From bc3825ae2d12c18ea3d3caf17eb23c93fef180b8 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 8 Oct 2020 09:31:35 +0200 Subject: Fix issues for release --- vignettes/FOCUS_L.html | 154 ++++++++++++++++++++++++------------------------- 1 file changed, 77 insertions(+), 77 deletions(-) (limited to 'vignettes/FOCUS_L.html') diff --git a/vignettes/FOCUS_L.html b/vignettes/FOCUS_L.html index 7573ef58..c7722f37 100644 --- a/vignettes/FOCUS_L.html +++ b/vignettes/FOCUS_L.html @@ -11,7 +11,7 @@ - + Example evaluation of FOCUS Laboratory Data L1 to L3 @@ -1518,7 +1518,7 @@ div.tocify {

Example evaluation of FOCUS Laboratory Data L1 to L3

Johannes Ranke

-

2020-05-26

+

2020-10-08

@@ -1538,30 +1538,30 @@ FOCUS_2006_L1_mkin <- mkin_wide_to_long(FOCUS_2006_L1) 
m.L1.SFO <- mkinfit("SFO", FOCUS_2006_L1_mkin, quiet = TRUE)
 summary(m.L1.SFO)
## mkin version used for fitting:    0.9.50.3 
-## R version used for fitting:       4.0.0 
-## Date of fit:     Tue May 26 17:01:08 2020 
-## Date of summary: Tue May 26 17:01:08 2020 
+## R version used for fitting:       4.0.2 
+## Date of fit:     Thu Oct  8 09:06:20 2020 
+## Date of summary: Thu Oct  8 09:06:20 2020 
 ## 
 ## Equations:
-## d_parent/dt = - k_parent_sink * parent
+## d_parent/dt = - k_parent * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 133 model solutions performed in 0.031 s
+## Fitted using 133 model solutions performed in 0.032 s
 ## 
 ## Error model: Constant variance 
 ## 
 ## Error model algorithm: OLS 
 ## 
 ## Starting values for parameters to be optimised:
-##               value   type
-## parent_0      89.85  state
-## k_parent_sink  0.10 deparm
+##          value   type
+## parent_0 89.85  state
+## k_parent  0.10 deparm
 ## 
 ## Starting values for the transformed parameters actually optimised:
-##                       value lower upper
-## parent_0          89.850000  -Inf   Inf
-## log_k_parent_sink -2.302585  -Inf   Inf
+##                  value lower upper
+## parent_0     89.850000  -Inf   Inf
+## log_k_parent -2.302585  -Inf   Inf
 ## 
 ## Fixed parameter values:
 ## None
@@ -1572,25 +1572,25 @@ summary(m.L1.SFO)
## 93.88778 96.5589 -43.94389 ## ## Optimised, transformed parameters with symmetric confidence intervals: -## Estimate Std. Error Lower Upper -## parent_0 92.470 1.28200 89.740 95.200 -## log_k_parent_sink -2.347 0.03763 -2.428 -2.267 -## sigma 2.780 0.46330 1.792 3.767 +## Estimate Std. Error Lower Upper +## parent_0 92.470 1.28200 89.740 95.200 +## log_k_parent -2.347 0.03763 -2.428 -2.267 +## sigma 2.780 0.46330 1.792 3.767 ## ## Parameter correlation: -## parent_0 log_k_parent_sink sigma -## parent_0 1.000e+00 6.186e-01 -1.516e-09 -## log_k_parent_sink 6.186e-01 1.000e+00 -3.124e-09 -## sigma -1.516e-09 -3.124e-09 1.000e+00 +## parent_0 log_k_parent sigma +## parent_0 1.000e+00 6.186e-01 -1.516e-09 +## log_k_parent 6.186e-01 1.000e+00 -3.124e-09 +## sigma -1.516e-09 -3.124e-09 1.000e+00 ## ## Backtransformed parameters: ## 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 72.13 8.824e-21 89.74000 95.2000 -## 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 +## Estimate t value Pr(>t) Lower Upper +## parent_0 92.47000 72.13 8.824e-21 89.74000 95.2000 +## k_parent 0.09561 26.57 2.487e-14 0.08824 0.1036 +## sigma 2.78000 6.00 1.216e-05 1.79200 3.7670 ## ## FOCUS Chi2 error levels in percent: ## err.min n.optim df @@ -1639,21 +1639,16 @@ summary(m.L1.SFO) 
## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is
 ## doubtful
## mkin version used for fitting:    0.9.50.3 
-## R version used for fitting:       4.0.0 
-## Date of fit:     Tue May 26 17:01:09 2020 
-## Date of summary: Tue May 26 17:01:09 2020 
-## 
-## 
-## Warning: Optimisation did not converge:
-## false convergence (8) 
-## 
+## R version used for fitting:       4.0.2 
+## Date of fit:     Thu Oct  8 09:06:21 2020 
+## Date of summary: Thu Oct  8 09:06:21 2020 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 380 model solutions performed in 0.08 s
+## Fitted using 380 model solutions performed in 0.088 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -1674,6 +1669,11 @@ summary(m.L1.SFO)
## Fixed parameter values: ## None ## +## +## Warning(s): +## Optimisation did not converge: +## false convergence (8) +## ## Results: ## ## AIC BIC logLik @@ -1744,16 +1744,16 @@ plot(m.L2.FOMC, show_residuals = TRUE, 

