fu'>summary</span>(<span class='no'>fit.1</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> mkin version: 0.9.45.1 +#> R version: 3.3.3 +#> Date of fit: Wed Mar 15 09:44:52 2017 +#> Date of summary: Wed Mar 15 09:44:52 2017 #> #> #> Warning: Optimisation by method Port did not converge. @@ -146,7 +151,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 590 model solutions performed in 3.474 s +#> Fitted with method Port using 590 model solutions performed in 3.519 s #> #> Weighting: none #> @@ -223,10 +228,10 @@ <span class='no'>fit.2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'>subset</span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='kw'>k_phenol_sink</span> <span class='kw'>=</span> <span class='fl'>0</span>), <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: 3.3.2 -#> Date of fit: Thu Dec 8 07:56:44 2016 -#> Date of summary: Thu Dec 8 07:56:44 2016 + <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: 0.9.45.1 +#> R version: 3.3.3 +#> Date of fit: Wed Mar 15 09:44:54 2017 +#> Date of summary: Wed Mar 15 09:44:54 2017 #> #> Equations: #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -236,7 +241,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 246 model solutions performed in 1.44 s +#> Fitted with method Port using 246 model solutions performed in 1.449 s #> #> Weighting: none #> diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html index af7daf7a..9b37726e 100644 --- a/docs/reference/mkin_long_to_wide.html +++ b/docs/reference/mkin_long_to_wide.html @@ -6,7 +6,8 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>Convert a dataframe from long to wide format — mkin_long_to_wide • mkin</title> +<title> + — mkin_long_to_wide • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -72,6 +73,9 @@ </li> </ul> </li> +<li> + <a href="../news/index.html">News</a> +</li> </ul> <ul class="nav navbar-nav navbar-right"> @@ -92,7 +96,8 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1>Convert a dataframe from long to wide format</h1> + <h1> +</h1> </div> diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html index 75417aec..378d3691 100644 --- a/docs/reference/mkin_wide_to_long.html +++ b/docs/reference/mkin_wide_to_long.html @@ -6,7 +6,8 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>Convert a dataframe with observations over time into long format — mkin_wide_to_long • mkin</title> +<title> + — mkin_wide_to_long • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -72,6 +73,9 @@ </li> </ul> </li> +<li> + <a href="../news/index.html">News</a> +</li> </ul> <ul class="nav navbar-nav navbar-right"> @@ -92,7 +96,8 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1>Convert a dataframe with observations over time into long format</h1> + <h1> +</h1> </div> diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html index a69920fd..97616a41 100644 --- a/docs/reference/mkinerrmin.html +++ b/docs/reference/mkinerrmin.html @@ -6,7 +6,8 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>Calculate the minimum error to assume in order to pass the variance test — mkinerrmin • mkin</title> +<title> + — mkinerrmin • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -72,6 +73,9 @@ </li> </ul> </li> +<li> + <a href="../news/index.html">News</a> +</li> </ul> <ul class="nav navbar-nav navbar-right"> @@ -92,7 +96,8 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1>Calculate the minimum error to assume in order to pass the variance test</h1> + <h1> +</h1> </div> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 3dd701d3..01c930e2 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -6,7 +6,8 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>Fit a kinetic model to data with one or more state variables — mkinfit • mkin</title> +<title> + — mkinfit • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -72,6 +73,9 @@ </li> </ul> </li> +<li> + <a href="../news/index.html">News</a> +</li> </ul> <ul class="nav navbar-nav navbar-right"> @@ -92,7 +96,8 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1>Fit a kinetic model to data with one or more state variables</h1> + <h1> +</h1> </div> @@ -372,17 +377,17 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='co'># Use shorthand notation for parent only degradation</span> <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: 3.3.2 -#> Date of fit: Thu Dec 8 07:56:46 2016 -#> Date of summary: Thu Dec 8 07:56:46 2016 +<span class='fu'>summary</span>(<span class='no'>fit</span>)</div><div class='output co'>#> mkin version: 0.9.45.1 +#> R version: 3.3.3 +#> Date of fit: Wed Mar 15 09:44:56 2017 +#> Date of summary: Wed Mar 15 09:44:56 2017 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent #> #> Model predictions using solution type analytical #> -#> Fitted with method Port using 64 model