diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2020-11-09 09:18:58 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2020-11-09 09:18:58 +0100 |
| commit | a3e058f8bceca903e7952e66abb4744f66115921 (patch) | |
| tree | f029eded457914459ecc111511e468905d56172d /docs/dev/reference/saem.html | |
| parent | e2cb0d4668f17f57c65f3ff94a7e17c784eaf4ba (diff) | |
Some work on example code, pkgdown update
Diffstat (limited to 'docs/dev/reference/saem.html')
| -rw-r--r-- | docs/dev/reference/saem.html | 180 |
1 files changed, 136 insertions, 44 deletions
diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html index 25608fc8..26f4c3e3 100644 --- a/docs/dev/reference/saem.html +++ b/docs/dev/reference/saem.html @@ -229,27 +229,27 @@ using <a href='mmkin.html'>mmkin</a>.</p> state.ini <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fl'>100</span><span class='op'>)</span>, fixed_initials <span class='op'>=</span> <span class='st'>"parent"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='va'>f_saem_p0_fixed</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent_p0_fixed</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Mon Nov 9 07:04:09 2020" +#> [1] "Mon Nov 9 09:03:11 2020" #> .... #> Minimisation finished -#> [1] "Mon Nov 9 07:04:11 2020"</div><div class='input'> +#> [1] "Mon Nov 9 09:03:13 2020"</div><div class='input'> <span class='va'>f_mmkin_parent</span> <span class='op'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>, <span class='st'>"DFOP"</span><span class='op'>)</span>, <span class='va'>ds</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='va'>f_saem_sfo</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"SFO"</span>, <span class='op'>]</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Mon Nov 9 07:04:12 2020" +#> [1] "Mon Nov 9 09:03:14 2020" #> .... #> Minimisation finished -#> [1] "Mon Nov 9 07:04:13 2020"</div><div class='input'><span class='va'>f_saem_fomc</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span> +#> [1] "Mon Nov 9 09:03:16 2020"</div><div class='input'><span class='va'>f_saem_fomc</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Mon Nov 9 07:04:14 2020" +#> [1] "Mon Nov 9 09:03:16 2020" #> .... #> Minimisation finished -#> [1] "Mon Nov 9 07:04:16 2020"</div><div class='input'><span class='va'>f_saem_dfop</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"DFOP"</span>, <span class='op'>]</span><span class='op'>)</span> +#> [1] "Mon Nov 9 09:03:18 2020"</div><div class='input'><span class='va'>f_saem_dfop</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"DFOP"</span>, <span class='op'>]</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Mon Nov 9 07:04:16 2020" +#> [1] "Mon Nov 9 09:03:19 2020" #> .... #> Minimisation finished -#> [1] "Mon Nov 9 07:04:19 2020"</div><div class='input'> +#> [1] "Mon Nov 9 09:03:22 2020"</div><div class='input'> <span class='co'># The returned saem.mmkin object contains an SaemixObject, therefore we can use</span> <span class='co'># functions from saemix</span> <span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'>saemix</span><span class='op'>)</span> @@ -258,14 +258,47 @@ using <a href='mmkin.html'>mmkin</a>.</p> </div><div class='output co'>#> Likelihoods computed by importance sampling </div><div class='output co'>#> AIC BIC #> 1 624.2428 622.2900 #> 2 467.7644 465.0305 -#> 3 491.3541 487.8391</div><div class='input'> +#> 3 491.3541 487.8391</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, plot.type <span class='op'>=</span> <span class='st'>"convergence"</span><span class='op'>)</span> +</div><div class='output co'>#> Plotting convergence plots</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, plot.type <span class='op'>=</span> <span class='st'>"individual.fit"</span><span class='op'>)</span> +</div><div class='img'><img src='saem-1.png' alt='' width='700' height='433' /></div><div class='output co'>#> Plotting individual fits</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, plot.type <span class='op'>=</span> <span class='st'>"npde"</span><span class='op'>)</span> +</div><div