diff options
Diffstat (limited to 'docs/dev/reference')
| -rw-r--r-- | docs/dev/reference/confint.mkinfit.html | 4 | ||||
| -rw-r--r-- | docs/dev/reference/create_deg_func.html | 8 | ||||
| -rw-r--r-- | docs/dev/reference/dimethenamid_2018.html | 6 | ||||
| -rw-r--r-- | docs/dev/reference/mkinfit.html | 16 | ||||
| -rw-r--r-- | docs/dev/reference/mkinmod.html | 4 | ||||
| -rw-r--r-- | docs/dev/reference/mkinpredict.html | 4 | ||||
| -rw-r--r-- | docs/dev/reference/mmkin.html | 4 | ||||
| -rw-r--r-- | docs/dev/reference/saem.html | 8 | ||||
| -rw-r--r-- | docs/dev/reference/summary.mkinfit.html | 6 | ||||
| -rw-r--r-- | docs/dev/reference/summary.mmkin.html | 2 | ||||
| -rw-r--r-- | docs/dev/reference/summary.nlme.mmkin.html | 6 | ||||
| -rw-r--r-- | docs/dev/reference/summary.saem.mmkin.html | 6 |
12 files changed, 37 insertions, 37 deletions
diff --git a/docs/dev/reference/confint.mkinfit.html b/docs/dev/reference/confint.mkinfit.html index a0051a85..aca693cc 100644 --- a/docs/dev/reference/confint.mkinfit.html +++ b/docs/dev/reference/confint.mkinfit.html @@ -217,7 +217,7 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, <span class="r-in"><span><span class="va">f_d_1</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">ci_profile</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f_d_1</span>, method <span class="op">=</span> <span class="st">"profile"</span>, cores <span class="op">=</span> <span class="fl">1</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> user system elapsed </span> -<span class="r-out co"><span class="r-pr">#></span> 1.182 0.004 1.186 </span> +<span class="r-out co"><span class="r-pr">#></span> 1.247 0.000 1.246 </span> <span class="r-in"><span><span class="co"># Using more cores does not save much time here, as parent_0 takes up most of the time</span></span></span> <span class="r-in"><span><span class="co"># If we additionally exclude parent_0 (the confidence of which is often of</span></span></span> <span class="r-in"><span><span class="co"># minor interest), we get a nice performance improvement if we use at least 4 cores</span></span></span> @@ -225,7 +225,7 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"k_parent_sink"</span>, <span class="st">"k_parent_m1"</span>, <span class="st">"k_m1_sink"</span>, <span class="st">"sigma"</span><span class="op">)</span>, cores <span class="op">=</span> <span class="va">n_cores</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Profiling the likelihood</span> <span class="r-out co"><span class="r-pr">#></span> user system elapsed </span> -<span class="r-out co"><span class="r-pr">#></span> 0.429 0.171 0.324 </span> +<span class="r-out co"><span class="r-pr">#></span> 0.444 0.131 0.303 </span> <span class="r-in"><span><span class="va">ci_profile</span></span></span> <span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 96.456003640 1.027703e+02</span> diff --git a/docs/dev/reference/create_deg_func.html b/docs/dev/reference/create_deg_func.html index 4c66c02b..75d21481 100644 --- a/docs/dev/reference/create_deg_func.html +++ b/docs/dev/reference/create_deg_func.html @@ -104,8 +104,8 @@ <span class="r-in"><span> replications <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Loading required package: rbenchmark</span> <span class="r-out co"><span class="r-pr">#></span> test replications elapsed relative user.self sys.self user.child</span> -<span class="r-out co"><span class="r-pr">#></span> 1 analytical 2 0.249 1.000 0.249 0 0</span> -<span class="r-out co"><span class="r-pr">#></span> 2 deSolve 2 0.307 1.233 0.306 0 0</span> +<span class="r-out co"><span class="r-pr">#></span> 1 analytical 2 0.243 1.000 0.244 0 0</span> +<span class="r-out co"><span class="r-pr">#></span> 2 deSolve 2 0.302 1.243 0.301 0 0</span> <span class="r-out co"><span class="r-pr">#></span> sys.child</span> <span class="r-out co"><span class="r-pr">#></span> 1 0</span> <span class="r-out co"><span class="r-pr">#></span> 2 0</span> @@ -118,8 +118,8 @@ <span class="r-in"><span> deSolve <span class="op">=</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">DFOP_SFO</span>, <span class="va">FOCUS_D</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span></span> <span class="r-in"><span> replications <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> test replications elapsed relative user.self sys.self user.child</span> -<span class="r-out co"><span class="r-pr">#></span> 1 analytical 2 0.391 1.000 0.391 0 0</span> -<span class="r-out co"><span class="r-pr">#></span> 2 deSolve 2 0.543 1.389 0.542 0 0</span> +<span class="r-out co"><span class="r-pr">#></span> 1 analytical 2 0.393 1.000 0.392 0 0</span> +<span class="r-out co"><span class="r-pr">#></span> 2 deSolve 2 0.534 1.359 0.535 0 0</span> <span class="r-out co"><span class="r-pr">#></span> sys.child</span> <span class="r-out co"><span class="r-pr">#></span> 1 0</span> <span class="r-out co"><span class="r-pr">#></span> 2 0</span> diff --git a/docs/dev/reference/dimethenamid_2018.html b/docs/dev/reference/dimethenamid_2018.html index 4bd35bc6..209405a9 100644 --- a/docs/dev/reference/dimethenamid_2018.html +++ b/docs/dev/reference/dimethenamid_2018.html @@ -185,8 +185,8 @@ specific pieces of information in the comments.