From a9427a09abdf7ce9aaeae7c7190f90c8f2e5ef52 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 15 Feb 2021 14:08:13 +0100 Subject: Improve README, introductory vignette and some other docs Also bump version to 1.0.3. --- docs/articles/web_only/FOCUS_Z.html | 32 ++-- .../accessible-code-block-0.0.1/empty-anchor.js | 15 ++ .../figure-html/FOCUS_2006_Z_fits_1-1.png | Bin 67049 -> 66640 bytes .../figure-html/FOCUS_2006_Z_fits_10-1.png | Bin 106768 -> 106038 bytes .../figure-html/FOCUS_2006_Z_fits_11-1.png | Bin 105777 -> 105042 bytes .../figure-html/FOCUS_2006_Z_fits_11a-1.png | Bin 76400 -> 75626 bytes .../figure-html/FOCUS_2006_Z_fits_11b-1.png | Bin 35734 -> 35744 bytes .../figure-html/FOCUS_2006_Z_fits_2-1.png | Bin 67049 -> 66640 bytes .../figure-html/FOCUS_2006_Z_fits_3-1.png | Bin 66804 -> 66424 bytes .../figure-html/FOCUS_2006_Z_fits_5-1.png | Bin 81025 -> 80520 bytes .../figure-html/FOCUS_2006_Z_fits_6-1.png | Bin 105745 -> 105149 bytes .../figure-html/FOCUS_2006_Z_fits_7-1.png | Bin 105161 -> 104479 bytes .../figure-html/FOCUS_2006_Z_fits_9-1.png | Bin 89419 -> 88890 bytes .../FOCUS_Z_files/header-attrs-2.6/header-attrs.js | 12 ++ docs/articles/web_only/NAFTA_examples.html | 178 ++++++++++----------- .../accessible-code-block-0.0.1/empty-anchor.js | 15 ++ .../NAFTA_examples_files/figure-html/p10-1.png | Bin 79145 -> 78793 bytes .../NAFTA_examples_files/figure-html/p11-1.png | Bin 75730 -> 75470 bytes .../NAFTA_examples_files/figure-html/p12a-1.png | Bin 81215 -> 80755 bytes .../NAFTA_examples_files/figure-html/p12b-1.png | Bin 70120 -> 69885 bytes .../NAFTA_examples_files/figure-html/p13-1.png | Bin 77502 -> 77126 bytes .../NAFTA_examples_files/figure-html/p14-1.png | Bin 79961 -> 79693 bytes .../NAFTA_examples_files/figure-html/p15a-1.png | Bin 76342 -> 75945 bytes .../NAFTA_examples_files/figure-html/p15b-1.png | Bin 78251 -> 78004 bytes .../NAFTA_examples_files/figure-html/p16-1.png | Bin 93322 -> 93075 bytes .../NAFTA_examples_files/figure-html/p5a-1.png | Bin 81873 -> 81521 bytes .../NAFTA_examples_files/figure-html/p5b-1.png | Bin 79970 -> 79783 bytes .../NAFTA_examples_files/figure-html/p6-1.png | Bin 82238 -> 81974 bytes .../NAFTA_examples_files/figure-html/p7-1.png | Bin 101821 -> 101606 bytes .../NAFTA_examples_files/figure-html/p8-1.png | Bin 92053 -> 91429 bytes .../NAFTA_examples_files/figure-html/p9a-1.png | Bin 78348 -> 77612 bytes .../NAFTA_examples_files/figure-html/p9b-1.png | Bin 75683 -> 75129 bytes .../header-attrs-2.6/header-attrs.js | 12 ++ docs/articles/web_only/benchmarks.html | 50 +++--- .../accessible-code-block-0.0.1/empty-anchor.js | 15 ++ .../header-attrs-2.6/header-attrs.js | 12 ++ docs/articles/web_only/compiled_models.html | 22 +-- .../accessible-code-block-0.0.1/empty-anchor.js | 15 ++ .../header-attrs-2.6/header-attrs.js | 12 ++ 39 files changed, 246 insertions(+), 144 deletions(-) create mode 100644 docs/articles/web_only/FOCUS_Z_files/accessible-code-block-0.0.1/empty-anchor.js create mode 100644 docs/articles/web_only/FOCUS_Z_files/header-attrs-2.6/header-attrs.js create mode 100644 docs/articles/web_only/NAFTA_examples_files/accessible-code-block-0.0.1/empty-anchor.js create mode 100644 docs/articles/web_only/NAFTA_examples_files/header-attrs-2.6/header-attrs.js create mode 100644 docs/articles/web_only/benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js create mode 100644 docs/articles/web_only/benchmarks_files/header-attrs-2.6/header-attrs.js create mode 100644 docs/articles/web_only/compiled_models_files/accessible-code-block-0.0.1/empty-anchor.js create mode 100644 docs/articles/web_only/compiled_models_files/header-attrs-2.6/header-attrs.js (limited to 'docs/articles/web_only') diff --git a/docs/articles/web_only/FOCUS_Z.html b/docs/articles/web_only/FOCUS_Z.html index 8bdcbe30..57fc3545 100644 --- a/docs/articles/web_only/FOCUS_Z.html +++ b/docs/articles/web_only/FOCUS_Z.html @@ -31,7 +31,7 @@ mkin - 1.0.0 + 1.0.3 @@ -94,13 +94,13 @@ -
+

