diff options
78 files changed, 450 insertions, 424 deletions
diff --git a/R/mkinfit.R b/R/mkinfit.R index 754e72b8..dca71ecf 100644 --- a/R/mkinfit.R +++ b/R/mkinfit.R @@ -21,6 +21,7 @@ if(getRversion() >= '2.15.1') utils::globalVariables(c("name", "time", "value")) mkinfit <- function(mkinmod, observed,
parms.ini = "auto",
state.ini = "auto",
+ err.ini = "auto",
fixed_parms = NULL,
fixed_initials = names(mkinmod$diffs)[-1],
from_max_mean = FALSE,
@@ -247,6 +248,26 @@ mkinfit <- function(mkinmod, observed, "obs" = paste0("sigma_", obs_vars),
"tc" = c("sigma_low", "rsd_high"))
+ # Define starting values for the error model
+ if (err.ini[1] != "auto") {
+ if (!identical(names(err.ini), errparm_names)) {
+ stop("Please supply initial values for error model components ", paste(errparm_names, collapse = ", "))
+ } else {
+ errparms = err.ini
+ }
+ } else {
+ if (err_mod == "const") {
+ errparms = 3
+ }
+ if (err_mod == "obs") {
+ errparms = rep(3, length(obs_vars))
+ }
+ if (err_mod == "tc") {
+ errparms <- c(sigma_low = 3, rsd_high = 0.01)
+ }
+ names(errparms) <- errparm_names
+ }
+
# Define outtimes for model solution.
# Include time points at which observed data are available
outtimes = sort(unique(c(observed$time, seq(min(observed$time),
@@ -407,14 +428,6 @@ mkinfit <- function(mkinmod, observed, fit <- fit.ols
fit$logLik <- - nlogLik(c(fit$par, sigma = sigma_mle), OLS = FALSE)
} else {
- if (err_mod == "obs") {
- errparms = rep(3, length(obs_vars))
- }
- if (err_mod == "tc") {
- errparms <- c(sigma_low = 0.5, rsd_high = 0.07)
- }
- names(errparms) <- errparm_names
-
fit <- nlminb(c(state.ini.optim, transparms.optim, errparms),
nlogLik, control = control,
lower = lower, upper = upper, ...)
@@ -6,5 +6,7 @@ * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories * looking to see if a ‘data/datalist’ file should be added -* building ‘mkin_0.9.49.4.tar.gz’ + NB: this package now depends on R (>= 3.5.0) + WARNING: Added dependency on R >= 3.5.0 because serialized objects in serialize/load version 3 cannot be read in older versions of R. File(s) containing such objects: 'mkin/inst/benchmark_data/mkin_benchmarks.rda' +* building 'mkin_0.9.49.4.tar.gz' diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index e63feb07..0ae6a391 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -88,7 +88,7 @@ <h1>Example evaluation of FOCUS Example Dataset D</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2019-04-10</h4> + <h4 class="date">2019-05-02</h4> <div class="hidden name"><code>FOCUS_D.Rmd</code></div> @@ -167,9 +167,9 @@ <p>A comprehensive report of the results is obtained using the <code>summary</code> method for <code>mkinfit</code> objects.</p> <div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(fit)</a></code></pre></div> <pre><code>## mkin version used for fitting: 0.9.49.4 -## R version used for fitting: 3.5.3 -## Date of fit: Wed Apr 10 10:11:31 2019 -## Date of summary: Wed Apr 10 10:11:31 2019 +## R version used for fitting: 3.6.0 +## Date of fit: Thu May 2 12:40:29 2019 +## Date of summary: Thu May 2 12:40:29 2019 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent @@ -177,10 +177,10 @@ ## ## Model predictions using solution type deSolve ## -## Fitted with method using 396 model solutions performed in 1.048 s +## Fitted using 396 model solutions performed in 1.048 s ## ## Error model: -## NULL +## Constant variance ## ## Starting values for parameters to be optimised: ## value type @@ -235,7 +235,7 @@ ## k_m1_sink 0.005261 7.510 6.165e-09 0.004012 6.898e-03 ## sigma 3.126000 8.718 2.235e-10 2.396000 3.855e+00 ## -## Chi2 error levels in percent: +## FOCUS Chi2 error levels in percent: ## err.min n.optim df ## All data 6.398 4 15 ## parent 6.827 3 6 diff --git a/docs/articles/FOCUS_D_files/figure-html/plot_2-1.png b/docs/articles/FOCUS_D_files/figure-html/plot_2-1.png Binary files differindex 79ec3aaf..64da1d2e 100644 --- a/docs/articles/FOCUS_D_files/figure-html/plot_2-1.png +++ b/docs/articles/FOCUS_D_files/figure-html/plot_2-1.png diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index 8af99f6c..b05963ae 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -88,7 +88,7 @@ <h1>Example evaluation of FOCUS Laboratory Data L1 to L3</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2019-04-10</h4> + <h4 class="date">2019-05-02</h4> <div class="hidden name"><code>FOCUS_L.Rmd</code></div> @@ -113,19 +113,19 @@ <div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" title="1">m.L1.SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(<span class="st">"SFO"</span>, FOCUS_<span class="dv">2006</span>_L1_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> <a class="sourceLine" id="cb2-2" title="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.L1.SFO)</a></code></pre></div> <pre><code>## mkin version used for fitting: 0.9.49.4 -## R version used for fitting: 3.5.3 -## Date of fit: Wed Apr 10 10:11:33 2019 -## Date of summary: Wed Apr 10 10:11:33 2019 +## R version used for fitting: 3.6.0 +## Date of fit: Thu May 2 12:40:31 2019 +## Date of summary: Thu May 2 12:40:31 2019 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method using 133 model solutions performed in 0.344 s +## Fitted using 133 model solutions performed in 0.289 s ## ## Error model: -## NULL +## Constant variance ## ## Starting values for parameters to be optimised: ## value type @@ -163,7 +163,7 @@ ## k_parent_sink 0.09561 26.57 2.487e-14 0.08824 0.1036 ## sigma 2.78000 6.00 1.216e-05 1.79200 3.7670 ## -## Chi2 error levels in percent: +## FOCUS Chi2 error levels in percent: ## err.min n.optim df ## All data 3.424 2 7 ## parent 3.424 2 7 @@ -214,9 +214,9 @@ <pre><code>## Warning in cov2cor(ans$cov.unscaled): diag(.) had 0 or NA entries; non- ## finite result is doubtful</code></pre> <pre><code>## mkin version used for fitting: 0.9.49.4 -## R version used for fitting: 3.5.3 -## Date of fit: Wed Apr 10 10:11:34 2019 -## Date of summary: Wed Apr 10 10:11:34 2019 +## R version used for fitting: 3.6.0 +## Date of fit: Thu May 2 12:40:33 2019 +## Date of summary: Thu May 2 12:40:33 2019 ## ## ## Warning: Optimisation did not converge: @@ -228,24 +228,24 @@ ## ## Model predictions using solution type analytical ## -## Fitted with method using 344 model solutions performed in 0.778 s +## Fitted using 599 model solutions performed in 1.277 s ## ## Error model: -## NULL +## Constant variance ## ## Starting values for parameters to be optimised: -## value type -## parent_0 89.85000 state -## alpha 1.00000 deparm -## beta 10.00000 deparm -## sigma 2.77987 error +## value type +## parent_0 89.850000 state +## alpha 1.000000 deparm +## beta 10.000000 deparm +## sigma 2.779868 error ## ## Starting values for the transformed parameters actually optimised: ## value lower upper ## parent_0 89.850000 -Inf Inf ## log_alpha 0.000000 -Inf Inf ## log_beta 2.302585 -Inf Inf -## sigma 2.779870 0 Inf +## sigma 2.779868 0 Inf ## ## Fixed parameter values: ## None @@ -253,16 +253,16 @@ ## Optimised, transformed parameters with symmetric confidence intervals: ## Estimate Std. Error Lower Upper ## parent_0 92.47 1.2810 89.720 95.220 -## log_alpha 10.60 NaN NaN NaN -## log_beta 12.95 NaN NaN NaN -## sigma 2.78 0.4554 1.803 3.757 +## log_alpha 10.66 NaN NaN NaN +## log_beta 13.01 NaN NaN NaN +## sigma 2.78 0.4599 1.794 3.766 ## ## Parameter correlation: ## parent_0 log_alpha log_beta sigma -## parent_0 1.000000 NaN NaN 0.008714 +## parent_0 1.000000 NaN NaN 0.003475 ## log_alpha NaN 1 NaN NaN ## log_beta NaN NaN 1 NaN -## sigma 0.008714 NaN NaN 1.000000 +## sigma 0.003475 NaN NaN 1.000000 ## ## Backtransformed parameters: ## Confidence intervals for internally transformed parameters are asymmetric. @@ -270,11 +270,11 @@ ## for estimators of untransformed parameters. ## Estimate t value Pr(>t) Lower Upper ## parent_0 92.47 72.13000 1.052e-19 89.720 95.220 -## alpha 40090.00 0.02388 4.906e-01 NA NA -## beta 419300.00 0.02388 4.906e-01 NA NA -## sigma 2.78 6.00000 1.628e-05 1.803 3.757 +## alpha 42700.00 0.02298 4.910e-01 NA NA +## beta 446600.00 0.02298 4.910e-01 NA NA +## sigma 2.78 6.00000 1.628e-05 1.794 3.766 ## -## Chi2 error levels in percent: +## FOCUS Chi2 error levels in percent: ## err.min n.optim df ## All data 3.619 3 6 ## parent 3.619 3 6 @@ -318,19 +318,19 @@ <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-9-1.png" width="672"></p> <div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.L2.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div> <pre><code>## mkin version used for fitting: 0.9.49.4 -## R version used for fitting: 3.5.3 -## Date of fit: Wed Apr 10 10:11:35 2019 -## Date of summary: Wed Apr 10 10:11:35 2019 +## R version used for fitting: 3.6.0 +## Date of fit: Thu May 2 12:40:34 2019 +## Date of summary: Thu May 2 12:40:34 2019 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted with method using 240 model solutions performed in 0.564 s +## Fitted using 240 model solutions performed in 0.506 s ## ## Error model: -## NULL +## Constant variance ## ## Starting values for parameters to be optimised: ## value type @@ -373,7 +373,7 @@ ## beta 1.234 4.012 1.942e-03 0.6945 2.192 ## sigma 2.276 4.899 5.977e-04 1.2050 3.347 ## -## Chi2 error levels in percent: +## FOCUS Chi2 error levels in percent: ## err.min n.optim df ## All data 6.205 3 3 ## parent 6.205 3 3 @@ -393,9 +393,9 @@ <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-10-1.png" width="672"></p> <div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.L2.DFOP, <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div> <pre><code>## mkin version used for fitting: 0.9.49.4 -## R version used for fitting: 3.5.3 -## Date of fit: Wed Apr 10 10:11:37 2019 -## Date of summary: Wed Apr 10 10:11:37 2019 +## R version used for fitting: 3.6.0 +## Date of fit: Thu May 2 12:40:35 2019 +## Date of summary: Thu May 2 12:40:35 2019 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -404,10 +404,10 @@ ## ## Model predictions using solution type analytical ## -## Fitted with method using 585 model solutions performed in 1.296 s +## Fitted using 587 model solutions performed in 1.273 s ## ## Error model: -## NULL +## Constant variance ## ## Starting values for parameters to be optimised: ## value type @@ -431,18 +431,18 @@ ## Optimised, transformed parameters with symmetric confidence intervals: ## Estimate Std. Error Lower Upper ## parent_0 93.9500 9.998e-01 91.5900 96.3100 -## log_k1 3.1350 2.336e+03 -5522.0000 5528.0000 +## log_k1 3.1330 2.265e+03 -5354.0000 5360.0000 ## log_k2 -1.0880 6.285e-02 -1.2370 -0.9394 ## g_ilr -0.2821 7.033e-02 -0.4484 -0.1158 ## sigma 1.4140 2.886e-01 0.7314 2.0960 ## ## Parameter correlation: ## parent_0 log_k1 log_k2 g_ilr sigma -## parent_0 1.000e+00 5.247e-07 -1.026e-10 2.665e-01 -8.076e-11 -## log_k1 5.247e-07 1.000e+00 8.592e-05 -1.690e-04 -7.938e-06 -## log_k2 -1.026e-10 8.592e-05 1.000e+00 -7.903e-01 5.048e-10 -## g_ilr 2.665e-01 -1.690e-04 -7.903e-01 1.000e+00 -6.476e-10 -## sigma -8.076e-11 -7.938e-06 5.048e-10 -6.476e-10 1.000e+00 +## parent_0 1.000e+00 5.434e-07 -9.989e-11 2.665e-01 -3.978e-10 +## log_k1 5.434e-07 1.000e+00 8.888e-05 -1.748e-04 -8.207e-06 +## log_k2 -9.989e-11 8.888e-05 1.000e+00 -7.903e-01 5.751e-10 +## g_ilr 2.665e-01 -1.748e-04 -7.903e-01 1.000e+00 -7.109e-10 +## sigma -3.978e-10 -8.207e-06 5.751e-10 -7.109e-10 1.000e+00 ## ## Backtransformed parameters: ## Confidence intervals for internally transformed parameters are asymmetric. @@ -450,19 +450,19 @@ ## for estimators of untransformed parameters. ## Estimate t value Pr(>t) Lower Upper ## parent_0 93.9500 9.397e+01 2.036e-12 91.5900 96.3100 -## k1 23.0000 4.377e-04 4.998e-01 0.0000 Inf +## k1 22.9300 4.514e-04 4.998e-01 0.0000 Inf ## k2 0.3369 1.591e+01 4.697e-07 0.2904 0.3909 ## g 0.4016 1.680e+01 3.238e-07 0.3466 0.4591 ## sigma 1.4140 4.899e+00 8.776e-04 0.7314 2.0960 ## -## Chi2 error levels in percent: +## FOCUS Chi2 error levels in percent: ## err.min n.optim df ## All data 2.53 4 2 ## parent 2.53 4 2 ## ## Estimated disappearance times: ## DT50 DT90 DT50_k1 DT50_k2 -## parent 0.5335 5.311 0.03014 2.058</code></pre> +## parent 0.5335 5.311 0.03023 2.058</code></pre> <p>Here, the DFOP model is clearly the best-fit model for dataset L2 based on the chi^2 error level criterion. However, the failure to calculate the covariance matrix indicates that the parameter estimates correlate excessively. Therefore, the FOMC model may be preferred for this dataset.</p> </div> </div> @@ -492,9 +492,9 @@ <p>We can extract the summary and plot for <em>e.g.</em> the DFOP fit, using square brackets for indexing which will result in the use of the summary and plot functions working on mkinfit objects.</p> <div class="sourceCode" id="cb24"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb24-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(mm.L3[[<span class="st">"DFOP"</span>, <span class="dv">1</span>]])</a></code></pre></div> <pre><code>## mkin version used for fitting: 0.9.49.4 -## R version used for fitting: 3.5.3 -## Date of fit: Wed Apr 10 10:11:39 2019 -## Date of summary: Wed Apr 10 10:11:39 2019 +## R version used for fitting: 3.6.0 +## Date of fit: Thu May 2 12:40:37 2019 +## Date of summary: Thu May 2 12:40:37 2019 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -503,10 +503,10 @@ ## ## Model predictions using solution type analytical ## -## Fitted with method using 372 model solutions performed in 0.809 s +## Fitted using 372 model solutions performed in 0.777 s ## ## Error model: -## NULL +## Constant variance ## ## Starting values for parameters to be optimised: ## value type @@ -537,11 +537,11 @@ ## ## Parameter correlation: ## parent_0 log_k1 log_k2 g_ilr sigma -## parent_0 1.000e+00 1.732e-01 2.282e-02 4.009e-01 1.656e-07 -## log_k1 1.732e-01 1.000e+00 4.945e-01 -5.809e-01 6.759e-08 -## log_k2 2.282e-02 4.945e-01 1.000e+00 -6.812e-01 3.867e-07 -## g_ilr 4.009e-01 -5.809e-01 -6.812e-01 1.000e+00 -3.839e-07 -## sigma 1.656e-07 6.759e-08 3.867e-07 -3.839e-07 1.000e+00 +## parent_0 1.000e+00 1.732e-01 2.282e-02 4.009e-01 1.660e-07 +## log_k1 1.732e-01 1.000e+00 4.945e-01 -5.809e-01 6.635e-08 +## log_k2 2.282e-02 4.945e-01 1.000e+00 -6.812e-01 3.880e-07 +## g_ilr 4.009e-01 -5.809e-01 -6.812e-01 1.000e+00 -3.822e-07 +## sigma 1.660e-07 6.635e-08 3.880e-07 -3.822e-07 1.000e+00 ## ## Backtransformed parameters: ## Confidence intervals for internally transformed parameters are asymmetric. @@ -554,7 +554,7 @@ ## g 0.45660 34.920 2.581e-05 0.41540 0.49850 ## sigma 1.01700 4.000 1.400e-02 0.20790 1.82700 ## -## Chi2 error levels in percent: +## FOCUS Chi2 error levels in percent: ## err.min n.optim df ## All data 2.225 4 4 ## parent 2.225 4 4 @@ -597,19 +597,19 @@ <p>The <span class="math inline">\(\chi^2\)</span> error level of 3.3% as well as the plot suggest that the SFO model fits very well. The error level at which the <span class="math inline">\(\chi^2\)</span> test passes is slightly lower for the FOMC model. However, the difference appears negligible.