</p> <span class="r-out co"><span class="r-pr">#></span> saemix version used for fitting: 3.3 </span> <span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.10 </span> <span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.4.2 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri Feb 14 07:29:22 2025 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri Feb 14 07:29:22 2025 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Sun Feb 16 16:58:17 2025 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Sun Feb 16 16:58:17 2025 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_DMTA/dt = - k_DMTA * DMTA</span> @@ -199,7 +199,7 @@ specific pieces of information in the comments.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type deSolve </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 295.57 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 294.206 s</span> <span class="r-out co"><span class="r-pr">#></span> Using 300, 100 iterations and 9 chains</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model: Two-component variance function </span> diff --git a/docs/dev/reference/mkinfit.html b/docs/dev/reference/mkinfit.html index 1c84b9b2..aa9c3d8f 100644 --- a/docs/dev/reference/mkinfit.html +++ b/docs/dev/reference/mkinfit.html @@ -368,8 +368,8 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.10 </span> <span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.4.2 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri Feb 14 07:30:02 2025 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri Feb 14 07:30:02 2025 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Sun Feb 16 16:58:54 2025 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Sun Feb 16 16:58:54 2025 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent</span> @@ -517,9 +517,9 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class="r-in"><span> solution_type <span class="op">=</span> <span class="st">"analytical"</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="op">}</span></span></span> <span class="r-out co"><span class="r-pr">#></span> test relative elapsed</span> -<span class="r-out co"><span class="r-pr">#></span> 3 analytical 1.000 0.242</span> -<span class="r-out co"><span class="r-pr">#></span> 2 eigen 1.913 0.463</span> -<span class="r-out co"><span class="r-pr">#></span> 1 deSolve_compiled 1.917 0.464</span> +<span class="r-out co"><span class="r-pr">#></span> 3 analytical 1.000 0.240</span> +<span class="r-out co"><span class="r-pr">#></span> 2 eigen 1.908 0.458</span> +<span class="r-out co"><span class="r-pr">#></span> 1 deSolve_compiled 1.933 0.464</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"># Use stepwise fitting, using optimised parameters from parent only fit, FOMC-SFO</span></span></span> @@ -547,8 +547,8 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>diag(V) had non-positive or NA entries; the non-finite result may be dubious</span> <span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.10 </span> <span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.4.2 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri Feb 14 07:30:07 2025 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri Feb 14 07:30:07 2025 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Sun Feb 16 16:58:58 2025 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Sun Feb 16 16:58:58 2025 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent</span> @@ -557,7 +557,7 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type deSolve </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted using 4062 model solutions performed in 0.77 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted using 4062 model solutions performed in 0.776 s</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Error model: Two-component variance function </span> <span class="r-out co"><span class="r-pr">#></span> </span> diff --git a/docs/dev/reference/mkinmod.html b/docs/dev/reference/mkinmod.html index d26086eb..9824bf3a 100644 --- a/docs/dev/reference/mkinmod.html +++ b/docs/dev/reference/mkinmod.html @@ -290,7 +290,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p> <span class="r-in"><span> m1 <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span>, full_name <span class="op">=</span> <span class="st">"Metabolite M1"</span><span class="op">)</span>,</span></span> <span class="r-in"><span> name <span class="op">=</span> <span class="st">"SFO_SFO"</span>, dll_dir <span class="op">=</span> <span class="va">DLL_dir</span>, unload <span class="op">=</span> <span class="cn">TRUE</span>, overwrite <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> -<span class="r-msg co"><span class="r-pr">#></span> Copied DLL from /tmp/RtmpSeNGYy/file226312370605e2.so to /home/jranke/.local/share/mkin/SFO_SFO.so</span> +<span class="r-msg co"><span class="r-pr">#></span> Copied DLL from /tmp/RtmpHpDSpx/file2445be5e83d15b.so