class='img'><img src='saem-2.png' alt='' width='700' height='433' /></div><div class='output co'>#> Simulating data using nsim = 1000 simulated datasets +#> Computing WRES and npde . +#> Plotting npde</div><div class='img'><img src='saem-3.png' alt='' width='700' height='433' /></div><div class='output co'>#> --------------------------------------------- +#> Distribution of npde: +#> mean= -0.01736 (SE= 0.098 ) +#> variance= 0.8562 (SE= 0.13 ) +#> skewness= 0.513 +#> kurtosis= 1.202 +#> --------------------------------------------- +#> +#> Statistical tests +#> Wilcoxon signed rank test : 0.652 +#> Fisher variance test : 0.338 +#> SW test of normality : 0.0757 . +#> Global adjusted p-value : 0.227 +#> --- +#> Signif. codes: '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 +#> ---------------------------------------------</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, plot.type <span class='op'>=</span> <span class='st'>"vpc"</span><span class='op'>)</span> +</div><div class='output co'>#> Performing simulations under the model. +#> Plotting VPC +#> Method used for VPC: binning by quantiles on X , dividing into the following intervals +#> Interval Centered.On +#> 1 (-1,3] 1.3 +#> 2 (3,8] 7.4 +#> 3 (8,14] 13.2 +#> 4 (14,21] 20.5 +#> 5 (21,37.7] 29.5 +#> 6 (37.7,60] 50.4 +#> 7 (60,90] 76.6 +#> 8 (90,120] 109.0 +#> 9 (120,180] 156.0 </div><div class='img'><img src='saem-4.png' alt='' width='700' height='433' /></div><div class='input'> <span class='va'>f_mmkin_parent_tc</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>f_mmkin_parent</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span> <span class='va'>f_saem_fomc_tc</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent_tc</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Mon Nov 9 07:04:21 2020" +#> [1] "Mon Nov 9 09:03:24 2020" #> .... #> Minimisation finished -#> [1] "Mon Nov 9 07:04:26 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/compare.saemix.html'>compare.saemix</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, <span class='va'>f_saem_fomc_tc</span><span class='op'>$</span><span class='va'>so</span><span class='op'>)</span><span class='op'>)</span> +#> [1] "Mon Nov 9 09:03:29 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/compare.saemix.html'>compare.saemix</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, <span class='va'>f_saem_fomc_tc</span><span class='op'>$</span><span class='va'>so</span><span class='op'>)</span><span class='op'>)</span> </div><div class='output co'>#> Likelihoods computed by importance sampling </div><div class='output co'>#> AIC BIC #> 1 467.7644 465.0305 #> 2 469.4862 466.3617</div><div class='input'> @@ -285,46 +318,105 @@ using <a href='mmkin.html'>mmkin</a>.</p> <span class='co'># solutions written for mkin this took around four minutes</span> <span class='va'>f_saem_sfo_sfo</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'>"SFO-SFO"</span>, <span class='op'>]</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Mon Nov 9 07:04:28 2020" +#> [1] "Mon Nov 9 09:03:31 2020" #> .... #> Minimisation finished -#> [1] "Mon Nov 9 07:04:33 2020"</div><div class='input'><span class='va'>f_saem_dfop_sfo</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'>"SFO-SFO"</span>, <span class='op'>]</span><span class='op'>)</span> +#> [1] "Mon Nov 9 09:03:36 2020"</div><div class='input'><span class='va'>f_saem_dfop_sfo</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><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Mon Nov 9 07:04:33 2020" +#> [1] "Mon Nov 9 09:03:37 2020" #> .... #> Minimisation finished -#> [1] "Mon Nov 9 07:04:39 2020"</div><div class='input'> +#> [1] "Mon Nov 9 09:03:46 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>f_saem_dfop_sfo</span>, data <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span> +</div><div class='output co'>#> saemix version used for fitting: 3.1.9000 +#> mkin version used for pre-fitting: 0.9.50.4 +#> R version used for fitting: 4.0.3 +#> Date of fit: Mon Nov 9 09:03:47 2020 +#> Date of summary: Mon Nov 9 09:03:47 2020 +#> +#> Equations: +#> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * +#> time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) +#> * parent +#> d_A1/dt = + f_parent_to_A1 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g) +#> * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * +#> exp(-k2 * time))) * parent - k_A1 * A1 +#> +#> Data: +#> 170 observations of 2 variable(s) grouped in 5 datasets +#> +#> Model predictions using solution type analytical +#> +#> Fitted in 9.758 s using 300, 100 iterations +#> +#> Variance model: Constant variance +#> +#> Mean of starting values for individual parameters: +#> parent_0 log_k_A1 f_parent_qlogis log_k1 log_k2 +#> 93.8101519 -9.7647455 -0.9711148 -1.8799371 -4.2708142 +#> g_qlogis +#> 0.1356441 +#> +#> Fixed degradation parameter values: +#> None +#> +#> Results: +#> +#> Likelihood computed by importance sampling +#> AIC BIC logLik +#> 841.3208 836.2435 -407.6604 +#> +#> Optimised, transformed parameters with symmetric confidence intervals: +#> est. lower upper +#> parent_0 93.7514328489 91.113651 96.3892150 +#> log_k_A1 -6.1262333211 -8.432492 -3.8199749 +#> f_parent_qlogis -0.9739851652 -1.371984 -0.5759863 +#> log_k1 -2.4818388836 -3.746899 -1.2167788 +#> log_k2 -3.6138616567 -5.294149 -1.9335743 +#> g_qlogis -0.0004613666 -1.063179 1.0622564 +#> +#> Correlation: +#> prnt_0 lg__A1 f_prn_ log_k1 log_k2 +#> log_k_A1 -0.013 +#> f_parent_qlogis -0.025 0.050 +#> log_k1 0.030 0.000 -0.005 +#> log_k2 0.013 0.005 -0.003 0.037 +#> g_qlogis -0.068 -0.016 0.011 -0.181 -0.181 +#> +#> Random effects: +#> est. lower upper +#> SD.parent_0 2.7857084 0.7825105 4.7889063 +#> SD.log_k_A1 2.1412505 0.4425207 3.8399803 +#> SD.f_parent_qlogis 0.4463087 0.1609059 0.7317116 +#> SD.log_k1 1.4097204 0.5240566 2.2953842 +#> SD.log_k2 1.8739067 0.6979362 3.0498773 +#> SD.g_qlogis 0.4559301 -0.8149852 1.7268453 +#> +#> Variance model: +#> est. lower upper +#> a.1 1.882757 1.665681 2.099832 +#> +#> Backtransformed parameters with asymmetric confidence intervals: +#> est. lower upper +#> parent_0 93.751432849 9.111365e+01 96.38921497 +#> k_A1 0.002184795 2.176784e-04 0.02192835 +#> f_parent_to_A1 0.274086887 2.022995e-01 0.35985666 +#> k1 0.083589373 2.359079e-02 0.29618269 +#> k2 0.026947583 5.020885e-03 0.14463032 +#> g 0.499884658 2.567024e-01 0.74312150 +#> +#> Resulting formation fractions: +#> ff +#> parent_A1 0.2741 +#> parent_sink 0.7259 +#> +#> Estimated disappearance times: +#> DT50 DT90 DT50back DT50_k1 DT50_k2 +#> parent 13.91 60.89 18.33 8.292 25.72 +#> A1 317.26 1053.91 NA NA NA</div><div class='input'> <span class='co'># Using a single core, the following takes about 6 minutes, using 10 cores</span> <span class='co'># it is slower instead of faster</span> -<span class='va'>f_saem_fomc</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'>"FOMC-SFO"</span>, <span class='op'>]</span>, cores <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span> -</div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Mon Nov 9 07:04:39 2020" -#> DLSODA- At current T (=R1), MXSTEP (=I1) steps -#> taken on this call before reaching TOUT -#> In above message, I1 = 5000 -#> -#> In above message, R1 = 0.00156238 -#> -#> DLSODA- At T (=R1) and step size H (=R2), the -#> corrector convergence failed repeatedly -#> or with ABS(H) = HMIN -#> In above message, R1 = 0, R2 = 1.1373e-10 -#> -#> DLSODA- At current T (=R1), MXSTEP (=I1) steps -#> taken on this call before reaching TOUT -#> In above message, I1 = 5000 -#> -#> In above message, R1 = 2.24752e-06 -#> -#> DLSODA- At current T (=R1), MXSTEP (=I1) steps -#> taken on this call before reaching TOUT -#> In above message, I1 = 5000 -#> -#> In above message, R1 = 0.000585935 -#> -#> .... -#> Minimisation finished -#> [1] "Mon Nov 9 07:11:24 2020"</div><div class='output co'>#> <span class='warning'>Warning: Creating predictions from the saemix model failed</span></div><div class='input'><span class='co'># }</span> +<span class='co'>#f_saem_fomc <- saem(f_mmkin["FOMC-SFO", ], cores = 1)</span> +<span class='co'># }</span> </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> |