</p> <div class="sourceCode" id="cb29"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb29-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(mm.L4[[<span class="st">"SFO"</span>, <span class="dv">1</span>]], <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div> <pre><code>## mkin version used for fitting: 0.9.49.4 -## R version used for fitting: 3.5.3 -## Date of fit: Wed Apr 10 10:11:39 2019 -## Date of summary: Wed Apr 10 10:11:40 2019 +## R version used for fitting: 3.6.0 +## Date of fit: Thu May 2 12:40:38 2019 +## Date of summary: Thu May 2 12:40:38 2019 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method using 146 model solutions performed in 0.306 s +## Fitted using 146 model solutions performed in 0.298 s ## ## Error model: -## NULL +## Constant variance ## ## Starting values for parameters to be optimised: ## value type @@ -634,9 +634,9 @@ ## ## Parameter correlation: ## parent_0 log_k_parent_sink sigma -## parent_0 1.000e+00 5.938e-01 5.612e-10 -## log_k_parent_sink 5.938e-01 1.000e+00 -4.994e-10 -## sigma 5.612e-10 -4.994e-10 1.000e+00 +## parent_0 1.000e+00 5.938e-01 4.256e-10 +## log_k_parent_sink 5.938e-01 1.000e+00 -7.280e-10 +## sigma 4.256e-10 -7.280e-10 1.000e+00 ## ## Backtransformed parameters: ## Confidence intervals for internally transformed parameters are asymmetric. @@ -647,7 +647,7 @@ ## k_parent_sink 0.006541 14.17 1.578e-05 0.005455 7.842e-03 ## sigma 3.162000 4.00 5.162e-03 1.130000 5.194e+00 ## -## Chi2 error levels in percent: +## FOCUS Chi2 error levels in percent: ## err.min n.optim df ## All data 3.287 2 6 ## parent 3.287 2 6 @@ -661,19 +661,19 @@ ## parent 106 352</code></pre> <div class="sourceCode" id="cb31"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb31-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(mm.L4[[<span class="st">"FOMC"</span>, <span class="dv">1</span>]], <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div> <pre><code>## mkin version used for fitting: 0.9.49.4 -## R version used for fitting: 3.5.3 -## Date of fit: Wed Apr 10 10:11:40 2019 -## Date of summary: Wed Apr 10 10:11:40 2019 +## R version used for fitting: 3.6.0 +## Date of fit: Thu May 2 12:40:38 2019 +## Date of summary: Thu May 2 12:40:38 2019 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted with method using 224 model solutions performed in 0.478 s +## Fitted using 224 model solutions performed in 0.458 s ## ## Error model: -## NULL +## Constant variance ## ## Starting values for parameters to be optimised: ## value type @@ -701,10 +701,10 @@ ## ## Parameter correlation: ## parent_0 log_alpha log_beta sigma -## parent_0 1.000e+00 -4.696e-01 -5.543e-01 -2.460e-07 -## log_alpha -4.696e-01 1.000e+00 9.889e-01 2.351e-08 -## log_beta -5.543e-01 9.889e-01 1.000e+00 5.079e-08 -## sigma -2.460e-07 2.351e-08 5.079e-08 1.000e+00 +## parent_0 1.000e+00 -4.696e-01 -5.543e-01 -2.473e-07 +## log_alpha -4.696e-01 1.000e+00 9.889e-01 2.429e-08 +## log_beta -5.543e-01 9.889e-01 1.000e+00 5.183e-08 +## sigma -2.473e-07 2.429e-08 5.183e-08 1.000e+00 ## ## Backtransformed parameters: ## Confidence intervals for internally transformed parameters are asymmetric. @@ -716,7 +716,7 @@ ## beta 64.9800 2.540 3.201e-02 21.7800 193.900 ## sigma 1.8300 4.000 8.065e-03 0.5598 3.100 ## -## Chi2 error levels in percent: +## FOCUS Chi2 error levels in percent: ## err.min n.optim df ## All data 2.029 3 5 ## parent 2.029 3 5 diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-10-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-10-1.png Binary files differindex f5f45ac6..7f695ecf 100644 --- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-10-1.png +++ b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-10-1.png diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-12-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-12-1.png Binary files differindex 6e4ccb9d..850df1e1 100644 --- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-12-1.png +++ b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-12-1.png diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-15-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-15-1.png Binary files differindex 6badc1bf..62b2ceb3 100644 --- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-15-1.png +++ b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-15-1.png diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-5-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-5-1.png Binary files differindex 12b4beea..93beb55f 100644 --- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-5-1.png +++ b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-5-1.png diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-6-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-6-1.png Binary files differindex 0a403808..5ed0b4de 100644 --- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-6-1.png +++ b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-6-1.png diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-8-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-8-1.png Binary files differindex 7b8e7f95..8d6531ea 100644 --- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-8-1.png +++ b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-8-1.png diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-9-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-9-1.png Binary files differindex 49c48168..a5e75b70 100644 --- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-9-1.png +++ b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-9-1.png diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html index 2e5cd759..bf52f364 100644 --- a/docs/articles/mkin.html +++ b/docs/articles/mkin.html @@ -88,7 +88,7 @@ <h1>Introduction to mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2019-04-10</h4> + <h4 class="date">2019-05-02</h4> <div class="hidden name"><code>mkin.Rmd</code></div> diff --git a/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png b/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png Binary files differindex fafe8afd..29ae1c43 100644 --- a/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png +++ b/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png diff --git a/docs/articles/twa.html b/docs/articles/twa.html index cdcea4d3..7d9d1c4e 100644 --- a/docs/articles/twa.html +++ b/docs/articles/twa.html @@ -88,7 +88,7 @@ <h1>Calculation of time weighted average concentrations with mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2019-04-10</h4> + <h4 class="date">2019-05-02</h4> <div class="hidden name"><code>twa.Rmd</code></div> diff --git a/docs/articles/web_only/FOCUS_Z.html b/docs/articles/web_only/FOCUS_Z.html index 33d0c90f..950e8eab 100644 --- a/docs/articles/web_only/FOCUS_Z.html +++ b/docs/articles/web_only/FOCUS_Z.html @@ -88,7 +88,7 @@ <h1>Example evaluation of FOCUS dataset Z</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2019-04-10</h4> + <h4 class="date">2019-05-02</h4> <div class="hidden name"><code>FOCUS_Z.Rmd</code></div> @@ -132,11 +132,11 @@ <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png" width="700"></p> <div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.Z<span class="fl">.2</span>a, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>bpar</a></code></pre></div> <pre><code>## Estimate se_notrans t value Pr(>t) Lower Upper -## Z0_0 9.7015e+01 3.39373 2.8587e+01 6.4606e-21 91.66556 102.3642 -## k_Z0_sink 4.0181e-10 0.22534 1.7831e-09 5.0000e-01 0.00000 Inf -## k_Z0_Z1 2.2360e+00 0.15915 1.4050e+01 1.1387e-13 1.95303 2.5600 -## k_Z1_sink 4.8212e-01 0.06547 7.3641e+00 5.1396e-08 0.40341 0.5762 -## sigma 4.8041e+00 0.63763 7.5343e+00 3.4444e-08 3.52677 6.0815</code></pre> +## Z0_0 9.7015e+01 3.394776 2.8578e+01 6.5093e-21 91.66556 102.3642 +## k_Z0_sink 4.0301e-10 0.225510 1.7871e-09 5.0000e-01 0.00000 Inf +## k_Z0_Z1 2.2360e+00 0.159161 1.4049e+01 1.1412e-13 1.95303 2.5600 +## k_Z1_sink 4.8212e-01 0.065499 7.3608e+00 5.1791e-08 0.40341 0.5762 +## sigma 4.8041e+00 0.637657 7.5340e+00 3.4468e-08 3.52677 6.0815</code></pre> <p>As obvious from the parameter summary (the component of the summary), the kinetic rate constant from parent compound Z to sink is very small and the t-test for this parameter suggests that it is not significantly different from zero. This suggests, in agreement with the analysis in the FOCUS kinetics report, to simplify the model by removing the pathway to sink.</p> <p>A similar result can be obtained when formation fractions are used in the model formulation:</p> <div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" title="1">Z<span class="fl">.2</span>a.ff <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z1"</span>),</a> @@ -335,14 +335,14 @@ ## ## $SFORB ## Z0_b1 Z0_b2 Z3_b1 Z3_b2 -## 2.4471355 0.0075125 0.0800068 0.0000000 +## 2.4471329 0.0075123 0.0800074 0.0000000 ## ## $distimes ## DT50 DT90 DT50_Z0_b1 DT50_Z0_b2 DT50_Z3_b1 DT50_Z3_b2 -## Z0 0.3043 1.1848 0.28325 92.266 NA NA +## Z0 0.3043 1.1848 0.28325 92.268 NA NA ## Z1 1.5148 5.0320 NA NA NA NA ## Z2 1.6414 5.4526 NA NA NA NA -## Z3 NA NA NA NA 8.6636 Inf</code></pre> +## Z3 NA NA NA NA 8.6635 Inf</code></pre> <p>It is clear the degradation rate of Z3 towards the end of the experiment is very low as DT50_Z3_b2 (the second Eigenvalue of the system of two differential equations representing the SFORB system for Z3, corresponding to the slower rate constant of the DFOP model) is reported to be infinity. However, this appears to be a feature of the data.</p> </div> <div id="references" class="section level1"> diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png Binary files differindex f371827f..0880ca60 100644 --- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png +++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png Binary files differindex c2fa5b46..bb909e98 100644 --- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png +++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png Binary files differindex 95553b43..c7cbb448 100644 --- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png +++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png Binary files differindex 8b69796f..e39a2e6a 100644 --- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png +++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.png Binary files differindex bac0a115..8e13b498 100644 --- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.png +++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.png diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png Binary files differindex 5b6c127f..7d490baa 100644 --- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png +++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png diff --git a/docs/articles/web_only/NAFTA_examples.html b/docs/articles/web_only/NAFTA_examples.html index 0bcfca27..0ae02f3c 100644 --- a/docs/articles/web_only/NAFTA_examples.html +++ b/docs/articles/web_only/NAFTA_examples.html @@ -88,7 +88,7 @@ <h1>Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2019-04-10</h4> + <h4 class="date">2019-05-02</h4> <div class="hidden name"><code>NAFTA_examples.Rmd</code></div> @@ -153,7 +153,7 @@ ## DFOP 55.5 3.70e+11 2.03e+11 ## ## Representative half-life: -## [1] 321.5119</code></pre> +## [1] 321.51</code></pre> </div> <div id="example-on-page-5-lower-panel" class="section level2"> <h2 class="hasAnchor"> @@ -189,7 +189,7 @@ ## Estimate Pr(>t) Lower Upper ## parent_0 9.84e+01 1.24e-27 97.8078 98.9187 ## k1 1.55e-02 4.10e-04 0.0143 0.0167 -## k2 1.09e-11 5.00e-01 0.0000 Inf +## k2 8.28e-12 5.00e-01 0.0000 Inf ## g 6.89e-01 2.92e-03 0.6626 0.7142 ## sigma 6.48e-01 2.38e-05 0.4147 0.8813 ## @@ -198,10 +198,10 @@ ## DT50 DT90 DT50_rep ## SFO 86.6 2.88e+02 8.66e+01 ## IORE 85.5 7.17e+02 2.16e+02 -## DFOP 83.6 1.04e+11 6.34e+10 +## DFOP 83.6 1.37e+11 8.37e+10 ## ## Representative half-life: -## [1] 215.8655</code></pre> +## [1] 215.87</code></pre> </div> <div id="example-on-page-6" class="section level2"> <h2 class="hasAnchor"> @@ -237,7 +237,7 @@ ## Estimate Pr(>t) Lower Upper ## parent_0 9.66e+01 1.57e-25 95.3476 97.8979 ## k1 2.55e-02 7.33e-06 0.0233 0.0278 -## k2 3.88e-11 5.00e-01 0.0000 Inf +## k2 3.87e-11 5.00e-01 0.0000 Inf ## g 8.61e-01 7.55e-06 0.8314 0.8867 ## sigma 1.46e+00 6.93e-06 0.9661 1.9483 ## @@ -246,10 +246,10 @@ ## DT50 DT90 DT50_rep ## SFO 38.6 1.28e+02 3.86e+01 ## IORE 34.0 1.77e+02 5.32e+01 -## DFOP 34.1 8.42e+09 1.79e+10 +## DFOP 34.1 8.43e+09 1.79e+10 ## ## Representative half-life: -## [1] 53.16582</code></pre> +## [1] 53.17</code></pre> </div> <div id="example-on-page-7" class="section level2"> <h2 class="hasAnchor"> @@ -285,7 +285,7 @@ ## Estimate Pr(>t) Lower Upper ## parent_0 9.89e+01 9.44e-49 95.4640 102.2573 ## k1 1.81e-02 1.75e-01 0.0116 0.0281 -## k2 2.57e-10 5.00e-01 0.0000 Inf +## k2 2.46e-10 5.00e-01 0.0000 Inf ## g 6.06e-01 2.19e-01 0.4826 0.7178 ## sigma 7.40e+00 2.97e-15 6.0201 8.7754 ## @@ -294,10 +294,10 @@ ## DT50 DT90 DT50_rep ## SFO 94.3 3.13e+02 9.43e+01 ## IORE 96.7 1.51e+03 4.55e+02 -## DFOP 96.4 5.32e+09 2.69e+09 +## DFOP 96.4 5.58e+09 2.82e+09 ## ## Representative half-life: -## [1] 454.5528</code></pre> +## [1] 454.55</code></pre> </div> </div> <div id="examples-where-the-representative-half-life-deviates-from-the-observed-dt50" class="section level1"> @@ -357,7 +357,7 @@ ## DFOP 55.6 517 253.0 ## ## Representative half-life: -## [1] 201.0316</code></pre> +## [1] 201.03</code></pre> </div> </div> <div id="examples-where-sfo-was-not-selected-for-an-abiotic-study" class="section level1"> @@ -409,23 +409,19 @@ ## DFOP 10.5 2.17e+12 1.21e+12 ## ## Representative half-life: -## [1] 101.4264</code></pre> +## [1] 101.43</code></pre> <p>In this example, the residuals of the SFO indicate a lack of fit of this model, so even if it was an abiotic experiment, the data do not suggest a simple exponential decline.</p> </div> <div id="example-on-page-9-lower-panel" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-9-lower-panel" class="anchor"></a>Example on page 9, lower panel</h2> <div class="sourceCode" id="cb38"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb38-1" title="1">p9b <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p9b"</span>]])</a></code></pre></div> -<pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre> <pre><code>## Warning in sqrt(diag(covar_notrans)): NaNs wurden erzeugt</code></pre> -<pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre> -<pre><code>## Warning in cov2cor(ans$cov.unscaled): diag(.) had 0 or NA entries; non- -## finite result is doubtful</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb45"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb45-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p9b)</a></code></pre></div> +<div class="sourceCode" id="cb42"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb42-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p9b)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p9b-1.png" width="700"></p> -<div class="sourceCode" id="cb46"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb46-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p9b)</a></code></pre></div> +<div class="sourceCode" id="cb43"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb43-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p9b)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 35.64867 23.22334 35.64867 @@ -450,9 +446,9 @@ ## $DFOP ## Estimate Pr(>t) Lower Upper ## parent_0 94.7123 1.61e-16 93.1355 96.2891 -## k1 0.0389 NaN 0.0316 0.0478 -## k2 0.0389 1.13e-08 0.0203 0.0743 -## g 0.7599 NaN NA NA +## k1 0.0389 NaN 0.0306 0.0495 +## k2 0.0389 1.10e-06 0.0186 0.0812 +## g 0.7598 NaN 0.0000 1.0000 ## sigma 1.5957 2.50e-04 0.9135 2.2779 ## ## @@ -463,18 +459,18 @@ ## DFOP 17.8 59.2 17.8 ## ## Representative half-life: -## [1] 14.80013</code></pre> +## [1] 14.8</code></pre> <p>Here, mkin gives a longer slow DT50 for the DFOP model (17.8 days) than PestDF (13.5 days). Presumably, this is related to the fact that PestDF gives a negative value for the proportion of the fast degradation which should be between 0 and 1, inclusive. This parameter is called f in PestDF and g in mkin. In mkin, it is restricted to the interval from 0 to 1.