summary(m.L2.FOMC, data = FALSE)
## mkin version used for fitting:    0.9.50.3 
-## R version used for fitting:       4.0.0 
-## Date of fit:     Tue May 26 17:01:09 2020 
-## Date of summary: Tue May 26 17:01:09 2020 
+## R version used for fitting:       4.0.2 
+## Date of fit:     Thu Oct  8 09:06:21 2020 
+## Date of summary: Thu Oct  8 09:06:21 2020 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 239 model solutions performed in 0.047 s
+## Fitted using 239 model solutions performed in 0.05 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -1822,9 +1822,9 @@ plot(m.L2.DFOP, show_residuals = TRUE, show_errmin = TRUE,
 

 
summary(m.L2.DFOP, data = FALSE)

 
## mkin version used for fitting:    0.9.50.3 
-## R version used for fitting:       4.0.0 
-## Date of fit:     Tue May 26 17:01:09 2020 
-## Date of summary: Tue May 26 17:01:09 2020 
+## R version used for fitting:       4.0.2 
+## Date of fit:     Thu Oct  8 09:06:21 2020 
+## Date of summary: Thu Oct  8 09:06:21 2020 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -1833,7 +1833,7 @@ plot(m.L2.DFOP, show_residuals = TRUE, show_errmin = TRUE,
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 572 model solutions performed in 0.13 s
+## Fitted using 572 model solutions performed in 0.136 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -1894,8 +1894,8 @@ plot(m.L2.DFOP, show_residuals = TRUE, show_errmin = TRUE,
 ## parent      2.53       4  2
 ## 
 ## Estimated disappearance times:
-##          DT50  DT90 DT50_k1 DT50_k2
-## parent 0.5335 5.311 0.03009   2.058

+##          DT50  DT90 DT50back DT50_k1 DT50_k2
+## parent 0.5335 5.311    1.599 0.03009   2.058

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.

@@ -1922,9 +1922,9 @@ plot(mm.L3)

We can extract the summary and plot for e.g. the DFOP fit, using square brackets for indexing which will result in the use of the summary and plot functions working on mkinfit objects.

summary(mm.L3[["DFOP", 1]])
## mkin version used for fitting:    0.9.50.3 
-## R version used for fitting:       4.0.0 
-## Date of fit:     Tue May 26 17:01:10 2020 
-## Date of summary: Tue May 26 17:01:10 2020 
+## R version used for fitting:       4.0.2 
+## Date of fit:     Thu Oct  8 09:06:22 2020 
+## Date of summary: Thu Oct  8 09:06:22 2020 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -1933,7 +1933,7 @@ plot(mm.L3)
## ## Model predictions using solution type analytical ## -## Fitted using 373 model solutions performed in 0.083 s +## Fitted using 373 model solutions performed in 0.085 s ## ## Error model: Constant variance ## @@ -1994,8 +1994,8 @@ plot(mm.L3) ## parent 2.225 4 4 ## ## Estimated disappearance times: -## DT50 DT90 DT50_k1 DT50_k2 -## parent 7.464 123 1.343 50.37 +## DT50 DT90 DT50back DT50_k1 DT50_k2 +## parent 7.464 123 37.03 1.343 50.37 ## ## Data: ## time variable observed predicted residual @@ -2030,30 +2030,30 @@ plot(mm.L4)

