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authorJohannes Ranke <jranke@uni-bremen.de>2022-11-24 09:02:26 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2022-11-24 09:02:26 +0100
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tree33c2963936ce6c38abe6533afcce3994a08d4ba9 /docs/dev/reference/ds_mixed.html
parent8e953c409e0020ea7e7c2a5121019c42cb66dde4 (diff)
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+ <h1>Synthetic data for hierarchical kinetic degradation models</h1>
+ <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/ds_mixed.R" class="external-link"><code>R/ds_mixed.R</code></a></small>
+ <div class="hidden name"><code>ds_mixed.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+ <p>The R code used to create this data object is installed with this package in
+the 'dataset_generation' directory.</p>
+ </div>
+
+
+
+ <div id="ref-examples">
+ <h2>Examples</h2>
+ <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \dontrun{</span></span></span>
+<span class="r-in"><span> <span class="va">sfo_mmkin</span> <span class="op">&lt;-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">ds_sfo</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>, cores <span class="op">=</span> <span class="fl">15</span><span class="op">)</span></span></span>
+<span class="r-in"><span> <span class="va">sfo_saem</span> <span class="op">&lt;-</span> <span class="fu"><a href="saem.html">saem</a></span><span class="op">(</span><span class="va">sfo_mmkin</span>, no_random_effect <span class="op">=</span> <span class="st">"parent_0"</span><span class="op">)</span></span></span>
+<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">sfo_saem</span><span class="op">)</span></span></span>
+<span class="r-plt img"><img src="ds_mixed-1.png" alt="" width="700" height="433"></span>
+<span class="r-in"><span><span class="co"># }</span></span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># This is the code used to generate the datasets</span></span></span>
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/cat.html" class="external-link">cat</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/readLines.html" class="external-link">readLines</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"dataset_generation/ds_mixed.R"</span>, package <span class="op">=</span> <span class="st">"mkin"</span><span class="op">)</span><span class="op">)</span>, sep <span class="op">=</span> <span class="st">"\n"</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> # Synthetic data for hierarchical kinetic models</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> # Refactored version of the code previously in tests/testthat/setup_script.R</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> # The number of datasets was 3 for FOMC, and 10 for HS in that script, now it</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> # is always 15 for consistency</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> library(mkin) # We use mkinmod and mkinpredict</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> n &lt;- 15</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> log_sd &lt;- 0.3</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> err_1 = list(const = 1, prop = 0.05)</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> tc &lt;- function(value) sigma_twocomp(value, err_1$const, err_1$prop)</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> const &lt;- function(value) 2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> set.seed(123456)</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> SFO &lt;- mkinmod(parent = mkinsub("SFO"))</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> sfo_pop &lt;- list(parent_0 = 100, k_parent = 0.03)</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> sfo_parms &lt;- as.matrix(data.frame(</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> k_parent = rlnorm(n, log(sfo_pop$k_parent), log_sd)))</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> set.seed(123456)</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> ds_sfo &lt;- lapply(1:n, function(i) {</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> ds_mean &lt;- mkinpredict(SFO, sfo_parms[i, ],</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> c(parent = sfo_pop$parent_0), sampling_times)</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> add_err(ds_mean, tc, n = 1)[[1]]</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> })</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> attr(ds_sfo, "pop") &lt;- sfo_pop</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> attr(ds_sfo, "parms") &lt;- sfo_parms</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> set.seed(123456)</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> FOMC &lt;- mkinmod(parent = mkinsub("FOMC"))</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> fomc_pop &lt;- list(parent_0 = 100, alpha = 2, beta = 8)</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> fomc_parms &lt;- as.matrix(data.frame(</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> alpha = rlnorm(n, log(fomc_pop$alpha), 0.4),</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> beta = rlnorm(n, log(fomc_pop$beta), 0.2)))</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> set.seed(123456)</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> ds_fomc &lt;- lapply(1:n, function(i) {</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> ds_mean &lt;- mkinpredict(FOMC, fomc_parms[i, ],</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> c(parent = fomc_pop$parent_0), sampling_times)</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> add_err(ds_mean, tc, n = 