Example evaluation of FOCUS dataset Z

Johannes Ranke

-

2021-02-03

+

Last change 16 January 2018 (rebuilt 2021-02-15)

Source: vignettes/web_only/FOCUS_Z.rmd @@ -237,12 +237,12 @@ 
 summary(m.Z.FOCUS, data = FALSE)$bpar
##             Estimate se_notrans t value     Pr(>t)     Lower      Upper
-## Z0_0       96.839001   1.994273 48.5585 4.0276e-42 92.827060 100.850943
-## k_Z0        2.215367   0.118456 18.7021 1.0410e-23  1.989432   2.466960
-## k_Z1        0.478310   0.028258 16.9265 6.2430e-22  0.424712   0.538673
-## k_Z2        0.451628   0.042139 10.7176 1.6313e-14  0.374337   0.544877
-## k_Z3        0.058692   0.015245  3.8498 1.7806e-04  0.034806   0.098972
-## f_Z2_to_Z3  0.471498   0.058350  8.0805 9.6614e-11  0.357741   0.588294
+## Z0_0       96.838822   1.994274 48.5584 4.0280e-42 92.826981 100.850664
+## k_Z0        2.215393   0.118458 18.7019 1.0413e-23  1.989456   2.466989
+## k_Z1        0.478305   0.028258 16.9266 6.2418e-22  0.424708   0.538666
+## k_Z2        0.451627   0.042139 10.7176 1.6314e-14  0.374339   0.544872
+## k_Z3        0.058692   0.015245  3.8499 1.7803e-04  0.034808   0.098965
+## f_Z2_to_Z3  0.471502   0.058351  8.0805 9.6608e-11  0.357769   0.588274
 ## sigma       3.984431   0.383402 10.3923 4.5575e-14  3.213126   4.755736
 endpoints(m.Z.FOCUS)
@@ -253,9 +253,9 @@ ## $distimes ## DT50 DT90 ## Z0 0.31288 1.0394 -## Z1 1.44916 4.8140 +## Z1 1.44917 4.8141 ## Z2 1.53478 5.0984 -## Z3 11.80983 39.2314 +## Z3 11.80986 39.2315

This fit corresponds to the final result chosen in Appendix 7 of the FOCUS report. Confidence intervals returned by mkin are based on internally transformed parameters, however.

@@ -351,13 +351,13 @@ ## ## $SFORB ## Z0_b1 Z0_b2 Z3_b1 Z3_b2 -## 2.4471371 0.0075126 0.0800070 0.0000000 +## 2.4471322 0.0075125 0.0800069 0.0000000 ## ## $distimes ## DT50 DT90 DT50back DT50_Z0_b1 DT50_Z0_b2 DT50_Z3_b1 DT50_Z3_b2 -## Z0 0.3043 1.1848 0.35666 0.28325 92.265 NA NA +## Z0 0.3043 1.1848 0.35666 0.28325 92.266 NA NA ## Z1 1.5148 5.0320 NA NA NA NA NA -## Z2 1.6414 5.4525 NA NA NA NA NA +## Z2 1.6414 5.4526 NA NA NA NA NA ## Z3 NA NA NA NA NA 8.6636 Inf

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.

