From d5ff53448c61134c46cc4df9ea88fd86fa376d66 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 17 Feb 2023 14:44:29 +0100 Subject: Finish adapting to upcoming deSolve --- vignettes/FOCUS_D.html | 12 +- vignettes/FOCUS_L.html | 64 +++++----- vignettes/dmta_pathway_2022_prebuilt.rnw | 2 +- vignettes/web_only/benchmarks.html | 92 +++++---------- vignettes/web_only/mkin_benchmarks.rda | Bin 1777 -> 1780 bytes vignettes/web_only/saem_benchmarks.html | 196 ++++++++++++++++++++++++------- vignettes/web_only/saem_benchmarks.rda | Bin 592 -> 673 bytes 7 files changed, 217 insertions(+), 149 deletions(-) (limited to 'vignettes') diff --git a/vignettes/FOCUS_D.html b/vignettes/FOCUS_D.html index c729e3c2..d1d51ddb 100644 --- a/vignettes/FOCUS_D.html +++ b/vignettes/FOCUS_D.html @@ -358,7 +358,7 @@ pre code {

Example evaluation of FOCUS Example Dataset D

Johannes Ranke

-

Last change 31 January 2019 (rebuilt 2023-01-05)

+

Last change 31 January 2019 (rebuilt 2023-02-17)

@@ -441,7 +441,7 @@ variables is obtained using the plot_sep method for mkinfit objects, which shows separate graphs for all compounds and their residuals.

plot_sep(fit, lpos = c("topright", "bottomright"))
-

+

Confidence intervals for the parameter estimates are obtained using the mkinparplot function.

mkinparplot(fit)
@@ -449,10 +449,10 @@ the mkinparplot function.

A comprehensive report of the results is obtained using the summary method for mkinfit objects.

summary(fit)
-
## mkin version used for fitting:    1.2.2 
+
## mkin version used for fitting:    1.3.0 
 ## R version used for fitting:       4.2.2 
-## Date of fit:     Thu Jan  5 14:50:13 2023 
-## Date of summary: Thu Jan  5 14:50:14 2023 
+## Date of fit:     Fri Feb 17 10:41:52 2023 
+## Date of summary: Fri Feb 17 10:41:52 2023 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent * parent
@@ -460,7 +460,7 @@ the mkinparplot function.

 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 401 model solutions performed in 0.049 s
+## Fitted using 401 model solutions performed in 0.048 s
 ## 
 ## Error model: Constant variance 
 ## 
diff --git a/vignettes/FOCUS_L.html b/vignettes/FOCUS_L.html
index 98fe86c1..190ab65b 100644
--- a/vignettes/FOCUS_L.html
+++ b/vignettes/FOCUS_L.html
@@ -1534,7 +1534,7 @@ div.tocify {
 
Example evaluation of FOCUS Laboratory Data
 L1 to L3

 
Johannes Ranke

-
Last change 18 May 2022 (rebuilt 2023-01-05)

+
Last change 18 May 2022 (rebuilt 2023-02-17)

 
 
 
@@ -1561,10 +1561,10 @@ 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)

-
## mkin version used for fitting:    1.2.2 
+
## mkin version used for fitting:    1.3.0 
 ## R version used for fitting:       4.2.2 
-## Date of fit:     Thu Jan  5 14:50:14 2023 
-## Date of summary: Thu Jan  5 14:50:14 2023 
+## Date of fit:     Fri Feb 17 10:41:53 2023 
+## Date of summary: Fri Feb 17 10:41:53 2023 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent * parent
@@ -1648,7 +1648,7 @@ summary(m.L1.SFO)

 
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")

-

+

 
The residual plot can be easily obtained by

 
mkinresplot(m.L1.SFO, ylab = "Observed", xlab = "Time")

 

@@ -1658,23 +1658,23 @@ checked.

 
## 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")

-

+

 
summary(m.L1.FOMC, data = FALSE)

 
## Warning in sqrt(diag(covar)): NaNs produced

 
## Warning in sqrt(1/diag(V)): NaNs produced

 
## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is
 ## doubtful

-
## mkin version used for fitting:    1.2.2 
+
## mkin version used for fitting:    1.3.0 
 ## R version used for fitting:       4.2.2 
-## Date of fit:     Thu Jan  5 14:50:15 2023 
-## Date of summary: Thu Jan  5 14:50:15 2023 
+## Date of fit:     Fri Feb 17 10:41:53 2023 
+## Date of summary: Fri Feb 17 10:41:53 2023 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 369 model solutions performed in 0.025 s
+## Fitted using 369 model solutions performed in 0.026 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -1785,7 +1785,7 @@ residual plot can be obtained simply by adding the argument
 
m.L2.SFO <- mkinfit("SFO", FOCUS_2006_L2_mkin, quiet=TRUE)
 plot(m.L2.SFO, show_residuals = TRUE, show_errmin = TRUE,
      main = "FOCUS L2 - SFO")

-

+

 
The χ2 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
@@ -1810,10 +1810,10 @@ plot(m.L2.FOMC, show_residuals = TRUE,
      main = "FOCUS L2 - FOMC")

 

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

-
## mkin version used for fitting:    1.2.2 
+
## mkin version used for fitting:    1.3.0 
 ## R version used for fitting:       4.2.2 
-## Date of fit:     Thu Jan  5 14:50:15 2023 
-## Date of summary: Thu Jan  5 14:50:15 2023 
+## Date of fit:     Fri Feb 17 10:41:54 2023 
+## Date of summary: Fri Feb 17 10:41:54 2023 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
@@ -1889,12 +1889,12 @@ order to explain the data.