to /home/jranke/.local/share/mkin/SFO_SFO.so</span> <span class="r-in"><span><span class="co"># Now we can save the model and restore it in a new session</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">saveRDS</a></span><span class="op">(</span><span class="va">SFO_SFO.2</span>, file <span class="op">=</span> <span class="st">"~/SFO_SFO.rds"</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="co"># Terminate the R session here if you would like to check, and then do</span></span></span> @@ -343,7 +343,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p> <span class="r-out co"><span class="r-pr">#></span> })</span> <span class="r-out co"><span class="r-pr">#></span> return(predicted)</span> <span class="r-out co"><span class="r-pr">#></span> }</span> -<span class="r-out co"><span class="r-pr">#></span> <environment: 0x5555577ec6d0></span> +<span class="r-out co"><span class="r-pr">#></span> <environment: 0x55555f1f7f68></span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># If we have several parallel metabolites</span></span></span> <span class="r-in"><span><span class="co"># (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)</span></span></span> diff --git a/docs/dev/reference/mkinpredict.html b/docs/dev/reference/mkinpredict.html index e11dacdf..4b6c54e3 100644 --- a/docs/dev/reference/mkinpredict.html +++ b/docs/dev/reference/mkinpredict.html @@ -353,10 +353,10 @@ as these always return mapped output.</p></dd> <span class="r-in"><span> solution_type <span class="op">=</span> <span class="st">"analytical"</span>, use_compiled <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">[</span><span class="fl">201</span>,<span class="op">]</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="op">}</span></span></span> <span class="r-out co"><span class="r-pr">#></span> test relative elapsed</span> -<span class="r-out co"><span class="r-pr">#></span> 2 deSolve_compiled 1.0 0.002</span> <span class="r-out co"><span class="r-pr">#></span> 4 analytical 1.0 0.002</span> +<span class="r-out co"><span class="r-pr">#></span> 2 deSolve_compiled 1.5 0.003</span> <span class="r-out co"><span class="r-pr">#></span> 1 eigen 4.0 0.008</span> -<span class="r-out co"><span class="r-pr">#></span> 3 deSolve 30.5 0.061</span> +<span class="r-out co"><span class="r-pr">#></span> 3 deSolve 31.0 0.062</span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># \dontrun{</span></span></span> <span class="r-in"><span> <span class="co"># Predict from a fitted model</span></span></span> diff --git a/docs/dev/reference/mmkin.html b/docs/dev/reference/mmkin.html index c2bbd3c4..275ac5d9 100644 --- a/docs/dev/reference/mmkin.html +++ b/docs/dev/reference/mmkin.html @@ -158,10 +158,10 @@ plotting.</p></div> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="va">time_default</span></span></span> <span class="r-out co"><span class="r-pr">#></span> user system elapsed </span> -<span class="r-out co"><span class="r-pr">#></span> 1.522 0.957 0.720 </span> +<span class="r-out co"><span class="r-pr">#></span> 1.617 0.819 0.699 </span> <span class="r-in"><span><span class="va">time_1</span></span></span> <span class="r-out co"><span class="r-pr">#></span> user system elapsed </span> -<span class="r-out co"><span class="r-pr">#></span> 1.991 0.024 2.015 </span> +<span class="r-out co"><span class="r-pr">#></span> 1.908 0.036 1.944 </span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">fits.0</span><span class="op">[[</span><span class="st">"SFO_lin"</span>, <span class="fl">2</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> $ff</span> diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html index 25eb03c7..d2ea6e1a 100644 --- a/docs/dev/reference/saem.html +++ b/docs/dev/reference/saem.html @@ -397,8 +397,8 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-out co"><span class="r-pr">#></span> saemix version used for fitting: 3.3 </span> <span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.10 </span> <span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.4.2 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri Feb 14 07:32:13 2025 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri Feb 14 07:32:13 2025 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Sun Feb 16 17:01:05 2025 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Sun Feb 16 17:01:05 2025 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span> @@ -413,7 +413,7 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type analytical </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 3.605 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 3.489 s</span> <span class="r-out co"><span class="r-pr">#></span> Using 300, 100 iterations and 10 chains</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model: Constant variance </span> @@ -695,7 +695,7 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> In above message, R1 = 91</span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Error in deSolve::lsoda(y = odeini, times = outtimes, func = lsoda_func, : </span> +<span class="r-out co"><span