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| author | Johannes Ranke <jranke@uni-bremen.de> | 2017-05-05 12:46:31 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2017-05-05 12:46:31 +0200 |
| commit | ccc70e82af4ba435f0a71ba1ae4e0e92045c3852 (patch) | |
| tree | d8ffd99be771f47eae876f244b049742481bdd25 /docs/reference/Extract.mmkin.html | |
| parent | 1c7dbeec335c404377381157d34db6e219ce3f21 (diff) | |
Static docs except articles rebuilt with current pkgdown
Diffstat (limited to 'docs/reference/Extract.mmkin.html')
| -rw-r--r-- | docs/reference/Extract.mmkin.html | 110 |
1 files changed, 64 insertions, 46 deletions
diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 0131342a..135297cd 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -25,12 +25,14 @@ <script src="../pkgdown.js"></script> <!-- mathjax --> -<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> +<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> <!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> <![endif]--> + + </head> <body> @@ -70,6 +72,9 @@ <li> <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> + <li> + <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + </li> </ul> </li> <li> @@ -102,23 +107,34 @@ <p>Subsetting method for mmkin objects.</p> - <pre># S3 method for mmkin + <pre class="usage"># S3 method for mmkin [(x, i, j, ..., drop = FALSE)</pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> - <dl class="dl-horizontal"> - <dt>x</dt> - <dd>An <code><a href='mmkin.html'>mmkin</a> object</code></dd> - <dt>i</dt> - <dd>Row index selecting the fits for specific models</dd> - <dt>j</dt> - <dd>Column index selecting the fits to specific datasets</dd> - <dt>...</dt> - <dd>Not used, only there to satisfy the generic method definition</dd> - <dt>drop</dt> - <dd>If FALSE, the method always returns an mmkin object, otherwise either - a list of mkinfit objects or a single mkinfit object.</dd> - </dl> + <table class="ref-arguments"> + <colgroup><col class="name" /><col class="desc" /></colgroup> + <tr> + <th>x</th> + <td><p>An <code><a href='mmkin.html'>mmkin</a> object</code></p></td> + </tr> + <tr> + <th>i</th> + <td><p>Row index selecting the fits for specific models</p></td> + </tr> + <tr> + <th>j</th> + <td><p>Column index selecting the fits to specific datasets</p></td> + </tr> + <tr> + <th>...</th> + <td><p>Not used, only there to satisfy the generic method definition</p></td> + </tr> + <tr> + <th>drop</th> + <td><p>If FALSE, the method always returns an mmkin object, otherwise either + a list of mkinfit objects or a single mkinfit object.</p></td> + </tr> + </table> <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> @@ -132,23 +148,23 @@ <span class='no'>fits</span>[<span class='st'>"FOMC"</span>, ]</div><div class='output co'>#> dataset #> model B C #> FOMC List,42 List,42 -#> attr(,"class") -#> [1] "mmkin"</div><div class='input'> <span class='no'>fits</span>[, <span class='st'>"B"</span>]</div><div class='output co'>#> dataset +#> attr(,"class") +#> [1] "mmkin"</div><div class='input'> <span class='no'>fits</span>[, <span class='st'>"B"</span>]</div><div class='output co'>#> dataset #> model B #> SFO List,42 #> FOMC List,42 -#> attr(,"class") -#> [1] "mmkin"</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 +#> attr(,"class") +#> [1] "mmkin"</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 #> model B #> SFO List,42 -#> attr(,"class") -#> [1] "mmkin"</div><div class='input'> +#> attr(,"class") +#> [1] "mmkin"</div><div class='input'> <span class='fu'>head</span>( <span class='co'># This extracts an mkinfit object with lots of components</span> <span class='no'>fits</span><span class='kw'>[[</span><span class='st'>"FOMC"</span>, <span class='st'>"B"</span>]] )</div><div class='output co'>#> $par #> parent_0 log_alpha log_beta -#> 99.666193 2.549849 5.050586 +#> 99.666192 2.549849 5.050586 #> #> $ssr #> [1] 28.58291 @@ -164,7 +180,7 @@ #> 25 78 #> #> $counts -#> [1] "both X-convergence and relative