solutions performed in 0.145 s +#> Fitted with method Port using 64 model solutions performed in 0.146 s #> #> Weighting: none #> @@ -451,7 +456,7 @@ <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 co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></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 -#> 1.172 1.232 0.904 </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 +#> 1.216 1.268 0.942 </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 #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 @@ -528,7 +533,7 @@ #> Model cost at call 152 : 371.2134 #> Optimisation by method Port successfully terminated. #> user system elapsed -#> 0.712 0.044 0.709 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 0.712 0.040 0.703 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit.deSolve</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.deSolve</span>)</div><div class='output co'>#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 @@ -569,10 +574,10 @@ <span class='co'># Weighted fits, including IRLS</span> <span class='no'>SFO_SFO.ff</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>f.noweight</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</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'>f.noweight</span>)</div><div class='output co'>#> mkin version: 0.9.44.9000 -#> R version: 3.3.2 -#> Date of fit: Thu Dec 8 07:56:57 2016 -#> Date of summary: Thu Dec 8 07:56:57 2016 +<span class='fu'>summary</span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#> mkin version: 0.9.45.1 +#> R version: 3.3.3 +#> Date of fit: Wed Mar 15 09:45:07 2017 +#> Date of summary: Wed Mar 15 09:45:07 2017 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -580,7 +585,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 185 model solutions performed in 0.77 s +#> Fitted with method Port using 185 model solutions performed in 0.753 s #> #> Weighting: none #> @@ -690,10 +695,10 @@ #> 100 m1 33.13 3.198e+01 1.148e+00 #> 120 m1 25.15 2.879e+01 -3.640e+00 #> 120 m1 33.31 2.879e+01 4.520e+00</div><div class='input'><span class='no'>f.irls</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='fu'>summary</span>(<span class='no'>f.irls</span>)</div><div class='output co'>#> mkin version: 0.9.44.9000 -#> R version: 3.3.2 -#> Date of fit: Thu Dec 8 07:56:59 2016 -#> Date of summary: Thu Dec 8 07:56:59 2016 +<span class='fu'>summary</span>(<span class='no'>f.irls</span>)</div><div class='output co'>#> mkin version: 0.9.45.1 +#> R version: 3.3.3 +#> Date of fit: Wed Mar 15 09:45:09 2017 +#> Date of summary: Wed Mar 15 09:45:09 2017 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -701,7 +706,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 486 model solutions performed in 2.019 s +#> Fitted with method Port using 486 model solutions performed in 2.091 s #> #> Weighting: none then iterative reweighting method obs #> @@ -811,10 +816,10 @@ #> 100 m1 33.13 3.199e+01 1.140e+00 2.722 #> 120 m1 25.15 2.881e+01 -3.659e+00 2.722 #> 120 m1 33.31 2.881e+01 4.501e+00 2.722</div><div class='input'><span class='no'>f.w.mean</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>weight</span> <span class='kw'>=</span> <span class='st'>"mean"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='fu'>summary</span>(<span class='no'>f.w.mean</span>)</div><div class='output co'>#> mkin version: 0.9.44.9000 -#> R version: 3.3.2 -#> Date of fit: Thu Dec 8 07:57:00 2016 -#> Date of summary: Thu Dec 8 07:57:00 2016 +<span class='fu'>summary</span>(<span class='no'>f.w.mean</span>)</div><div class='output co'>#> mkin version: 0.9.45.1 +#> R version: 3.3.3 +#> Date of fit: Wed Mar 15 09:45:10 2017 +#> Date of summary: Wed Mar 15 09:45:10 2017 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -822,7 +827,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 155 model solutions performed in 0.65 s +#> Fitted with method Port using 155 model solutions performed in 0.661 s #> #> Weighting: mean #> @@ -933,10 +938,10 @@ #> 120 m1 25.15 28.824128 -3.674128 #> 120 m1 33.31 28.824128 4.485872</div><div class='input'><span class='no'>f.w.value</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='fu'>subset</span>(<span class='no'>FOCUS_2006_D</span>, <span class='no'>value</span> <span class='kw'>!