diff options
Diffstat (limited to 'vignettes')
| -rw-r--r-- | vignettes/FOCUS_D.html | 50 | ||||
| -rw-r--r-- | vignettes/FOCUS_L.html | 357 | ||||
| -rw-r--r-- | vignettes/FOCUS_Z.Rnw | 2 | ||||
| -rw-r--r-- | vignettes/FOCUS_Z.pdf | bin | 215014 -> 224256 bytes | |||
| -rw-r--r-- | vignettes/compiled_models.html | 42 | ||||
| -rw-r--r-- | vignettes/mkin.pdf | bin | 160260 -> 160260 bytes |
6 files changed, 232 insertions, 219 deletions
diff --git a/vignettes/FOCUS_D.html b/vignettes/FOCUS_D.html index 6573cc7a..b1ea64ea 100644 --- a/vignettes/FOCUS_D.html +++ b/vignettes/FOCUS_D.html @@ -215,13 +215,7 @@ library we look a the data. We have observed concentrations in the column named named <code>parent</code> and <code>m1</code>.</p> <pre><code class="r">library("mkin") -</code></pre> - -<pre><code>## Loading required package: minpack.lm -## Loading required package: rootSolve -</code></pre> - -<pre><code class="r">print(FOCUS_2006_D) +print(FOCUS_2006_D) </code></pre> <pre><code>## name time value @@ -276,7 +270,7 @@ kinetics (SFO) to one metabolite named m1, which also degrades with SFO kinetics <p>The call to mkinmod returns a degradation model. The differential equations represented in R code can be found in the character vector <code>$diffs</code> of the <code>mkinmod</code> object. If -the <code>ccSolve</code> package is installed and functional, the differential equation model +the gcc compiler is installed and functional, the differential equation model will be compiled from auto-generated C code.</p> <pre><code class="r">SFO_SFO <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO")) @@ -312,7 +306,7 @@ using the <code>plot</code> method for <code>mkinfit</code> objects.</p> <pre><code class="r">mkinparplot(fit) </code></pre> -<p><img src="data:image/png;base64,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alt="plot of chunk unnamed-chunk-6"/> </p> +<p><img 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" alt="plot of chunk unnamed-chunk-6"/> </p> <p>A comprehensive report of the results is obtained using the <code>summary</code> method for <code>mkinfit</code> objects.</p> @@ -321,9 +315,9 @@ objects.</p> </code></pre> <pre><code>## mkin version: 0.9.36 -## R version: 3.2.0 -## Date of fit: Fri Jun 5 14:20:31 2015 -## Date of summary: Fri Jun 5 14:20:31 2015 +## R version: 3.2.1 +## Date of fit: Sun Jun 21 01:47:59 2015 +## Date of summary: Sun Jun 21 01:47:59 2015 ## ## Equations: ## d_parent = - k_parent_sink * parent - k_parent_m1 * parent @@ -331,7 +325,7 @@ objects.</p> ## ## Model predictions using solution type deSolve ## -## Fitted with method Port using 153 model solutions performed in 0.621 s +## Fitted with method Port using 153 model solutions performed in 0.698 s ## ## Weighting: none ## @@ -353,17 +347,12 @@ objects.</p> ## value type ## m1_0 0 state ## -## Optimised, transformed parameters: -## Estimate Std. Error Lower Upper t value Pr(>|t|) -## parent_0 99.600 1.61400 96.330 102.900 61.72 4.048e-38 -## log_k_parent_sink -3.038 0.07826 -3.197 -2.879 -38.82 5.601e-31 -## log_k_parent_m1 -2.980 0.04124 -3.064 -2.897 -72.27 1.446e-40 -## log_k_m1_sink -5.248 0.13610 -5.523 -4.972 -38.56 7.087e-31 -## Pr(>t) -## parent_0 2.024e-38 -## log_k_parent_sink 2.800e-31 -## log_k_parent_m1 7.228e-41 -## log_k_m1_sink 3.543e-31 +## Optimised, transformed parameters with symmetric confidence intervals: +## Estimate Std. Error Lower Upper +## parent_0 99.600 1.61400 96.330 102.900 +## log_k_parent_sink -3.038 0.07826 -3.197 -2.879 +## log_k_parent_m1 -2.980 0.04124 -3.064 -2.897 +## log_k_m1_sink -5.248 0.13610 -5.523 -4.972 ## ## Parameter correlation: ## parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink @@ -375,11 +364,14 @@ objects.