@@ -365,9 +365,9 @@

References

-
+
-

FOCUS Work Group on Degradation Kinetics. 2014. Generic Guidance for Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in Eu Registration. 1.1 ed. http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics.

+

FOCUS Work Group on Degradation Kinetics. 2014. Generic Guidance for Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in Eu Registration. 1.1 ed. http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics.

diff --git a/docs/articles/web_only/FOCUS_Z_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/web_only/FOCUS_Z_files/accessible-code-block-0.0.1/empty-anchor.js new file mode 100644 index 00000000..ca349fd6 --- /dev/null +++ b/docs/articles/web_only/FOCUS_Z_files/accessible-code-block-0.0.1/empty-anchor.js @@ -0,0 +1,15 @@ +// Hide empty tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) --> +// v0.0.1 +// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. + +document.addEventListener('DOMContentLoaded', function() { + const codeList = document.getElementsByClassName("sourceCode"); + for (var i = 0; i < codeList.length; i++) { + var linkList = codeList[i].getElementsByTagName('a'); + for (var j = 0; j < linkList.length; j++) { + if (linkList[j].innerHTML === "") { + linkList[j].setAttribute('aria-hidden', 'true'); + } + } + } +}); diff --git 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We remove the former (to +// be compatible with the behavior of Pandoc < 2.8). +document.addEventListener('DOMContentLoaded', function(e) { + var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); + var i, h, a; + for (i = 0; i < hs.length; i++) { + h = hs[i]; + if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 + a = h.attributes; + while (a.length > 0) h.removeAttribute(a[0].name); + } +}); diff --git a/docs/articles/web_only/NAFTA_examples.html b/docs/articles/web_only/NAFTA_examples.html index d3e23253..e79375b3 100644 --- a/docs/articles/web_only/NAFTA_examples.html +++ b/docs/articles/web_only/NAFTA_examples.html @@ -31,7 +31,7 @@ mkin - 1.0.0 + 1.0.3
@@ -94,13 +94,13 @@ -
+

Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance

Johannes Ranke

-

2021-02-03

+

26 February 2019 (rebuilt 2021-02-15)

Source: vignettes/web_only/NAFTA_examples.rmd @@ -156,7 +156,7 @@ ## Estimate Pr(>t) Lower Upper ## parent_0 9.99e+01 1.41e-26 98.8116 101.0810 ## k1 2.67e-02 5.05e-06 0.0243 0.0295 -## k2 2.42e-12 5.00e-01 0.0000 Inf +## k2 2.26e-12 5.00e-01 0.0000 Inf ## g 6.47e-01 3.67e-06 0.6248 0.6677 ## sigma 1.27e+00 8.91e-06 0.8395 1.6929 ## @@ -165,7 +165,7 @@ ## DT50 DT90 DT50_rep ## SFO 67.7 2.25e+02 6.77e+01 ## IORE 58.2 1.07e+03 3.22e+02 -## DFOP 55.5 5.22e+11 2.86e+11 +## DFOP 55.5 5.59e+11 3.07e+11 ## ## Representative half-life: ## [1] 321.51 @@ -207,7 +207,7 @@ ## 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 1.10e-11 5.00e-01 0.0000 Inf +## k2 8.63e-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 ## @@ -216,7 +216,7 @@ ## 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 1.03e+11 6.29e+10 +## DFOP 83.6 1.32e+11 8.04e+10 ## ## Representative half-life: ## [1] 215.87 @@ -258,7 +258,7 @@ ## 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 3.60e-11 5.00e-01 0.0000 Inf +## k2 3.22e-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 ## @@ -267,7 +267,7 @@ ## 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 9.07e+09 1.93e+10 +## DFOP 34.1 1.01e+10 2.15e+10 ## ## Representative half-life: ## [1] 53.17 @@ -309,7 +309,7 @@ ## 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 2.89e-10 5.00e-01 0.0000 Inf +## k2 3.63e-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 ## @@ -318,7 +318,7 @@ ## 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 4.75e+09 2.40e+09 +## DFOP 96.4 3.77e+09 1.91e+09 ## ## Representative half-life: ## [1] 454.55 @@ -420,7 +420,7 @@ ## Estimate Pr(>t) Lower Upper ## parent_0 9.85e+01 2.54e-20 97.390 99.672 ## k1 1.38e-01 3.52e-05 0.131 0.146 -## k2 9.03e-13 5.00e-01 0.000 Inf +## k2 9.02e-13 5.00e-01 0.000 Inf ## g 6.52e-01 8.13e-06 0.642 0.661 ## sigma 7.88e-01 6.13e-02 0.481 1.095 ## @@ -429,7 +429,7 @@ ## DT50 DT90 DT50_rep ## SFO 16.9 5.63e+01 1.69e+01 ## IORE 11.6 3.37e+02 1.01e+02 -## DFOP 10.5 1.38e+12 7.67e+11 +## DFOP 10.5 1.38e+12 7.69e+11 ## ## Representative half-life: ## [1] 101.43 @@ -441,15 +441,16 @@ 
 p9b <- nafta(NAFTA_SOP_Attachment[["p9b"]])
## Warning in sqrt(diag(covar)): NaNs produced
+
## Warning in sqrt(diag(covar_notrans)): 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
## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
## The half-life obtained from the IORE model may be used
-
+
 plot(p9b)