</p> </div> <div id="example-on-page-10" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-10" class="anchor"></a>Example on page 10</h2> -<div class="sourceCode" id="cb48"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb48-1" title="1">p10 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p10"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb45"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb45-1" title="1">p10 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p10"</span>]])</a></code></pre></div> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb51"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb51-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p10)</a></code></pre></div> +<div class="sourceCode" id="cb48"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb48-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p10)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p10-1.png" width="700"></p> -<div class="sourceCode" id="cb52"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb52-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p10)</a></code></pre></div> +<div class="sourceCode" id="cb49"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb49-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p10)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 899.4089 336.4348 899.4089 @@ -512,7 +508,7 @@ ## DFOP 14.0 46.5 14.00 ## ## Representative half-life: -## [1] 8.862193</code></pre> +## [1] 8.86</code></pre> <p>Here, a value below N is given for the IORE model, because the data suggests a faster decline towards the end of the experiment, which appears physically rather unlikely in the case of a photolysis study. It seems PestDF does not constrain N to values above zero, thus the slight difference in IORE model parameters between PestDF and mkin.</p> </div> </div> @@ -522,12 +518,12 @@ <div id="example-on-page-11" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-11" class="anchor"></a>Example on page 11</h2> -<div class="sourceCode" id="cb54"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb54-1" title="1">p11 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p11"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb51"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb51-1" title="1">p11 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p11"</span>]])</a></code></pre></div> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb57"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb57-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p11)</a></code></pre></div> +<div class="sourceCode" id="cb54"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb54-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p11)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p11-1.png" width="700"></p> -<div class="sourceCode" id="cb58"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb58-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p11)</a></code></pre></div> +<div class="sourceCode" id="cb55"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb55-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p11)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 579.6805 204.7932 144.7783 @@ -576,7 +572,7 @@ <div id="example-on-page-12-upper-panel" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-12-upper-panel" class="anchor"></a>Example on page 12, upper panel</h2> -<div class="sourceCode" id="cb60"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb60-1" title="1">p12a <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p12a"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb57"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb57-1" title="1">p12a <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p12a"</span>]])</a></code></pre></div> <pre><code>## Warning in summary.mkinfit(x): Could not estimate covariance matrix; ## singular system.</code></pre> <pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre> @@ -586,9 +582,9 @@ ## finite result is doubtful</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb68"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb68-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p12a)</a></code></pre></div> +<div class="sourceCode" id="cb65"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb65-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p12a)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p12a-1.png" width="700"></p> -<div class="sourceCode" id="cb69"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb69-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p12a)</a></code></pre></div> +<div class="sourceCode" id="cb66"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb66-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p12a)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 695.4440 220.0685 695.4440 @@ -626,12 +622,12 @@ ## DFOP 5.58 18.5 5.58 ## ## Representative half-life: -## [1] 3.987308</code></pre> +## [1] 3.99</code></pre> </div> <div id="example-on-page-12-lower-panel" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-12-lower-panel" class="anchor"></a>Example on page 12, lower panel</h2> -<div class="sourceCode" id="cb71"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb71-1" title="1">p12b <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p12b"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb68"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb68-1" title="1">p12b <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p12b"</span>]])</a></code></pre></div> <pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre> <pre><code>## Warning in qt(alpha/2, rdf): NaNs wurden erzeugt</code></pre> <pre><code>## Warning in qt(1 - alpha/2, rdf): NaNs wurden erzeugt</code></pre> @@ -642,9 +638,9 @@ ## finite result is doubtful</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb81"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb81-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p12b)</a></code></pre></div> +<div class="sourceCode" id="cb78"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb78-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p12b)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p12b-1.png" width="700"></p> -<div class="sourceCode" id="cb82"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb82-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p12b)</a></code></pre></div> +<div class="sourceCode" id="cb79"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb79-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p12b)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 58.90242 19.06353 58.90242 @@ -682,17 +678,17 @@ ## DFOP 11.8 39.1 11.80 ## ## Representative half-life: -## [1] 9.461912</code></pre> +## [1] 9.46</code></pre> </div> <div id="example-on-page-13" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-13" class="anchor"></a>Example on page 13</h2> -<div class="sourceCode" id="cb84"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb84-1" title="1">p13 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p13"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb81"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb81-1" title="1">p13 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p13"</span>]])</a></code></pre></div> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb87"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb87-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p13)</a></code></pre></div> +<div class="sourceCode" id="cb84"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb84-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p13)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p13-1.png" width="700"></p> -<div class="sourceCode" id="cb88"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb88-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p13)</a></code></pre></div> +<div class="sourceCode" id="cb85"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb85-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p13)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 174.5971 142.3951 174.5971 @@ -717,7 +713,7 @@ ## $DFOP ## Estimate Pr(>t) Lower Upper ## parent_0 92.73500 9.25e-15 8.95e+01 9.59e+01 -## k1 0.00258 4.28e-01 1.38e-08 4.82e+02 +## k1 0.00258 4.28e-01 1.25e-08 5.31e+02 ## k2 0.00258 3.69e-08 2.20e-03 3.03e-03 ## g 0.00442 5.00e-01 0.00e+00 1.00e+00 ## sigma 3.41172 1.35e-04 2.02e+00 4.80e+00 @@ -730,22 +726,22 @@ ## DFOP 269 892 269 ## ## Representative half-life: -## [1] 168.5123</code></pre> +## [1] 168.51</code></pre> </div> </div> <div id="dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf" class="section level1"> <h1 class="hasAnchor"> <a href="#dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf" class="anchor"></a>DT50 not observed in the study and DFOP problems in PestDF</h1> -<div class="sourceCode" id="cb90"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb90-1" title="1">p14 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p14"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb87"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb87-1" title="1">p14 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p14"</span>]])</a></code></pre></div> <pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre> <pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre> <pre><code>## Warning in cov2cor(ans$cov.unscaled): diag(.) had 0 or NA entries; non- ## finite result is doubtful</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb96"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb96-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p14)</a></code></pre></div> +<div class="sourceCode" id="cb93"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb93-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p14)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p14-1.png" width="700"></p> -<div class="sourceCode" id="cb97"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb97-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p14)</a></code></pre></div> +<div class="sourceCode" id="cb94"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb94-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p14)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 48.43249 28.67746 27.26248 @@ -771,7 +767,7 @@ ## Estimate Pr(>t) Lower Upper ## parent_0 1.00e+02 2.96e-28 99.40280 101.2768 ## k1 9.53e-03 1.20e-01 0.00638 0.0143 -## k2 6.17e-12 5.00e-01 0.00000 Inf +## k2 5.42e-12 5.00e-01 0.00000 Inf ## g 3.98e-01 2.19e-01 0.30481 0.4998 ## sigma 1.17e+00 7.68e-06 0.77406 1.5610 ## @@ -780,16 +776,16 @@ ## DT50 DT90 DT50_rep ## SFO 2.48e+02 8.25e+02 2.48e+02 ## IORE 4.34e+02 2.22e+04 6.70e+03 -## DFOP 3.00e+10 2.91e+11 1.12e+11 +## DFOP 3.41e+10 3.31e+11 1.28e+11 ## ## Representative half-life: -## [1] 6697.437</code></pre> +## [1] 6697.44</code></pre> <p>The slower rate constant reported by PestDF is negative, which is not physically realistic, and not possible in mkin. The other fits give the same results in mkin and PestDF.</p> </div> <div id="n-is-less-than-1-and-dfop-fraction-parameter-is-below-zero" class="section level1"> <h1 class="hasAnchor"> <a href="#n-is-less-than-1-and-dfop-fraction-parameter-is-below-zero" class="anchor"></a>N is less than 1 and DFOP fraction parameter is below zero</h1> -<div class="sourceCode" id="cb99"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb99-1" title="1">p15a <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p15a"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb96"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb96-1" title="1">p15a <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p15a"</span>]])</a></code></pre></div> <pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre> <pre><code>## Warning in sqrt(diag(covar_notrans)): NaNs wurden erzeugt</code></pre> <pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre> @@ -797,9 +793,9 @@ ## finite result is doubtful</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb106"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb106-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p15a)</a></code></pre></div> +<div class="sourceCode" id="cb103"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb103-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p15a)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p15a-1.png" width="700"></p> -<div class="sourceCode" id="cb107"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb107-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p15a)</a></code></pre></div> +<div class="sourceCode" id="cb104"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb104-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p15a)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 245.5248 135.0132 245.5248 @@ -837,13 +833,13 @@ ## DFOP 72.8 242 72.8 ## ## Representative half-life: -## [1] 41.32749</code></pre> -<div class="sourceCode" id="cb109"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb109-1" title="1">p15b <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p15b"</span>]])</a></code></pre></div> +## [1] 41.33</code></pre> +<div class="sourceCode" id="cb106"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb106-1" title="1">p15b <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p15b"</span>]])</a></code></pre></div> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb112"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb112-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p15b)</a></code></pre></div> +<div class="sourceCode" id="cb109"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb109-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p15b)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p15b-1.png" width="700"></p> -<div class="sourceCode" id="cb113"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb113-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p15b)</a></code></pre></div> +<div class="sourceCode" id="cb110"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb110-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p15b)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 106.91629 68.55574 106.91629 @@ -881,20 +877,20 @@ ## DFOP 143 474 143.0 ## ## Representative half-life: -## [1] 71.18014</code></pre> +## [1] 71.18</code></pre> <p>In mkin, only the IORE fit is affected (deemed unrealistic), as the fraction parameter of the DFOP model is restricted to the interval between 0 and 1 in mkin. The SFO fits give the same results for both mkin and PestDF.</p> </div> <div id="the-dfop-fraction-parameter-is-greater-than-1" class="section level1"> <h1 class="hasAnchor"> <a href="#the-dfop-fraction-parameter-is-greater-than-1" class="anchor"></a>The DFOP fraction parameter is greater than 1</h1> -<div class="sourceCode" id="cb115"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb115-1" title="1">p16 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p16"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb112"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb112-1" title="1">p16 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p16"</span>]])</a></code></pre></div> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The representative half-life of the IORE model is longer than the one corresponding</code></pre> <pre><code>## to the terminal degradation rate found with the DFOP model.</code></pre> <pre><code>## The representative half-life obtained from the DFOP model may be used</code></pre> -<div class="sourceCode" id="cb120"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb120-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p16)</a></code></pre></div> +<div class="sourceCode" id="cb117"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb117-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p16)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p16-1.png" width="700"></p> -<div class="sourceCode" id="cb121"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb121-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p16)</a></code></pre></div> +<div class="sourceCode" id="cb118"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb118-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p16)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 3831.804 2062.008 1550.980 @@ -919,7 +915,7 @@ ## $DFOP ## Estimate Pr(>t) Lower Upper ## parent_0 88.5333 7.40e-18 79.9836 97.083 -## k1 18.6317 5.00e-01 0.0000 Inf +## k1 18.6315 5.00e-01 0.0000 Inf ## k2 0.0776 1.41e-05 0.0518 0.116 ## g 0.4733 1.41e-09 0.3674 0.582 ## sigma 7.1902 2.11e-08 5.2785 9.102 @@ -932,7 +928,7 @@ ## DFOP 0.67 21.4 8.93 ## ## Representative half-life: -## [1] 8.932679</code></pre> +## [1] 8.93</code></pre> <p>In PestDF, the DFOP fit seems to have stuck in a local minimum, as mkin finds a solution with a much lower <span class="math inline">\(\chi^2\)</span> error level. As the half-life from the slower rate constant of the DFOP model is larger than the IORE derived half-life, the NAFTA recommendation obtained with mkin is to use the DFOP representative half-life of 8.9 days.