diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2016-11-04 17:11:50 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2016-11-04 17:11:50 +0100 |
| commit | 517d9378284bb4341c1bbce6716b89b341c8b61e (patch) | |
| tree | e4ebb4ac0b7e6c91bd8fdf127b69baf66c4b26d7 /docs/reference | |
| parent | 2bd7610ecb5f4aa2ed564bd0d581adb49a1baa41 (diff) | |
Rebuild docs with updated PR for pkgdown
Diffstat (limited to 'docs/reference')
43 files changed, 325 insertions, 191 deletions
diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html index 7d036804..c0690f41 100644 --- a/docs/reference/DFOP.solution.html +++ b/docs/reference/DFOP.solution.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — DFOP.solution • mkin</title> +<title>Double First-Order in Parallel kinetics — DFOP.solution • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -61,7 +60,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -73,8 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Double First-Order in Parallel kinetics</h1> </div> diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index cfe6329b..ad4614fb 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -60,7 +60,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -188,7 +193,7 @@ #> #> $time #> user system elapsed -#> 0.316 0.000 0.317 +#> 0.264 0.000 0.262 #> #> $mkinmod #> <mkinmod> model generated with @@ -374,7 +379,7 @@ #> } #> return(mC) #> } -#> <environment: 0x5d4a3b0> +#> <environment: 0x50d32d0> #> #> $cost_notrans #> function (P) @@ -396,7 +401,7 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x5d4a3b0> +#> <environment: 0x50d32d0> #> #> $hessian_notrans #> parent_0 alpha beta @@ -462,7 +467,7 @@ #> 99.66619 #> #> $date -#> [1] "Fri Nov 4 15:36:31 2016" +#> [1] "Fri Nov 4 17:08:52 2016" #> #> attr(,"class") #> [1] "mkinfit" "modFit" </div><div class='input'> <span class='no'>fits</span>[<span class='st'>"SFO"</span>, <span class='st'>"B"</span>]</div><div class='output co'>#> dataset @@ -541,7 +546,7 @@ #> #> $time #> user system elapsed -#> 0.076 0.000 0.077 +#> 0.068 0.000 0.067 #> #> $mkinmod #> <mkinmod> model generated with @@ -728,7 +733,7 @@ #> } #> return(mC) #> } -#> <environment: 0x5d98970> +#> <environment: 0x4f17408> #> #> $cost_notrans #> function (P) @@ -750,7 +755,7 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x5d98970> +#> <environment: 0x4f17408> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -813,7 +818,7 @@ #> 99.17407 #> #> $date -#> [1] "Fri Nov 4 15:36:30 2016" +#> [1] "Fri Nov 4 17:08:51 2016" #> #> attr(,"class") #> [1] "mkinfit" "modFit" </div><div class='input'> <span class='no'>fits</span>[<span class='st'>"SFO"</span>, <span class='st'>"B"</span>, <span class='kw'>drop</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>]</div><div class='output co'>#> [[1]] @@ -889,7 +894,7 @@ #> #> $time #> user system elapsed -#> 0.076 0.000 0.077 +#> 0.068 0.000 0.067 #> #> $mkinmod #> <mkinmod> model generated with @@ -1076,7 +1081,7 @@ #> } #> return(mC) #> } -#> <environment: 0x5d98970> +#> <environment: 0x4f17408> #> #> $cost_notrans #> function (P) @@ -1098,7 +1103,7 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x5d98970> +#> <environment: 0x4f17408> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -1161,7 +1166,7 @@ #> 99.17407 #> #> $date -#> [1] "Fri Nov 4 15:36:30 2016" +#> [1] "Fri Nov 4 17:08:51 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 97af2f9c..13dfa186 100644 --- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html +++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — FOCUS_2006_DFOP_ref_A_to_B • mkin</title> +<title>Results of fitting the DFOP model to Datasets A to B of FOCUS (2006) — 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> @@ -61,7 +60,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -73,8 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Results of fitting the DFOP model to Datasets A to B of FOCUS (2006)</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 1487e2c9..5b36ac74 100644 --- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — FOCUS_2006_FOMC_ref_A_to_F • mkin</title> +<title>Results of fitting the FOMC model to Datasets A to F of FOCUS (2006) — 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> @@ -61,7 +60,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -73,8 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Results of fitting the FOMC model to Datasets A to F of FOCUS (2006)</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 4571c175..446ce4d7 100644 --- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — FOCUS_2006_HS_ref_A_to_F • mkin</title> +<title>Results of fitting the HS model to Datasets A to F of FOCUS (2006) — 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> @@ -61,7 +60,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -73,8 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Results of fitting the HS model to Datasets A to F of FOCUS (2006)</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 7003fa0e..db462f10 100644 --- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — FOCUS_2006_SFO_ref_A_to_F • mkin</title> +<title>Results of fitting the SFO model to Datasets A to F of FOCUS (2006) — 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> @@ -61,7 +60,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -73,8 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Results of fitting the SFO model to Datasets A to F of FOCUS (2006)</h1> </div> diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html index 83edd323..ffc7558e 100644 --- a/docs/reference/FOCUS_2006_datasets.html +++ b/docs/reference/FOCUS_2006_datasets.