</p> ## Residual standard error: 3.211 on 36 degrees of freedom ## ## Backtransformed parameters: -## Estimate Lower Upper -## parent_0 99.600000 96.330000 1.029e+02 -## k_parent_sink 0.047920 0.040890 5.616e-02 -## k_parent_m1 0.050780 0.046700 5.521e-02 -## k_m1_sink 0.005261 0.003992 6.933e-03 +## Confidence intervals for internally transformed parameters are asymmetric. +## t-test (unrealistically) based on the assumption of normal distribution +## for estimators of untransformed parameters. +## Estimate t value Pr(>t) Lower Upper +## parent_0 99.600000 61.720 2.024e-38 96.330000 1.029e+02 +## k_parent_sink 0.047920 12.780 3.050e-15 0.040890 5.616e-02 +## k_parent_m1 0.050780 24.250 3.407e-24 0.046700 5.521e-02 +## k_m1_sink 0.005261 7.349 5.758e-09 0.003992 6.933e-03 ## ## Chi2 error levels in percent: ## err.min n.optim df diff --git a/vignettes/FOCUS_L.html b/vignettes/FOCUS_L.html index 96ea70ce..692caf93 100644 --- a/vignettes/FOCUS_L.html +++ b/vignettes/FOCUS_L.html @@ -214,13 +214,7 @@ hr { report, p. 284:</p> <pre><code class="r">library("mkin") -</code></pre> - -<pre><code>## Loading required package: minpack.lm -## Loading required package: rootSolve -</code></pre> - -<pre><code class="r">FOCUS_2006_L1 = data.frame( +FOCUS_2006_L1 = data.frame( t = rep(c(0, 1, 2, 3, 5, 7, 14, 21, 30), each = 2), parent = c(88.3, 91.4, 85.6, 84.5, 78.9, 77.6, 72.0, 71.9, 50.3, 59.4, 47.0, 45.1, @@ -242,17 +236,17 @@ given in the FOCUS report. </p> summary(m.L1.SFO) </code></pre> -<pre><code>## mkin version: 0.9.35 -## R version: 3.1.2 -## Date of fit: Sat Feb 21 14:44:53 2015 -## Date of summary: Sat Feb 21 14:44:53 2015 +<pre><code>## mkin version: 0.9.36 +## R version: 3.2.1 +## Date of fit: Sun Jun 21 01:47:59 2015 +## Date of summary: Sun Jun 21 01:47:59 2015 ## ## Equations: ## d_parent = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 37 model solutions performed in 0.098 s +## Fitted with method Port using 37 model solutions performed in 0.093 s ## ## Weighting: none ## @@ -269,13 +263,10 @@ summary(m.L1.SFO) ## Fixed parameter values: ## None ## -## Optimised, transformed parameters: -## Estimate Std. Error Lower Upper t value Pr(>|t|) -## parent_0 92.470 1.36800 89.570 95.370 67.58 4.339e-21 -## log_k_parent_sink -2.347 0.04057 -2.433 -2.261 -57.86 5.155e-20 -## Pr(>t) -## parent_0 2.170e-21 -## log_k_parent_sink 2.577e-20 +## Optimised, transformed parameters with symmetric confidence intervals: +## Estimate Std. Error Lower Upper +## parent_0 92.470 1.36800 89.570 95.370 +## log_k_parent_sink -2.347 0.04057 -2.433 -2.261 ## ## Parameter correlation: ## parent_0 log_k_parent_sink @@ -285,9 +276,12 @@ summary(m.L1.SFO) ## Residual standard error: 2.948 on 16 degrees of freedom ## ## Backtransformed parameters: -## Estimate Lower Upper -## parent_0 92.47000 89.57000 95.3700 -## k_parent_sink 0.09561 0.08773 0.1042 +## Confidence intervals for internally transformed parameters are asymmetric. +## t-test (unrealistically) based on the assumption of normal distribution +## for estimators of untransformed parameters. +## Estimate t value Pr(>t) Lower Upper +## parent_0 92.47000 67.58 2.170e-21 89.57000 95.3700 +## k_parent_sink 0.09561 24.65 1.867e-14 0.08773 0.1042 ## ## Chi2 error levels in percent: ## err.min n.optim df @@ -341,20 +335,31 @@ The residual plot can be easily obtained by</p> is checked.</p> <pre><code class="r">m.L1.FOMC <- mkinfit("FOMC", FOCUS_2006_L1_mkin, quiet=TRUE) -summary(m.L1.FOMC, data = FALSE) </code></pre> -<pre><code>## mkin version: 0.9.35 -## R version: 3.1.2 -## Date of fit: Sat Feb 21 14:44:55 2015 -## Date of summary: Sat Feb 21 14:44:55 2015 +<pre><code>## Warning in mkinfit("FOMC", FOCUS_2006_L1_mkin, quiet = TRUE): Optimisation by method Port did not converge. +## Convergence code is 1 +</code></pre> + +<pre><code class="r">summary(m.L1.FOMC, data = FALSE) +</code></pre> + +<pre><code>## mkin version: 0.9.36 +## R version: 3.2.1 +## Date of fit: Sun Jun 21 01:48:00 2015 +## Date of summary: Sun Jun 21 01:48:00 2015 +## +## +## Warning: Optimisation by method Port did not converge. +## Convergence code is 1 +## ## ## Equations: -## d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent +## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 611 model solutions performed in 1.509 s +## Fitted with method Port using 188 model solutions performed in 0.463 s ## ## Weighting: none ## @@ -373,29 +378,28 @@ summary(m.L1.FOMC, data = FALSE) ## Fixed parameter values: ## None ## -## Optimised, transformed parameters: -## Estimate Std. Error Lower Upper t value Pr(>|t|) -## parent_0 92.47 1.482 89.31 95.63 62.39000 1.546e-19 -## log_alpha 11.25 598.200 -1264.00 1286.00 0.01880 9.852e-01 -## log_beta 13.60 598.200 -1261.00 1289.00 0.02273 9.822e-01 -## Pr(>t) -## parent_0 7.730e-20 -## log_alpha 4.926e-01 -## log_beta 4.911e-01 +## Optimised, transformed parameters with symmetric confidence intervals: +## Estimate Std. Error Lower Upper +## parent_0 92.47 1.422 89.44 95.50 +## log_alpha 15.43 15.080 -16.71 47.58 +## log_beta 17.78 15.090 -14.37 49.93 ## ## Parameter correlation: ## parent_0 log_alpha log_beta -## parent_0 1.0000 -0.3016 -0.3016 -## log_alpha -0.3016 1.0000 1.0000 -## log_beta -0.3016 1.0000 1.0000 +## parent_0 1.0000 0.1129 0.1112 +## log_alpha 0.1129 1.0000 1.0000 +## log_beta 0.1112 1.0000 1.0000 ## ## Residual standard error: 3.045 on 15 degrees of freedom ## ## Backtransformed parameters: -## Estimate Lower Upper -## parent_0 92.47 89.31 95.63 -## alpha 76830.00 0.00 Inf -## beta 803500.00 0.00 Inf +## Confidence intervals for internally transformed parameters are asymmetric. +## t-test (unrealistically) based on the assumption of normal distribution +## for estimators of untransformed parameters. +## Estimate t value Pr(>t) Lower Upper +## parent_0 9.247e+01 65.150 4.044e-20 8.944e+01 9.550e+01 +## alpha 5.044e+06 1.271 1.115e-01 5.510e-08 4.618e+20 +## beta 5.276e+07 1.259 1.137e-01 5.732e-07 4.857e+21 ## ## Chi2 error levels in percent: ## err.min n.optim df @@ -403,8 +407,8 @@ summary(m.L1.FOMC, data = FALSE) ## parent 3.619 3 6 ## ## Estimated disappearance times: -## DT50 DT90 DT50back -## parent 7.249 24.08 7.249 +## DT50 DT90 DT50back +## parent 7.25 24.08 7.25 </code></pre> <p>Due to the higher number of parameters, and the lower number of degrees of @@ -442,17 +446,17 @@ FOCUS_2006_L2_mkin <- mkin_wide_to_long(FOCUS_2006_L2) summary(m.L2.SFO) </code></pre> -<pre><code>## mkin version: 0.9.35 -## R version: 3.1.2 -## Date of fit: Sat Feb 21 14:44:55 2015 -## Date of summary: Sat Feb 21 14:44:55 2015 +<pre><code>## mkin version: 0.9.36 +## R version: 3.2.1 +## Date of fit: Sun Jun 21 01:48:00 2015 +## Date of summary: Sun Jun 21 01:48:00 2015 ## ## Equations: ## d_parent = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 41 model solutions performed in 0.1 s +## Fitted with method Port using 41 model solutions performed in 0.097 s ## ## Weighting: none ## @@ -469,13 +473,10 @@ summary(m.L2.SFO) ## Fixed parameter values: ## None ## -## Optimised, transformed parameters: -## Estimate Std. Error Lower Upper t value Pr(>|t|) -## parent_0 91.4700 3.8070 82.9800 99.9500 24.030 3.545e-10 -## log_k_parent_sink -0.4112 0.1074 -0.6505 -0.1719 -3.828 3.329e-03 -## Pr(>t) -## parent_0 1.773e-10 -## log_k_parent_sink 1.664e-03 +## Optimised, transformed parameters with symmetric confidence intervals: +## Estimate Std. Error Lower Upper +## parent_0 91.4700 3.8070 82.9800 99.9500 +## log_k_parent_sink -0.4112 0.1074 -0.6505 -0.1719 ## ## Parameter correlation: ## parent_0 log_k_parent_sink @@ -485,9 +486,12 @@ summary(m.L2.SFO) ## Residual standard error: 5.51 on 10 degrees of freedom ## ## Backtransformed parameters: -## Estimate Lower Upper -## parent_0 91.4700 82.9800 99.9500 -## k_parent_sink 0.6629 0.5218 0.8421 +## Confidence intervals for