</p> </div> <div id="conclusions" class="section level1"> diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p10-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p10-1.png Binary files differindex e4062661..f84439e8 100644 --- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p10-1.png +++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p10-1.png diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p11-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p11-1.png Binary files differindex cc4ce2d7..2f659bca 100644 --- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p11-1.png +++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p11-1.png diff --git 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a/docs/articles/web_only/benchmarks.html +++ b/docs/articles/web_only/benchmarks.html @@ -88,7 +88,7 @@ <h1>Benchmark timings for mkin on various systems</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2019-04-10</h4> + <h4 class="date">2019-05-02</h4> <div class="hidden name"><code>benchmarks.Rmd</code></div> @@ -115,32 +115,32 @@ <a class="sourceLine" id="cb1-12" title="12">}</a></code></pre></div> <div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" title="1"><span class="co"># Parent only</span></a> <a class="sourceLine" id="cb2-2" title="2">t1 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span>, <span class="st">"HS"</span>), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(FOCUS_<span class="dv">2006</span>_C, FOCUS_<span class="dv">2006</span>_D)))[[<span class="st">"elapsed"</span>]]</a> -<a class="sourceLine" id="cb2-3" title="3">t2 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span>, <span class="st">"HS"</span>), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(FOCUS_<span class="dv">2006</span>_C, FOCUS_<span class="dv">2006</span>_D), <span class="dt">error_model =</span> <span class="st">"tc"</span>))[[<span class="st">"elapsed"</span>]]</a> -<a class="sourceLine" id="cb2-4" title="4"></a> -<a class="sourceLine" id="cb2-5" title="5"><span class="co"># One metabolite</span></a> -<a class="sourceLine" id="cb2-6" title="6">SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(</a> -<a class="sourceLine" id="cb2-7" title="7"> <span class="dt">parent =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"m1"</span>),</a> -<a class="sourceLine" id="cb2-8" title="8"> <span class="dt">m1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></code></pre></div> +<a class="sourceLine" id="cb2-3" title="3">t2 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span>, <span class="st">"HS"</span>), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(FOCUS_<span class="dv">2006</span>_C, FOCUS_<span class="dv">2006</span>_D), <span class="dt">error_model =</span> <span class="st">"tc"</span>))[[<span class="st">"elapsed"</span>]]</a></code></pre></div> +<pre><code>## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): Optimisation did not converge: +## false convergence (8)</code></pre> +<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1"><span class="co"># One metabolite</span></a> +<a class="sourceLine" id="cb4-2" title="2">SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(</a> +<a class="sourceLine" id="cb4-3" title="3"> <span class="dt">parent =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"m1"</span>),</a> +<a class="sourceLine" id="cb4-4" title="4"> <span class="dt">m1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1">FOMC_SFO <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(</a> -<a class="sourceLine" id="cb4-2" title="2"> <span class="dt">parent =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"FOMC"</span>, <span class="st">"m1"</span>),</a> -<a class="sourceLine" id="cb4-3" title="3"> <span class="dt">m1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></code></pre></div> -<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" title="1">DFOP_SFO <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(</a> +<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" title="1">FOMC_SFO <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(</a> <a class="sourceLine" id="cb6-2" title="2"> <span class="dt">parent =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"FOMC"</span>, <span class="st">"m1"</span>),</a> <a class="sourceLine" id="cb6-3" title="3"> <span class="dt">m1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" title="1">t3 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(SFO_SFO, FOMC_SFO, DFOP_SFO), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(FOCUS_<span class="dv">2006</span>_D)))[[<span class="st">"elapsed"</span>]]</a></code></pre></div> +<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" title="1">DFOP_SFO <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(</a> +<a class="sourceLine" id="cb8-2" title="2"> <span class="dt">parent =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"FOMC"</span>, <span class="st">"m1"</span>),</a> +<a class="sourceLine" id="cb8-3" title="3"> <span class="dt">m1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></code></pre></div> +<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> +<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" title="1">t3 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(SFO_SFO, FOMC_SFO, DFOP_SFO), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(FOCUS_<span class="dv">2006</span>_D)))[[<span class="st">"elapsed"</span>]]</a></code></pre></div> +<pre><code>## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): +## Observations with value of zero were removed from the data</code></pre> <pre><code>## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): -## Observations with value of zero were removed from the data - -## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): ## Observations with value of zero were removed from the data ## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): ## Observations with value of zero were removed from the data</code></pre> -<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" title="1">t4 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(SFO_SFO, FOMC_SFO, DFOP_SFO), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/subset">subset</a></span>(FOCUS_<span class="dv">2006</span>_D, value <span class="op">!=</span><span class="st"> </span><span class="dv">0</span>)), <span class="dt">error_model =</span> <span class="st">"tc"</span>))[[<span class="st">"elapsed"</span>]]</a> -<a class="sourceLine" id="cb10-2" title="2">t5 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(SFO_SFO, FOMC_SFO, DFOP_SFO), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(FOCUS_<span class="dv">2006</span>_D), <span class="dt">error_model =</span> <span class="st">"obs"</span>))[[<span class="st">"elapsed"</span>]]</a></code></pre></div> +<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" title="1">t4 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(SFO_SFO, FOMC_SFO, DFOP_SFO), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/subset">subset</a></span>(FOCUS_<span class="dv">2006</span>_D, value <span class="op">!=</span><span class="st"> </span><span class="dv">0</span>)), <span class="dt">error_model =</span> <span class="st">"tc"</span>))[[<span class="st">"elapsed"</span>]]</a> +<a class="sourceLine" id="cb13-2" title="2">t5 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(SFO_SFO, FOMC_SFO, DFOP_SFO), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(FOCUS_<span class="dv">2006</span>_D), <span class="dt">error_model =</span> <span class="st">"obs"</span>))[[<span class="st">"elapsed"</span>]]</a></code></pre></div> <pre><code>## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): ## Observations with value of zero were removed from the data @@ -149,32 +149,32 @@ ## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): ## Observations with value of zero were removed from the data</code></pre> -<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" title="1"><span class="co"># Two metabolites, synthetic data</span></a> -<a class="sourceLine" id="cb12-2" title="2">m_synth_SFO_lin <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">parent =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"M1"</span>),</a> -<a class="sourceLine" id="cb12-3" title="3"> <span class="dt">M1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"M2"</span>),</a> -<a class="sourceLine" id="cb12-4" title="4"> <span class="dt">M2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>),</a> -<a class="sourceLine" id="cb12-5" title="5"> <span class="dt">use_of_ff =</span> <span class="st">"max"</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb12-6" title="6"></a> -<a class="sourceLine" id="cb12-7" title="7">m_synth_DFOP_par <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">parent =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"DFOP"</span>, <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"M1"</span>, <span class="st">"M2"</span>)),</a> -<a class="sourceLine" id="cb12-8" title="8"> <span class="dt">M1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>),</a> -<a class="sourceLine" id="cb12-9" title="9"> <span class="dt">M2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>),</a> -<a class="sourceLine" id="cb12-10" title="10"> <span class="dt">use_of_ff =</span> <span class="st">"max"</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb12-11" title="11"></a> -<a class="sourceLine" id="cb12-12" title="12">SFO_lin_a <-<span class="st"> </span>synthetic_data_for_UBA_<span class="dv">2014</span>[[<span class="dv">1</span>]]<span class="op">$</span>data</a> -<a class="sourceLine" id="cb12-13" title="13"></a> -<a class="sourceLine" id="cb12-14" title="14">DFOP_par_c <-<span class="st"> </span>synthetic_data_for_UBA_<span class="dv">2014</span>[[<span class="dv">12</span>]]<span class="op">$</span>data</a> -<a class="sourceLine" id="cb12-15" title="15"></a> -<a class="sourceLine" id="cb12-16" title="16">t6 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(m_synth_SFO_lin), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(SFO_lin_a)))[<span class="st">"elapsed"</span>]</a> -<a class="sourceLine" id="cb12-17" title="17">t7 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(m_synth_DFOP_par), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(DFOP_par_c)))[<span class="st">"elapsed"</span>]</a> -<a class="sourceLine" id="cb12-18" title="18"></a> -<a class="sourceLine" id="cb12-19" title="19">t8 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(m_synth_SFO_lin), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(SFO_lin_a), <span class="dt">error_model =</span> <span class="st">"tc"</span>))[<span class="st">"elapsed"</span>]</a> -<a class="sourceLine" id="cb12-20" title="20">t9 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(m_synth_DFOP_par), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(DFOP_par_c), <span class="dt">error_model =</span> <span class="st">"tc"</span>))[<span class="st">"elapsed"</span>]</a> -<a class="sourceLine" id="cb12-21" title="21"></a> -<a class="sourceLine" id="cb12-22" title="22">t10 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(m_synth_SFO_lin), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(SFO_lin_a), <span class="dt">error_model =</span> <span class="st">"obs"</span>))[<span class="st">"elapsed"</span>]</a> -<a class="sourceLine" id="cb12-23" title="23">t11 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(m_synth_DFOP_par), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(DFOP_par_c), <span class="dt">error_model =</span> <span class="st">"obs"</span>))[<span class="st">"elapsed"</span>]</a> -<a class="sourceLine" id="cb12-24" title="24"></a> -<a class="sourceLine" id="cb12-25" title="25">mkin_benchmarks[system_string, <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/paste">paste0</a></span>(<span class="st">"t"</span>, <span class="dv">1</span><span class="op">:</span><span class="dv">11</span>)] <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(t1, t2, t3, t4, t5, t6, t7, t8, t9, t10, t11)</a> -<a class="sourceLine" id="cb12-26" title="26">mkin_benchmarks</a></code></pre></div> +<div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" title="1"><span class="co"># Two metabolites, synthetic data</span></a> +<a class="sourceLine" id="cb15-2" title="2">m_synth_SFO_lin <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">parent =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"M1"</span>),</a> +<a class="sourceLine" id="cb15-3" title="3"> <span class="dt">M1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"M2"</span>),</a> +<a class="sourceLine" id="cb15-4" title="4"> <span class="dt">M2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>),</a> +<a class="sourceLine" id="cb15-5" title="5"> <span class="dt">use_of_ff =</span> <span class="st">"max"</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> +<a class="sourceLine" id="cb15-6" title="6"></a> +<a class="sourceLine" id="cb15-7" title="7">m_synth_DFOP_par <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">parent =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"DFOP"</span>, <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"M1"</span>, <span class="st">"M2"</span>)),</a> +<a class="sourceLine" id="cb15-8" title="8"> <span class="dt">M1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>),</a> +<a class="sourceLine" id="cb15-9" title="9"> <span class="dt">M2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>),</a> +<a class="sourceLine" id="cb15-10" title="10"> <span class="dt">use_of_ff =</span> <span class="st">"max"</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> +<a class="sourceLine" id="cb15-11" title="11"></a> +<a class="sourceLine" id="cb15-12" title="12">SFO_lin_a <-<span class="st"> </span>synthetic_data_for_UBA_<span class="dv">2014</span>[[<span class="dv">1</span>]]<span class="op">$</span>data</a> +<a class="sourceLine" id="cb15-13" title="13"></a> +<a class="sourceLine" id="cb15-14" title="14">DFOP_par_c <-<span class="st"> </span>synthetic_data_for_UBA_<span class="dv">2014</span>[[<span class="dv">12</span>]]<span class="op">$</span>data</a> +<a class="sourceLine" id="cb15-15" title="15"></a> +<a class="sourceLine" id="cb15-16" title="16">t6 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(m_synth_SFO_lin), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(SFO_lin_a)))[<span class="st">"elapsed"</span>]</a> +<a class="sourceLine" id="cb15-17" title="17">t7 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(m_synth_DFOP_par), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(DFOP_par_c)))[<span class="st">"elapsed"</span>]</a> +<a class="sourceLine" id="cb15-18" title="18"></a> +<a class="sourceLine" id="cb15-19" title="19">t8 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(m_synth_SFO_lin), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(SFO_lin_a), <span