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — FOCUS_2006_datasets • mkin</title> +<title>Datasets A to F from the FOCUS Kinetics report from 2006 — FOCUS_2006_datasets • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -61,7 +60,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -73,8 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Datasets A to F from the FOCUS Kinetics report from 2006</h1> </div> diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html index 83bca886..fdbf0d1f 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> @@ -60,7 +60,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -72,7 +77,7 @@ <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 13db29aa..fbe0b590 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> @@ -60,7 +60,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -72,7 +77,7 @@ <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 56c2b48e..553c38b0 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> @@ -60,7 +60,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -72,7 +77,7 @@ <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 8ff5b5ba..2ead8f24 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> @@ -60,7 +60,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -72,7 +77,7 @@ <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 43b6028a..be425d83 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> @@ -60,7 +60,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -72,7 +77,7 @@ <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 8e491bc9..0a126c5c 100644 --- a/docs/reference/add_err.html +++ b/docs/reference/add_err.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — add_err • mkin</title> +<title>Add normally distributed errors to simulated kinetic degradation data — add_err • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -61,7 +60,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -73,8 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Add normally distributed errors to simulated kinetic degradation data</h1> </div> diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html index a3716060..44a8f4c4 100644 --- a/docs/reference/endpoints.html +++ b/docs/reference/endpoints.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — endpoints • mkin</title> +<title>Function to calculate endpoints for further use from kinetic models fitted with mkinfit — endpoints • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -61,7 +60,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -73,8 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Function to calculate endpoints for further use from kinetic models fitted with mkinfit</h1> </div> diff --git a/docs/reference/geometric_mean.html b/docs/reference/geometric_mean.html index 633e0865..97352ff8 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> @@ -60,7 +60,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -72,7 +77,7 @@ <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 955b5c58..95fed72e 100644 --- a/docs/reference/ilr.html +++ b/docs/reference/ilr.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — ilr • mkin</title> +<title>Function to perform isometric log-ratio transformation — ilr • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -61,7 +60,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -73,8 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Function to perform isometric log-ratio transformation</h1> </div> diff --git a/docs/reference/index.html b/docs/reference/index.html index b7d59a21..32455baa 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -60,7 +60,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://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/mccall81_245T.html b/docs/reference/mccall81_245T.html index d32acb5b..6eb4741b 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — mccall81_245T • mkin</title> +<title>Datasets on aerobic soil metabolism of 2,4,5-T in six soils — mccall81_245T • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -61,7 +60,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -73,8 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Datasets on aerobic soil metabolism of 2,4,5-T in six soils</h1> </div> @@ -119,8 +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: 3.3.2 -#> Date of fit: Fri Nov 4 15:36:38 2016 -#> Date of summary: Fri Nov 4 15:36:38 2016 +#> Date of fit: Fri Nov 4 17:08:59 2016 +#> Date of summary: Fri Nov 4 17:08:59 2016 #> #> Equations: #> d_T245 = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -130,7 +133,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 246 model solutions performed in 1.886 s +#> Fitted with method Port using 246 model solutions performed in 1.497 s #> #> Weighting: none #> diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html index 21a8a8f8..fa131a6d 100644 --- a/docs/reference/mkin_long_to_wide.html +++ b/docs/reference/mkin_long_to_wide.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — mkin_long_to_wide • mkin</title> +<title>Convert a dataframe from long to wide format — 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> @@ -61,7 +60,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -73,8 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Convert a dataframe from long to wide format</h1> </div> diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html index fe6e47e4..077c0b7d 100644 --- a/docs/reference/mkin_wide_to_long.html +++ b/docs/reference/mkin_wide_to_long.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — mkin_wide_to_long • mkin</title> +<title>Convert a dataframe with observations over time into long format — 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> @@ -61,7 +60,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -73,8 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Convert a dataframe with observations over time into long format</h1> </div> diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html index f5dd4c88..522aab33 100644 --- a/docs/reference/mkinds.html +++ b/docs/reference/mkinds.html @@ -60,7 +60,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://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 8d420165..d212e3b2 100644 --- a/docs/reference/mkinerrmin.html +++ b/docs/reference/mkinerrmin.