diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2019-09-18 13:03:50 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2019-09-18 13:03:50 +0200 |
| commit | e05656d57668688b971c28e32b4cfd4d3eac4662 (patch) | |
| tree | 597df9a638c0ce68ae9efcb5b45d42b2f2927a15 /docs/reference/synthetic_data_for_UBA.html | |
| parent | 0818986e2d9a0e68d3d1de26ac381836e0cf5a6f (diff) | |
Correct and rebuild docs
- Reconcile docs and code for max_twa_parent
- Correct links to docs in twa vignette
- Static documentation rebuilt by pkgdown
Diffstat (limited to 'docs/reference/synthetic_data_for_UBA.html')
| -rw-r--r-- | docs/reference/synthetic_data_for_UBA.html | 124 |
1 files changed, 16 insertions, 108 deletions
diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html index 1f8bc914..b3da0016 100644 --- a/docs/reference/synthetic_data_for_UBA.html +++ b/docs/reference/synthetic_data_for_UBA.html @@ -16,13 +16,15 @@ <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" /> +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" /> +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" /> <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script> -<!-- sticky kit --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> +<!-- headroom.js --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> @@ -62,6 +64,7 @@ Compare also the code in the example section to see the degradation models." /> <![endif]--> + </head> <body> @@ -131,6 +134,7 @@ Compare also the code in the example section to see the degradation models." /> </div><!--/.navbar --> + </header> <div class="row"> @@ -170,7 +174,9 @@ Compare also the code in the example section to see the degradation models." /> each containing, among others, the following components</p><dl class='dl-horizontal'> <dt><code>title</code></dt><dd><p>The name of the dataset, e.g. <code>SFO_lin_a</code></p></dd> <dt><code>data</code></dt><dd><p>A data frame with the data in the form expected by <code><a href='mkinfit.html'>mkinfit</a></code></p></dd> - </dl> + +</dl> + <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> @@ -181,109 +187,7 @@ Compare also the code in the example section to see the degradation models." /> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'># The data have been generated using the following kinetic models -m_synth_SFO_lin <- mkinmod(parent = list(type = "SFO", to = "M1"), - M1 = list(type = "SFO", to = "M2"), - M2 = list(type = "SFO"), use_of_ff = "max") - - -m_synth_SFO_par <- mkinmod(parent = list(type = "SFO", to = c("M1", "M2"), - sink = FALSE), - M1 = list(type = "SFO"), - M2 = list(type = "SFO"), use_of_ff = "max") - -m_synth_DFOP_lin <- mkinmod(parent = list(type = "DFOP", to = "M1"), - M1 = list(type = "SFO", to = "M2"), - M2 = list(type = "SFO"), use_of_ff = "max") - -m_synth_DFOP_par <- mkinmod(parent = list(type = "DFOP", to = c("M1", "M2"), - sink = FALSE), - M1 = list(type = "SFO"), - M2 = list(type = "SFO"), use_of_ff = "max") - -# The model predictions without intentional error were generated as follows -sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120) - -d_synth_SFO_lin <- mkinpredict(m_synth_SFO_lin, - c(k_parent = 0.7, f_parent_to_M1 = 0.8, - k_M1 = 0.3, f_M1_to_M2 = 0.7, - k_M2 = 0.02), - c(parent = 100, M1 = 0, M2 = 0), - sampling_times) - -d_synth_DFOP_lin <- mkinpredict(m_synth_DFOP_lin, - c(k1 = 0.2, k2 = 0.02, g = 0.5, - f_parent_to_M1 = 0.5, k_M1 = 0.3, - f_M1_to_M2 = 0.7, k_M2 = 0.02), - c(parent = 100, M1 = 0, M2 = 0), - sampling_times) - -d_synth_SFO_par <- mkinpredict(m_synth_SFO_par, - c(k_parent = 0.2, - f_parent_to_M1 = 0.8, k_M1 = 0.01, - f_parent_to_M2 = 0.2, k_M2 = 0.02), - c(parent = 100, M1 = 0, M2 = 0), - sampling_times) - -d_synth_DFOP_par <- mkinpredict(m_synth_DFOP_par, - c(k1 = 0.3, k2 = 0.02, g = 0.7, - f_parent_to_M1 = 0.6, k_M1 = 0.04, - f_parent_to_M2 = 0.4, k_M2 = 0.01), - c(parent = 100, M1 = 0, M2 = 0), - sampling_times) - -# Construct names for datasets with errors -d_synth_names = paste0("d_synth_", c("SFO_lin", "SFO_par", - "DFOP_lin", "DFOP_par")) - -# Function for adding errors. The add_err function now published with this -# package is a slightly generalised version where the names of secondary -# compartments that should have an initial value of zero (M1 and M2 in this -# case) are not hardcoded any more. -add_err = function(d, sdfunc, LOD = 0.1, reps = 2, seed = 123456789) -{ - set.seed(seed) - d_long = mkin_wide_to_long(d, time = "time") - d_rep = data.frame(lapply(d_long, rep, each = 2)) - d_rep$value = rnorm(length(d_rep$value), d_rep$value, sdfunc(d_rep$value)) - - d_rep[d_rep$time == 0 & d_rep$name <!-- %in% c("M1", "M2"), "value"] <- 0 --> - d_NA <- transform(d_rep, value = ifelse(value < LOD, NA, value)) - d_NA$value <- round(d_NA$value, 1) - return(d_NA) -} - -# The following is the simplified version of the two-component model of Rocke -# and Lorenzato (1995) -sdfunc_twocomp = function(value, sd_low, rsd_high) { - sqrt(sd_low^2 + value^2 * rsd_high^2) -} - -# Add the errors. -for (d_synth_name in d_synth_names) -{ - d_synth = get(d_synth_name) - assign(paste0(d_synth_name, "_a"), add_err(d_synth, function(value) 3)) - assign(paste0(d_synth_name, "_b"), add_err(d_synth, function(value) 7)) - assign(paste0(d_synth_name, "_c"), add_err(d_synth, - function(value) sdfunc_twocomp(value, 0.5, 0.07))) - -} - -d_synth_err_names = c( - paste(rep(d_synth_names, each = 3), letters[1:3], sep = "_") -) - -# This is just one example of an evaluation using the kinetic model used for -# the generation of the data -fit <- mkinfit(m_synth_SFO_lin, synthetic_data_for_UBA_2014[[1]]$data, - quiet = TRUE) -plot_sep(fit) -summary(fit) -</div><div class='output co'>#> <span class='error'>Error: <text>:67:43: Unerwartete(s) SPECIAL</span> -#> <span class='error'>66: </span> -#> <span class='error'>67: d_rep[d_rep$time == 0 & d_rep$name <!-- %in%</span> -#> <span class='error'> ^</span></div></pre> + <pre class="examples"></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> @@ -299,19 +203,23 @@ summary(fit) </div> </div> + <footer> <div class="copyright"> <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> </div> + </footer> </div> + </body> </html> + |