diff options
| -rw-r--r-- | vignettes/web_only/benchmarks.Rmd | 23 | ||||
| -rw-r--r-- | vignettes/web_only/benchmarks.html | 198 | ||||
| -rw-r--r-- | vignettes/web_only/mkin_benchmarks.rda | bin | 885 -> 852 bytes |
3 files changed, 182 insertions, 39 deletions
diff --git a/vignettes/web_only/benchmarks.Rmd b/vignettes/web_only/benchmarks.Rmd index 27f5d366..990c2fee 100644 --- a/vignettes/web_only/benchmarks.Rmd +++ b/vignettes/web_only/benchmarks.Rmd @@ -92,18 +92,18 @@ SFO_lin_a <- synthetic_data_for_UBA_2014[[1]]$data DFOP_par_c <- synthetic_data_for_UBA_2014[[12]]$data -t6 <- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a)))["elapsed"] -t7 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c)))["elapsed"] +t6 <- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a)))[["elapsed"]] +t7 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c)))[["elapsed"]] t8 <- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a), - error_model = "tc"))["elapsed"] + error_model = "tc"))[["elapsed"]] t9 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c), - error_model = "tc"))["elapsed"] + error_model = "tc"))[["elapsed"]] t10 <- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a), - error_model = "obs"))["elapsed"] + error_model = "obs"))[["elapsed"]] t11 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c), - error_model = "obs"))["elapsed"] + error_model = "obs"))[["elapsed"]] ``` ```{r results} @@ -117,6 +117,11 @@ save(mkin_benchmarks, file = "~/git/mkin/vignettes/web_only/mkin_benchmarks.rda" Currently, we only have benchmark information on one system, therefore only the mkin version is shown with the results below. Timings are in seconds, shorter is better. +```{r} +rownames(mkin_benchmarks) <- as.character(mkin_benchmarks$mkin) +``` + + Benchmarks for all available error models are shown. ### Parent only @@ -124,7 +129,7 @@ Benchmarks for all available error models are shown. Constant variance and two-component error model: ```{r} -print(mkin_benchmarks[, c("mkin", "t1", "t2")], row.names = FALSE) +kable(mkin_benchmarks[, c("t1", "t2")]) ``` ### One metabolite @@ -132,7 +137,7 @@ print(mkin_benchmarks[, c("mkin", "t1", "t2")], row.names = FALSE) Constant variance, variance by variable and two-component error model: ```{r} -print(mkin_benchmarks[, c("mkin", "t3", "t4", "t5")], row.names = FALSE) +kable(mkin_benchmarks[, c("t3", "t4", "t5")]) ``` ### Two metabolites @@ -141,5 +146,5 @@ Two different datasets, for each constant variance, variance by variable and two-component error model are shown: ```{r} -print(mkin_benchmarks[, c("mkin", paste0("t", 6:11))], row.names = FALSE) +kable(mkin_benchmarks[, paste0("t", 6:11)]) ``` diff --git a/vignettes/web_only/benchmarks.html b/vignettes/web_only/benchmarks.html index 5c9cc67e..821399e4 100644 --- a/vignettes/web_only/benchmarks.html +++ b/vignettes/web_only/benchmarks.html @@ -1649,18 +1649,18 @@ SFO_lin_a <- synthetic_data_for_UBA_2014[[1]]$data DFOP_par_c <- synthetic_data_for_UBA_2014[[12]]$data -t6 <- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a)))["elapsed"] -t7 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c)))["elapsed"] +t6 <- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a)))[["elapsed"]] +t7 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c)))[["elapsed"]] t8 <- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a), - error_model = "tc"))["elapsed"] + error_model = "tc"))[["elapsed"]] t9 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c), - error_model = "tc"))["elapsed"] + error_model = "tc"))[["elapsed"]] t10 <- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a), - error_model = "obs"))["elapsed"] + error_model = "obs"))[["elapsed"]] t11 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c), - error_model = "obs"))["elapsed"]</code></pre> + error_model = "obs"))[["elapsed"]]</code></pre> <pre class="r"><code>mkin_benchmarks[system_string, paste0("t", 1:11)] <- c(t1, t2, t3, t4, t5, t6, t7, t8, t9, t10, t11) save(mkin_benchmarks, file = "~/git/mkin/vignettes/web_only/mkin_benchmarks.rda")</code></pre> @@ -1668,42 +1668,180 @@ save(mkin_benchmarks, file = "~/git/mkin/vignettes/web_only/mkin_benchmarks <div id="results" class="section level2"> <h2>Results</h2> <p>Currently, we only have benchmark information on one system, therefore only the mkin version is shown with the results below. Timings are in seconds, shorter is better.</p> +<pre class="r"><code>rownames(mkin_benchmarks) <- as.character(mkin_benchmarks$mkin)</code></pre> <p>Benchmarks for all available error models are shown.</p> <div id="parent-only" class="section level3"> <h3>Parent only</h3> <p>Constant variance and two-component error model:</p> -<pre class="r"><code>print(mkin_benchmarks[, c("mkin", "t1", "t2")], row.names = FALSE)</code></pre> -<pre><code>## mkin t1 t2 -## 0.9.48.1 3.610 11.019 -## 0.9.49.1 8.184 22.889 -## 0.9.49.2 7.064 12.558 -## 0.9.49.3 7.296 21.239 -## 0.9.49.4 5.936 20.545 -## 0.9.50.2 1.547 3.955</code></pre> +<pre class="r"><code>kable(mkin_benchmarks[, c("t1", "t2")])</code></pre> +<table> +<thead> +<tr class="header"> +<th></th> +<th align="right">t1</th> +<th align="right">t2</th> +</tr> +</thead> +<tbody> +<tr class="odd"> +<td>0.9.48.1</td> +<td align="right">3.610</td> +<td align="right">11.019</td> +</tr> +<tr class="even"> +<td>0.9.49.1</td> +<td align="right">8.184</td> +<td align="right">22.889</td> +</tr> +<tr class="odd"> +<td>0.9.49.2</td> +<td align="right">7.064</td> +<td align="right">12.558</td> +</tr> +<tr class="even"> +<td>0.9.49.3</td> +<td align="right">7.296</td> +<td align="right">21.239</td> +</tr> +<tr class="odd"> +<td>0.9.49.4</td> +<td align="right">5.936</td> +<td align="right">20.545</td> +</tr> +<tr class="even"> +<td>0.9.50.2</td> +<td align="right">1.559</td> +<td align="right">3.929</td> +</tr> +</tbody> +</table> </div> <div id="one-metabolite" class="section level3"> <h3>One metabolite</h3> <p>Constant variance, variance by variable and two-component error model:</p> -<pre class="r"><code>print(mkin_benchmarks[, c("mkin", "t3", "t4", "t5")], row.names = FALSE)</code></pre> -<pre><code>## mkin t3 t4 t5 -## 0.9.48.1 3.764 14.347 9.495 -## 0.9.49.1 4.649 13.789 6.395 -## 0.9.49.2 4.786 8.461 5.675 -## 0.9.49.3 4.510 13.805 7.386 -## 0.9.49.4 4.446 15.335 6.002 -## 0.9.50.2 1.379 6.176 2.713</code></pre> +<pre class="r"><code>kable(mkin_benchmarks[, c("t3", "t4", "t5")])</code></pre> +<table> +<thead> +<tr class="header"> +<th></th> +<th align="right">t3</th> +<th align="right">t4</th> +<th align="right">t5</th> +</tr> +</thead> +<tbody> +<tr class="odd"> +<td>0.9.48.1</td> +<td align="right">3.764</td> +<td