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — mkinerrmin • mkin</title> +<title>Calculate the minimum error to assume in order to pass the variance test — mkinerrmin • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -61,7 +60,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -73,8 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Calculate the minimum error to assume in order to pass the variance test</h1> </div> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index b298d90a..93185eff 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — mkinfit • mkin</title> +<title>Fit a kinetic model to data with one or more state variables — mkinfit • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -61,7 +60,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -73,8 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Fit a kinetic model to data with one or more state variables</h1> </div> @@ -356,8 +359,8 @@ <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: Fri Nov 4 15:36:41 2016 -#> Date of summary: Fri Nov 4 15:36:41 2016 +#> Date of fit: Fri Nov 4 17:09:01 2016 +#> Date of summary: Fri Nov 4 17:09:01 2016 #> #> Equations: #> d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent @@ -433,7 +436,7 @@ <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 -#> 1.244 1.208 0.933 </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 +#> 1.256 1.216 0.946 </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 diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index 7dba1b6d..f328c34a 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — mkinmod • mkin</title> +<title>Function to set up a kinetic model with one or more state variables — mkinmod • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -61,7 +60,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -73,8 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Function to set up a kinetic model with one or more state variables</h1> </div> diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html index 923abc6d..764f1ab4 100644 --- a/docs/reference/mkinparplot.html +++ b/docs/reference/mkinparplot.html @@ -6,8 +6,8 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — mkinparplot • mkin</title> +<title>Function to plot the confidence intervals obtained using + list(list("mkinfit")) — mkinparplot • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -61,7 +61,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -73,8 +78,8 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Function to plot the confidence intervals obtained using + list(list("mkinfit"))</h1> </div> diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html index 5fe94a8a..921affdc 100644 --- a/docs/reference/mkinplot.html +++ b/docs/reference/mkinplot.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — mkinplot • mkin</title> +<title>Plot the observed data and the fitted model of an mkinfit object — mkinplot • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -61,7 +60,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -73,8 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Plot the observed data and the fitted model of an mkinfit object</h1> </div> diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index f7eb950a..9f00dab7 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — mkinpredict • mkin</title> +<title>Produce predictions from a kinetic model using specific parameters — mkinpredict • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -61,7 +60,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -73,8 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Produce predictions from a kinetic model using specific parameters</h1> </div> @@ -272,7 +275,7 @@ <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 -#> 0.008 0.024 0.005 </div><div class='input'> <span class='fu'>system.time</span>( +#> 0.004 0.028 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 @@ -282,7 +285,7 @@ <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 0.037 </div></pre> +#> 0.052 0.000 0.052 </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 a0dcd06d..ae9131ac 100644 --- a/docs/reference/mkinresplot.html +++ b/docs/reference/mkinresplot.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — mkinresplot • mkin</title> +<title>Function to plot residuals stored in an mkin object — mkinresplot • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -61,7 +60,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -73,8 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Function to plot residuals stored in an mkin object</h1> </div> diff --git a/docs/reference/mkinsub.html b/docs/reference/mkinsub.html index 8424eaab..8bb2ce1c 100644 --- a/docs/reference/mkinsub.html +++ b/docs/reference/mkinsub.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — mkinsub • mkin</title> +<title>Function to set up a kinetic submodel for one state variable — mkinsub • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -61,7 +60,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -73,8 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Function to set up a kinetic submodel for one state variable</h1> </div> diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index 5613a720..a21a980b 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — mmkin • mkin</title> +<title>Fit one or more kinetic models with one or more state variables to one or more datasets — mmkin • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -61,7 +60,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -73,8 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Fit one or more kinetic models with one or more state variables to one or more datasets</h1> </div> diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html index e7158180..52db9bc6 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — plot.mkinfit • mkin</title> +<title>Plot the observed data and the fitted model of an mkinfit object — plot.mkinfit • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -61,7 +60,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -73,8 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Plot the observed data and the fitted model of an mkinfit object</h1> </div> diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html index ef5c04b7..eac31273 100644 --- a/docs/reference/plot.mmkin.html +++ b/docs/reference/plot.mmkin.