 

-
+
 print(p9b)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
@@ -473,12 +474,12 @@
 ## sigma             1.288 1.76e-04  0.7456  1.830
 ## 
 ## $DFOP
-##          Estimate Pr(>t)   Lower   Upper
-## parent_0  94.7123     NA 93.1355 96.2891
-## k1         0.0389     NA  0.0266  0.0569
-## k2         0.0389     NA  0.0255  0.0592
-## g          0.5256     NA      NA      NA
-## sigma      1.5957     NA  0.9135  2.2779
+##          Estimate   Pr(>t)   Lower   Upper
+## parent_0  94.7123 1.61e-16 93.1355 96.2891
+## k1         0.0389 1.08e-04  0.0266  0.0569
+## k2         0.0389 2.23e-04  0.0255  0.0592
+## g          0.5256      NaN      NA      NA
+## sigma      1.5957 2.50e-04  0.9135  2.2779
 ## 
 ## 
 ## DTx values:
@@ -494,15 +495,18 @@
 

 

 Example on page 10

-
+
 p10 <- nafta(NAFTA_SOP_Attachment[["p10"]])

-
## Warning in sqrt(diag(covar_notrans)): NaNs produced

+
## 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

 
## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c

 
## The half-life obtained from the IORE model may be used

-
+
 plot(p10)

 

-
+
 print(p10)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
@@ -528,9 +532,9 @@
 ## $DFOP
 ##          Estimate   Pr(>t)   Lower    Upper
 ## parent_0 101.7315 1.41e-09 91.6534 111.8097
-## k1         0.0495 5.63e-03  0.0240   0.1020
-## k2         0.0495 1.93e-03  0.0272   0.0903
-## g          0.4487      NaN  0.0000   1.0000
+## k1         0.0495 6.58e-03  0.0303   0.0809
+## k2         0.0495 2.60e-03  0.0410   0.0598
+## g          0.4487 5.00e-01      NA       NA
 ## sigma      8.0152 2.50e-04  4.5886  11.4418
 ## 
 ## 
@@ -551,14 +555,14 @@
 

 

 Example on page 11

-
+
 p11 <- nafta(NAFTA_SOP_Attachment[["p11"]])

 
## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c

 
## The half-life obtained from the IORE model may be used

-
+
 plot(p11)

 

-
+
 print(p11)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
@@ -594,10 +598,10 @@
 ##          DT50     DT90 DT50_rep
 ## SFO  2.16e+02 7.18e+02 2.16e+02
 ## IORE 9.73e+02 1.37e+08 4.11e+07
-## DFOP 3.07e+11 1.93e+12 6.97e+11
+## DFOP 3.07e+11 1.93e+12 6.98e+11
 ## 
 ## Representative half-life:
-## [1] 41148171

+## [1] 41148170

 
In this case, the DFOP fit reported for PestDF resulted in a negative value for the slower rate constant, which is not possible in mkin. The other results are in agreement.