class="dt">error_model =</span> <span class="st">"tc"</span>))[<span class="st">"elapsed"</span>]</a> +<a class="sourceLine" id="cb15-20" title="20">t9 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(m_synth_DFOP_par), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(DFOP_par_c), <span class="dt">error_model =</span> <span class="st">"tc"</span>))[<span class="st">"elapsed"</span>]</a> +<a class="sourceLine" id="cb15-21" title="21"></a> +<a class="sourceLine" id="cb15-22" title="22">t10 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(m_synth_SFO_lin), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(SFO_lin_a), <span class="dt">error_model =</span> <span class="st">"obs"</span>))[<span class="st">"elapsed"</span>]</a> +<a class="sourceLine" id="cb15-23" title="23">t11 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(m_synth_DFOP_par), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(DFOP_par_c), <span class="dt">error_model =</span> <span class="st">"obs"</span>))[<span class="st">"elapsed"</span>]</a> +<a class="sourceLine" id="cb15-24" title="24"></a> +<a class="sourceLine" id="cb15-25" title="25">mkin_benchmarks[system_string, <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/paste">paste0</a></span>(<span class="st">"t"</span>, <span class="dv">1</span><span class="op">:</span><span class="dv">11</span>)] <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(t1, t2, t3, t4, t5, t6, t7, t8, t9, t10, t11)</a> +<a class="sourceLine" id="cb15-26" title="26">mkin_benchmarks</a></code></pre></div> <pre><code>## CPU ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 AMD Ryzen 7 1700 Eight-Core Processor ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 AMD Ryzen 7 1700 Eight-Core Processor @@ -198,68 +198,68 @@ ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 8.184 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 7.064 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.296 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 6.303 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.936 ## t2 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 11.019 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 22.889 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 12.558 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 21.239 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 21.837 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 20.545 ## t3 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 3.764 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.649 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.786 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 4.510 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.487 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.446 ## t4 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 14.347 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 13.789 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 8.461 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 13.805 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 14.162 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 15.335 ## t5 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 9.495 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 6.395 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 5.675 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.386 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 6.021 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 6.002 ## t6 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 2.623 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 2.542 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 2.723 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 2.643 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 2.657 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 2.635 ## t7 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 4.587 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.128 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.478 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 4.374 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.523 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.259 ## t8 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 7.525 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.632 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.862 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.02 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.72 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.737 ## t9 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 16.621 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 8.171 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 7.618 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 11.124 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 8.364 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 7.763 ## t10 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 8.576 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 3.676 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 3.579 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 5.388 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 3.623 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 3.427 ## t11 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 31.267 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 5.636 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 5.574 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.365 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.95</code></pre> -<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/save">save</a></span>(mkin_benchmarks, <span class="dt">file =</span> <span class="st">"~/git/mkin/inst/benchmark_data/mkin_benchmarks.rda"</span>)</a></code></pre></div> +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.626</code></pre> +<div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/save">save</a></span>(mkin_benchmarks, <span class="dt">file =</span> <span class="st">"~/git/mkin/inst/benchmark_data/mkin_benchmarks.rda"</span>)</a></code></pre></div> </div> </div> diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html index 597b7c55..ee279f51 100644 --- a/docs/articles/web_only/compiled_models.html +++ b/docs/articles/web_only/compiled_models.html @@ -88,7 +88,7 @@ <h1>Performance benefit by using compiled model definitions in mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2019-04-10</h4> + <h4 class="date">2019-05-02</h4> <div class="hidden name"><code>compiled_models.Rmd</code></div> @@ -163,14 +163,14 @@ ## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve", quiet ## = TRUE): Observations with value of zero were removed from the data</code></pre> <pre><code>## test replications elapsed relative user.self sys.self -## 3 deSolve, compiled 3 3.215 1.000 3.213 0 -## 1 deSolve, not compiled 3 42.468 13.209 42.445 0 -## 2 Eigenvalue based 3 4.666 1.451 4.663 0 +## 3 deSolve, compiled 3 3.178 1.000 3.176 0 +## 1 deSolve, not compiled 3 28.700 9.031 28.685 0 +## 2 Eigenvalue based 3 4.401 1.385 4.398 0 ## user.child sys.child ## 3 0 0 ## 1 0 0 ## 2 0 0</code></pre> -<p>We see that using the compiled model is by a factor of around 13 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs.</p> +<p>We see that using the compiled model is by a factor of around 9 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs.</p> </div> <div id="model-that-can-not-be-solved-with-eigenvalues" class="section level2"> <h2 class="hasAnchor"> @@ -214,14 +214,14 @@ ## Warning in mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE): Observations with ## value of zero were removed from the data</code></pre> <pre><code>## test replications elapsed relative user.self sys.self -## 2 deSolve, compiled 3 4.906 1.000 4.902 0 -## 1 deSolve, not compiled 3 70.459 14.362 70.421 0 +## 2 deSolve, compiled 3 4.549 1.000 4.547 0 +## 1 deSolve, not compiled 3 49.752 10.937 49.729 0 ## user.child sys.child ## 2 0 0 ## 1 0 0</code></pre> -<p>Here we get a performance benefit of a factor of 14 using the version of the differential equation model compiled from C code!</p> +<p>Here we get a performance benefit of a factor of 11 using the version of the differential equation model compiled from C code!</p> <p>This vignette was built with mkin 0.9.49.4 on</p> -<pre><code>## R version 3.5.3 (2019-03-11) +<pre><code>## R version 3.6.0 (2019-04-26) ## Platform: x86_64-pc-linux-gnu (64-bit) ## Running under: Debian GNU/Linux 9 (stretch)</code></pre> <pre><code>## CPU model: AMD Ryzen 7 1700 Eight-Core Processor</code></pre> diff --git a/docs/reference/AIC.mmkin.html b/docs/reference/AIC.mmkin.html index d5386145..c797567c 100644 --- a/docs/reference/AIC.mmkin.html +++ b/docs/reference/AIC.mmkin.html @@ -169,10 +169,10 @@ <span class='co'># of parameters, the higher (worse) the AIC</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/AIC'>AIC</a></span>(<span class='no'>f</span>[, <span class='st'>"FOCUS A"</span>])</div><div class='output co'>#> df AIC #> SFO 3 55.28197 -#> FOMC 4 57.28198 +#> FOMC 4 57.28202 #> DFOP 5 59.28197</div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/AIC'>AIC</a></span>(<span class='no'>f</span>[, <span class='st'>"FOCUS A"</span>], <span class='kw'>k</span> <span class='kw'>=</span> <span class='fl'>0</span>) <span class='co'># If we do not penalize additional parameters, we get nearly the same</span></div><div class='output co'>#> df AIC #> SFO 3 49.28197 -#> FOMC 4 49.28198 +#> FOMC 4 49.28202 #> DFOP 5 49.28197</div><div class='input'> <span class='co'># For FOCUS C, the more complex models fit better</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/AIC'>AIC</a></span>(<span class='no'>f</span>[, <span class='st'>"FOCUS C"</span>])</div><div class='output co'>#> df AIC diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 77eff52e..3b7209b1 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -189,7 +189,7 @@ <span class='no'>fits</span><span class='kw'>[[</span><span class='st'>"FOMC"</span>, <span class='st'>"B"</span>]] )</div><div class='output co'>#> $par #> parent_0 log_alpha log_beta sigma -#> 99.666193 2.549849 5.050586 1.890202 +#> 99.666193 2.549850 5.050586 1.890202 #> #> $objective #> [1] 28.58291 diff --git a/docs/reference/NAFTA_SOP_2015-1.png b/docs/reference/NAFTA_SOP_2015-1.png Binary files differindex c4f9f048..bcf5d12c 100644 --- a/docs/reference/NAFTA_SOP_2015-1.png +++ b/docs/reference/NAFTA_SOP_2015-1.png diff --git a/docs/reference/NAFTA_SOP_2015.html b/docs/reference/NAFTA_SOP_2015.html index 513cb128..84341a17 100644 --- a/docs/reference/NAFTA_SOP_2015.html +++ b/docs/reference/NAFTA_SOP_2015.html @@ -192,7 +192,7 @@ #> DFOP 429 2380 841 #> #> Representative half-life: -#> [1] 841.4094</div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>nafta_evaluation</span>)</div><div class='img'><img src='NAFTA_SOP_2015-1.png' alt='' width='700' height='433' /></div></pre> +#> [1] 841.41</div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>nafta_evaluation</span>)</div><div class='img'><img src='NAFTA_SOP_2015-1.png' alt='' width='700' height='433' /></div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/NAFTA_SOP_Attachment-1.png b/docs/reference/NAFTA_SOP_Attachment-1.png Binary files differindex 7c6c723f..87068d7c 100644 --- a/docs/reference/NAFTA_SOP_Attachment-1.png +++ b/docs/reference/NAFTA_SOP_Attachment-1.png diff --git a/docs/reference/NAFTA_SOP_Attachment.html b/docs/reference/NAFTA_SOP_Attachment.html index ead06a54..48a1495f 100644 --- a/docs/reference/NAFTA_SOP_Attachment.html +++ b/docs/reference/NAFTA_SOP_Attachment.html @@ -189,7 +189,7 @@ #> DFOP 55.5 3.70e+11 2.03e+11 #> #> Representative half-life: -#> [1] 321.5119</div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>nafta_att_p5a</span>)</div><div class='img'><img src='NAFTA_SOP_Attachment-1.png' alt='' width='700' height='433' /></div></pre> +#> [1] 321.51</div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>nafta_att_p5a</span>)</div><div class='img'><img src='NAFTA_SOP_Attachment-1.png' alt='' width='700' height='433' /></div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/add_err-1.png b/docs/reference/add_err-1.png Binary files differindex e2107cc2..2f60fdf7 100644 --- a/docs/reference/add_err-1.png +++ b/docs/reference/add_err-1.png diff --git a/docs/reference/add_err-3.png b/docs/reference/add_err-3.png Binary files differindex 6e6592a5..06f877c2 100644 --- a/docs/reference/add_err-3.png +++ b/docs/reference/add_err-3.png diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index a336a840..1f0f6b50 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -160,14 +160,14 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='no'>SFO_SFO_SFO</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>T245</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"phenol"</span>), <span class='kw'>phenol</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"anisole"</span>), - <span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> </div><div class='input'> <span class='no'>fit.1</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/subset'>subset</a></span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.1</span>)$<span class='no'>bpar</span></div><div class='output co'>#> <span class='warning'>Warning: NaNs wurden erzeugt</span></div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower -#> T245_0 1.038550e+02 2.1508106806 48.286460 3.542223e-18 99.246062186 -#> k_T245_sink 1.636106e-02 NaN NaN NaN 0.012661557 -#> k_T245_phenol 2.700936e-02 NaN NaN NaN 0.024487315 -#> k_phenol_sink 1.054519e-10 NaN NaN NaN 0.000000000 -#> k_phenol_anisole 4.050581e-01 0.1053797258 3.843795 7.969973e-04 0.218013983 -#> k_anisole_sink 6.678742e-03 0.0006205825 10.762053 9.427693e-09 0.005370739 -#> sigma 2.514628e+00 0.3383657682 7.431685 1.054052e-06 1.706607296 + <span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> </div><div class='input'> <span class='no'>fit.1</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/subset'>subset</a></span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.1</span>)$<span class='no'>bpar</span></div><div class='output co'>#> <span class='warning'>Warning: NaNs wurden erzeugt</span></div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower +#> T245_0 1.038550e+02 2.150809526 48.286486 3.542195e-18 99.246062243 +#> k_T245_sink 1.636106e-02 NaN NaN NaN 0.012661558 +#> k_T245_phenol 2.700936e-02 NaN NaN NaN 0.024487315 +#> k_phenol_sink 1.187912e-10 NaN NaN NaN 0.000000000 +#> k_phenol_anisole 4.050581e-01 0.105378416 3.843843 7.969195e-04 0.218013983 +#> k_anisole_sink 6.678742e-03 0.000620576 10.762166 9.426361e-09 0.005370739 +#> sigma 2.514628e+00 0.338361458 7.431780 1.053891e-06 1.706607296 #> Upper #> T245_0 1.084640e+02 #> k_T245_sink 2.114150e-02 @@ -177,7 +177,7 @@ #> k_anisole_sink 8.305299e-03 #> sigma 3.322649e+00</div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.1</span>)</div><div class='output co'>#> $ff #> T245_sink T245_phenol phenol_sink phenol_anisole anisole_sink -#> 3.772401e-01 6.227599e-01 2.603376e-10 1.000000e+00 1.000000e+00 +#> 3.772401e-01 6.227599e-01 2.932696e-10 1.000000e+00 1.000000e+00 #> #> $SFORB #> logical(0) @@ -205,7 +205,7 @@ #> k_anisole_sink 8.295501e-03 #> sigma 3.318272e+00</div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.1</span>)</div><div class='output co'>#> $ff #> T245_sink T245_phenol phenol_sink phenol_anisole anisole_sink -#> 3.772401e-01 6.227599e-01 2.603376e-10 1.000000e+00 1.000000e+00 +#> 3.772401e-01 6.227599e-01 2.932696e-10 1.000000e+00 1.000000e+00 #> #> $SFORB #> logical(0) diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index d3a826b9..7693287e 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -151,6 +151,7 @@ Per default, parameters in the kinetic models are internally transformed in <pre class="usage"><span class='fu'>mkinfit</span>(<span class='no'>mkinmod</span>, <span class='no'>observed</span>, <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>state.ini</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, + <span class='kw'>err.ini</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>fixed_initials</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/names'>names</a></span>(<span class='no'>mkinmod</span>$<span class='no'>diffs</span>)[-<span class='fl'>1</span>], <span class='kw'>from_max_mean</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"auto"</span>, <span class='st'>"analytical"</span>, <span class='st'>"eigen"</span>, <span class='st'>"deSolve"</span>), @@ -210,6 +211,13 @@ Per default, parameters in the kinetic models are internally transformed in If this variable has no time zero observations, its initial value is set to 100.