From e05656d57668688b971c28e32b4cfd4d3eac4662 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 18 Sep 2019 13:03:50 +0200 Subject: Correct and rebuild docs - Reconcile docs and code for max_twa_parent - Correct links to docs in twa vignette - Static documentation rebuilt by pkgdown --- docs/articles/FOCUS_L.html | 133 +++++++++++++++++++++++---------------------- 1 file changed, 69 insertions(+), 64 deletions(-) (limited to 'docs/articles/FOCUS_L.html') diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index 779635cd..81659030 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -7,8 +7,9 @@ Example evaluation of FOCUS Laboratory Data L1 to L3 • mkin - - + + + @@ -82,13 +83,14 @@ +

Example evaluation of FOCUS Laboratory Data L1 to L3

Johannes Ranke

-

2019-07-09

+

2019-09-18

@@ -101,28 +103,28 @@

Laboratory Data L1

The following code defines example dataset L1 from the FOCUS kinetics report, p. 284:

-
library("mkin", quietly = TRUE)
-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,
+
library("mkin", quietly = TRUE)
+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,
              27.7, 27.3, 10.0, 10.4, 2.9, 4.0))
 FOCUS_2006_L1_mkin <- mkin_wide_to_long(FOCUS_2006_L1)

 
Here we use the assumptions of simple first order (SFO), the case of declining rate constant over time (FOMC) and the case of two different phases of the kinetics (DFOP). For a more detailed discussion of the models, please see the FOCUS kinetics report.

 
Since mkin version 0.9-32 (July 2014), we can use shorthand notation like "SFO" for parent only degradation models. The following two lines fit the model and produce the summary report of the model fit. This covers the numerical analysis given in the FOCUS report.

 
m.L1.SFO <- mkinfit("SFO", FOCUS_2006_L1_mkin, quiet = TRUE)
-summary(m.L1.SFO)

+summary(m.L1.SFO)
## mkin version used for fitting:    0.9.49.6 
-## R version used for fitting:       3.6.0 
-## Date of fit:     Tue Jul  9 09:00:20 2019 
-## Date of summary: Tue Jul  9 09:00:20 2019 
+## R version used for fitting:       3.6.1 
+## Date of fit:     Wed Sep 18 12:57:35 2019 
+## Date of summary: Wed Sep 18 12:57:35 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 133 model solutions performed in 0.282 s
+## Fitted using 133 model solutions performed in 0.287 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -198,7 +200,7 @@
 ##    30   parent      2.9     5.251  -2.3513
 ##    30   parent      4.0     5.251  -1.2513

A plot of the fit is obtained with the plot function for mkinfit objects.

-
plot(m.L1.SFO, show_errmin = TRUE, main = "FOCUS L1 - SFO")
+
plot(m.L1.SFO, show_errmin = TRUE, main = "FOCUS L1 - SFO")

The residual plot can be easily obtained by

mkinresplot(m.L1.SFO, ylab = "Observed", xlab = "Time")
@@ -207,17 +209,17 @@ 
m.L1.FOMC <- mkinfit("FOMC", FOCUS_2006_L1_mkin, quiet=TRUE)
## Warning in mkinfit("FOMC", FOCUS_2006_L1_mkin, quiet = TRUE): Optimisation did not converge:
 ## false convergence (8)
-
plot(m.L1.FOMC, show_errmin = TRUE, main = "FOCUS L1 - FOMC")
+
plot(m.L1.FOMC, show_errmin = TRUE, main = "FOCUS L1 - FOMC")

-
summary(m.L1.FOMC, data = FALSE)
+
summary(m.L1.FOMC, data = FALSE)
## Warning in sqrt(diag(covar)): NaNs wurden erzeugt
## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt
## Warning in cov2cor(ans$cov.unscaled): diag(.) had 0 or NA entries; non-
 ## finite result is doubtful
## mkin version used for fitting:    0.9.49.6 
-## R version used for fitting:       3.6.0 
-## Date of fit:     Tue Jul  9 09:00:22 2019 
-## Date of summary: Tue Jul  9 09:00:22 2019 
+## R version used for fitting:       3.6.1 
+## Date of fit:     Wed Sep 18 12:57:37 2019 
+## Date of summary: Wed Sep 18 12:57:37 2019 
 ## 
 ## 
 ## Warning: Optimisation did not converge:
@@ -229,7 +231,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 899 model solutions performed in 1.881 s
+## Fitted using 899 model solutions performed in 1.921 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -292,9 +294,9 @@
 

 Laboratory Data L2

 
The following code defines example dataset L2 from the FOCUS kinetics report, p. 287:

