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Diffstat (limited to 'vignettes/web_only/benchmarks.html')
| -rw-r--r-- | vignettes/web_only/benchmarks.html | 40 |
1 files changed, 23 insertions, 17 deletions
diff --git a/vignettes/web_only/benchmarks.html b/vignettes/web_only/benchmarks.html index 4afe49c4..5f81f39f 100644 --- a/vignettes/web_only/benchmarks.html +++ b/vignettes/web_only/benchmarks.html @@ -1599,13 +1599,23 @@ div.tocify { <h1 class="title toc-ignore">Benchmark timings for mkin</h1> <h4 class="author">Johannes Ranke</h4> -<h4 class="date">Last change 1 July 2022 (rebuilt 2022-07-12)</h4> +<h4 class="date">Last change 14 July 2022 (rebuilt 2022-07-14)</h4> </div> <p>Each system is characterized by the operating system type, the CPU type, the mkin version, and, as in June 2022 the current R version lead to worse performance, the R version. A compiler was available, so if no analytical solution was available, compiled ODE models are used.</p> <p>Every fit is only performed once, so the accuracy of the benchmarks is limited.</p> +<p>The following wrapper function for <code>mmkin</code> is used because the way the error model is specified was changed in mkin version 0.9.49.1.</p> +<pre class="r"><code>if (packageVersion("mkin") > "0.9.48.1") { + mmkin_bench <- function(models, datasets, error_model = "const") { + mmkin(models, datasets, error_model = error_model, cores = 1, quiet = TRUE) + } +} else { + mmkin_bench <- function(models, datasets, error_model = NULL) { + mmkin(models, datasets, reweight.method = error_model, cores = 1, quiet = TRUE) + } +}</code></pre> <div id="test-cases" class="section level2"> <h2>Test cases</h2> <p>Parent only:</p> @@ -1613,6 +1623,7 @@ div.tocify { FOCUS_D <- subset(FOCUS_2006_D, value != 0) parent_datasets <- list(FOCUS_C, FOCUS_D) + t1 <- system.time(mmkin_bench(c("SFO", "FOMC", "DFOP", "HS"), parent_datasets))[["elapsed"]] t2 <- system.time(mmkin_bench(c("SFO", "FOMC", "DFOP", "HS"), parent_datasets, error_model = "tc"))[["elapsed"]]</code></pre> @@ -1658,11 +1669,6 @@ t10 <- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a), error_model = "obs"))[["elapsed"]] t11 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c), error_model = "obs"))[["elapsed"]]</code></pre> -<pre class="r"><code>mkin_benchmarks[system_string, paste0("t", 1:11)] <- - c(t1, t2, t3, t4, t5, t6, t7, t8, t9, t10, t11) -save(mkin_benchmarks, file = benchmark_path) -# Hide rownames from kable for results section -rownames(mkin_benchmarks) <- NULL</code></pre> </div> <div id="results" class="section level2"> <h2>Results</h2> @@ -1807,8 +1813,8 @@ rownames(mkin_benchmarks) <- NULL</code></pre> <td align="left">Ryzen 7 1700</td> <td align="left">4.2.1</td> <td align="left">1.1.1</td> -<td align="right">1.767</td> -<td align="right">3.396</td> +<td align="right">1.770</td> +<td align="right">3.377</td> </tr> </tbody> </table> @@ -1969,9 +1975,9 @@ rownames(mkin_benchmarks) <- NULL</code></pre> <td align="left">Ryzen 7 1700</td> <td align="left">4.2.1</td> <td align="left">1.1.1</td> -<td align="right">1.320</td> -<td align="right">5.774</td> -<td align="right">2.575</td> +<td align="right">1.308</td> +<td align="right">5.758</td> +<td align="right">2.558</td> </tr> </tbody> </table> @@ -2180,12 +2186,12 @@ rownames(mkin_benchmarks) <- NULL</code></pre> <td align="left">Ryzen 7 1700</td> <td align="left">4.2.1</td> <td align="left">1.1.1</td> -<td align="right">0.700</td> -<td align="right">1.146</td> -<td align="right">1.334</td> -<td align="right">2.807</td> -<td align="right">1.750</td> -<td align="right">2.593</td> +<td align="right">0.696</td> +<td align="right">1.124</td> +<td align="right">1.321</td> +<td align="right">2.786</td> +<td align="right">1.744</td> +<td align="right">2.566</td> </tr> </tbody> </table> |