internally transformed parameters are asymmetric. +## t-test (unrealistically) based on the assumption of normal distribution +## for estimators of untransformed parameters. +## Estimate t value Pr(>t) Lower Upper +## parent_0 91.4700 24.03 1.773e-10 82.9800 99.9500 +## k_parent_sink 0.6629 9.31 1.525e-06 0.5218 0.8421 ## ## Chi2 error levels in percent: ## err.min n.optim df @@ -552,17 +556,17 @@ mkinresplot(m.L2.FOMC) <pre><code class="r">summary(m.L2.FOMC, data = FALSE) </code></pre> -<pre><code>## mkin version: 0.9.35 -## R version: 3.1.2 -## Date of fit: Sat Feb 21 14:44:55 2015 -## Date of summary: Sat Feb 21 14:44:55 2015 +<pre><code>## mkin version: 0.9.36 +## R version: 3.2.1 +## Date of fit: Sun Jun 21 01:48:00 2015 +## Date of summary: Sun Jun 21 01:48:00 2015 ## ## Equations: -## d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent +## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 81 model solutions performed in 0.201 s +## Fitted with method Port using 81 model solutions performed in 0.191 s ## ## Weighting: none ## @@ -581,11 +585,11 @@ mkinresplot(m.L2.FOMC) ## Fixed parameter values: ## None ## -## Optimised, transformed parameters: -## Estimate Std. Error Lower Upper t value Pr(>|t|) Pr(>t) -## parent_0 93.7700 1.8560 89.5700 97.9700 50.5100 2.345e-12 1.173e-12 -## log_alpha 0.3180 0.1867 -0.1044 0.7405 1.7030 1.227e-01 6.137e-02 -## log_beta 0.2102 0.2943 -0.4555 0.8759 0.7142 4.932e-01 2.466e-01 +## Optimised, transformed parameters with symmetric confidence intervals: +## Estimate Std. Error Lower Upper +## parent_0 93.7700 1.8560 89.5700 97.9700 +## log_alpha 0.3180 0.1867 -0.1044 0.7405 +## log_beta 0.2102 0.2943 -0.4555 0.8759 ## ## Parameter correlation: ## parent_0 log_alpha log_beta @@ -596,10 +600,13 @@ mkinresplot(m.L2.FOMC) ## Residual standard error: 2.628 on 9 degrees of freedom ## ## Backtransformed parameters: -## Estimate Lower Upper -## parent_0 93.770 89.5700 97.970 -## alpha 1.374 0.9009 2.097 -## beta 1.234 0.6341 2.401 +## Confidence intervals for internally transformed parameters are asymmetric. +## t-test (unrealistically) based on the assumption of normal distribution +## for estimators of untransformed parameters. +## Estimate t value Pr(>t) Lower Upper +## parent_0 93.770 50.510 1.173e-12 89.5700 97.970 +## alpha 1.374 5.355 2.296e-04 0.9009 2.097 +## beta 1.234 3.398 3.949e-03 0.6341 2.401 ## ## Chi2 error levels in percent: ## err.min n.optim df @@ -638,10 +645,10 @@ plot(m.L2.DFOP) <pre><code class="r">summary(m.L2.DFOP, data = FALSE) </code></pre> -<pre><code>## mkin version: 0.9.35 -## R version: 3.1.2 -## Date of fit: Sat Feb 21 14:44:57 2015 -## Date of summary: Sat Feb 21 14:44:57 2015 +<pre><code>## mkin version: 0.9.36 +## R version: 3.2.1 +## Date of fit: Sun Jun 21 01:48:02 2015 +## Date of summary: Sun Jun 21 01:48:02 2015 ## ## Equations: ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -650,7 +657,7 @@ plot(m.L2.DFOP) ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 336 model solutions performed in 0.856 s +## Fitted with method Port using 336 model solutions performed in 0.835 s ## ## Weighting: none ## @@ -671,12 +678,12 @@ plot(m.L2.DFOP) ## Fixed parameter values: ## None ## -## Optimised, transformed parameters: -## Estimate Std. Error Lower Upper t value Pr(>|t|) Pr(>t) -## parent_0 93.9500 NA NA NA NA NA NA -## log_k1 3.1210 NA NA NA NA NA NA -## log_k2 -1.0880 NA NA NA NA NA NA -## g_ilr -0.2821 NA NA NA NA NA NA +## Optimised, transformed parameters with symmetric confidence intervals: +## Estimate Std. Error Lower Upper +## parent_0 93.9500 NA NA NA +## log_k1 3.1210 NA NA NA +## log_k2 -1.0880 NA NA NA +## g_ilr -0.2821 NA NA NA ## ## Parameter correlation: ## Could not estimate covariance matrix; singular system: @@ -684,11 +691,14 @@ plot(m.L2.DFOP) ## Residual standard error: 1.732 on 8 degrees of