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

-

+

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

-
## mkin version used for fitting:    1.2.2 
+
## mkin version used for fitting:    1.3.0 
 ## R version used for fitting:       4.2.2 
-## Date of fit:     Thu Jan  5 14:50:15 2023 
-## Date of summary: Thu Jan  5 14:50:15 2023 
+## Date of fit:     Fri Feb 17 10:41:54 2023 
+## Date of summary: Fri Feb 17 10:41:54 2023 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -1988,7 +1988,7 @@ only the L3 dataset prepared above.

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

-

+

 
The χ2 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
@@ -2004,10 +2004,10 @@ as a row index and datasets as a column index.

 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:    1.2.2 
+
## mkin version used for fitting:    1.3.0 
 ## R version used for fitting:       4.2.2 
-## Date of fit:     Thu Jan  5 14:50:15 2023 
-## Date of summary: Thu Jan  5 14:50:15 2023 
+## Date of fit:     Fri Feb 17 10:41:54 2023 
+## Date of summary: Fri Feb 17 10:41:54 2023 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -2016,7 +2016,7 @@ summary and plot functions working on mkinfit objects.

 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 376 model solutions performed in 0.024 s
+## Fitted using 376 model solutions performed in 0.023 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -2091,7 +2091,7 @@ summary and plot functions working on mkinfit objects.

 ##    91   parent     15.0     15.18 -0.18181
 ##   120   parent     12.0     10.19  1.81395

 
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
@@ -2119,24 +2119,24 @@ mm.L4 <- mmkin(c("SFO", "FOMC"), cores = 1,
                list("FOCUS L4" = FOCUS_2006_L4_mkin),
                quiet = TRUE)
 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:    1.2.2 
+
## mkin version used for fitting:    1.3.0 
 ## R version used for fitting:       4.2.2 
-## Date of fit:     Thu Jan  5 14:50:16 2023 
-## Date of summary: Thu Jan  5 14:50:16 2023 
+## Date of fit:     Fri Feb 17 10:41:54 2023 
+## Date of summary: Fri Feb 17 10:41:54 2023 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 142 model solutions performed in 0.01 s
+## Fitted using 142 model solutions performed in 0.009 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -2190,10 +2190,10 @@ negligible.

 ##        DT50 DT90
 ## parent  106  352

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

-
## mkin version used for fitting:    1.2.2 
+
## mkin version used for fitting:    1.3.0 
 ## R version used for fitting:       4.2.2 
-## Date of fit:     Thu Jan  5 14:50:16 2023 
-## Date of summary: Thu Jan  5 14:50:16 2023 
+## Date of fit:     Fri Feb 17 10:41:54 2023 
+## Date of summary: Fri Feb 17 10:41:54 2023 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
diff --git a/vignettes/dmta_pathway_2022_prebuilt.rnw b/vignettes/dmta_pathway_2022_prebuilt.rnw
index 0a3aaaa8..a310633b 100644
--- a/vignettes/dmta_pathway_2022_prebuilt.rnw
+++ b/vignettes/dmta_pathway_2022_prebuilt.rnw
@@ -3,5 +3,5 @@
 %\VignetteIndexEntry{Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P}
 
 \begin{document}
-\includepdf[pages=-, fitpaper=true]{2022_wp_1/2022_dmta_pathway.pdf}
+\includepdf[pages=-, fitpaper=true]{prebuilt/2022_dmta_pathway.pdf}
 \end{document}
diff --git a/vignettes/web_only/benchmarks.html b/vignettes/web_only/benchmarks.html
index fb799462..6cce41e6 100644
--- a/vignettes/web_only/benchmarks.html
+++ b/vignettes/web_only/benchmarks.html
@@ -1592,7 +1592,7 @@ div.tocify {
 
 
Benchmark timings for mkin

 
Johannes Ranke

-
Last change 14 July 2022 (rebuilt 2023-02-13)

+
Last change 14 July 2022 (rebuilt 2023-02-17)

 
 
 
@@ -1636,31 +1636,11 @@ FOMC_SFO <- mkinmod(
 DFOP_SFO <- mkinmod(
   parent = mkinsub("FOMC", "m1"), # erroneously used FOMC twice, not fixed for consistency
   m1 = mkinsub("SFO"))
-t3 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_D)))[["elapsed"]]