</p></td> </tr> <tr> + <th>err.ini</th> + <td><p>A named vector of initial values for the error model parameters to be + optimised. If set to "auto", initial values are set to default values. + Otherwise, inital values for all error model parameters must be + given.</p></td> + </tr> + <tr> <th>fixed_parms</th> <td><p>The names of parameters that should not be optimised but rather kept at the values specified in <code>parms.ini</code>.</p></td> @@ -353,19 +361,19 @@ Per default, parameters in the kinetic models are internally transformed in <pre class="examples"><div class='input'><span class='co'># Use shorthand notation for parent only degradation</span> <span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.49.4 -#> R version used for fitting: 3.5.3 -#> Date of fit: Wed Apr 10 10:10:01 2019 -#> Date of summary: Wed Apr 10 10:10:01 2019 +#> R version used for fitting: 3.6.0 +#> Date of fit: Thu May 2 12:38:56 2019 +#> Date of summary: Thu May 2 12:38:56 2019 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent #> #> Model predictions using solution type analytical #> -#> Fitted with method using 221 model solutions performed in 0.508 s +#> Fitted using 221 model solutions performed in 0.455 s #> #> Error model: -#> NULL +#> Constant variance #> #> Starting values for parameters to be optimised: #> value type @@ -393,10 +401,10 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Parameter correlation: #> parent_0 log_alpha log_beta sigma -#> parent_0 1.000e+00 -1.565e-01 -3.142e-01 -1.313e-07 -#> log_alpha -1.565e-01 1.000e+00 9.564e-01 -2.634e-07 -#> log_beta -3.142e-01 9.564e-01 1.000e+00 -2.200e-07 -#> sigma -1.313e-07 -2.634e-07 -2.200e-07 1.000e+00 +#> parent_0 1.000e+00 -1.565e-01 -3.142e-01 -1.317e-07 +#> log_alpha -1.565e-01 1.000e+00 9.564e-01 -2.640e-07 +#> log_beta -3.142e-01 9.564e-01 1.000e+00 -2.205e-07 +#> sigma -1.317e-07 -2.640e-07 -2.205e-07 1.000e+00 #> #> Backtransformed parameters: #> Confidence intervals for internally transformed parameters are asymmetric. @@ -408,7 +416,7 @@ Per default, parameters in the kinetic models are internally transformed in #> beta 1.917 4.373 3.601e-03 1.0650 3.451 #> sigma 1.857 4.243 4.074e-03 0.7320 2.983 #> -#> Chi2 error levels in percent: +#> FOCUS Chi2 error levels in percent: #> err.min n.optim df #> All data 6.657 3 6 #> parent 6.657 3 6 @@ -435,7 +443,7 @@ Per default, parameters in the kinetic models are internally transformed in <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>(<span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)))</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#> User System verstrichen -#> 1.653 0.000 1.653 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> NULL</div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> $ff +#> 1.551 0.000 1.552 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> NULL</div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 #> @@ -448,71 +456,71 @@ Per default, parameters in the kinetic models are internally transformed in #> m1 131.760715 437.69962 #> </div><div class='input'><span class='co'># deSolve is slower when no C compiler (gcc) was available during model generation</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>(<span class='no'>fit.deSolve</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, - <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)))</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#> Negative log-likelihood at call 1: 18915.53 -#> Negative log-likelihood at call 2: 18915.53 -#> Negative log-likelihood at call 6: 11424.02 -#> Negative log-likelihood at call 10: 11424 -#> Negative log-likelihood at call 13: 2367.052 -#> Negative log-likelihood at call 14: 2367.05 -#> Negative log-likelihood at call 19: 1314.716 -#> Negative log-likelihood at call 22: 1314.714 -#> Negative log-likelihood at call 25: 991.8311 -#> Negative log-likelihood at call 28: 991.8305 -#> Negative log-likelihood at call 30: 893.6462 -#> Negative log-likelihood at call 33: 893.6457 -#> Negative log-likelihood at call 35: 569.4049 -#> Negative log-likelihood at call 38: 569.4047 -#> Negative log-likelihood at call 40: 565.0651 -#> Negative log-likelihood at call 41: 565.065 -#> Negative log-likelihood at call 42: 565.0637 -#> Negative log-likelihood at call 45: 428.0188 -#> Negative log-likelihood at call 46: 428.0185 -#> Negative log-likelihood at call 50: 406.732 -#> Negative log-likelihood at call 52: 406.732 -#> Negative log-likelihood at call 55: 398.9115 -#> Negative log-likelihood at call 57: 398.9113 -#> Negative log-likelihood at call 60: 394.5943 -#> Negative log-likelihood at call 62: 394.5943 -#> Negative log-likelihood at call 66: 385.26 -#> Negative log-likelihood at call 67: 385.2599 -#> Negative log-likelihood at call 69: 385.2599 -#> Negative log-likelihood at call 70: 385.2597 -#> Negative log-likelihood at call 71: 374.7604 -#> Negative log-likelihood at call 72: 374.7603 -#> Negative log-likelihood at call 76: 373.199 -#> Negative log-likelihood at call 79: 373.199 -#> Negative log-likelihood at call 80: 373.199 -#> Negative log-likelihood at call 81: 372.3772 -#> Negative log-likelihood at call 84: 372.3772 -#> Negative log-likelihood at call 86: 371.2615 -#> Negative log-likelihood at call 89: 371.2615 -#> Negative log-likelihood at call 90: 371.2615 -#> Negative log-likelihood at call 92: 371.2439 -#> Negative log-likelihood at call 93: 371.2439 -#> Negative log-likelihood at call 94: 371.2439 -#> Negative log-likelihood at call 97: 371.2198 -#> Negative log-likelihood at call 98: 371.2198 -#> Negative log-likelihood at call 102: 371.2174 -#> Negative log-likelihood at call 104: 371.2174 -#> Negative log-likelihood at call 107: 371.2147 -#> Negative log-likelihood at call 110: 371.2147 -#> Negative log-likelihood at call 111: 371.2147 -#> Negative log-likelihood at call 112: 371.2145 -#> Negative log-likelihood at call 113: 371.2145 -#> Negative log-likelihood at call 116: 371.2145 -#> Negative log-likelihood at call 119: 371.2135 -#> Negative log-likelihood at call 121: 371.2135 -#> Negative log-likelihood at call 124: 371.2135 -#> Negative log-likelihood at call 126: 371.2135 -#> Negative log-likelihood at call 127: 371.2135 -#> Negative log-likelihood at call 133: 371.2134 -#> Negative log-likelihood at call 135: 371.2134 -#> Negative log-likelihood at call 138: 371.2134 -#> Negative log-likelihood at call 142: 371.2134 + <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)))</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#> Sum of squared residuals at call 1: 18915.53 +#> Sum of squared residuals at call 2: 18915.53 +#> Sum of squared residuals at call 6: 11424.02 +#> Sum of squared residuals at call 10: 11424 +#> Sum of squared residuals at call 13: 2367.052 +#> Sum of squared residuals at call 14: 2367.05 +#> Sum of squared residuals at call 19: 1314.716 +#> Sum of squared residuals at call 22: 1314.714 +#> Sum of squared residuals at call 25: 991.8311 +#> Sum of squared residuals at call 28: 991.8305 +#> Sum of squared residuals at call 30: 893.6462 +#> Sum of squared residuals at call 33: 893.6457 +#> Sum of squared residuals at call 35: 569.4049 +#> Sum of squared residuals at call 38: 569.4047 +#> Sum of squared residuals at call 40: 565.0651 +#> Sum of squared residuals at call 41: 565.065 +#> Sum of squared residuals at call 42: 565.0637 +#> Sum of squared residuals at call 45: 428.0188 +#> Sum of squared residuals at call 46: 428.0185 +#> Sum of squared residuals at call 50: 406.732 +#> Sum of squared residuals at call 52: 406.732 +#> Sum of squared residuals at call 55: 398.9115 +#> Sum of squared residuals at call 57: 398.9113 +#> Sum of squared residuals at call 60: 394.5943 +#> Sum of squared residuals at call 62: 394.5943 +#> Sum of squared residuals at call 66: 385.26 +#> Sum of squared residuals at call 67: 385.2599 +#> Sum of squared residuals at call 69: 385.2599 +#> Sum of squared residuals at call 70: 385.2597 +#> Sum of squared residuals at call 71: 374.7604 +#> Sum of squared residuals at call 72: 374.7603 +#> Sum of squared residuals at call 76: 373.199 +#> Sum of squared residuals at call 79: 373.199 +#> Sum of squared residuals at call 80: 373.199 +#> Sum of squared residuals at call 81: 372.3772 +#> Sum of squared residuals at call 84: 372.3772 +#> Sum of squared residuals at call 86: 371.2615 +#> Sum of squared residuals at call 89: 371.2615 +#> Sum of squared residuals at call 90: 371.2615 +#> Sum of squared residuals at call 92: 371.2439 +#> Sum of squared residuals at call 93: 371.2439 +#> Sum of squared residuals at call 94: 371.2439 +#> Sum of squared residuals at call 97: 371.2198 +#> Sum of squared residuals at call 98: 371.2198 +#> Sum of squared residuals at call 102: 371.2174 +#> Sum of squared residuals at call 104: 371.2174 +#> Sum of squared residuals at call 107: 371.2147 +#> Sum of squared residuals at call 110: 371.2147 +#> Sum of squared residuals at call 111: 371.2147 +#> Sum of squared residuals at call 112: 371.2145 +#> Sum of squared residuals at call 113: 371.2145 +#> Sum of squared residuals at call 116: 371.2145 +#> Sum of squared residuals at call 119: 371.2135 +#> Sum of squared residuals at call 121: 371.2135 +#> Sum of squared residuals at call 124: 371.2135 +#> Sum of squared residuals at call 126: 371.2135 +#> Sum of squared residuals at call 127: 371.2135 +#> Sum of squared residuals at call 133: 371.2134 +#> Sum of squared residuals at call 135: 371.2134 +#> Sum of squared residuals at call 138: 371.2134 +#> Sum of squared residuals at call 142: 371.2134 #> Negative log-likelihood at call 152: 97.22429 #> Optimisation successfully terminated. #> User System verstrichen -#> 1.136 0.000 1.135 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#> NULL</div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#> $ff +#> 1.152 0.000 1.153 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#> NULL</div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 #> @@ -543,9 +551,9 @@ Per default, parameters in the kinetic models are internally transformed in </div><div class='input'><span class='co'># Weighted fits, including IRLS</span> <span class='no'>SFO_SFO.ff</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>f.noweight</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.49.4 -#> R version used for fitting: 3.5.3 -#> Date of fit: Wed Apr 10 10:10:17 2019 -#> Date of summary: Wed Apr 10 10:10:17 2019 +#> R version used for fitting: 3.6.0 +#> Date of fit: Thu May 2 12:39:13 2019 +#> Date of summary: Thu May 2 12:39:13 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -553,10 +561,10 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Model predictions using solution type deSolve #> -#> Fitted with method using 404 model solutions performed in 1.105 s +#> Fitted using 404 model solutions performed in 1.178 s #> #> Error model: -#> NULL +#> Constant variance #> #> Starting values for parameters to be optimised: #> value type @@ -605,7 +613,7 @@ Per default, parameters in the kinetic models are internally transformed in #> f_parent_to_m1 0.514500 23.070 3.104e-22 0.469100 5.596e-01 #> sigma 3.126000 8.718 2.235e-10 2.396000 3.855e+00 #> -#> Chi2 error levels in percent: +#> FOCUS Chi2 error levels in percent: #> err.min n.optim df #> All data 6.398 4 15 #> parent 6.459 2 7 @@ -661,9 +669,9 @@ Per default, parameters in the kinetic models are internally transformed in #> 100 m1 33.13 31.98163 1.148e+00 #> 120 m1 25.15 28.78984 -3.640e+00 #> 120 m1 33.31 28.78984 4.520e+00</div><div class='input'><span class='no'>f.obs</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"obs"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.obs</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.49.4 -#> R version used for fitting: 3.5.3 -#> Date of fit: Wed Apr 10 10:10:19 2019 -#> Date of summary: Wed Apr 10 10:10:19 2019 +#> R version used for fitting: 3.6.0 +#> Date of fit: Thu May 2 12:39:14 2019 +#> Date of summary: Thu May 2 12:39:14 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -671,10 +679,10 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Model predictions using solution type deSolve #> -#> Fitted with method using 558 model solutions performed in 1.602 s +#> Fitted using 558 model solutions performed in 1.518 s #> #> Error model: -#> NULL +#> Variance unique to each observed variable #> #> Starting values for parameters to be optimised: #> value type @@ -735,7 +743,7 @@ Per default, parameters in the kinetic models are internally transformed in #> sigma_parent 3.401000 5.985 5.662e-07 2.244000 4.559e+00 #> sigma_m1 2.855000 6.311 2.215e-07 1.934000 3.777e+00 #> -#> Chi2 error levels in percent: +#> FOCUS Chi2 error levels in percent: #> err.min n.optim df #> All data 6.398 4 15 #> parent 6.464 2 7 @@ -791,9 +799,9 @@ Per default, parameters in the kinetic models are internally transformed in #> 100 m1 33.13 31.98774 1.142e+00 #> 120 m1 25.15 28.80430 -3.654e+00 #> 120 m1 33.31 28.80430 4.506e+00</div><div class='input'><span class='no'>f.tc</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.tc</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.49.4 -#> R version used for fitting: 3.5.3 -#> Date of fit: Wed Apr 10 10:10:22 2019 -#> Date of summary: Wed Apr 10 10:10:22 2019 +#> R version used for fitting: 3.6.0 +#> Date of fit: Thu May 2 12:39:18 2019 +#> Date of summary: Thu May 2 12:39:18 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -801,10 +809,10 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Model predictions using solution type deSolve #> -#> Fitted with method using 756 model solutions performed in 3.222 s +#> Fitted using 844 model solutions performed in 3.501 s #> #> Error model: -#> NULL +#> Two-component variance function #> #> Starting values for parameters to be optimised: #> value type @@ -812,8 +820,8 @@ Per default, parameters in the kinetic models are internally transformed in #> k_parent 0.1000 deparm #> k_m1 0.1001 deparm #> f_parent_to_m1 0.5000 deparm -#> sigma_low 0.5000 error -#> rsd_high 0.0700 error +#> sigma_low 3.0000 error +#> rsd_high 0.0100 error #> #> Starting values for the transformed parameters actually optimised: #> value lower upper @@ -821,8 +829,8 @@ Per default, parameters in the kinetic models are internally transformed in #> log_k_parent -2.302585 -Inf Inf #> log_k_m1 -2.301586 -Inf Inf #> f_parent_ilr_1 0.000000 -Inf Inf -#> sigma_low 0.500000 0 Inf -#> rsd_high 0.070000 0 Inf +#> sigma_low 3.000000 0 Inf +#> rsd_high 0.010000 0 Inf #> #> Fixed parameter values: #> value type @@ -858,7 +866,7 @@ Per default, parameters in the kinetic models are internally transformed in #> sigma_low 3.050e-03 0.6314 2.661e-01 -0.006786 1.289e-02 #> rsd_high 7.928e-02 8.4170 6.418e-10 