=</span> <span class='fl'>0</span>), <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"value"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='fu'>summary</span>(<span class='no'>f.w.value</span>)</div><div class='output co'>#> mkin version: 0.9.44.9000 -#> R version: 3.3.2 -#> Date of fit: Thu Dec 8 07:57:01 2016 -#> Date of summary: Thu Dec 8 07:57:01 2016 +<span class='fu'>summary</span>(<span class='no'>f.w.value</span>)</div><div class='output co'>#> mkin version: 0.9.45.1 +#> R version: 3.3.3 +#> Date of fit: Wed Mar 15 09:45:11 2017 +#> Date of summary: Wed Mar 15 09:45:11 2017 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -944,7 +949,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 174 model solutions performed in 0.713 s +#> Fitted with method Port using 174 model solutions performed in 0.724 s #> #> Weighting: manual #> @@ -1055,10 +1060,10 @@ <span class='no'>errors</span> <span class='kw'><-</span> <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>1</span>) <span class='no'>dw</span>$<span class='no'>err.man</span> <span class='kw'><-</span> <span class='no'>errors</span>[<span class='no'>FOCUS_2006_D</span>$<span class='no'>name</span>] <span class='no'>f.w.man</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>dw</span>, <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"err.man"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='fu'>summary</span>(<span class='no'>f.w.man</span>)</div><div class='output co'>#> mkin version: 0.9.44.9000 -#> R version: 3.3.2 -#> Date of fit: Thu Dec 8 07:57:02 2016 -#> Date of summary: Thu Dec 8 07:57:02 2016 +<span class='fu'>summary</span>(<span class='no'>f.w.man</span>)</div><div class='output co'>#> mkin version: 0.9.45.1 +#> R version: 3.3.3 +#> Date of fit: Wed Mar 15 09:45:12 2017 +#> Date of summary: Wed Mar 15 09:45:12 2017 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -1066,7 +1071,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 316 model solutions performed in 1.322 s +#> Fitted with method Port using 316 model solutions performed in 1.31 s #> #> Weighting: manual #> @@ -1177,10 +1182,10 @@ #> 120 m1 25.15 28.760615 -3.610615 2 #> 120 m1 33.31 28.760615 4.549385 2</div><div class='input'><span class='no'>f.w.man.irls</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>dw</span>, <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"err.man"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>) -<span class='fu'>summary</span>(<span class='no'>f.w.man.irls</span>)</div><div class='output co'>#> mkin version: 0.9.44.9000 -#> R version: 3.3.2 -#> Date of fit: Thu Dec 8 07:57:05 2016 -#> Date of summary: Thu Dec 8 07:57:05 2016 +<span class='fu'>summary</span>(<span class='no'>f.w.man.irls</span>)</div><div class='output co'>#> mkin version: 0.9.45.1 +#> R version: 3.3.3 +#> Date of fit: Wed Mar 15 09:45:15 2017 +#> Date of summary: Wed Mar 15 09:45:15 2017 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -1188,7 +1193,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 648 model solutions performed in 2.818 s +#> Fitted with method Port using 648 model solutions performed in 2.766 s #> #> Weighting: manual then iterative reweighting method obs #> diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index 1044af6b..1343abcc 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -6,7 +6,8 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>Function to set up a kinetic model with one or more state variables — mkinmod • mkin</title> +<title> + — mkinmod • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -72,6 +73,9 @@ </li> </ul> </li> +<li> + <a href="../news/index.html">News</a> +</li> </ul> <ul class="nav navbar-nav navbar-right"> @@ -92,7 +96,8 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1>Function to set up a kinetic model with one or more state variables</h1> + <h1> +</h1> </div> @@ -188,7 +193,7 @@ <span class='no'>SFO_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>( <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> Compilation argument: -#> /usr/lib/R/bin/R CMD SHLIB file386742883b12.c 2> file386742883b12.c.err.txt +#> /usr/lib/R/bin/R CMD SHLIB file2ac5b2884c1.c 2> file2ac5b2884c1.c.err.txt #> Program source: #> 1: #include <R.h> #> 2: diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html index 744de866..0682211b 100644 --- a/docs/reference/mkinparplot.html +++ b/docs/reference/mkinparplot.html @@ -6,7 +6,8 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>Function to plot the confidence intervals obtained using mkinfit — mkinparplot • mkin</title> +<title> + — mkinparplot • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -72,6 +73,9 @@ </li> </ul> </li> +<li> + <a href="../news/index.html">News</a> +</li> </ul> <ul class="nav navbar-nav navbar-right"> @@ -92,7 +96,8 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1>Function to plot the confidence intervals obtained using mkinfit</h1> + <h1> +</h1> </div> diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html index 898b1b9f..fdc61af4 100644 --- a/docs/reference/mkinplot.html +++ b/docs/reference/mkinplot.html @@ -6,7 +6,8 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>Plot the observed data and the fitted model of an mkinfit object — mkinplot • mkin</title> +<title> + — mkinplot • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -95,7 +96,8 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1>Plot the observed data and the fitted model of an mkinfit object</h1> + <h1> +</h1> </div> diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 766b6613..2348d40e 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -6,7 +6,8 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>Produce predictions from a kinetic model using specific parameters — mkinpredict • mkin</title> +<title> + — mkinpredict • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -72,6 +73,9 @@ </li> </ul> </li> +<li> + <a href="../news/index.html">News</a> +</li> </ul> <ul class="nav navbar-nav navbar-right"> @@ -92,7 +96,8 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1>Produce predictions from a kinetic model using specific parameters</h1> + <h1> +</h1> </div> @@ -290,17 +295,17 @@ <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'>"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 -#> 0.012 0.020 0.005 </div><div class='input'> <span class='fu'>system.time</span>( +#> 0.016 0.016 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 0.003 </div><div class='input'> <span class='fu'>system.time</span>( +#> 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 -#> 0.032 0.000 0.035 </div></pre> +#> 0.032 0.000 0.034 </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html index a6527aa4..fd5722bc 100644 --- a/docs/reference/mkinresplot.html +++ b/docs/reference/mkinresplot.html @@ -6,7 +6,8 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>Function to plot residuals stored in an mkin object — mkinresplot • mkin</title> +<title> + — mkinresplot • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -95,7 +96,8 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1>Function to plot residuals stored in an mkin object</h1> + <h1> +</h1> </div> diff --git a/docs/reference/mkinsub.html b/docs/reference/mkinsub.html index bad034ee..aff0b593 100644 --- a/docs/reference/mkinsub.html +++ b/docs/reference/mkinsub.html @@ -6,7 +6,8 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>Function to set up a kinetic submodel for one state variable — mkinsub • mkin</title> +<title> + — mkinsub • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -72,6 +73,9 @@ </li> </ul> </li> +<li> + <a href="../news/index.html">News</a> +</li> </ul> <ul class="nav navbar-nav navbar-right"> @@ -92,7 +96,8 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1>Function to set up a kinetic submodel for one state variable</h1> + <h1> +</h1> </div> diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index 0127f114..67397827 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -6,7 +6,8 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>Fit one or more kinetic models with one or more state variables to one or more datasets — mmkin • mkin</title> +<title> + — mmkin • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -72,6 +73,9 @@ </li> </ul> </li> +<li> + <a href="../news/index.html">News</a> +</li> </ul> <ul class="nav navbar-nav navbar-right"> @@ -92,7 +96,8 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1>Fit one or more kinetic models with one or more state variables to one or more datasets</h1> + <h1> +</h1> </div> @@ -158,8 +163,8 @@ <span class='no'>time_1</span> <span class='kw'><-</span> <span class='fu'>system.time</span>(<span class='no'>fits.4</span> <span class='kw'><-</span> <span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)) <span class='no'>time_default</span></div><div class='output co'>#> user system elapsed -#> 16.776 0.108 9.353 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#> user system elapsed -#> 22.696 0.000 22.701 </div><div class='input'> +#> 16.360 0.128 9.017 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#> user system elapsed +#> 21.888 0.004 21.892 </div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='st'>"SFO_lin"</span>, <span class='fl'>2</span>]])</div><div class='output co'>#> $ff #> parent_M1 parent_sink M1_M2 M1_sink #> 0.7340479 0.2659521 0.7505687 0.2494313 diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html index 9969e198..e77b7b54 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -6,7 +6,8 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>Plot the observed data and the fitted model of an mkinfit object — plot.mkinfit • mkin</title> +<title> + — plot.mkinfit • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -72,6 +73,9 @@ </li> </ul> </li> +<li> + <a href="../news/index.html">News</a> +</li> </ul> <ul class="nav navbar-nav navbar-right"> @@ -92,7 +96,8 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1>Plot the observed data and the fitted model of an mkinfit object</h1> + <h1> +</h1> </div> |