aboutsummaryrefslogtreecommitdiff
path: root/docs/dev/reference/saem.html
diff options
context:
space:
mode:
Diffstat (limited to 'docs/dev/reference/saem.html')
-rw-r--r--docs/dev/reference/saem.html180
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'>&lt;-</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'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Mon Nov 9 07:04:09 2020"
+#&gt; [1] "Mon Nov 9 09:03:11 2020"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Mon Nov 9 07:04:11 2020"</div><div class='input'>
+#&gt; [1] "Mon Nov 9 09:03:13 2020"</div><div class='input'>
<span class='va'>f_mmkin_parent</span> <span class='op'>&lt;-</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'>&lt;-</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'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Mon Nov 9 07:04:12 2020"
+#&gt; [1] "Mon Nov 9 09:03:14 2020"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Mon Nov 9 07:04:13 2020"</div><div class='input'><span class='va'>f_saem_fomc</span> <span class='op'>&lt;-</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>
+#&gt; [1] "Mon Nov 9 09:03:16 2020"</div><div class='input'><span class='va'>f_saem_fomc</span> <span class='op'>&lt;-</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'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Mon Nov 9 07:04:14 2020"
+#&gt; [1] "Mon Nov 9 09:03:16 2020"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Mon Nov 9 07:04:16 2020"</div><div class='input'><span class='va'>f_saem_dfop</span> <span class='op'>&lt;-</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>
+#&gt; [1] "Mon Nov 9 09:03:18 2020"</div><div class='input'><span class='va'>f_saem_dfop</span> <span class='op'>&lt;-</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'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Mon Nov 9 07:04:16 2020"
+#&gt; [1] "Mon Nov 9 09:03:19 2020"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Mon Nov 9 07:04:19 2020"</div><div class='input'>
+#&gt; [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'>#&gt; Likelihoods computed by importance sampling </div><div class='output co'>#&gt; AIC BIC
#&gt; 1 624.2428 622.2900
#&gt; 2 467.7644 465.0305
-#&gt; 3 491.3541 487.8391</div><div class='input'>
+#&gt; 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'>$</span><span class='va'>so</span>, plot.type <span class='op'>=</span> <span class='st'>"convergence"</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; Plotting convergence plots</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</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'>#&gt; 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'>$</span><span class='va'>so</span>, plot.type <span class='op'>=</span> <span class='st'>"npde"</span><span class='op'>)</span>
+</div><div class='img'><img src='saem-2.png' alt='' width='700' height='433' /></div><div class='output co'>#&gt; Simulating data using nsim = 1000 simulated datasets
+#&gt; Computing WRES and npde .
+#&gt; Plotting npde</div><div class='img'><img src='saem-3.png' alt='' width='700' height='433' /></div><div class='output co'>#&gt; ---------------------------------------------
+#&gt; Distribution of npde:
+#&gt; mean= -0.01736 (SE= 0.098 )
+#&gt; variance= 0.8562 (SE= 0.13 )
+#&gt; skewness= 0.513
+#&gt; kurtosis= 1.202
+#&gt; ---------------------------------------------
+#&gt;
+#&gt; Statistical tests
+#&gt; Wilcoxon signed rank test : 0.652
+#&gt; Fisher variance test : 0.338
+#&gt; SW test of normality : 0.0757 .
+#&gt; Global adjusted p-value : 0.227
+#&gt; ---
+#&gt; Signif. codes: '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1
+#&gt; ---------------------------------------------</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</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'>#&gt; Performing simulations under the model.
+#&gt; Plotting VPC
+#&gt; Method used for VPC: binning by quantiles on X , dividing into the following intervals
+#&gt; Interval Centered.On
+#&gt; 1 (-1,3] 1.3
+#&gt; 2 (3,8] 7.4
+#&gt; 3 (8,14] 13.2
+#&gt; 4 (14,21] 20.5
+#&gt; 5 (21,37.7] 29.5
+#&gt; 6 (37.7,60] 50.4
+#&gt; 7 (60,90] 76.6
+#&gt; 8 (90,120] 109.0
+#&gt; 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'>&lt;-</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'>&lt;-</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'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Mon Nov 9 07:04:21 2020"
+#&gt; [1] "Mon Nov 9 09:03:24 2020"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [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>
+#&gt; [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'>#&gt; Likelihoods computed by importance sampling </div><div class='output co'>#&gt; AIC BIC
#&gt; 1 467.7644 465.0305
#&gt; 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'>&lt;-</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'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Mon Nov 9 07:04:28 2020"
