From cf54ccca37d27480dbf8d59eb027300518f7ad75 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 19 May 2023 17:08:43 +0200 Subject: Prepare release of v1.2.4 - Update DESCRIPTION - Update Makefile to document how to use R-patched - Remove markup from two URLs to avoid CRAN NOTE - Switch two vignettes from html_document to html_vignette to save space in the docs directory, also avoiding a CRAN NOTE - Complete rebuild of pkgdown docs for release --- docs/articles/web_only/NAFTA_examples.html | 189 ++++++++++++++--------------- 1 file changed, 91 insertions(+), 98 deletions(-) (limited to 'docs/articles/web_only/NAFTA_examples.html') diff --git a/docs/articles/web_only/NAFTA_examples.html b/docs/articles/web_only/NAFTA_examples.html index 49d1db33..87cef18a 100644 --- a/docs/articles/web_only/NAFTA_examples.html +++ b/docs/articles/web_only/NAFTA_examples.html @@ -33,7 +33,7 @@ mkin - 1.2.3 + 1.2.4 @@ -135,7 +135,7 @@ to the US EPA SOP for the NAFTA guidance Ranke

26 February 2019 (rebuilt -2023-04-20)

+2023-05-19) Source: vignettes/web_only/NAFTA_examples.rmd @@ -171,7 +171,7 @@ same.

## 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(p5a)
+plot(p5a) 

 print(p5a)
@@ -200,7 +200,7 @@ same.

## 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 2.26e-12 5.00e-01 0.0000 Inf +## k2 3.41e-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 ## @@ -209,7 +209,7 @@ same.

## 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 5.59e+11 3.07e+11 +## DFOP 55.5 3.70e+11 2.03e+11 ## ## Representative half-life: ## [1] 321.51 @@ -222,7 +222,7 @@ same.

## 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(p5b)
+plot(p5b) 

 print(p5b)
@@ -251,7 +251,7 @@ same.

## 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 8.63e-12 5.00e-01 0.0000 Inf +## k2 9.07e-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 ## @@ -260,7 +260,7 @@ same.

## 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 1.32e+11 8.04e+10 +## DFOP 83.6 1.25e+11 7.64e+10 ## ## Representative half-life: ## [1] 215.87 @@ -273,7 +273,7 @@ same.

## 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(p6)
+plot(p6) 

 print(p6)
@@ -302,7 +302,7 @@ same.

## 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 3.22e-11 5.00e-01 0.0000 Inf +## k2 3.84e-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 ## @@ -311,7 +311,7 @@ same.

## 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 1.01e+10 2.15e+10 +## DFOP 34.1 8.50e+09 1.80e+10 ## ## Representative half-life: ## [1] 53.17 @@ -324,7 +324,7 @@ same.

## 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(p7)
+plot(p7) 

 print(p7)
@@ -353,7 +353,7 @@ same.

## 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 3.63e-10 5.00e-01 0.0000 Inf +## k2 3.62e-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 ## @@ -362,7 +362,7 @@ same.

## 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 3.77e+09 1.91e+09 +## DFOP 96.4 3.79e+09 1.92e+09 ## ## Representative half-life: ## [1] 454.55 @@ -383,7 +383,7 @@ lower value for the rate constant is used here.

## 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(p8)
+plot(p8) 

 print(p8)
@@ -438,7 +438,7 @@ lower value for the rate constant is used here.

## 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(p9a)
+plot(p9a) 

 print(p9a)
@@ -476,7 +476,7 @@ lower value for the rate constant is used here.

## 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 7.69e+11 +## DFOP 10.5 1.38e+12 7.68e+11 ## ## Representative half-life: ## [1] 101.43 @@ -489,17 +489,12 @@ suggest a simple exponential decline.

 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)
+
+plot(p9b)

-
+
 print(p9b)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
@@ -526,8 +521,8 @@ suggest a simple exponential decline.

 ##          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
+## k2         0.0389 2.24e-04  0.0255  0.0592
+## g          0.5256 5.00e-01  0.0000  1.0000
 ## sigma      1.5957 2.50e-04  0.9135  2.2779
 ## 
 ## 
@@ -549,18 +544,15 @@ in PestDF and g in mkin. In mkin, it is restricted to the interval from
 

 
Example on page 10
 

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

-
## 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

+
## Warning in sqrt(diag(covar_notrans)): 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(p10)

+
+plot(p10)

 

-
+
 print(p10)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
@@ -584,12 +576,12 @@ in PestDF and g in mkin. In mkin, it is restricted to the interval from
 ## sigma              4.90 1.77e-04  2.837   6.968
 ## 
 ## $DFOP
-##          Estimate   Pr(>t)   Lower    Upper
-## parent_0 101.7315 1.41e-09 91.6534 111.8097
-## 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
+##          Estimate   Pr(>t)   Lower   Upper
+## parent_0 101.7315 1.41e-09 91.6534 111.810
+## k1         0.0495 3.04e-03  0.0188   0.131
+## k2         0.0495 4.92e-04  0.0197   0.124
+## g          0.4487      NaN  0.0000   1.000
+## sigma      8.0152 2.50e-04  4.5886  11.442
 ## 
 ## 
 ## DTx values:
@@ -613,14 +605,14 @@ difference in IORE model parameters between PestDF and mkin.