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — plot.mmkin • mkin</title> +<title>Plot model fits (observed and fitted) and the residuals for a row or column of an mmkin object — plot.mmkin • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -61,7 +60,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -73,8 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Plot model fits (observed and fitted) and the residuals for a row or column of an mmkin object</h1> </div> diff --git a/docs/reference/print.mkinds.html b/docs/reference/print.mkinds.html index c578f4ee..9057114d 100644 --- a/docs/reference/print.mkinds.html +++ b/docs/reference/print.mkinds.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — print.mkinds • mkin</title> +<title>Print mkinds objects — print.mkinds • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -61,7 +60,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -73,8 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Print mkinds objects</h1> </div> diff --git a/docs/reference/print.mkinmod.html b/docs/reference/print.mkinmod.html index 3f653971..2034ea10 100644 --- a/docs/reference/print.mkinmod.html +++ b/docs/reference/print.mkinmod.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — print.mkinmod • mkin</title> +<title>Print mkinmod objects — print.mkinmod • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -61,7 +60,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -73,8 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Print mkinmod objects</h1> </div> diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html index c63ba490..e2f845d9 100644 --- a/docs/reference/schaefer07_complex_case.html +++ b/docs/reference/schaefer07_complex_case.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — schaefer07_complex_case • mkin</title> +<title>Metabolism data set used for checking the software quality of KinGUI — schaefer07_complex_case • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -61,7 +60,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -73,8 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Metabolism data set used for checking the software quality of KinGUI</h1> </div> diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index 241964a7..f67bc1d1 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — summary.mkinfit • mkin</title> +<title>Summary method for class "mkinfit" — summary.mkinfit • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -61,7 +60,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -73,8 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Summary method for class "mkinfit"</h1> </div> @@ -139,8 +142,8 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</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: 3.3.2 -#> Date of fit: Fri Nov 4 15:36:49 2016 -#> Date of summary: Fri Nov 4 15:36:49 2016 +#> Date of fit: Fri Nov 4 17:09:10 2016 +#> Date of summary: Fri Nov 4 17:09:10 2016 #> #> Equations: #> d_parent = - k_parent_sink * parent diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html index 333b3dbf..c6f29582 100644 --- a/docs/reference/synthetic_data_for_UBA.html +++ b/docs/reference/synthetic_data_for_UBA.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — synthetic_data_for_UBA_2014 • mkin</title> +<title>Synthetic datasets for one parent compound with two metabolites — synthetic_data_for_UBA_2014 • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -61,7 +60,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -73,8 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Synthetic datasets for one parent compound with two metabolites</h1> </div> diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index 5ee1e9cc..60208ff4 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — transform_odeparms • mkin</title> +<title>Functions to transform and backtransform kinetic parameters for fitting — transform_odeparms • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -61,7 +60,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> @@ -73,8 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Functions to transform and backtransform kinetic parameters for fitting</h1> </div> @@ -146,8 +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: 3.3.2 -#> Date of fit: Fri Nov 4 15:36:50 2016 -#> Date of summary: Fri Nov 4 15:36:50 2016 +#> Date of fit: Fri Nov 4 17:09:11 2016 +#> Date of summary: Fri Nov 4 17:09:11 2016 #> #> Equations: #> d_parent = - k_parent_sink * parent - k_parent_m1 * parent @@ -155,7 +158,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 153 model solutions performed in 0.663 s +#> Fitted with method Port using 153 model solutions performed in 0.638 s #> #> Weighting: none #> diff --git a/docs/reference/unknown-10.png b/docs/reference/unknown-10.png Binary files differdeleted file mode 100644 index 09bb687c..00000000 --- a/docs/reference/unknown-10.png +++ /dev/null diff --git a/docs/reference/unknown-2.png b/docs/reference/unknown-2.png Binary files differdeleted file mode 100644 index a26e413f..00000000 --- a/docs/reference/unknown-2.png +++ /dev/null diff --git a/docs/reference/unknown-4.png b/docs/reference/unknown-4.png Binary files differdeleted file mode 100644 index f23ed172..00000000 --- a/docs/reference/unknown-4.png +++ /dev/null diff --git a/docs/reference/unknown-6.png b/docs/reference/unknown-6.png Binary files differdeleted file mode 100644 index dc24d92f..00000000 --- a/docs/reference/unknown-6.png +++ /dev/null diff --git a/docs/reference/unknown-8.png b/docs/reference/unknown-8.png Binary files differdeleted file mode 100644 index e4ab674a..00000000 --- a/docs/reference/unknown-8.png +++ /dev/null |