+#&gt; [1] "Mon Nov 9 09:03:31 2020"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Mon Nov 9 07:04:33 2020"</div><div class='input'><span class='va'>f_saem_dfop_sfo</span> <span class='op'>&lt;-</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>
+#&gt; [1] "Mon Nov 9 09:03:36 2020"</div><div class='input'><span class='va'>f_saem_dfop_sfo</span> <span class='op'>&lt;-</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'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Mon Nov 9 07:04:33 2020"
+#&gt; [1] "Mon Nov 9 09:03:37 2020"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Mon Nov 9 07:04:39 2020"</div><div class='input'>
+#&gt; [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'>#&gt; saemix version used for fitting: 3.1.9000
+#&gt; mkin version used for pre-fitting: 0.9.50.4
+#&gt; R version used for fitting: 4.0.3
+#&gt; Date of fit: Mon Nov 9 09:03:47 2020
+#&gt; Date of summary: Mon Nov 9 09:03:47 2020
+#&gt;
+#&gt; Equations:
+#&gt; d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
+#&gt; time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time)))
+#&gt; * parent
+#&gt; d_A1/dt = + f_parent_to_A1 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g)
+#&gt; * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) *
+#&gt; exp(-k2 * time))) * parent - k_A1 * A1
+#&gt;
+#&gt; Data:
+#&gt; 170 observations of 2 variable(s) grouped in 5 datasets
+#&gt;
+#&gt; Model predictions using solution type analytical
+#&gt;
+#&gt; Fitted in 9.758 s using 300, 100 iterations
+#&gt;
+#&gt; Variance model: Constant variance
+#&gt;
+#&gt; Mean of starting values for individual parameters:
+#&gt; parent_0 log_k_A1 f_parent_qlogis log_k1 log_k2
+#&gt; 93.8101519 -9.7647455 -0.9711148 -1.8799371 -4.2708142
+#&gt; g_qlogis
+#&gt; 0.1356441
+#&gt;
+#&gt; Fixed degradation parameter values:
+#&gt; None
+#&gt;
+#&gt; Results:
+#&gt;
+#&gt; Likelihood computed by importance sampling
+#&gt; AIC BIC logLik
+#&gt; 841.3208 836.2435 -407.6604
+#&gt;
+#&gt; Optimised, transformed parameters with symmetric confidence intervals:
+#&gt; est. lower upper
+#&gt; parent_0 93.7514328489 91.113651 96.3892150
+#&gt; log_k_A1 -6.1262333211 -8.432492 -3.8199749
+#&gt; f_parent_qlogis -0.9739851652 -1.371984 -0.5759863
+#&gt; log_k1 -2.4818388836 -3.746899 -1.2167788
+#&gt; log_k2 -3.6138616567 -5.294149 -1.9335743
+#&gt; g_qlogis -0.0004613666 -1.063179 1.0622564
+#&gt;
+#&gt; Correlation:
+#&gt; prnt_0 lg__A1 f_prn_ log_k1 log_k2
+#&gt; log_k_A1 -0.013
+#&gt; f_parent_qlogis -0.025 0.050
+#&gt; log_k1 0.030 0.000 -0.005
+#&gt; log_k2 0.013 0.005 -0.003 0.037
+#&gt; g_qlogis -0.068 -0.016 0.011 -0.181 -0.181
+#&gt;
+#&gt; Random effects:
+#&gt; est. lower upper
+#&gt; SD.parent_0 2.7857084 0.7825105 4.7889063
+#&gt; SD.log_k_A1 2.1412505 0.4425207 3.8399803
+#&gt; SD.f_parent_qlogis 0.4463087 0.1609059 0.7317116
+#&gt; SD.log_k1 1.4097204 0.5240566 2.2953842
+#&gt; SD.log_k2 1.8739067 0.6979362 3.0498773
+#&gt; SD.g_qlogis 0.4559301 -0.8149852 1.7268453
+#&gt;
+#&gt; Variance model:
+#&gt; est. lower upper
+#&gt; a.1 1.882757 1.665681 2.099832
+#&gt;
+#&gt; Backtransformed parameters with asymmetric confidence intervals:
+#&gt; est. lower upper
+#&gt; parent_0 93.751432849 9.111365e+01 96.38921497
+#&gt; k_A1 0.002184795 2.176784e-04 0.02192835
+#&gt; f_parent_to_A1 0.274086887 2.022995e-01 0.35985666
+#&gt; k1 0.083589373 2.359079e-02 0.29618269
+#&gt; k2 0.026947583 5.020885e-03 0.14463032
+#&gt; g 0.499884658 2.567024e-01 0.74312150
+#&gt;
+#&gt; Resulting formation fractions:
+#&gt; ff
+#&gt; parent_A1 0.2741
+#&gt; parent_sink 0.7259
+#&gt;
+#&gt; Estimated disappearance times:
+#&gt; DT50 DT90 DT50back DT50_k1 DT50_k2
+#&gt; parent 13.91 60.89 18.33 8.292 25.72
+#&gt; 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'>&lt;-</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'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Mon Nov 9 07:04:39 2020"
-#&gt; DLSODA- At current T (=R1), MXSTEP (=I1) steps
-#&gt; taken on this call before reaching TOUT
-#&gt; In above message, I1 = 5000
-#&gt;
-#&gt; In above message, R1 = 0.00156238
-#&gt;
-#&gt; DLSODA- At T (=R1) and step size H (=R2), the
-#&gt; corrector convergence failed repeatedly
-#&gt; or with ABS(H) = HMIN
-#&gt; In above message, R1 = 0, R2 = 1.1373e-10
-#&gt;
-#&gt; DLSODA- At current T (=R1), MXSTEP (=I1) steps
-#&gt; taken on this call before reaching TOUT
-#&gt; In above message, I1 = 5000
-#&gt;
-#&gt; In above message, R1 = 2.24752e-06
-#&gt;
-#&gt; DLSODA- At current T (=R1), MXSTEP (=I1) steps
-#&gt; taken on this call before reaching TOUT
-#&gt; In above message, I1 = 5000
-#&gt;
-#&gt; In above message, R1 = 0.000585935
-#&gt;
-#&gt; ....
-#&gt; Minimisation finished
-#&gt; [1] "Mon Nov 9 07:11:24 2020"</div><div class='output co'>#&gt; <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 &lt;- 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">

Contact - Imprint