0.060100 9.847e-02 #> -#> Chi2 error levels in percent: +#> FOCUS Chi2 error levels in percent: #> err.min n.optim df #> All data 6.475 4 15 #> parent 6.573 2 7 @@ -876,18 +884,18 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Data: #> time variable observed predicted residual -#> 0 parent 99.46 100.73434 -1.274340 -#> 0 parent 102.04 100.73434 1.305660 +#> 0 parent 99.46 100.73434 -1.274339 +#> 0 parent 102.04 100.73434 1.305661 #> 1 parent 93.50 91.09751 2.402486 #> 1 parent 92.50 91.09751 1.402486 #> 3 parent 63.23 74.50141 -11.271410 #> 3 parent 68.99 74.50141 -5.511410 -#> 7 parent 52.32 49.82880 2.491200 -#> 7 parent 55.13 49.82880 5.301200 +#> 7 parent 52.32 49.82880 2.491201 +#> 7 parent 55.13 49.82880 5.301201 #> 14 parent 27.27 24.64809 2.621908 #> 14 parent 26.64 24.64809 1.991908 -#> 21 parent 11.50 12.19232 -0.692316 -#> 21 parent 11.64 12.19232 -0.552316 +#> 21 parent 11.50 12.19232 -0.692315 +#> 21 parent 11.64 12.19232 -0.552315 #> 35 parent 2.85 2.98327 -0.133266 #> 35 parent 2.91 2.98327 -0.073266 #> 50 parent 0.69 0.66013 0.029874 @@ -900,20 +908,20 @@ Per default, parameters in the kinetic models are internally transformed in #> 3 m1 12.96 13.22867 -0.268669 #> 7 m1 22.97 25.36417 -2.394167 #> 7 m1 24.47 25.36417 -0.894167 -#> 14 m1 41.69 37.00974 4.680262 -#> 14 m1 33.21 37.00974 -3.799738 +#> 14 m1 41.69 37.00974 4.680263 +#> 14 m1 33.21 37.00974 -3.799737 #> 21 m1 44.37 41.90133 2.468668 #> 21 m1 46.44 41.90133 4.538668 #> 35 m1 41.22 43.45691 -2.236914 #> 35 m1 37.95 43.45691 -5.506914 #> 50 m1 41.19 41.34199 -0.151986 #> 50 m1 40.01 41.34199 -1.331986 -#> 75 m1 40.09 36.61470 3.475295 -#> 75 m1 33.85 36.61470 -2.764705 -#> 100 m1 31.04 32.20082 -1.160823 -#> 100 m1 33.13 32.20082 0.929177 -#> 120 m1 25.15 29.04130 -3.891303 -#> 120 m1 33.31 29.04130 4.268697</div><div class='input'> +#> 75 m1 40.09 36.61471 3.475294 +#> 75 m1 33.85 36.61471 -2.764706 +#> 100 m1 31.04 32.20082 -1.160824 +#> 100 m1 33.13 32.20082 0.929176 +#> 120 m1 25.15 29.04130 -3.891305 +#> 120 m1 33.31 29.04130 4.268695</div><div class='input'> </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index b100f251..b545dad1 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -234,7 +234,7 @@ For the definition of model types and their parameters, the equations given <span class='no'>SFO_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>( <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> Compilation argument: -#> /usr/lib/R/bin/R CMD SHLIB file27ad440ff595.c 2> file27ad440ff595.c.err.txt +#> /usr/lib/R/bin/R CMD SHLIB file35fe67db2b2a.c 2> file35fe67db2b2a.c.err.txt #> Program source: #> 1: #include <R.h> #> 2: diff --git a/docs/reference/mkinparplot-1.png b/docs/reference/mkinparplot-1.png Binary files differindex 82b9c212..798722a2 100644 --- a/docs/reference/mkinparplot-1.png +++ b/docs/reference/mkinparplot-1.png diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 56c1ed27..4b75603f 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -328,7 +328,7 @@ <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#> time parent m1 #> 201 20 4.978707 27.46227</div><div class='output co'>#> User System verstrichen -#> 0.004 0.000 0.003 </div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>( +#> 0.003 0.000 0.003 </div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>( <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>), <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#> time parent m1 @@ -338,34 +338,34 @@ <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#> time parent m1 #> 201 20 4.978707 27.46227</div><div class='output co'>#> User System verstrichen -#> 0.04 0.00 0.04 </div><div class='input'> +#> 0.021 0.000 0.021 </div><div class='input'> </div><div class='input'> <span class='co'># Predict from a fitted model</span> - <span class='no'>f</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_C</span>)</div><div class='output co'>#> Negative log-likelihood at call 1: 552.5739 -#> Negative log-likelihood at call 3: 552.5739 -#> Negative log-likelihood at call 4: 552.5739 -#> Negative log-likelihood at call 6: 279.9345 -#> Negative log-likelihood at call 7: 279.9344 -#> Negative log-likelihood at call 8: 279.9294 -#> Negative log-likelihood at call 9: 279.9294 -#> Negative log-likelihood at call 12: 200.3629 -#> Negative log-likelihood at call 13: 200.3629 -#> Negative log-likelihood at call 18: 197.9039 -#> Negative log-likelihood at call 25: 196.6754 -#> Negative log-likelihood at call 27: 196.6754 -#> Negative log-likelihood at call 32: 196.5742 -#> Negative log-likelihood at call 33: 196.5742 -#> Negative log-likelihood at call 34: 196.5742 -#> Negative log-likelihood at call 38: 196.5361 -#> Negative log-likelihood at call 40: 196.5361 -#> Negative log-likelihood at call 44: 196.5336 -#> Negative log-likelihood at call 45: 196.5336 -#> Negative log-likelihood at call 50: 196.5334 -#> Negative log-likelihood at call 51: 196.5334 -#> Negative log-likelihood at call 52: 196.5334 -#> Negative log-likelihood at call 56: 196.5334 -#> Negative log-likelihood at call 58: 196.5334 -#> Negative log-likelihood at call 59: 196.5334 -#> Negative log-likelihood at call 65: 196.5334 + <span class='no'>f</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_C</span>)</div><div class='output co'>#> Sum of squared residuals at call 1: 552.5739 +#> Sum of squared residuals at call 3: 552.5739 +#> Sum of squared residuals at call 4: 552.5739 +#> Sum of squared residuals at call 6: 279.9345 +#> Sum of squared residuals at call 7: 279.9344 +#> Sum of squared residuals at call 8: 279.9294 +#> Sum of squared residuals at call 9: 279.9294 +#> Sum of squared residuals at call 12: 200.3629 +#> Sum of squared residuals at call 13: 200.3629 +#> Sum of squared residuals at call 18: 197.9039 +#> Sum of squared residuals at call 25: 196.6754 +#> Sum of squared residuals at call 27: 196.6754 +#> Sum of squared residuals at call 32: 196.5742 +#> Sum of squared residuals at call 33: 196.5742 +#> Sum of squared residuals at call 34: 196.5742 +#> Sum of squared residuals at call 38: 196.5361 +#> Sum of squared residuals at call 40: 196.5361 +#> Sum of squared residuals at call 44: 196.5336 +#> Sum of squared residuals at call 45: 196.5336 +#> Sum of squared residuals at call 50: 196.5334 +#> Sum of squared residuals at call 51: 196.5334 +#> Sum of squared residuals at call 52: 196.5334 +#> Sum of squared residuals at call 56: 196.5334 +#> Sum of squared residuals at call 58: 196.5334 +#> Sum of squared residuals at call 59: 196.5334 +#> Sum of squared residuals at call 65: 196.5334 #> Negative log-likelihood at call 75: 26.64668 #> Negative log-likelihood at call 103: 26.64668 #> Optimisation successfully terminated.</div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/utils/topics/head'>head</a></span>(<span class='fu'>mkinpredict</span>(<span class='no'>f</span>))</div><div class='output co'>#> time parent m1 diff --git a/docs/reference/mmkin-1.png b/docs/reference/mmkin-1.png Binary files differindex 6f24b369..9d86a2df 100644 --- a/docs/reference/mmkin-1.png +++ b/docs/reference/mmkin-1.png diff --git a/docs/reference/mmkin-2.png b/docs/reference/mmkin-2.png Binary files differindex 1ed2b216..c66b0beb 100644 --- a/docs/reference/mmkin-2.png +++ b/docs/reference/mmkin-2.png diff --git a/docs/reference/mmkin-3.png b/docs/reference/mmkin-3.png Binary files differindex 4743eabd..761778f8 100644 --- a/docs/reference/mmkin-3.png +++ b/docs/reference/mmkin-3.png diff --git a/docs/reference/mmkin-4.png b/docs/reference/mmkin-4.png Binary files differindex cad6ee11..89048ea3 100644 --- a/docs/reference/mmkin-4.png +++ b/docs/reference/mmkin-4.png diff --git a/docs/reference/mmkin-5.png b/docs/reference/mmkin-5.png Binary files differindex 5e1527fa..0c81649c 100644 --- a/docs/reference/mmkin-5.png +++ b/docs/reference/mmkin-5.png diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index 68451ca6..a16cb6d7 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -194,8 +194,8 @@ <span class='no'>time_1</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>(<span class='no'>fits.4</span> <span class='kw'><-</span> <span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)) <span class='no'>time_default</span></div><div class='output co'>#> User System verstrichen -#> 0.034 0.041 5.124 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#> User System verstrichen -#> 19.594 0.000 19.605 </div><div class='input'> +#> 0.040 0.035 7.515 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#> User System verstrichen +#> 21.597 0.000 21.609 </div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='st'>"SFO_lin"</span>, <span class='fl'>2</span>]])</div><div class='output co'>#> $ff #> parent_M1 parent_sink M1_M2 M1_sink #> 0.7340481 0.2659519 0.7505683 0.2494317 diff --git a/docs/reference/nafta-1.png b/docs/reference/nafta-1.png Binary files differindex c4f9f048..bcf5d12c 100644 --- a/docs/reference/nafta-1.png +++ b/docs/reference/nafta-1.png diff --git a/docs/reference/nafta.html b/docs/reference/nafta.html index 93bc3955..a9ee2f76 100644 --- a/docs/reference/nafta.html +++ b/docs/reference/nafta.html @@ -219,7 +219,7 @@ #> DFOP 429 2380 841 #> #> Representative half-life: -#> [1] 841.4094</div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>nafta_evaluation</span>)</div><div class='img'><img src='nafta-1.png' alt='' width='700' height='433' /></div></pre> +#> [1] 841.41</div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>nafta_evaluation</span>)</div><div class='img'><img src='nafta-1.png' alt='' width='700' height='433' /></div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/plot.mkinfit-3.png b/docs/reference/plot.mkinfit-3.png Binary files differindex 9a074f31..52de09bd 100644 --- a/docs/reference/plot.mkinfit-3.png +++ b/docs/reference/plot.mkinfit-3.png diff --git a/docs/reference/plot.mkinfit-4.png b/docs/reference/plot.mkinfit-4.png Binary files differindex f8ae39c2..a832ede2 100644 --- a/docs/reference/plot.mkinfit-4.png +++ b/docs/reference/plot.mkinfit-4.png diff --git a/docs/reference/plot.mmkin-1.png b/docs/reference/plot.mmkin-1.png Binary files differindex 60e602d4..03d334f7 100644 --- a/docs/reference/plot.mmkin-1.png +++ b/docs/reference/plot.mmkin-1.png diff --git a/docs/reference/plot.mmkin-2.png b/docs/reference/plot.mmkin-2.png Binary files differindex f1e4318c..555cb7d6 100644 --- a/docs/reference/plot.mmkin-2.png +++ b/docs/reference/plot.mmkin-2.png diff --git a/docs/reference/plot.mmkin-3.png b/docs/reference/plot.mmkin-3.png Binary files differindex 04762756..412c7244 100644 --- a/docs/reference/plot.mmkin-3.png +++ b/docs/reference/plot.mmkin-3.png diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html index fec2a187..f645e6a7 100644 --- a/docs/reference/schaefer07_complex_case.html +++ b/docs/reference/schaefer07_complex_case.html @@ -167,7 +167,7 @@ <span class='kw'>A2</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> </div><div class='input'> <span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>model</span>, <span class='no'>data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>fit</span>)</div><div class='img'><img src='schaefer07_complex_case-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> $ff #> parent_A1 parent_B1 parent_C1 parent_sink A1_A2 A1_sink -#> 0.3809619 0.1954667 0.4235714 0.0000000 0.4479605 0.5520395 +#> 0.3809619 0.1954667 0.4235714 0.0000000 0.4479603 0.5520397 #> #> $SFORB #> logical(0) @@ -175,10 +175,10 @@ #> $distimes #> DT50 DT90 #> parent 13.95078 46.34350 -#> A1 49.75344 165.27734 -#> B1 37.26908 123.80520 -#> C1 11.23130 37.30958 -#> A2 28.50644 94.69634 +#> A1 49.75343 165.27733 +#> B1 37.26907 123.80518 +#> C1 11.23131 37.30959 +#> A2 28.50644 94.69635 #> </div><div class='input'> </div><div class='input'> <span class='co'># Compare with the results obtained in the original publication</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>schaefer07_complex_results</span>)</div><div class='output co'>#> compound parameter KinGUI ModelMaker deviation #> 1 parent degradation rate 0.0496 0.0506 2.0 diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index e5565990..1a08132f 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -210,19 +210,19 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>)), <span class='no'>FOCUS_2006_A</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#> mkin version used for fitting: 0.9.49.4 -#> R version used for fitting: 3.5.3 -#> Date of fit: Wed Apr 10 10:11:15 2019 -#> Date of summary: Wed Apr 10 10:11:15 2019 +#> R version used for fitting: 3.6.0 +#> Date of fit: Thu May 2 12:40:14 2019 +#> Date of summary: Thu May 2 12:40:14 2019 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent #> #> Model predictions using solution type analytical #> -#> Fitted with method using 131 model solutions performed in 0.284 s +#> Fitted using 131 model solutions performed in 0.269 s #> #> Error model: -#> NULL +#> Constant variance #> #> Starting values for parameters to be optimised: #> value type @@ -260,7 +260,7 @@ #> k_parent_sink 0.03722 10.90 5.650e-05 0.0294 0.04712 #> sigma 5.26600 4.00 5.162e-03 1.8820 8.64900 #> -#> Chi2 error levels in percent: +#> FOCUS Chi2 error levels in percent: #> err.min n.optim df #> All data 8.385 2 6 #> parent 8.385 2 6 diff --git a/docs/reference/test_data_from_UBA_2014-1.png b/docs/reference/test_data_from_UBA_2014-1.png Binary files differindex 9157a6a1..a9aeea21 100644 --- a/docs/reference/test_data_from_UBA_2014-1.png +++ b/docs/reference/test_data_from_UBA_2014-1.png diff --git a/docs/reference/test_data_from_UBA_2014-2.png b/docs/reference/test_data_from_UBA_2014-2.png Binary files differindex 528f3987..f6c91bff 100644 --- a/docs/reference/test_data_from_UBA_2014-2.png +++ b/docs/reference/test_data_from_UBA_2014-2.png diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html index dfb49619..688baf32 100644 --- a/docs/reference/test_data_from_UBA_2014.html +++ b/docs/reference/test_data_from_UBA_2014.html @@ -184,25 +184,25 @@ <span class='kw'>M3</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> <span class='no'>f_soil</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_soil</span>, <span class='no'>test_data_from_UBA_2014</span><span class='kw'>[[</span><span class='fl'>3</span>]]$<span class='no'>data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>f_soil</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>))</div><div class='img'><img src='test_data_from_UBA_2014-2.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f_soil</span>)$<span class='no'>bpar</span></div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower -#> parent_0 76.55425584 0.859186614 89.1008479 1.113866e-26 74.755959751 -#> k_parent 0.12081956 0.004601922 26.2541548 1.077373e-16 0.111561582 -#> k_M1 0.84258651 0.806231481 1.0450925 1.545475e-01 0.113839756 +#> parent_0 76.55425583 0.859186612 89.1008482 1.113866e-26 74.755959748 +#> k_parent 0.12081956 0.004601921 26.2541551 1.077372e-16 0.111561582 +#> k_M1 0.84258650 0.806231456 1.0450926 1.545475e-01 0.113839804 #> k_M2 0.04210878 0.017083049 2.4649452 1.170195e-02 0.018013807 #> k_M3 0.01122919 0.007245890 1.5497322 6.885127e-02 0.002909463 -#> f_parent_to_M1 0.32240199 0.240803570 1.3388589 9.820821e-02 NA +#> f_parent_to_M1 0.32240199 0.240803564 1.3388589 9.820820e-02 NA #> f_parent_to_M2 0.16099854 0.033691991 4.7785403 6.531225e-05 NA -#> f_M1_to_M3 0.27921500 0.269443517 1.0362654 1.565440e-01 0.022992921 -#> f_M2_to_M3 0.55641333 0.595125456 0.9349513 1.807725e-01 0.008003316 +#> f_M1_to_M3 0.27921500 0.269443517 1.0362654 1.565440e-01 0.022992933 +#> f_M2_to_M3 0.55641333 0.595125466 0.9349513 1.807725e-01 0.008003317 #> sigma 1.14005399 0.149696423 7.6157731 1.727024e-07 0.826735778 #> Upper #> parent_0 78.35255192 #> k_parent 0.13084582 -#> k_M1 6.23641562 +#> k_M1 6.23641283 #> k_M2 0.09843279 #> k_M3 0.04333950 #> f_parent_to_M1 NA #> f_parent_to_M2 NA -#> f_M1_to_M3 0.86443090 +#> f_M1_to_M3 0.86443084 #> f_M2_to_M3 0.99489847 #> sigma 1.45337221</div><div class='input'> <span class='fu'><a href='mkinerrmin.html'>mkinerrmin</a></span>(<span class='no'>f_soil</span>)</div><div class='output co'>#> err.min n.optim df #> All data 0.09649963 9 20 diff --git a/inst/benchmark_data/mkin_benchmarks.rda b/inst/benchmark_data/mkin_benchmarks.rda Binary files differindex c02d745a..388a7886 100644 --- a/inst/benchmark_data/mkin_benchmarks.rda +++ b/inst/benchmark_data/mkin_benchmarks.rda diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd index d9efe05f..78a53ee0 100644 --- a/man/mkinfit.Rd +++ b/man/mkinfit.Rd @@ -19,6 +19,7 @@ mkinfit(mkinmod, observed, parms.ini = "auto", state.ini = "auto", + err.ini = "auto", fixed_parms = NULL, fixed_initials = names(mkinmod$diffs)[-1], from_max_mean = FALSE, solution_type = c("auto", "analytical", "eigen", "deSolve"), @@ -72,6 +73,12 @@ mkinfit(mkinmod, observed, values for the variable with the maximum observed value, and all others to 0. If this variable has no time zero observations, its initial value is set to 100. } + \item{err.ini}{ + A named vector of initial values for the error model parameters to be + optimised. If set to "auto", initial values are set to default values. + Otherwise, inital values for all error model parameters must be + given. + } \item{fixed_parms}{ The names of parameters that should not be optimised but rather kept at the values specified in \code{parms.ini}. @@ -2,26 +2,26 @@ Loading mkin Testing mkin ✔ | OK F W S | Context