freedom ## ## Backtransformed parameters: -## Estimate Lower Upper -## parent_0 93.9500 NA NA -## k1 22.6700 NA NA -## k2 0.3369 NA NA -## g 0.4016 NA NA +## Confidence intervals for internally transformed parameters are asymmetric. +## t-test (unrealistically) based on the assumption of normal distribution +## for estimators of untransformed parameters. +## Estimate t value Pr(>t) Lower Upper +## parent_0 93.9500 NA NA NA NA +## k1 22.6700 NA NA NA NA +## k2 0.3369 NA NA NA NA +## g 0.4016 NA NA NA NA ## ## Chi2 error levels in percent: ## err.min n.optim df @@ -727,17 +737,17 @@ plot(m.L3.SFO) <pre><code class="r">summary(m.L3.SFO) </code></pre> -<pre><code>## mkin version: 0.9.35 -## R version: 3.1.2 -## Date of fit: Sat Feb 21 14:44:57 2015 -## Date of summary: Sat Feb 21 14:44:57 2015 +<pre><code>## mkin version: 0.9.36 +## R version: 3.2.1 +## Date of fit: Sun Jun 21 01:48:03 2015 +## Date of summary: Sun Jun 21 01:48:03 2015 ## ## Equations: ## d_parent = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 43 model solutions performed in 0.109 s +## Fitted with method Port using 43 model solutions performed in 0.104 s ## ## Weighting: none ## @@ -754,13 +764,10 @@ plot(m.L3.SFO) ## Fixed parameter values: ## None ## -## Optimised, transformed parameters: -## Estimate Std. Error Lower Upper t value Pr(>|t|) -## parent_0 74.870 8.4570 54.180 95.57 8.853 1.155e-04 -## log_k_parent_sink -3.678 0.3261 -4.476 -2.88 -11.280 2.903e-05 -## Pr(>t) -## parent_0 5.776e-05 -## log_k_parent_sink 1.451e-05 +## Optimised, transformed parameters with symmetric confidence intervals: +## Estimate Std. Error Lower Upper +## parent_0 74.870 8.4570 54.180 95.57 +## log_k_parent_sink -3.678 0.3261 -4.476 -2.88 ## ## Parameter correlation: ## parent_0 log_k_parent_sink @@ -770,9 +777,12 @@ plot(m.L3.SFO) ## Residual standard error: 12.91 on 6 degrees of freedom ## ## Backtransformed parameters: -## Estimate Lower Upper -## parent_0 74.87000 54.18000 95.57000 -## k_parent_sink 0.02527 0.01138 0.05612 +## Confidence intervals for internally transformed parameters are asymmetric. +## t-test (unrealistically) based on the assumption of normal distribution +## for estimators of untransformed parameters. +## Estimate t value Pr(>t) Lower Upper +## parent_0 74.87000 8.853 5.776e-05 54.18000 95.57000 +## k_parent_sink 0.02527 3.067 1.102e-02 0.01138 0.05612 ## ## Chi2 error levels in percent: ## err.min n.optim df @@ -813,17 +823,17 @@ plot(m.L3.FOMC) <pre><code class="r">summary(m.L3.FOMC, data = FALSE) </code></pre> -<pre><code>## mkin version: 0.9.35 -## R version: 3.1.2 -## Date of fit: Sat Feb 21 14:44:58 2015 -## Date of summary: Sat Feb 21 14:44:58 2015 +<pre><code>## mkin version: 0.9.36 +## R version: 3.2.1 +## Date of fit: Sun Jun 21 01:48:03 2015 +## Date of summary: Sun Jun 21 01:48:03 2015 ## ## Equations: -## d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent +## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 83 model solutions performed in 0.203 s +## Fitted with method Port using 83 model solutions performed in 0.196 s ## ## Weighting: none ## @@ -842,11 +852,11 @@ plot(m.L3.FOMC) ## Fixed parameter values: ## None ## -## Optimised, transformed parameters: -## Estimate Std. Error Lower Upper t value Pr(>|t|) Pr(>t) -## parent_0 96.9700 4.5500 85.2800 108.7000 21.310 4.216e-06 2.108e-06 -## log_alpha -0.8619 0.1704 -1.3000 -0.4238 -5.057 3.911e-03 1.955e-03 -## log_beta 0.6193 0.4744 -0.6003 1.8390 1.305 2.486e-01 1.243e-01 +## Optimised, transformed parameters with symmetric confidence intervals: +## Estimate Std. Error Lower Upper +## parent_0 96.9700 4.5500 85.2800 108.7000 +## log_alpha -0.8619 0.1704 -1.3000 -0.4238 +## log_beta 0.6193 0.4744 -0.6003 1.8390 ## ## Parameter correlation: ## parent_0 log_alpha log_beta @@ -857,10 +867,13 @@ plot(m.L3.FOMC) ## Residual standard error: 4.572 