-
FOCUS_2006_L2 = data.frame(
-  t = rep(c(0, 1, 3, 7, 14, 28), each = 2),
-  parent = c(96.1, 91.8, 41.4, 38.7,
+
@@ -303,7 +305,7 @@
 SFO fit for L2
 
Again, the SFO model is fitted and the result is plotted. The residual plot can be obtained simply by adding the argument show_residuals to the plot command.

 
m.L2.SFO <- mkinfit("SFO", FOCUS_2006_L2_mkin, quiet=TRUE)
-plot(m.L2.SFO, show_residuals = TRUE, show_errmin = TRUE,
+plot(m.L2.SFO, show_residuals = TRUE, show_errmin = TRUE,
      main = "FOCUS L2 - SFO")

 

 
The \(\chi^2\) error level of 14% suggests that the model does not fit very well. This is also obvious from the plots of the fit, in which we have included the residual plot.

@@ -315,21 +317,21 @@
 FOMC fit for L2
 
For comparison, the FOMC model is fitted as well, and the \(\chi^2\) error level is checked.

 
m.L2.FOMC <- mkinfit("FOMC", FOCUS_2006_L2_mkin, quiet = TRUE)
-plot(m.L2.FOMC, show_residuals = TRUE,
+plot(m.L2.FOMC, show_residuals = TRUE,
      main = "FOCUS L2 - FOMC")

 

-
summary(m.L2.FOMC, data = FALSE)

+
summary(m.L2.FOMC, data = FALSE)

 
## mkin version used for fitting:    0.9.49.6 
-## R version used for fitting:       3.6.0 
-## Date of fit:     Tue Jul  9 09:00:23 2019 
-## Date of summary: Tue Jul  9 09:00:23 2019 
+## R version used for fitting:       3.6.1 
+## Date of fit:     Wed Sep 18 12:57:38 2019 
+## Date of summary: Wed Sep 18 12:57:38 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 239 model solutions performed in 0.495 s
+## Fitted using 239 model solutions performed in 0.49 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -391,14 +393,14 @@
 DFOP fit for L2
 
Fitting the four parameter DFOP model further reduces the \(\chi^2\) error level.

 
m.L2.DFOP <- mkinfit("DFOP", FOCUS_2006_L2_mkin, quiet = TRUE)
-plot(m.L2.DFOP, show_residuals = TRUE, show_errmin = TRUE,
+plot(m.L2.DFOP, show_residuals = TRUE, show_errmin = TRUE,
      main = "FOCUS L2 - DFOP")

 

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

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

 
## mkin version used for fitting:    0.9.49.6 
-## R version used for fitting:       3.6.0 
-## Date of fit:     Tue Jul  9 09:00:24 2019 
-## Date of summary: Tue Jul  9 09:00:25 2019 
+## R version used for fitting:       3.6.1 
+## Date of fit:     Wed Sep 18 12:57:40 2019 
+## Date of summary: Wed Sep 18 12:57:40 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -407,7 +409,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 572 model solutions performed in 1.193 s
+## Fitted using 572 model solutions performed in 1.209 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -474,18 +476,18 @@
 

 Laboratory Data L3

 
The following code defines example dataset L3 from the FOCUS kinetics report, p. 290.

-
FOCUS_2006_L3 = data.frame(
-  t = c(0, 3, 7, 14, 30, 60, 91, 120),
-  parent = c(97.8, 60, 51, 43, 35, 22, 15, 12))
+
FOCUS_2006_L3 = data.frame(
+  t = c(0, 3, 7, 14, 30, 60, 91, 120),
+  parent = c(97.8, 60, 51, 43, 35, 22, 15, 12))
 FOCUS_2006_L3_mkin <- mkin_wide_to_long(FOCUS_2006_L3)

 

 

 Fit multiple models

 
As of mkin version 0.9-39 (June 2015), we can fit several models to one or more datasets in one call to the function mmkin. The datasets have to be passed in a list, in this case a named list holding only the L3 dataset prepared above.

 
# Only use one core here, not to offend the CRAN checks
-mm.L3 <- mmkin(c("SFO", "FOMC", "DFOP"), cores = 1,
-               list("FOCUS L3" = FOCUS_2006_L3_mkin), quiet = TRUE)
-plot(mm.L3)

+mm.L3 <- mmkin(c("SFO", "FOMC", "DFOP"), cores = 1,
+               list("FOCUS L3" = FOCUS_2006_L3_mkin), quiet = TRUE)
+plot(mm.L3)

 

 
The \(\chi^2\) error level of 21% as well as the plot suggest that the SFO model does not fit very well. The FOMC model performs better, with an error level at which the \(\chi^2\) test passes of 7%. Fitting the four parameter DFOP model further reduces the \(\chi^2\) error level considerably.