 

 

@@ -608,19 +612,21 @@
 

 

 Example on page 12, upper panel

-
+
 p12a <- nafta(NAFTA_SOP_Attachment[["p12a"]])

 
## Warning in summary.mkinfit(x): Could not calculate correlation; no covariance
-## matrix
-
-## Warning in summary.mkinfit(x): Could not calculate correlation; no covariance
 ## matrix

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

+
## Warning in sqrt(diag(covar_notrans)): 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

 
## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c

 
## The half-life obtained from the IORE model may be used

-
+
 plot(p12a)

 

-
+
 print(p12a)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
@@ -644,12 +650,12 @@
 ## sigma             3.965     NA    NA    NA
 ## 
 ## $DFOP
-##          Estimate   Pr(>t) Lower Upper
-## parent_0  100.521 2.74e-10    NA    NA
-## k1          0.124 2.53e-05    NA    NA
-## k2          0.124 2.52e-02    NA    NA
-## g           0.793 5.00e-01    NA    NA
-## sigma       7.048 2.50e-04    NA    NA
+##          Estimate   Pr(>t)   Lower   Upper
+## parent_0  100.521 2.74e-10 92.2366 108.805
+## k1          0.124 2.53e-05  0.0908   0.170
+## k2          0.124 2.52e-02  0.0456   0.339
+## g           0.793      NaN      NA      NA
+## sigma       7.048 2.50e-04  4.0349  10.061
 ## 
 ## 
 ## DTx values:
@@ -664,20 +670,18 @@
 

 

 Example on page 12, lower panel

-
+
 p12b <- nafta(NAFTA_SOP_Attachment[["p12b"]])

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

 
## Warning in qt(alpha/2, rdf): NaNs produced

 
## Warning in qt(1 - alpha/2, rdf): 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

+
## Warning in sqrt(diag(covar_notrans)): NaNs produced

+
## Warning in pt(abs(tval), rdf, lower.tail = FALSE): NaNs produced

 
## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c

 
## The half-life obtained from the IORE model may be used

-
+
 plot(p12b)

 

-
+
 print(p12b)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
@@ -702,11 +706,11 @@
 ## 
 ## $DFOP
 ##          Estimate Pr(>t) Lower Upper
-## parent_0  97.6840     NA   NaN   NaN
-## k1         0.0589     NA    NA    NA
-## k2         0.0589     NA    NA    NA
-## g          0.6473     NA    NA    NA
-## sigma      3.4323     NA   NaN   NaN
+## parent_0  97.6840    NaN   NaN   NaN
+## k1         0.0589    NaN    NA    NA
+## k2         0.0589    NaN    NA    NA
+## g          0.6473    NaN    NA    NA
+## sigma      3.4323    NaN   NaN   NaN
 ## 
 ## 
 ## DTx values:
@@ -721,18 +725,14 @@
 

 

 Example on page 13

-
+
 p13 <- nafta(NAFTA_SOP_Attachment[["p13"]])

-
## 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

 
## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c

 
## The half-life obtained from the IORE model may be used

-
+
 plot(p13)

 

-
+
 print(p13)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
@@ -758,9 +758,9 @@
 ## $DFOP
 ##          Estimate Pr(>t)    Lower    Upper
 ## parent_0 92.73500     NA 8.95e+01 95.92118
-## k1        0.00258     NA 4.25e-04  0.01569
-## k2        0.00258     NA 1.76e-03  0.00379
-## g         0.16452     NA       NA       NA
+## k1        0.00258     NA 4.14e-04  0.01611
+## k2        0.00258     NA 1.74e-03  0.00383
+## g         0.16452     NA 0.00e+00  1.00000
 ## sigma     3.41172     NA 2.02e+00  4.79960
 ## 
 ## 
@@ -777,7 +777,7 @@
 

 

 DT50 not observed in the study and DFOP problems in PestDF

-
+
 p14 <- nafta(NAFTA_SOP_Attachment[["p14"]])

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

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

@@ -785,10 +785,10 @@
 ## doubtful

 
## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c

 
## The half-life obtained from the IORE model may be used

-
+
 plot(p14)

 

-
+
 print(p14)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
@@ -815,7 +815,7 @@
 ##          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       5.33e-12 5.00e-01  0.00000      Inf
+## k2       6.08e-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
 ## 
@@ -824,7 +824,7 @@
 ##          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 3.48e+10 3.37e+11 1.30e+11
+## DFOP 3.05e+10 2.95e+11 1.14e+11
 ## 
 ## Representative half-life:
 ## [1] 6697.44

@@ -833,14 +833,14 @@
 

 

 N is less than 1 and DFOP fraction parameter is below zero

-
+
 p15a <- nafta(NAFTA_SOP_Attachment[["p15a"]])