on 5 degrees of freedom ## ## Backtransformed parameters: -## Estimate Lower Upper -## parent_0 96.9700 85.2800 108.7000 -## alpha 0.4224 0.2725 0.6546 -## beta 1.8580 0.5487 6.2890 +## Confidence intervals for internally transformed parameters are asymmetric. +## t-test (unrealistically) based on the assumption of normal distribution +## for estimators of untransformed parameters. +## Estimate t value Pr(>t) Lower Upper +## parent_0 96.9700 21.310 2.108e-06 85.2800 108.7000 +## alpha 0.4224 5.867 1.020e-03 0.2725 0.6546 +## beta 1.8580 2.108 4.444e-02 0.5487 6.2890 ## ## Chi2 error levels in percent: ## err.min n.optim df @@ -886,10 +899,10 @@ plot(m.L3.DFOP) <pre><code class="r">summary(m.L3.DFOP, data = FALSE) </code></pre> -<pre><code>## mkin version: 0.9.35 -## R version: 3.1.2 -## Date of fit: Sat Feb 21 14:44:58 2015 -## Date of summary: Sat Feb 21 14:44:58 2015 +<pre><code>## mkin version: 0.9.36 +## R version: 3.2.1 +## Date of fit: Sun Jun 21 01:48:03 2015 +## Date of summary: Sun Jun 21 01:48:03 2015 ## ## Equations: ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -898,7 +911,7 @@ plot(m.L3.DFOP) ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 137 model solutions performed in 0.346 s +## Fitted with method Port using 137 model solutions performed in 0.35 s ## ## Weighting: none ## @@ -919,12 +932,12 @@ plot(m.L3.DFOP) ## Fixed parameter values: ## None ## -## Optimised, transformed parameters: -## Estimate Std. Error Lower Upper t value Pr(>|t|) Pr(>t) -## parent_0 97.7500 1.43800 93.7500 101.70000 67.970 2.808e-07 1.404e-07 -## log_k1 -0.6612 0.13340 -1.0310 -0.29100 -4.958 7.715e-03 3.858e-03 -## log_k2 -4.2860 0.05902 -4.4500 -4.12200 -72.620 2.155e-07 1.077e-07 -## g_ilr -0.1229 0.05121 -0.2651 0.01925 -2.401 7.431e-02 3.716e-02 +## Optimised, transformed parameters with symmetric confidence intervals: +## Estimate Std. Error Lower Upper +## parent_0 97.7500 1.43800 93.7500 101.70000 +## log_k1 -0.6612 0.13340 -1.0310 -0.29100 +## log_k2 -4.2860 0.05902 -4.4500 -4.12200 +## g_ilr -0.1229 0.05121 -0.2651 0.01925 ## ## Parameter correlation: ## parent_0 log_k1 log_k2 g_ilr @@ -936,11 +949,14 @@ plot(m.L3.DFOP) ## Residual standard error: 1.439 on 4 degrees of freedom ## ## Backtransformed parameters: -## Estimate Lower Upper -## parent_0 97.75000 93.75000 101.70000 -## k1 0.51620 0.35650 0.74750 -## k2 0.01376 0.01168 0.01621 -## g 0.45660 0.40730 0.50680 +## Confidence intervals for internally transformed parameters are asymmetric. +## t-test (unrealistically) based on the assumption of normal distribution +## for estimators of untransformed parameters. +## Estimate t value Pr(>t) Lower Upper +## parent_0 97.75000 67.970 1.404e-07 93.75000 101.70000 +## k1 0.51620 7.499 8.460e-04 0.35650 0.74750 +## k2 0.01376 16.940 3.557e-05 0.01168 0.01621 +## g 0.45660 25.410 7.121e-06 0.40730 0.50680 ## ## Chi2 error levels in percent: ## err.min n.optim df @@ -984,17 +1000,17 @@ plot(m.L4.SFO) <pre><code class="r">summary(m.L4.SFO, data = FALSE) </code></pre> -<pre><code>## mkin version: 0.9.35 -## R version: 3.1.2 -## Date of fit: Sat Feb 21 14:44:58 2015 -## Date of summary: Sat Feb 21 14:44:58 2015 +<pre><code>## mkin version: 0.9.36 +## R version: 3.2.1 +## Date of fit: Sun Jun 21 01:48:04 2015 +## Date of summary: Sun Jun 21 01:48:04 2015 ## ## Equations: ## d_parent = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 46 model solutions performed in 0.109 s +## Fitted with method Port using 46 model solutions performed in 0.105 s ## ## Weighting: none ## @@ -1011,13 +1027,10 @@ plot(m.L4.SFO) ## Fixed parameter values: ## None ## -## Optimised, transformed parameters: -## Estimate Std. Error Lower Upper t value Pr(>|t|) -## parent_0 96.44 1.94900 91.670 101.200 49.49 4.566e-09 -## log_k_parent_sink -5.03 0.07999 -5.225 -4.834 -62.88 1.088e-09 -## Pr(>t) -## parent_0 