 

 
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)

+
+plot(p11)

 

-
+
 print(p11)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
@@ -659,7 +651,7 @@ difference in IORE model parameters between PestDF and mkin.

 ## DFOP 3.07e+11 1.93e+12 6.98e+11
 ## 
 ## Representative half-life:
-## [1] 41148170

+## [1] 41148169

 
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.

@@ -676,21 +668,17 @@ overparameterisation.

 

 
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 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)

+
+plot(p12a)

 

-
+
 print(p12a)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
@@ -718,7 +706,7 @@ overparameterisation.

 ## 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
+## g           0.793      NaN  0.0000   1.000
 ## sigma       7.048 2.50e-04  4.0349  10.061
 ## 
 ## 
@@ -734,18 +722,21 @@ overparameterisation.

 

 
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(diag(covar_notrans)): NaNs produced

 
## Warning in pt(abs(tval), rdf, lower.tail = FALSE): 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(p12b)

+
+plot(p12b)

 

-
+
 print(p12b)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
@@ -789,14 +780,14 @@ overparameterisation.

 

 
Example on page 13
 

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

 
## 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)

+
+plot(p13)

 

-
+
 print(p13)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
@@ -822,8 +813,8 @@ overparameterisation.

 ## $DFOP
 ##          Estimate Pr(>t)    Lower    Upper
 ## parent_0 92.73500     NA 8.95e+01 95.92118
-## k1        0.00258     NA 4.14e-04  0.01611
-## k2        0.00258     NA 1.74e-03  0.00383
+## k1        0.00258     NA 4.18e-04  0.01592
+## k2        0.00258     NA 1.75e-03  0.00381
 ## g         0.16452     NA 0.00e+00  1.00000
 ## sigma     3.41172     NA 2.02e+00  4.79960
 ## 
@@ -841,7 +832,7 @@ overparameterisation.

 

 
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

@@ -849,10 +840,10 @@ overparameterisation.

 ## 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(p14)

+
+plot(p14)

 

-
+
 print(p14)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
@@ -879,7 +870,7 @@ overparameterisation.

 ##          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       6.08e-12 5.00e-01  0.00000      Inf
+## k2       5.21e-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
 ## 
@@ -888,7 +879,7 @@ overparameterisation.

 ##          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 3.05e+10 2.95e+11 1.14e+11
+## DFOP 3.55e+10 3.44e+11 1.33e+11
 ## 
 ## Representative half-life:
 ## [1] 6697.44

@@ -899,14 +890,18 @@ same results in mkin and PestDF.

 

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

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

+
## 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(p15a)

+
+plot(p15a)

 

-
+
 print(p15a)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
@@ -932,9 +927,9 @@ same results in mkin and PestDF.

 ## $DFOP
 ##          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
+## k1        0.00952 6.28e-02  0.00260   0.0349
+## k2        0.00952 1.27e-04  0.00652   0.0139
+## g         0.21241 5.00e-01       NA       NA
 ## sigma     4.18778 2.50e-04  2.39747   5.9781
 ## 
 ## 
@@ -946,18 +941,16 @@ same results in mkin and PestDF.

 ## 
 ## 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

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

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

 
## 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)

+
+plot(p15b)

 

-
+
 print(p15b)

 
## Sums of squares:
 ##       SFO      IORE      DFOP 
@@ -975,18 +968,18 @@ same results in mkin and PestDF.

 ## 
 ## $IORE
 ##                Estimate   Pr(>t)    Lower  Upper
-## parent_0          99.83 1.81e-16 97.51349 102.14
+## parent_0          99.83 1.81e-16 97.51348 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
 ## 
 ## $DFOP
-##          Estimate Pr(>t)    Lower    Upper
-## parent_0 1.01e+02     NA 9.82e+01 1.04e+02
-## k1       4.86e-03     NA 8.63e-04 2.73e-02
-## k2       4.86e-03     NA 3.21e-03 7.35e-03
-## g        1.88e-01     NA       NA       NA
-## sigma    2.76e+00     NA 1.58e+00 3.94e+00
+##          Estimate Pr(>t) Lower Upper
+## parent_0 1.01e+02     NA    NA    NA
+## k1       4.86e-03     NA    NA    NA
+## k2       4.86e-03     NA    NA    NA
+## g        1.88e-01     NA    NA    NA
+## sigma    2.76e+00     NA    NA    NA
 ## 
 ## 
 ## DTx values:
@@ -1005,16 +998,16 @@ mkin and PestDF.

 

 
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)

+
+plot(p16)

 

-
+
 print(p16)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
-- 
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