 
## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c

 
## The half-life obtained from the IORE model may be used

-
+
 plot(p15a)

 

-
+
 print(p15a)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
@@ -864,12 +864,12 @@
 ## sigma             3.105 1.78e-04  1.795  4.416
 ## 
 ## $DFOP
-##          Estimate Pr(>t)    Lower    Upper
-## parent_0 97.96751     NA 94.21913 101.7159
-## k1        0.00952     NA  0.00221   0.0411
-## k2        0.00952     NA  0.00626   0.0145
-## g         0.21241     NA  0.00000   1.0000
-## sigma     4.18778     NA  2.39747   5.9781
+##          Estimate   Pr(>t)    Lower    Upper
+## parent_0 97.96751 2.85e-13 94.21913 101.7159
+## k1        0.00952 6.28e-02  0.00250   0.0363
+## k2        0.00952 1.27e-04  0.00646   0.0140
+## g         0.21241 5.00e-01  0.00000   1.0000
+## sigma     4.18778 2.50e-04  2.39747   5.9781
 ## 
 ## 
 ## DTx values:
@@ -880,7 +880,7 @@
 ## 
 ## Representative half-life:
 ## [1] 41.33

-
+
 p15b <- nafta(NAFTA_SOP_Attachment[["p15b"]])

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

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

@@ -888,10 +888,10 @@
 ## doubtful

 
## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c

 
## The half-life obtained from the IORE model may be used

-
+
 plot(p15b)

 

-
+
 print(p15b)

 
## Sums of squares:
 ##       SFO      IORE      DFOP 
@@ -909,7 +909,7 @@
 ## 
 ## $IORE
 ##                Estimate   Pr(>t)    Lower  Upper
-## parent_0          99.83 1.81e-16 97.51348 102.14
+## parent_0          99.83 1.81e-16 97.51349 102.14
 ## k__iore_parent     0.38 3.22e-01  0.00352  41.05
 ## N_parent           0.00 5.00e-01 -1.07696   1.08
 ## sigma              2.21 2.57e-04  1.23245   3.19
@@ -936,16 +936,16 @@
 

 

 The DFOP fraction parameter is greater than 1

-
+
 p16 <- nafta(NAFTA_SOP_Attachment[["p16"]])

 
## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c

 
## The representative half-life of the IORE model is longer than the one corresponding

 
## to the terminal degradation rate found with the DFOP model.

 
## The representative half-life obtained from the DFOP model may be used

-
+
 plot(p16)

 

-
+
 print(p16)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
@@ -996,7 +996,7 @@
 

 

 References

-

+

 

 
US EPA. 2015. “Standard Operating Procedure for Using the NAFTA Guidance to Calculate Representative Half-Life Values and Characterizing Pesticide Degradation.”

 

diff --git a/docs/articles/web_only/NAFTA_examples_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/web_only/NAFTA_examples_files/accessible-code-block-0.0.1/empty-anchor.js
new file mode 100644
index 00000000..ca349fd6
--- /dev/null
+++ b/docs/articles/web_only/NAFTA_examples_files/accessible-code-block-0.0.1/empty-anchor.js
@@ -0,0 +1,15 @@
+// Hide empty  tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
+// v0.0.1
+// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
+
+document.addEventListener('DOMContentLoaded', function() {
+  const codeList = document.getElementsByClassName("sourceCode");
+  for (var i = 0; i < codeList.length; i++) {
+    var linkList = codeList[i].getElementsByTagName('a');
+    for (var j = 0; j < linkList.length; j++) {
+      if (linkList[j].innerHTML === "") {
+        linkList[j].setAttribute('aria-hidden', 'true');
+      }
+    }
+  }
+});
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
index bfe9b278..f5420ce8 100644
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diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p16-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p16-1.png
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diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p9a-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p9a-1.png
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diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p9b-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p9b-1.png
index 73b85767..e2cf2f83 100644
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diff --git a/docs/articles/web_only/NAFTA_examples_files/header-attrs-2.6/header-attrs.js b/docs/articles/web_only/NAFTA_examples_files/header-attrs-2.6/header-attrs.js
new file mode 100644
index 00000000..dd57d92e
--- /dev/null
+++ b/docs/articles/web_only/NAFTA_examples_files/header-attrs-2.6/header-attrs.js
@@ -0,0 +1,12 @@
+// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
+// be compatible with the behavior of Pandoc < 2.8).
+document.addEventListener('DOMContentLoaded', function(e) {
+  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
+  var i, h, a;
+  for (i = 0; i < hs.length; i++) {
+    h = hs[i];
+    if (!/^h[1-6]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
+    a = h.attributes;
+    while (a.length > 0) h.removeAttribute(a[0].name);
+  }
+});
diff --git a/docs/articles/web_only/benchmarks.html b/docs/articles/web_only/benchmarks.html
index e15358a0..d7b81f20 100644
--- a/docs/articles/web_only/benchmarks.html
+++ b/docs/articles/web_only/benchmarks.html
@@ -31,7 +31,7 @@
       