1)[[1]]</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> })</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> attr(ds_fomc, "pop") &lt;- fomc_pop</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> attr(ds_fomc, "parms") &lt;- fomc_parms</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> set.seed(123456)</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> DFOP &lt;- mkinmod(parent = mkinsub("DFOP"))</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> dfop_pop &lt;- list(parent_0 = 100, k1 = 0.06, k2 = 0.015, g = 0.4)</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> dfop_parms &lt;- as.matrix(data.frame(</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> k1 = rlnorm(n, log(dfop_pop$k1), log_sd),</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> k2 = rlnorm(n, log(dfop_pop$k2), log_sd),</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> g = plogis(rnorm(n, qlogis(dfop_pop$g), log_sd))))</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> set.seed(123456)</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> ds_dfop &lt;- lapply(1:n, function(i) {</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> ds_mean &lt;- mkinpredict(DFOP, dfop_parms[i, ],</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> c(parent = dfop_pop$parent_0), sampling_times)</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> add_err(ds_mean, tc, n = 1)[[1]]</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> })</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> attr(ds_dfop, "pop") &lt;- dfop_pop</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> attr(ds_dfop, "parms") &lt;- dfop_parms</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> set.seed(123456)</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> HS &lt;- mkinmod(parent = mkinsub("HS"))</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> hs_pop &lt;- list(parent_0 = 100, k1 = 0.08, k2 = 0.01, tb = 15)</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> hs_parms &lt;- as.matrix(data.frame(</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> k1 = rlnorm(n, log(hs_pop$k1), log_sd),</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> k2 = rlnorm(n, log(hs_pop$k2), log_sd),</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> tb = rlnorm(n, log(hs_pop$tb), 0.1)))</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> set.seed(123456)</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> ds_hs &lt;- lapply(1:n, function(i) {</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> ds_mean &lt;- mkinpredict(HS, hs_parms[i, ],</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> c(parent = hs_pop$parent_0), sampling_times)</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> add_err(ds_mean, const, n = 1)[[1]]</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> })</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> attr(ds_hs, "pop") &lt;- hs_pop</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> attr(ds_hs, "parms") &lt;- hs_parms</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> set.seed(123456)</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> DFOP_SFO &lt;- mkinmod(</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> parent = mkinsub("DFOP", "m1"),</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> m1 = mkinsub("SFO"),</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> quiet = TRUE)</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> dfop_sfo_pop &lt;- list(parent_0 = 100,</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> k_m1 = 0.007, f_parent_to_m1 = 0.5,</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> k1 = 0.1, k2 = 0.02, g = 0.5)</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> dfop_sfo_parms &lt;- as.matrix(data.frame(</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> k1 = rlnorm(n, log(dfop_sfo_pop$k1), log_sd),</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> k2 = rlnorm(n, log(dfop_sfo_pop$k2), log_sd),</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> g = plogis(rnorm(n, qlogis(dfop_sfo_pop$g), log_sd)),</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> f_parent_to_m1 = plogis(rnorm(n,</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> qlogis(dfop_sfo_pop$f_parent_to_m1), log_sd)),</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> k_m1 = rlnorm(n, log(dfop_sfo_pop$k_m1), log_sd)))</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> ds_dfop_sfo_mean &lt;- lapply(1:n,</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> function(i) {</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> mkinpredict(DFOP_SFO, dfop_sfo_parms[i, ],</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> c(parent = dfop_sfo_pop$parent_0, m1 = 0), sampling_times)</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> }</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> )</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> set.seed(123456)</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> ds_dfop_sfo &lt;- lapply(ds_dfop_sfo_mean, function(ds) {</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> add_err(ds,</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> sdfunc = function(value) sqrt(err_1$const^2 + value^2 * err_1$prop^2),</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> n = 1, secondary = "m1")[[1]]</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> })</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> attr(ds_dfop_sfo, "pop") &lt;- dfop_sfo_pop</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> attr(ds_dfop_sfo, "parms") &lt;- dfop_sfo_parms</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> #save(ds_sfo, ds_fomc, ds_dfop, ds_hs, ds_dfop_sfo, file = "data/ds_mixed.rda", version = 2)</span>
+</code></pre></div>
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