2.283e-09 -## log_k_parent_sink 5.438e-10 +## Optimised, transformed parameters with symmetric confidence intervals: +## Estimate Std. Error Lower Upper +## parent_0 96.44 1.94900 91.670 101.200 +## log_k_parent_sink -5.03 0.07999 -5.225 -4.834 ## ## Parameter correlation: ## parent_0 log_k_parent_sink @@ -1027,9 +1040,12 @@ plot(m.L4.SFO) ## Residual standard error: 3.651 on 6 degrees of freedom ## ## Backtransformed parameters: -## Estimate Lower Upper -## parent_0 96.440000 91.670000 1.012e+02 -## k_parent_sink 0.006541 0.005378 7.955e-03 +## Confidence intervals for internally transformed parameters are asymmetric. +## t-test (unrealistically) based on the assumption of normal distribution +## for estimators of untransformed parameters. +## Estimate t value Pr(>t) Lower Upper +## parent_0 96.440000 49.49 2.283e-09 91.670000 1.012e+02 +## k_parent_sink 0.006541 12.50 8.008e-06 0.005378 7.955e-03 ## ## Chi2 error levels in percent: ## err.min n.optim df @@ -1059,17 +1075,17 @@ plot(m.L4.FOMC) <pre><code class="r">summary(m.L4.FOMC, data = FALSE) </code></pre> -<pre><code>## mkin version: 0.9.35 -## R version: 3.1.2 -## Date of fit: Sat Feb 21 14:44:58 2015 -## Date of summary: Sat Feb 21 14:44:58 2015 +<pre><code>## mkin version: 0.9.36 +## R version: 3.2.1 +## Date of fit: Sun Jun 21 01:48:04 2015 +## Date of summary: Sun Jun 21 01:48:04 2015 ## ## Equations: -## d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent +## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 66 model solutions performed in 0.161 s +## Fitted with method Port using 66 model solutions performed in 0.159 s ## ## Weighting: none ## @@ -1088,11 +1104,11 @@ plot(m.L4.FOMC) ## Fixed parameter values: ## None ## -## Optimised, transformed parameters: -## Estimate Std. Error Lower Upper t value Pr(>|t|) Pr(>t) -## parent_0 99.1400 1.6800 94.820 103.5000 59.0200 2.643e-08 1.322e-08 -## log_alpha -0.3506 0.3725 -1.308 0.6068 -0.9414 3.897e-01 1.949e-01 -## log_beta 4.1740 0.5635 2.726 5.6230 7.4070 7.059e-04 3.530e-04 +## Optimised, transformed parameters with symmetric confidence intervals: +## Estimate Std. Error Lower Upper +## parent_0 99.1400 1.6800 94.820 103.5000 +## log_alpha -0.3506 0.3725 -1.308 0.6068 +## log_beta 4.1740 0.5635 2.726 5.6230 ## ## Parameter correlation: ## parent_0 log_alpha log_beta @@ -1103,10 +1119,13 @@ plot(m.L4.FOMC) ## Residual standard error: 2.315 on 5 degrees of freedom ## ## Backtransformed parameters: -## Estimate Lower Upper -## parent_0 99.1400 94.8200 103.500 -## alpha 0.7042 0.2703 1.835 -## beta 64.9800 15.2600 276.600 +## Confidence intervals for internally transformed parameters are asymmetric. +## t-test (unrealistically) based on the assumption of normal distribution +## for estimators of untransformed parameters. +## Estimate t value Pr(>t) Lower Upper +## parent_0 99.1400 59.020 1.322e-08 94.8200 103.500 +## alpha 0.7042 2.685 2.178e-02 0.2703 1.835 +## beta 64.9800 1.775 6.807e-02 15.2600 276.600 ## ## Chi2 error levels in percent: ## err.min n.optim df diff --git a/vignettes/FOCUS_Z.Rnw b/vignettes/FOCUS_Z.Rnw index 5e2e0251..1df0ee9c 100644 --- a/vignettes/FOCUS_Z.Rnw +++ b/vignettes/FOCUS_Z.Rnw @@ -265,11 +265,13 @@ summary(m.Z.mkin.5a, data = FALSE)$bpar @ A graphical representation of the confidence intervals can finally be obtained. + <<FOCUS_2006_Z_fits_11b, echo=TRUE>>= mkinparplot(m.Z.mkin.5a) @ The endpoints obtained with this model are + <<FOCUS_2006_Z_fits_11b_endpoints, echo=TRUE>>= endpoints(m.Z.mkin.5a) @ diff --git a/vignettes/FOCUS_Z.pdf b/vignettes/FOCUS_Z.pdf Binary files differindex 3174a23a..36f3dc14 100644 --- a/vignettes/FOCUS_Z.pdf +++ b/vignettes/FOCUS_Z.pdf diff --git a/vignettes/compiled_models.html b/vignettes/compiled_models.html index 2f2a6edb..e6f21b09 100644 --- a/vignettes/compiled_models.html +++ b/vignettes/compiled_models.html @@ -77,7 +77,7 @@ img { --> <div id="benchmark-for-a-model-that-can-also-be-solved-with-eigenvalues" class="section level1"> <h1>Benchmark for a model that can also be solved with Eigenvalues</h1> -<p>This evaluation is taken from the example section of mkinfit. When using an mkin version greater than 0.9-36 and the ccSolve package is installed and functional, you will get a message that the model is being compiled when defining a model using mkinmod.