       
         mkin
-        1.0.0
+        1.0.3
       
     

 
@@ -94,13 +94,13 @@
 
       
 
-      

+      

   

     

       
Benchmark timings for mkin

                         
Johannes Ranke

             
-            
2021-02-03

+            
Last change 13 May 2020 (rebuilt 2021-02-15)

       
       Source: vignettes/web_only/benchmarks.rmd
       
@@ -135,17 +135,11 @@
   m1 = mkinsub("SFO"))
 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"]]

-
## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): Optimisation did not converge:
-## iteration limit reached without convergence (10)
-
-## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): Optimisation did not converge:
-## iteration limit reached without convergence (10)

-
-t5 <- 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"]]

 
Two metabolites, synthetic data:

-
+
 m_synth_SFO_lin <- mkinmod(parent = mkinsub("SFO", "M1"),
                            M1 = mkinsub("SFO", "M2"),
                            M2 = mkinsub("SFO"),
@@ -172,7 +166,7 @@
     error_model = "obs"))[["elapsed"]]
 t11 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c),
     error_model = "obs"))[["elapsed"]]

-
+
 mkin_benchmarks[system_string, paste0("t", 1:11)] <-
   c(t1, t2, t3, t4, t5, t6, t7, t8, t9, t10, t11)
 save(mkin_benchmarks, file = "~/git/mkin/vignettes/web_only/mkin_benchmarks.rda")

@@ -234,9 +228,9 @@
 3.729
 
 
-1.0.0
-1.770
-3.703
+1.0.3
+1.722
+3.419
 
 
 
@@ -302,10 +296,10 @@
 2.810
 
 
-1.0.0
-1.373
-7.127
-2.762
+1.0.3
+1.402
+6.343
+2.802
 
 
 
@@ -313,7 +307,7 @@
 

 

 Two metabolites

-
Constant variance (t6 and t7), two-component error model (t8 and t9), and variance by variable (t10 and t11) for one model fitted to one dataset, i.e. one fit for each test.

+
Constant variance (t6 and t7), two-component error model (t8 and t9), and variance by variable (t10 and t11) for one model fitted to one dataset, i.e. one fit for each test.

 
@@ -398,13 +392,13 @@
 
-
-
-
-
-
-
-
+
+
+
+
+
+
+

 

 mkin version3.105
 

 
1.0.00.7751.2691.4673.7671.9192.9421.0.30.7711.2511.4643.0741.9402.831
 

 
 

diff --git a/docs/articles/web_only/benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/web_only/benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js
new file mode 100644
index 00000000..ca349fd6
--- /dev/null
+++ b/docs/articles/web_only/benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js
@@ -0,0 +1,15 @@
+// Hide empty  tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
+// v0.0.1
+// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
+
+document.addEventListener('DOMContentLoaded', function() {
+  const codeList = document.getElementsByClassName("sourceCode");
+  for (var i = 0; i < codeList.length; i++) {
+    var linkList = codeList[i].getElementsByTagName('a');
+    for (var j = 0; j < linkList.length; j++) {
+      if (linkList[j].innerHTML === "") {
+        linkList[j].setAttribute('aria-hidden', 'true');
+      }
+    }
+  }
+});
diff --git a/docs/articles/web_only/benchmarks_files/header-attrs-2.6/header-attrs.js b/docs/articles/web_only/benchmarks_files/header-attrs-2.6/header-attrs.js
new file mode 100644
index 00000000..dd57d92e
--- /dev/null
+++ b/docs/articles/web_only/benchmarks_files/header-attrs-2.6/header-attrs.js
@@ -0,0 +1,12 @@
+// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
+// be compatible with the behavior of Pandoc < 2.8).
+document.addEventListener('DOMContentLoaded', function(e) {
+  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
+  var i, h, a;
+  for (i = 0; i < hs.length; i++) {
+    h = hs[i];
+    if (!/^h[1-6]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
+    a = h.attributes;
+    while (a.length > 0) h.removeAttribute(a[0].name);
+  }
+});
diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html
index e45655b6..ce8d8481 100644
--- a/docs/articles/web_only/compiled_models.html
+++ b/docs/articles/web_only/compiled_models.html
@@ -31,7 +31,7 @@
       