align="right">14.347</td> +<td align="right">9.495</td> +</tr> +<tr class="even"> +<td>0.9.49.1</td> +<td align="right">4.649</td> +<td align="right">13.789</td> +<td align="right">6.395</td> +</tr> +<tr class="odd"> +<td>0.9.49.2</td> +<td align="right">4.786</td> +<td align="right">8.461</td> +<td align="right">5.675</td> +</tr> +<tr class="even"> +<td>0.9.49.3</td> +<td align="right">4.510</td> +<td align="right">13.805</td> +<td align="right">7.386</td> +</tr> +<tr class="odd"> +<td>0.9.49.4</td> +<td align="right">4.446</td> +<td align="right">15.335</td> +<td align="right">6.002</td> +</tr> +<tr class="even"> +<td>0.9.50.2</td> +<td align="right">1.352</td> +<td align="right">6.110</td> +<td align="right">2.841</td> +</tr> +</tbody> +</table> </div> <div id="two-metabolites" class="section level3"> <h3>Two metabolites</h3> <p>Two different datasets, for each constant variance, variance by variable and two-component error model are shown:</p> -<pre class="r"><code>print(mkin_benchmarks[, c("mkin", paste0("t", 6:11))], row.names = FALSE)</code></pre> -<pre><code>## mkin t6 t7 t8 t9 t10 t11 -## 0.9.48.1 2.623 4.587 7.525 16.621 8.576 31.267 -## 0.9.49.1 2.542 4.128 4.632 8.171 3.676 5.636 -## 0.9.49.2 2.723 4.478 4.862 7.618 3.579 5.574 -## 0.9.49.3 2.643 4.374 7.02 11.124 5.388 7.365 -## 0.9.49.4 2.635 4.259 4.737 7.763 3.427 5.626 -## 0.9.50.2 0.742 1.202 1.269 2.97 2.028 2.959</code></pre> +<pre class="r"><code>kable(mkin_benchmarks[, paste0("t", 6:11)])</code></pre> +<table> +<thead> +<tr class="header"> +<th></th> +<th align="right">t6</th> +<th align="right">t7</th> +<th align="right">t8</th> +<th align="right">t9</th> +<th align="right">t10</th> +<th align="right">t11</th> +</tr> +</thead> +<tbody> +<tr class="odd"> +<td>0.9.48.1</td> +<td align="right">2.623</td> +<td align="right">4.587</td> +<td align="right">7.525</td> +<td align="right">16.621</td> +<td align="right">8.576</td> +<td align="right">31.267</td> +</tr> +<tr class="even"> +<td>0.9.49.1</td> +<td align="right">2.542</td> +<td align="right">4.128</td> +<td align="right">4.632</td> +<td align="right">8.171</td> +<td align="right">3.676</td> +<td align="right">5.636</td> +</tr> +<tr class="odd"> +<td>0.9.49.2</td> +<td align="right">2.723</td> +<td align="right">4.478</td> +<td align="right">4.862</td> +<td align="right">7.618</td> +<td align="right">3.579</td> +<td align="right">5.574</td> +</tr> +<tr class="even"> +<td>0.9.49.3</td> +<td align="right">2.643</td> +<td align="right">4.374</td> +<td align="right">7.020</td> +<td align="right">11.124</td> +<td align="right">5.388</td> +<td align="right">7.365</td> +</tr> +<tr class="odd"> +<td>0.9.49.4</td> +<td align="right">2.635</td> +<td align="right">4.259</td> +<td align="right">4.737</td> +<td align="right">7.763</td> +<td align="right">3.427</td> +<td align="right">5.626</td> +</tr> +<tr class="even"> +<td>0.9.50.2</td> +<td align="right">0.759</td> +<td align="right">1.204</td> +<td align="right">1.275</td> +<td align="right">2.837</td> +<td align="right">2.026</td> +<td align="right">2.976</td> +</tr> +</tbody> +</table> </div> </div> diff --git a/vignettes/web_only/mkin_benchmarks.rda b/vignettes/web_only/mkin_benchmarks.rda Binary files differindex 870ecc2b..8e3f0b3b 100644 --- a/vignettes/web_only/mkin_benchmarks.rda +++ b/vignettes/web_only/mkin_benchmarks.rda |