⠏ | 0 | Export dataset for reading into CAKE
⠋ | 1 | Export dataset for reading into CAKE
✔ | 1 | Export dataset for reading into CAKE -
⠏ | 0 | Error model fitting
⠋ | 1 | Error model fitting
⠙ | 2 | Error model fitting
⠹ | 3 | Error model fitting
⠸ | 4 | Error model fitting
⠼ | 5 | Error model fitting
⠴ | 6 | Error model fitting
⠦ | 7 | Error model fitting
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⠇ | 9 | Error model fitting
⠏ | 10 | Error model fitting
⠋ | 11 | Error model fitting
⠙ | 12 | Error model fitting
✔ | 12 | Error model fitting [164.6 s] +
⠏ | 0 | Error model fitting
⠋ | 1 | Error model fitting
⠙ | 2 | Error model fitting
⠹ | 3 | Error model fitting
⠸ | 4 | Error model fitting
⠼ | 5 | Error model fitting
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⠧ | 8 | Error model fitting
⠇ | 9 | Error model fitting
⠏ | 10 | Error model fitting
⠋ | 11 | Error model fitting
⠙ | 12 | Error model fitting
✔ | 12 | Error model fitting [148.0 s]
⠏ | 0 | Calculation of FOCUS chi2 error levels
⠋ | 1 | Calculation of FOCUS chi2 error levels
⠙ | 2 | Calculation of FOCUS chi2 error levels
⠹ | 3 | Calculation of FOCUS chi2 error levels
✔ | 3 | Calculation of FOCUS chi2 error levels [2.3 s] -
⠏ | 0 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠋ | 1 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠙ | 2 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠹ | 3 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠸ | 4 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠼ | 5 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠴ | 6 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠦ | 7 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠧ | 8 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠇ | 9 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠏ | 10 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠋ | 11 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠙ | 12 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠹ | 13 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
✔ | 13 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [3.8 s] +
⠏ | 0 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠋ | 1 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠙ | 2 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠹ | 3 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠸ | 4 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠼ | 5 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠴ | 6 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠦ | 7 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠧ | 8 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠇ | 9 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠏ | 10 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠋ | 11 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠙ | 12 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠹ | 13 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
✔ | 13 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [3.7 s]
⠏ | 0 | Test fitting the decline of metabolites from their maximum
⠋ | 1 | Test fitting the decline of metabolites from their maximum
⠙ | 2 | Test fitting the decline of metabolites from their maximum
⠹ | 3 | Test fitting the decline of metabolites from their maximum
⠸ | 4 | Test fitting the decline of metabolites from their maximum
⠼ | 5 | Test fitting the decline of metabolites from their maximum
⠴ | 6 | Test fitting the decline of metabolites from their maximum
✔ | 6 | Test fitting the decline of metabolites from their maximum [0.9 s] -
⠏ | 0 | Fitting the logistic model
⠋ | 1 | Fitting the logistic model
✔ | 1 | Fitting the logistic model [1.0 s] +
⠏ | 0 | Fitting the logistic model
⠋ | 1 | Fitting the logistic model
✔ | 1 | Fitting the logistic model [0.9 s]
⠏ | 0 | Test dataset class mkinds used in gmkin
⠋ | 1 | Test dataset class mkinds used in gmkin
✔ | 1 | Test dataset class mkinds used in gmkin -
⠏ | 0 | Special cases of mkinfit calls
⠋ | 1 | Special cases of mkinfit calls
⠙ | 2 | Special cases of mkinfit calls
⠹ | 3 | Special cases of mkinfit calls
⠸ | 4 | Special cases of mkinfit calls
⠼ | 5 | Special cases of mkinfit calls
⠴ | 6 | Special cases of mkinfit calls
⠦ | 7 | Special cases of mkinfit calls
⠧ | 8 | Special cases of mkinfit calls
⠇ | 9 | Special cases of mkinfit calls
⠏ | 10 | Special cases of mkinfit calls
⠋ | 11 | Special cases of mkinfit calls
⠙ | 12 | Special cases of mkinfit calls
✔ | 12 | Special cases of mkinfit calls [2.8 s] +
⠏ | 0 | Special cases of mkinfit calls
⠋ | 1 | Special cases of mkinfit calls
⠙ | 2 | Special cases of mkinfit calls
⠹ | 3 | Special cases of mkinfit calls
⠸ | 4 | Special cases of mkinfit calls
⠼ | 5 | Special cases of mkinfit calls
⠴ | 6 | Special cases of mkinfit calls
⠦ | 7 | Special cases of mkinfit calls
⠧ | 8 | Special cases of mkinfit calls
⠇ | 9 | Special cases of mkinfit calls
⠏ | 10 | Special cases of mkinfit calls
⠋ | 11 | Special cases of mkinfit calls
⠙ | 12 | Special cases of mkinfit calls
✔ | 12 | Special cases of mkinfit calls [2.7 s]
⠏ | 0 | mkinmod model generation and printing
⠋ | 1 | mkinmod model generation and printing
⠙ | 2 | mkinmod model generation and printing
⠹ | 3 | mkinmod model generation and printing
⠸ | 4 | mkinmod model generation and printing
⠼ | 5 | mkinmod model generation and printing
⠴ | 6 | mkinmod model generation and printing
⠦ | 7 | mkinmod model generation and printing
⠧ | 8 | mkinmod model generation and printing
⠇ | 9 | mkinmod model generation and printing
✔ | 9 | mkinmod model generation and printing [0.2 s] -
⠏ | 0 | Model predictions with mkinpredict
⠋ | 1 | Model predictions with mkinpredict
⠙ | 2 | Model predictions with mkinpredict
⠹ | 3 | Model predictions with mkinpredict
✔ | 3 | Model predictions with mkinpredict [0.4 s] -
⠏ | 0 | Evaluations according to 2015 NAFTA guidance
⠋ | 1 | Evaluations according to 2015 NAFTA guidance
⠙ | 2 | Evaluations according to 2015 NAFTA guidance
⠹ | 3 | Evaluations according to 2015 NAFTA guidance
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⠏ | 10 | Evaluations according to 2015 NAFTA guidance
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⠙ | 12 | Evaluations according to 2015 NAFTA guidance
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⠸ | 14 | Evaluations according to 2015 NAFTA guidance
⠼ | 15 | Evaluations according to 2015 NAFTA guidance
⠴ | 16 | Evaluations according to 2015 NAFTA guidance
✔ | 16 | Evaluations according to 2015 NAFTA guidance [4.1 s] -
⠏ | 0 | Fitting of parent only models
⠋ | 1 | Fitting of parent only models
⠙ | 2 | Fitting of parent only models
⠹ | 3 | Fitting of parent only models
⠸ | 4 | Fitting of parent only models
⠼ | 5 | Fitting of parent only models
⠴ | 6 | Fitting of parent only models
⠦ | 7 | Fitting of parent only models
⠧ | 8 | Fitting of parent only models
⠇ | 9 | Fitting of parent only models
⠏ | 10 | Fitting of parent only models
⠋ | 11 | Fitting of parent only models
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⠴ | 16 | Fitting of parent only models
⠦ | 17 | Fitting of parent only models
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⠇ | 19 | Fitting of parent only models
⠏ | 20 | Fitting of parent only models
⠋ | 21 | Fitting of parent only models
✔ | 21 | Fitting of parent only models [58.1 s] -
⠏ | 0 | Calculation of maximum time weighted average concentrations (TWAs)
⠋ | 1 | Calculation of maximum time weighted average concentrations (TWAs)
⠙ | 2 | Calculation of maximum time weighted average concentrations (TWAs)
⠹ | 3 | Calculation of maximum time weighted average concentrations (TWAs)
⠸ | 4 | Calculation of maximum time weighted average concentrations (TWAs)
✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [3.7 s] +
⠏ | 0 | Model predictions with mkinpredict
⠋ | 1 | Model predictions with mkinpredict
⠙ | 2 | Model predictions with mkinpredict
⠹ | 3 | Model predictions with mkinpredict
✔ | 3 | Model predictions with mkinpredict [0.3 s] +
⠏ | 0 | Evaluations according to 2015 NAFTA guidance
⠋ | 1 | Evaluations according to 2015 NAFTA guidance
⠙ | 2 | Evaluations according to 2015 NAFTA guidance
⠹ | 3 | Evaluations according to 2015 NAFTA guidance
⠸ | 4 | Evaluations according to 2015 NAFTA guidance
⠼ | 5 | Evaluations according to 2015 NAFTA guidance
⠴ | 6 | Evaluations according to 2015 NAFTA guidance
⠦ | 7 | Evaluations according to 2015 NAFTA guidance
⠧ | 8 | Evaluations according to 2015 NAFTA guidance
⠇ | 9 | Evaluations according to 2015 NAFTA guidance
⠏ | 10 | Evaluations according to 2015 NAFTA guidance
⠋ | 11 | Evaluations according to 2015 NAFTA guidance
⠙ | 12 | Evaluations according to 2015 NAFTA guidance
⠹ | 13 | Evaluations according to 2015 NAFTA guidance
⠸ | 14 | Evaluations according to 2015 NAFTA guidance
⠼ | 15 | Evaluations according to 2015 NAFTA guidance
⠴ | 16 | Evaluations according to 2015 NAFTA guidance
✔ | 16 | Evaluations according to 2015 NAFTA guidance [3.9 s] +
⠏ | 0 | Fitting of parent only models
⠋ | 1 | Fitting of parent only models
⠙ | 2 | Fitting of parent only models
⠹ | 3 | Fitting of parent only models
⠸ | 4 | Fitting of parent only models
⠼ | 5 | Fitting of parent only models
⠴ | 6 | Fitting of parent only models
⠦ | 7 | Fitting of parent only models
⠧ | 8 | Fitting of parent only models
⠇ | 9 | Fitting of parent only models
⠏ | 10 | Fitting of parent only models
⠋ | 11 | Fitting of parent only models
⠙ | 12 | Fitting of parent only models
⠹ | 13 | Fitting of parent only models
⠸ | 14 | Fitting of parent only models
⠼ | 15 | Fitting of parent only models
⠴ | 16 | Fitting of parent only models
⠦ | 17 | Fitting of parent only models
⠧ | 18 | Fitting of parent only models
⠇ | 19 | Fitting of parent only models
⠏ | 20 | Fitting of parent only models
⠋ | 21 | Fitting of parent only models
✔ | 21 | Fitting of parent only models [40.0 s] +
⠏ | 0 | Calculation of maximum time weighted average concentrations (TWAs)
⠋ | 1 | Calculation of maximum time weighted average concentrations (TWAs)
⠙ | 2 | Calculation of maximum time weighted average concentrations (TWAs)
⠹ | 3 | Calculation of maximum time weighted average concentrations (TWAs)
⠸ | 4 | Calculation of maximum time weighted average concentrations (TWAs)
✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.3 s]
⠏ | 0 | Summary
⠋ | 1 | Summary
✔ | 1 | Summary
⠏ | 0 | Plotting
⠋ | 1 | Plotting
⠙ | 2 | Plotting
⠹ | 3 | Plotting
⠸ | 4 | Plotting
✔ | 4 | Plotting [0.3 s]
⠏ | 0 | AIC calculation
⠋ | 1 | AIC calculation
⠙ | 2 | AIC calculation
✔ | 2 | AIC calculation -
⠏ | 0 | Complex test case from Schaefer et al. (2007) Piacenza paper
⠋ | 1 | Complex test case from Schaefer et al. (2007) Piacenza paper
⠙ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper
✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [5.5 s] -
⠏ | 0 | Results for synthetic data established in expertise for UBA (Ranke 2014)
⠋ | 1 | Results for synthetic data established in expertise for UBA (Ranke 2014)
⠙ | 2 | Results for synthetic data established in expertise for UBA (Ranke 2014)
⠹ | 3 | Results for synthetic data established in expertise for UBA (Ranke 2014)
⠸ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014)
✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [7.2 s] +
⠏ | 0 | Complex test case from Schaefer et al. (2007) Piacenza paper
⠋ | 1 | Complex test case from Schaefer et al. (2007) Piacenza paper
⠙ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper
✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [5.3 s] +
⠏ | 0 | Results for synthetic data established in expertise for UBA (Ranke 2014)
⠋ | 1 | Results for synthetic data established in expertise for UBA (Ranke 2014)
⠙ | 2 | Results for synthetic data established in expertise for UBA (Ranke 2014)
⠹ | 3 | Results for synthetic data established in expertise for UBA (Ranke 2014)
⠸ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014)
✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [7.1 s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 261.0 s +Duration: 223.4 s OK: 115 Failed: 0 diff --git a/tests/testthat/DFOP_FOCUS_C_messages.txt b/tests/testthat/DFOP_FOCUS_C_messages.txt index 9abde683..4718cea6 100644 --- a/tests/testthat/DFOP_FOCUS_C_messages.txt +++ b/tests/testthat/DFOP_FOCUS_C_messages.txt @@ -81,7 +81,7 @@ Sum of squared residuals at call 55: 4.364078 85.01633 -0.7763163 -4.027611 1.248897 Sum of squared residuals at call 56: 4.364078 85.01633 -0.7763164 -4.027611 1.248897 -Sum of squared residuals at call 57: 4.364077 +Sum of squared residuals at call 57: 4.364078 85.01633 -0.7763163 -4.027611 1.248897 85.01633 -0.7763163 -4.027611 1.248897 85.00894 -0.7777917 -4.026307 1.24772 diff --git a/tests/testthat/FOCUS_2006_D.csf b/tests/testthat/FOCUS_2006_D.csf index 9e912a28..07488d5e 100644 --- a/tests/testthat/FOCUS_2006_D.csf +++ b/tests/testthat/FOCUS_2006_D.csf @@ -5,7 +5,7 @@ Description: MeasurementUnits: % AR TimeUnits: days Comments: Created using mkin::CAKE_export -Date: 2019-04-24 +Date: 2019-05-02 Optimiser: IRLS [Data] diff --git a/tests/testthat/summary_DFOP_FOCUS_C.txt b/tests/testthat/summary_DFOP_FOCUS_C.txt index b0a6bb6d..c4800f35 100644 --- a/tests/testthat/summary_DFOP_FOCUS_C.txt +++ b/tests/testthat/summary_DFOP_FOCUS_C.txt @@ -44,11 +44,11 @@ sigma 0.6962 0.16410 0.2406 1.1520 Parameter correlation: parent_0 log_k1 log_k2 g_ilr sigma -parent_0 1.000e+00 4.393e-01 8.805e-02 -3.176e-02 5.405e-07 -log_k1 4.393e-01 1.000e+00 4.821e-01 -6.716e-01 4.395e-07 -log_k2 8.805e-02 4.821e-01 1.000e+00 -7.532e-01 -1.151e-07 -g_ilr -3.176e-02 -6.716e-01 -7.532e-01 1.000e+00 -2.142e-08 -sigma 5.405e-07 4.395e-07 -1.151e-07 -2.142e-08 1.000e+00 +parent_0 1.000e+00 4.393e-01 8.805e-02 -3.176e-02 5.407e-07 +log_k1 4.393e-01 1.000e+00 4.821e-01 -6.716e-01 4.399e-07 +log_k2 8.805e-02 4.821e-01 1.000e+00 -7.532e-01 -1.143e-07 +g_ilr -3.176e-02 -6.716e-01 -7.532e-01 1.000e+00 -2.196e-08 +sigma 5.407e-07 4.399e-07 -1.143e-07 -2.196e-08 1.000e+00 Backtransformed parameters: Confidence intervals for internally transformed parameters are asymmetric. |