class="r-pr">#></span> Error in deSolve::lsoda(y = odeini, times = outtimes_deSolve, func = lsoda_func, : </span> <span class="r-out co"><span class="r-pr">#></span> illegal input detected before taking any integration steps - see written message</span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co">#anova(</span></span></span> diff --git a/docs/dev/reference/summary.mkinfit.html b/docs/dev/reference/summary.mkinfit.html index 63a08d05..a9d124b9 100644 --- a/docs/dev/reference/summary.mkinfit.html +++ b/docs/dev/reference/summary.mkinfit.html @@ -193,15 +193,15 @@ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">FOCUS_2006_A</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.10 </span> <span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.4.2 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri Feb 14 07:34:16 2025 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri Feb 14 07:34:16 2025 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Sun Feb 16 17:03:11 2025 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Sun Feb 16 17:03:11 2025 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - k_parent * parent</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type analytical </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted using 131 model solutions performed in 0.009 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted using 131 model solutions performed in 0.01 s</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Error model: Constant variance </span> <span class="r-out co"><span class="r-pr">#></span> </span> diff --git a/docs/dev/reference/summary.mmkin.html b/docs/dev/reference/summary.mmkin.html index dad19e59..27b8c8a5 100644 --- a/docs/dev/reference/summary.mmkin.html +++ b/docs/dev/reference/summary.mmkin.html @@ -113,7 +113,7 @@ and gives an overview of ill-defined parameters calculated by <a href="illparms. <span class="r-wrn co"><span class="r-pr">#></span> false convergence (8)</span> <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fits</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Error model: Constant variance </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 0.512 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 0.471 s</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Status:</span> <span class="r-out co"><span class="r-pr">#></span> dataset</span> diff --git a/docs/dev/reference/summary.nlme.mmkin.html b/docs/dev/reference/summary.nlme.mmkin.html index dd4c4771..a1206833 100644 --- a/docs/dev/reference/summary.nlme.mmkin.html +++ b/docs/dev/reference/summary.nlme.mmkin.html @@ -214,8 +214,8 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> <span class="r-out co"><span class="r-pr">#></span> nlme version used for fitting: 3.1.166 </span> <span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.10 </span> <span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.4.2 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri Feb 14 07:34:18 2025 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri Feb 14 07:34:18 2025 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Sun Feb 16 17:03:13 2025 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Sun Feb 16 17:03:13 2025 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - k_parent * parent</span> @@ -225,7 +225,7 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type analytical </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 0.187 s using 4 iterations</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 0.189 s using 4 iterations</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model: Two-component variance function </span> <span class="r-out co"><span class="r-pr">#></span> </span> diff --git a/docs/dev/reference/summary.saem.mmkin.html b/docs/dev/reference/summary.saem.mmkin.html index e6138f37..271dddfa 100644 --- a/docs/dev/reference/summary.saem.mmkin.html +++ b/docs/dev/reference/summary.saem.mmkin.html @@ -290,8 +290,8 @@ saemix authors for the parts inherited from saemix.</p> <span class="r-out co"><span class="r-pr">#></span> saemix version used for fitting: 3.3 </span> <span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.10 </span> <span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.4.2 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri Feb 14 07:34:33 2025 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri Feb 14 07:34:33 2025 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Sun Feb 16 17:03:28 2025 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Sun Feb 16 17:03:28 2025 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span> @@ -306,7 +306,7 @@ saemix authors for the parts inherited from saemix.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type analytical </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 8.903 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 8.612 s</span> <span class="r-out co"><span class="r-pr">#></span> Using 300, 100 iterations and 10 chains</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model: Two-component variance function </span> |