</p> +<p>This evaluation is taken from the example section of mkinfit. When using an mkin version equal to or greater than 0.9-36 and a compiler (gcc) is installed, you will see a message that the model is being compiled from autogenerated C code when defining a model using mkinmod.</p> <pre class="r"><code>library("mkin") SFO_SFO <- mkinmod( parent = list(type = "SFO", to = "m1", sink = TRUE), @@ -94,20 +94,20 @@ mb.1 <- microbenchmark( smb.1 <- summary(mb.1)[-1] rownames(smb.1) <- c("deSolve, not compiled", "Eigenvalue based", "deSolve, compiled") print(smb.1)</code></pre> -<pre><code>## min lq mean median uq -## deSolve, not compiled 6192.0125 6195.3470 6211.0309 6198.6816 6220.5401 -## Eigenvalue based 956.7604 1008.7224 1026.2572 1060.6844 1061.0055 -## deSolve, compiled 869.6880 871.9315 883.4929 874.1751 890.3953 +<pre><code>## min lq mean median uq +## deSolve, not compiled 4969.585 5033.7311 5092.7389 5097.8773 5154.3160 +## Eigenvalue based 868.731 891.7239 909.6449 914.7169 930.1018 +## deSolve, compiled 4935.049 4935.4796 4968.2150 4935.9097 4984.7978 ## max neval -## deSolve, not compiled 6242.3986 3 -## Eigenvalue based 1061.3266 3 -## deSolve, compiled 906.6155 3</code></pre> +## deSolve, not compiled 5210.7547 3 +## Eigenvalue based 945.4867 3 +## deSolve, compiled 5033.6858 3</code></pre> <p>We see that using the compiled model is almost a factor of 8 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> <pre class="r"><code>smb.1["median"]/smb.1["deSolve, compiled", "median"]</code></pre> -<pre><code>## median -## deSolve, not compiled 7.120877 -## Eigenvalue based 1.205328 -## deSolve, compiled 1.000000</code></pre> +<pre><code>## median +## deSolve, not compiled 1.0328141 +## Eigenvalue based 0.1853188 +## deSolve, compiled 1.0000000</code></pre> </div> <div id="benchmark-for-a-model-that-can-not-be-solved-with-eigenvalues" class="section level1"> <h1>Benchmark for a model that can not be solved with Eigenvalues</h1> @@ -124,16 +124,16 @@ smb.2 <- summary(mb.2)[-1] rownames(smb.2) <- c("deSolve, not compiled", "deSolve, compiled") print(smb.2)</code></pre> <pre><code>## min lq mean median uq -## deSolve, not compiled 13.297283 13.427702 13.481155 13.558121 13.573092 -## deSolve, compiled 1.486926 1.526887 1.546851 1.566848 1.576813 -## max neval -## deSolve, not compiled 13.588063 3 -## deSolve, compiled 1.586778 3</code></pre> +## deSolve, not compiled 11.745276 11.754288 11.820726 11.763300 11.858451 +## deSolve, compiled 1.385829 1.386407 1.400841 1.386985 1.408347 +## max neval +## deSolve, not compiled 11.95360 3 +## deSolve, compiled 1.42971 3</code></pre> <pre class="r"><code>smb.2["median"]/smb.2["deSolve, compiled", "median"]</code></pre> -<pre><code>## median -## deSolve, not compiled 8.653119 -## deSolve, compiled 1.000000</code></pre> -<p>Here we get a performance benefit of more than a factor of 8 using the version of the differential equation model compiled from C code using the ccSolve package!</p> +<pre><code>## median +## deSolve, not compiled 8.4812 +## deSolve, compiled 1.0000</code></pre> +<p>Here we get a performance benefit of more than a factor of 10 using the version of the differential equation model compiled from C code using the inline package!</p> </div> diff --git a/vignettes/mkin.pdf b/vignettes/mkin.pdf Binary files differindex 8f1e0884..5786c5bf 100644 --- a/vignettes/mkin.pdf +++ b/vignettes/mkin.pdf |