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Diffstat (limited to 'docs/reference/saem.html')
| -rw-r--r-- | docs/reference/saem.html | 99 |
1 files changed, 70 insertions, 29 deletions
diff --git a/docs/reference/saem.html b/docs/reference/saem.html index 957c098e..e308af61 100644 --- a/docs/reference/saem.html +++ b/docs/reference/saem.html @@ -19,13 +19,13 @@ Expectation Maximisation algorithm (SAEM)."><!-- mathjax --><script src="https:/ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.1</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.3</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"><li> - <a href="../reference/index.html">Functions and data</a> + <a href="../reference/index.html">Reference</a> </li> <li class="dropdown"> <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> @@ -36,6 +36,8 @@ Expectation Maximisation algorithm (SAEM)."><!-- mathjax --><script src="https:/ <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> + <li class="divider"> + <li class="dropdown-header">Example evaluations with (generalised) nonlinear least squares</li> <li> <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> </li> @@ -43,22 +45,29 @@ Expectation Maximisation algorithm (SAEM)."><!-- mathjax --><script src="https:/ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> + <li class="divider"> + <li class="dropdown-header">Example evaluations with hierarchical models (nonlinear mixed-effects models)</li> <li> - <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> + <a href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a> </li> <li> - <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> - <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + <a href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a> </li> <li> - <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> + </li> + <li class="divider"> + <li class="dropdown-header">Performance</li> + <li> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> @@ -66,6 +75,14 @@ Expectation Maximisation algorithm (SAEM)."><!-- mathjax --><script src="https:/ <li> <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> + <li class="divider"> + <li class="dropdown-header">Miscellaneous</li> + <li> + <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + </li> + <li> + <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </li> </ul></li> <li> <a href="../news/index.html">News</a> @@ -143,10 +160,7 @@ Expectation Maximisation algorithm (SAEM).</p> <span> <span class="va">...</span></span> <span><span class="op">)</span></span> <span></span> -<span><span class="fu">saemix_data</span><span class="op">(</span><span class="va">object</span>, covariates <span class="op">=</span> <span class="cn">NULL</span>, verbose <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span> -<span></span> -<span><span class="co"># S3 method for saem.mmkin</span></span> -<span><span class="fu"><a href="parms.html">parms</a></span><span class="op">(</span><span class="va">object</span>, ci <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> +<span><span class="fu">saemix_data</span><span class="op">(</span><span class="va">object</span>, covariates <span class="op">=</span> <span class="cn">NULL</span>, verbose <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> </div> <div id="arguments"> @@ -257,11 +271,6 @@ and the end of the optimisation process?</p></dd> <dt>digits</dt> <dd><p>Number of digits to use for printing</p></dd> - -<dt>ci</dt> -<dd><p>Should a matrix with estimates and confidence interval boundaries -be returned? If FALSE (default), a vector of estimates is returned.</p></dd> - </dl></div> <div id="value"> <h2>Value</h2> @@ -430,10 +439,10 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-plt img"><img src="saem-4.png" alt="" width="700" height="433"></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">f_saem_dfop_sfo</span>, data <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> saemix version used for fitting: 3.2 </span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.1 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.2 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri Nov 18 19:19:25 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri Nov 18 19:19:25 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.3 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.3 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Apr 20 07:34:38 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Apr 20 07:34:38 2023 </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> @@ -448,12 +457,12 @@ 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 9.068 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 3.757 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> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Mean of starting values for individual parameters:</span> +<span class="r-out co"><span class="r-pr">#></span> Starting values for degradation parameters:</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 log_k_A1 f_parent_qlogis log_k1 log_k2 </span> <span class="r-out co"><span class="r-pr">#></span> 93.8102 -5.3734 -0.9711 -1.8799 -4.2708 </span> <span class="r-out co"><span class="r-pr">#></span> g_qlogis </span> @@ -462,6 +471,19 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-out co"><span class="r-pr">#></span> Fixed degradation parameter values:</span> <span class="r-out co"><span class="r-pr">#></span> None</span> <span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Starting values for random effects (square root of initial entries in omega):</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 log_k_A1 f_parent_qlogis log_k1 log_k2 g_qlogis</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 4.941 0.000 0.0000 0.000 0.000 0.0000</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_A1 0.000 2.551 0.0000 0.000 0.000 0.0000</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis 0.000 0.000 0.7251 0.000 0.000 0.0000</span> +<span class="r-out co"><span class="r-pr">#></span> log_k1 0.000 0.000 0.0000 1.449 0.000 0.0000</span> +<span class="r-out co"><span class="r-pr">#></span> log_k2 0.000 0.000 0.0000 0.000 2.228 0.0000</span> +<span class="r-out co"><span class="r-pr">#></span> g_qlogis 0.000 0.000 0.0000 0.000 0.000 0.7814</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Starting values for error model parameters:</span> +<span class="r-out co"><span class="r-pr">#></span> a.1 </span> +<span class="r-out co"><span class="r-pr">#></span> 1 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Results:</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Likelihood computed by importance sampling</span> @@ -698,12 +720,31 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 120 12.1 12.79238 -0.69238 1.882 -0.36791</span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># The following takes about 6 minutes</span></span></span> -<span class="r-in"><span><span class="co">#f_saem_dfop_sfo_deSolve <- saem(f_mmkin["DFOP-SFO", ], solution_type = "deSolve",</span></span></span> -<span class="r-in"><span><span class="co"># control = list(nbiter.saemix = c(200, 80), nbdisplay = 10))</span></span></span> +<span class="r-in"><span><span class="va">f_saem_dfop_sfo_deSolve</span> <span class="op"><-</span> <span class="fu">saem</span><span class="op">(</span><span class="va">f_mmkin</span><span class="op">[</span><span class="st">"DFOP-SFO"</span>, <span class="op">]</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span>,</span></span> +<span class="r-in"><span> nbiter.saemix <span class="op">=</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="fl">200</span>, <span class="fl">80</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> DINTDY- T (=R1) illegal </span> +<span class="r-out co"><span class="r-pr">#></span> In above message, R1 = 70</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> T not in interval TCUR - HU (= R1) to TCUR (=R2) </span> +<span class="r-out co"><span class="r-pr">#></span> In above message, R1 = 53.1122, R2 = 56.6407</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> DINTDY- T (=R1) illegal </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> T not in interval TCUR - HU (= R1) to TCUR (=R2) </span> +<span class="r-out co"><span class="r-pr">#></span> In above message, R1 = 53.1122, R2 = 56.6407</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> DLSODA- Trouble in DINTDY. ITASK = I1, TOUT = R1</span> +<span class="r-out co"><span class="r-pr">#></span> In above message, I1 = 1</span> +<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> 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">#saemix::compare.saemix(list(</span></span></span> -<span class="r-in"><span><span class="co"># f_saem_dfop_sfo$so,</span></span></span> -<span class="r-in"><span><span class="co"># f_saem_dfop_sfo_deSolve$so))</span></span></span> +<span class="r-in"><span><span class="co">#anova(</span></span></span> +<span class="r-in"><span><span class="co"># f_saem_dfop_sfo,</span></span></span> +<span class="r-in"><span><span class="co"># f_saem_dfop_sfo_deSolve))</span></span></span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># If the model supports it, we can also use eigenvalue based solutions, which</span></span></span> <span class="r-in"><span><span class="co"># take a similar amount of time</span></span></span> @@ -724,7 +765,7 @@ using <a href="mmkin.html">mmkin</a>.</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> </footer></div> |