 

@@ -494,11 +496,11 @@
 Accessing mmkin objects
 
The objects returned by mmkin are arranged like a matrix, with models as a row index and datasets as a column index.

 
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]])

+
summary(mm.L3[["DFOP", 1]])

 
## mkin version used for fitting:    0.9.49.6 
-## R version used for fitting:       3.6.0 
-## Date of fit:     Tue Jul  9 09:00:26 2019 
-## Date of summary: Tue Jul  9 09:00:27 2019 
+## R version used for fitting:       3.6.1 
+## Date of fit:     Wed Sep 18 12:57:42 2019 
+## Date of summary: Wed Sep 18 12:57:42 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -507,7 +509,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 373 model solutions performed in 0.797 s
+## Fitted using 373 model solutions performed in 0.783 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -578,7 +580,7 @@
 ##    60   parent     22.0     23.26 -1.25919
 ##    91   parent     15.0     15.18 -0.18181
 ##   120   parent     12.0     10.19  1.81395

-
plot(mm.L3[["DFOP", 1]], show_errmin = TRUE)

+
plot(mm.L3[["DFOP", 1]], show_errmin = TRUE)

 

 
Here, a look to the model plot, the confidence intervals of the parameters and the correlation matrix suggest that the parameter estimates are reliable, and the DFOP model can be used as the best-fit model based on the \(\chi^2\) error level criterion for laboratory data L3.

 
This is also an example where the standard t-test for the parameter g_ilr is misleading, as it tests for a significant difference from zero. In this case, zero appears to be the correct value for this parameter, and the confidence interval for the backtransformed parameter g is quite narrow.

@@ -588,30 +590,30 @@
 

 Laboratory Data L4

 
The following code defines example dataset L4 from the FOCUS kinetics report, p. 293:

-
FOCUS_2006_L4 = data.frame(
-  t = c(0, 3, 7, 14, 30, 60, 91, 120),
-  parent = c(96.6, 96.3, 94.3, 88.8, 74.9, 59.9, 53.5, 49.0))
+
FOCUS_2006_L4 = data.frame(
+  t = c(0, 3, 7, 14, 30, 60, 91, 120),
+  parent = c(96.6, 96.3, 94.3, 88.8, 74.9, 59.9, 53.5, 49.0))
 FOCUS_2006_L4_mkin <- mkin_wide_to_long(FOCUS_2006_L4)

 
Fits of the SFO and FOMC models, plots and summaries are produced below:

 
# Only use one core here, not to offend the CRAN checks
-mm.L4 <- mmkin(c("SFO", "FOMC"), cores = 1,
-               list("FOCUS L4" = FOCUS_2006_L4_mkin),
+mm.L4 <- mmkin(c("SFO", "FOMC"), cores = 1,
+               list("FOCUS L4" = FOCUS_2006_L4_mkin),
                quiet = TRUE)
-plot(mm.L4)

+plot(mm.L4)

 

 
The \(\chi^2\) error level of 3.3% as well as the plot suggest that the SFO model fits very well. The error level at which the \(\chi^2\) test passes is slightly lower for the FOMC model. However, the difference appears negligible.

-
summary(mm.L4[["SFO", 1]], data = FALSE)

+
summary(mm.L4[["SFO", 1]], data = FALSE)

 
## mkin version used for fitting:    0.9.49.6 
-## R version used for fitting:       3.6.0 
-## Date of fit:     Tue Jul  9 09:00:27 2019 
-## Date of summary: Tue Jul  9 09:00:28 2019 
+## R version used for fitting:       3.6.1 
+## Date of fit:     Wed Sep 18 12:57:42 2019 
+## Date of summary: Wed Sep 18 12:57:43 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 142 model solutions performed in 0.299 s
+## Fitted using 142 model solutions performed in 0.288 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -665,18 +667,18 @@
 ## Estimated disappearance times:
 ##        DT50 DT90
 ## parent  106  352

-
summary(mm.L4[["FOMC", 1]], data = FALSE)

+
summary(mm.L4[["FOMC", 1]], data = FALSE)

 
## mkin version used for fitting:    0.9.49.6 
-## R version used for fitting:       3.6.0 
-## Date of fit:     Tue Jul  9 09:00:28 2019 
-## Date of summary: Tue Jul  9 09:00:28 2019 
+## R version used for fitting:       3.6.1 
+## Date of fit:     Wed Sep 18 12:57:43 2019 
+## Date of summary: Wed Sep 18 12:57:43 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 224 model solutions performed in 0.478 s
+## Fitted using 224 model solutions performed in 0.463 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -771,17 +773,20 @@
+

Developed by Johannes Ranke.

-

Site built with pkgdown 1.3.0.

+

Site built with pkgdown 1.4.1.

+
+ -- cgit v1.2.1