convergence (5)" +#> [1] "both X-convergence and relative convergence (5)" #> </div><div class='input'> <span class='fu'>head</span>( <span class='co'># The same can be achieved by</span> @@ -188,7 +204,7 @@ #> 8 15 #> #> $counts -#> [1] "relative convergence (4)" +#> [1] "relative convergence (4)" #> #> $hessian #> parent_0 log_k_parent_sink @@ -223,7 +239,7 @@ #> [1] 6 #> #> $solution_type -#> [1] "analytical" +#> [1] "analytical" #> #> $transform_rates #> [1] TRUE @@ -232,17 +248,17 @@ #> [1] TRUE #> #> $method.modFit -#> [1] "Port" +#> [1] "Port" #> #> $maxit.modFit -#> [1] "auto" +#> [1] "auto" #> #> $calls #> [1] 29 #> #> $time #> user system elapsed -#> 0.068 0.000 0.066 +#> 0.064 0.000 0.063 #> #> $mkinmod #> <mkinmod> model generated with @@ -266,7 +282,7 @@ #> 8 parent 118 0.08 #> #> $obs_vars -#> [1] "parent" +#> [1] "parent" #> #> $predicted #> name time value @@ -380,9 +396,9 @@ #> $cost #> function (P) #> { -#> assign("calls", calls + 1, inherits = TRUE) +#> assign("calls", calls + 1, inherits = TRUE) #> if (trace_parms) -#> cat(P, "\n") +#> cat(P, "\n") #> if (length(state.ini.optim) > 0) { #> odeini <- c(P[1:length(state.ini.optim)], state.ini.fixed) #> names(odeini) <- c(state.ini.optim.boxnames, state.ini.fixed.boxnames) @@ -398,13 +414,13 @@ #> out <- mkinpredict(mkinmod, parms, odeini, outtimes, solution_type = solution_type, #> use_compiled = use_compiled, method.ode = method.ode, #> atol = atol, rtol = rtol, ...) -#> assign("out_predicted", out, inherits = TRUE) -#> mC <- modCost(out, observed, y = "value", err = err, weight = weight, +#> assign("out_predicted", out, inherits = TRUE) +#> mC <- modCost(out, observed, y = "value", err = err, weight = weight, #> scaleVar = scaleVar) #> if (mC$model < cost.old) { #> if (!quiet) -#> cat("Model cost at call ", calls, ": ", mC$model, -#> "\n") +#> cat("Model cost at call ", calls, ": ", mC$model, +#> "\n") #> if (plot) { #> outtimes_plot = seq(min(observed$time), max(observed$time), #> length.out = 100) @@ -412,9 +428,9 @@ #> solution_type = solution_type, use_compiled = use_compiled, #> method.ode = method.ode, atol = atol, rtol = rtol, #> ...) -#> plot(0, type = "n", xlim = range(observed$time), +#> plot(0, type = "n", xlim = range(observed$time), #> ylim = c(0, max(observed$value, na.rm = TRUE)), -#> xlab = "Time", ylab = "Observed") +#> xlab = "Time", ylab = "Observed") #> col_obs <- pch_obs <- 1:length(obs_vars) #> lty_obs <- rep(1, length(obs_vars)) #> names(col_obs) <- names(pch_obs) <- names(lty_obs) <- obs_vars @@ -424,14 +440,15 @@ #> } #> matlines(out_plot$time, out_plot[-1], col = col_obs, #> lty = lty_obs) -#> legend("topright", inset = c(0.05, 0.05), legend = obs_vars, +#> legend("topright", inset = c(0.05, 0.05), legend = obs_vars, #> col = col_obs, pch = pch_obs, lty = 1:length(pch_obs)) #> } -#> assign("cost.old", mC$model, inherits = TRUE) +#> assign("cost.old", mC$model, inherits = TRUE) #> } #> return(mC) #> } -#> <environment: 0x3b9eeb8> +#> <bytecode: 0x5554250> +#> <environment: 0x4eb4b18> #> #> $cost_notrans #> function (P) @@ -449,11 +466,12 @@ #> out <- mkinpredict(mkinmod, odeparms, odeini, outtimes, solution_type = solution_type, #> use_compiled = use_compiled, method.ode = method.ode, #> atol = atol, rtol = rtol, ...) -#> mC <- modCost(out, observed, y = "value", err = err, weight = weight, +#> mC <- modCost(out, observed, y = "value", err = err, weight = weight, #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x3b9eeb8> +#> <bytecode: 0x5073868> +#> <environment: 0x4eb4b18> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -492,7 +510,7 @@ #> [1] 1e-10 #> #> $weight.ini -#> [1] "none" +#> [1] "none" #> #> $reweight.tol #> [1] 1e-08 @@ -516,10 +534,10 @@ #> 99.17407 #> #> $date -#> [1] "Wed Mar 15 09:44:44 2017" +#> [1] "Fri May 5 12:44:53 2017" #> -#> attr(,"class") -#> [1] "mkinfit" "modFit" +#> attr(,"class") +#> [1] "mkinfit" "modFit" #> </div></pre> </div> <div 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