       
         mkin
-        1.0.0
+        1.0.3
       
     

 
@@ -94,13 +94,13 @@
 
       
 
-      

+      

   

     

       
Performance benefit by using compiled model definitions in mkin

                         
Johannes Ranke

             
-            
2021-02-03

+            
2021-02-15

       
       Source: vignettes/web_only/compiled_models.rmd
       
@@ -159,9 +159,9 @@
 }

 
##                    test replications relative elapsed
 ## 4            analytical            1    1.000   0.181
-## 3     deSolve, compiled            1    1.818   0.329
-## 2      Eigenvalue based            1    2.061   0.373
-## 1 deSolve, not compiled            1   43.923   7.950

+## 3     deSolve, compiled            1    1.812   0.328
+## 2      Eigenvalue based            1    2.088   0.378
+## 1 deSolve, not compiled            1   45.923   8.312

 
We see that using the compiled model is by more than a factor of 10 faster than using deSolve without compiled code.

 

 

@@ -188,13 +188,13 @@
 }

 
## Temporary DLL for differentials generated and loaded

 
##                    test replications relative elapsed
-## 2     deSolve, compiled            1    1.000   0.474
-## 1 deSolve, not compiled            1   30.179  14.305

-
Here we get a performance benefit of a factor of 30 using the version of the differential equation model compiled from C code!

-
This vignette was built with mkin 1.0.0 on

+## 2     deSolve, compiled            1    1.000   0.486
+## 1 deSolve, not compiled            1   31.597  15.356

+
Here we get a performance benefit of a factor of 32 using the version of the differential equation model compiled from C code!

+
This vignette was built with mkin 1.0.3 on

 
## R version 4.0.3 (2020-10-10)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
-## Running under: Debian GNU/Linux 10 (buster)

+## Running under: Debian GNU/Linux bullseye/sid

 
## CPU model: AMD Ryzen 7 1700 Eight-Core Processor

 

   

diff --git a/docs/articles/web_only/compiled_models_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/web_only/compiled_models_files/accessible-code-block-0.0.1/empty-anchor.js
new file mode 100644
index 00000000..ca349fd6
--- /dev/null
+++ b/docs/articles/web_only/compiled_models_files/accessible-code-block-0.0.1/empty-anchor.js
@@ -0,0 +1,15 @@
+// Hide empty  tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
+// v0.0.1
+// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
+
+document.addEventListener('DOMContentLoaded', function() {
+  const codeList = document.getElementsByClassName("sourceCode");
+  for (var i = 0; i < codeList.length; i++) {
+    var linkList = codeList[i].getElementsByTagName('a');
+    for (var j = 0; j < linkList.length; j++) {
+      if (linkList[j].innerHTML === "") {
+        linkList[j].setAttribute('aria-hidden', 'true');
+      }
+    }
+  }
+});
diff --git a/docs/articles/web_only/compiled_models_files/header-attrs-2.6/header-attrs.js b/docs/articles/web_only/compiled_models_files/header-attrs-2.6/header-attrs.js
new file mode 100644
index 00000000..dd57d92e
--- /dev/null
+++ b/docs/articles/web_only/compiled_models_files/header-attrs-2.6/header-attrs.js
@@ -0,0 +1,12 @@
+// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
+// be compatible with the behavior of Pandoc < 2.8).
+document.addEventListener('DOMContentLoaded', function(e) {
+  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
+  var i, h, a;
+  for (i = 0; i < hs.length; i++) {
+    h = hs[i];
+    if (!/^h[1-6]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
+    a = h.attributes;
+    while (a.length > 0) h.removeAttribute(a[0].name);
+  }
+});
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