The χ2 error level of 3.3% as well as the plot suggest that the SFO model fits very well. The error level at which the χ2 test passes is slightly lower for the FOMC model. However, the difference appears negligible.

summary(mm.L4[["SFO", 1]], data = FALSE)
## mkin version used for fitting:    0.9.50.3 
-## R version used for fitting:       4.0.0 
-## Date of fit:     Tue May 26 17:01:10 2020 
-## Date of summary: Tue May 26 17:01:10 2020 
+## R version used for fitting:       4.0.2 
+## Date of fit:     Thu Oct  8 09:06:22 2020 
+## Date of summary: Thu Oct  8 09:06:22 2020 
 ## 
 ## Equations:
-## d_parent/dt = - k_parent_sink * parent
+## d_parent/dt = - k_parent * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 142 model solutions performed in 0.029 s
+## Fitted using 142 model solutions performed in 0.03 s
 ## 
 ## Error model: Constant variance 
 ## 
 ## Error model algorithm: OLS 
 ## 
 ## Starting values for parameters to be optimised:
-##               value   type
-## parent_0       96.6  state
-## k_parent_sink   0.1 deparm
+##          value   type
+## parent_0  96.6  state
+## k_parent   0.1 deparm
 ## 
 ## Starting values for the transformed parameters actually optimised:
-##                       value lower upper
-## parent_0          96.600000  -Inf   Inf
-## log_k_parent_sink -2.302585  -Inf   Inf
+##                  value lower upper
+## parent_0     96.600000  -Inf   Inf
+## log_k_parent -2.302585  -Inf   Inf
 ## 
 ## Fixed parameter values:
 ## None
@@ -2064,25 +2064,25 @@ plot(mm.L4)
## 47.12133 47.35966 -20.56067 ## ## Optimised, transformed parameters with symmetric confidence intervals: -## Estimate Std. Error Lower Upper -## parent_0 96.440 1.69900 92.070 100.800 -## log_k_parent_sink -5.030 0.07059 -5.211 -4.848 -## sigma 3.162 0.79050 1.130 5.194 +## Estimate Std. Error Lower Upper +## parent_0 96.440 1.69900 92.070 100.800 +## log_k_parent -5.030 0.07059 -5.211 -4.848 +## sigma 3.162 0.79050 1.130 5.194 ## ## Parameter correlation: -## parent_0 log_k_parent_sink sigma -## parent_0 1.000e+00 5.938e-01 3.387e-07 -## log_k_parent_sink 5.938e-01 1.000e+00 5.830e-07 -## sigma 3.387e-07 5.830e-07 1.000e+00 +## parent_0 log_k_parent sigma +## parent_0 1.000e+00 5.938e-01 3.387e-07 +## log_k_parent 5.938e-01 1.000e+00 5.830e-07 +## sigma 3.387e-07 5.830e-07 1.000e+00 ## ## Backtransformed parameters: ## 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 56.77 1.604e-08 92.070000 1.008e+02 -## 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 +## Estimate t value Pr(>t) Lower Upper +## parent_0 96.440000 56.77 1.604e-08 92.070000 1.008e+02 +## k_parent 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 ## ## FOCUS Chi2 error levels in percent: ## err.min n.optim df @@ -2094,16 +2094,16 @@ plot(mm.L4) ## parent 106 352 
summary(mm.L4[["FOMC", 1]], data = FALSE)
## mkin version used for fitting:    0.9.50.3 
-## R version used for fitting:       4.0.0 
-## Date of fit:     Tue May 26 17:01:10 2020 
-## Date of summary: Tue May 26 17:01:10 2020 
+## R version used for fitting:       4.0.2 
+## Date of fit:     Thu Oct  8 09:06:22 2020 
+## Date of summary: Thu Oct  8 09:06:22 2020 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 224 model solutions performed in 0.044 s
+## Fitted using 224 model solutions performed in 0.046 s
 ## 
 ## Error model: Constant variance 
 ## 
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