-
## Error in mkinmod[["symbols"]] : 
-##   object of type 'closure' is not subsettable
-## Error in mkinmod[["symbols"]] : 
-##   object of type 'closure' is not subsettable

-
t4 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_D),
-    error_model = "tc"))[["elapsed"]]

-
## Error in mkinmod[["symbols"]] : 
-##   object of type 'closure' is not subsettable
-## Error in mkinmod[["symbols"]] : 
-##   object of type 'closure' is not subsettable
-## Error in mkinmod[["symbols"]] : 
-##   object of type 'closure' is not subsettable
-## Error in mkinmod[["symbols"]] : 
-##   object of type 'closure' is not subsettable

-
t5 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_D),
+t3 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_D)))[["elapsed"]]
+t4 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_D),
+    error_model = "tc"))[["elapsed"]]
+t5 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_D),
     error_model = "obs"))[["elapsed"]]

-
## Error in mkinmod[["symbols"]] : 
-##   object of type 'closure' is not subsettable
-## Error in mkinmod[["symbols"]] : 
-##   object of type 'closure' is not subsettable
-## Error in mkinmod[["symbols"]] : 
-##   object of type 'closure' is not subsettable
-## Error in mkinmod[["symbols"]] : 
-##   object of type 'closure' is not subsettable

 
Two metabolites, synthetic data:

 
m_synth_SFO_lin <- mkinmod(parent = mkinsub("SFO", "M1"),
                            M1 = mkinsub("SFO", "M2"),
@@ -1676,36 +1656,18 @@ SFO_lin_a <- synthetic_data_for_UBA_2014[[1]]$data
 
 DFOP_par_c <- synthetic_data_for_UBA_2014[[12]]$data
 
-t6 <- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a)))[["elapsed"]]

-
## Error in mkinmod[["symbols"]] : 
-##   object of type 'closure' is not subsettable

-
t7 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c)))[["elapsed"]]

-
## Error in mkinmod[["symbols"]] : 
-##   object of type 'closure' is not subsettable

-
t8 <- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a),
-    error_model = "tc"))[["elapsed"]]

-
## Error in mkinmod[["symbols"]] : 
-##   object of type 'closure' is not subsettable
-## Error in mkinmod[["symbols"]] : 
-##   object of type 'closure' is not subsettable

-
t9 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c),
-    error_model = "tc"))[["elapsed"]]

-
## Error in mkinmod[["symbols"]] : 
-##   object of type 'closure' is not subsettable
-## Error in mkinmod[["symbols"]] : 
-##   object of type 'closure' is not subsettable

-
t10 <- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a),
-    error_model = "obs"))[["elapsed"]]

-
## Error in mkinmod[["symbols"]] : 
-##   object of type 'closure' is not subsettable
-## Error in mkinmod[["symbols"]] : 
-##   object of type 'closure' is not subsettable

-
t11 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c),
+t6 <- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a)))[["elapsed"]]
+t7 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c)))[["elapsed"]]
+
+t8 <- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a),
+    error_model = "tc"))[["elapsed"]]
+t9 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c),
+    error_model = "tc"))[["elapsed"]]
+
+t10 <- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a),
+    error_model = "obs"))[["elapsed"]]
+t11 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c),
     error_model = "obs"))[["elapsed"]]

-
## Error in mkinmod[["symbols"]] : 
-##   object of type 'closure' is not subsettable
-## Error in mkinmod[["symbols"]] : 
-##   object of type 'closure' is not subsettable

 
 

 
Results

@@ -1901,8 +1863,8 @@ models fitted to two datasets, i.e. eight fits for each test.

 Ryzen 9 7950X 16-Core Processor
 4.2.2
 1.3.0
-1.271
-1.787
+1.287
+1.805
 
 
 
@@ -2119,9 +2081,9 @@ for each test.

 Ryzen 9 7950X 16-Core Processor
 4.2.2
 1.3.0
-0.526
-0.623
-0.631
+0.731
+1.984
+1.100
 
 
 
@@ -2404,12 +2366,12 @@ dataset, i.e. one fit for each test.

 Ryzen 9 7950X 16-Core Processor
 4.2.2
 1.3.0
-0.242
-0.237
-0.238
-0.239
-0.237
-0.237
+0.400
+0.518
+0.580
+0.990
+0.701
+0.935
 
 
 
diff --git a/vignettes/web_only/mkin_benchmarks.rda b/vignettes/web_only/mkin_benchmarks.rda
index 93138541..389e2738 100644
Binary files a/vignettes/web_only/mkin_benchmarks.rda and b/vignettes/web_only/mkin_benchmarks.rda differ
diff --git a/vignettes/web_only/saem_benchmarks.html b/vignettes/web_only/saem_benchmarks.html
index 714dc1ff..a3bbafef 100644
--- a/vignettes/web_only/saem_benchmarks.html
+++ b/vignettes/web_only/saem_benchmarks.html
@@ -31,7 +31,7 @@ document.addEventListener('DOMContentLoaded', function(e) {
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