From d0a358a8f4fd03c95536409523e492eb15726f44 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 4 Mar 2019 10:12:43 +0100 Subject: Review tests and examples based on winbuilder results Static documentation rebuilt by pkgdown --- docs/articles/web_only/NAFTA_examples.html | 533 +++++++++++++++-------------- 1 file changed, 283 insertions(+), 250 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 cae0cd6b..db1fc478 100644 --- a/docs/articles/web_only/NAFTA_examples.html +++ b/docs/articles/web_only/NAFTA_examples.html @@ -88,7 +88,7 @@

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

Johannes Ranke

-

2019-02-26

+

2019-03-04

@@ -110,12 +110,14 @@

Example on page 5, upper panel

-
p5a <- nafta(NAFTA_SOP_Attachment[["p5a"]])
+
p5a <- nafta(NAFTA_SOP_Attachment[["p5a"]])
+
## Warning in summary.mkinfit(x): Could not estimate covariance matrix;
+## singular system.
## 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)
+
print(p5a)
## Sums of squares:
 ##       SFO      IORE      DFOP 
 ## 465.21753  56.27506  32.06401 
@@ -125,22 +127,22 @@
 ## 
 ## Parameters:
 ## $SFO
-##                  Estimate       Pr(>t)        Lower       Upper
-## parent_0      95.84012168 1.095639e-21 92.120517864 99.55972549
-## k_parent_sink  0.01024015 1.710227e-12  0.008996874  0.01165524
+##               Estimate   Pr(>t)  Lower   Upper
+## parent_0       95.8401 1.10e-21 92.121 99.5597
+## k_parent_sink   0.0102 1.71e-12  0.009  0.0117
 ## 
 ## $IORE
-##                         Estimate       Pr(>t)        Lower        Upper
-## parent_0            1.007532e+02 2.365797e-26 9.891170e+01 1.025947e+02
-## k__iore_parent_sink 1.544192e-05 8.733384e-02 3.482391e-06 6.847393e-05
-## N_parent            2.569877e+00 1.140446e-11 2.215298e+00 2.924456e+00
+##                     Estimate   Pr(>t)    Lower    Upper
+## parent_0            1.01e+02 2.37e-26 9.89e+01 1.03e+02
+## k__iore_parent_sink 1.54e-05 8.73e-02 3.48e-06 6.85e-05
+## N_parent            2.57e+00 1.14e-11 2.22e+00 2.92e+00
 ## 
 ## $DFOP
-##              Estimate       Pr(>t) Lower Upper
-## parent_0 9.994630e+01 4.330861e-27    NA    NA
-## k1       2.674255e-02 3.171390e-05    NA    NA
-## k2       2.161318e-12 5.000000e-01    NA    NA
-## g        6.465276e-01 2.129114e-05    NA    NA
+##          Estimate   Pr(>t) Lower Upper
+## parent_0 9.99e+01 4.33e-27    NA    NA
+## k1       2.67e-02 3.17e-05    NA    NA
+## k2       2.16e-12 5.00e-01    NA    NA
+## g        6.47e-01 2.13e-05    NA    NA
 ## 
 ## 
 ## DTx values:
@@ -155,12 +157,14 @@
 

 

 Example on page 5, lower panel

-
p5b <- nafta(NAFTA_SOP_Attachment[["p5b"]])

+
p5b <- nafta(NAFTA_SOP_Attachment[["p5b"]])

+
## Warning in summary.mkinfit(x): Could not estimate covariance matrix;
+## singular system.

 
## 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)

+
print(p5b)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
 ## 94.81123 10.10936  7.55871 
@@ -170,22 +174,22 @@
 ## 
 ## Parameters:
 ## $SFO
-##                   Estimate       Pr(>t)        Lower        Upper
-## parent_0      96.497133849 2.623748e-25 94.776528606 98.217739092
-## k_parent_sink  0.008002704 1.352275e-14  0.007356108  0.008706135
+##               Estimate   Pr(>t)    Lower    Upper
+## parent_0        96.497 2.62e-25 94.77653 98.21774
+## k_parent_sink    0.008 1.35e-14  0.00736  0.00871
 ## 
 ## $IORE
-##                         Estimate       Pr(>t)        Lower        Upper
-## parent_0            9.854518e+01 1.019174e-29 9.780760e+01 9.928276e+01
-## k__iore_parent_sink 1.532766e-04 1.152046e-02 6.603390e-05 3.557826e-04
-## N_parent            1.939125e+00 8.177751e-13 1.741616e+00 2.136633e+00
+##                     Estimate   Pr(>t)    Lower    Upper
+## parent_0            9.85e+01 1.02e-29 9.78e+01 9.93e+01
+## k__iore_parent_sink 1.53e-04 1.15e-02 6.60e-05 3.56e-04
+## N_parent            1.94e+00 8.18e-13 1.74e+00 2.14e+00
 ## 
 ## $DFOP
-##              Estimate       Pr(>t) Lower Upper
-## parent_0 9.836323e+01 1.896304e-28    NA    NA
-## k1       1.546859e-02 2.833415e-03    NA    NA
-## k2       8.172408e-12 5.000000e-01    NA    NA
-## g        6.889941e-01 1.306276e-02    NA    NA
+##          Estimate   Pr(>t) Lower Upper
+## parent_0 9.84e+01 1.90e-28    NA    NA
+## k1       1.55e-02 2.83e-03    NA    NA
+## k2       8.17e-12 5.00e-01    NA    NA
+## g        6.89e-01 1.31e-02    NA    NA
 ## 
 ## 
 ## DTx values:
@@ -200,12 +204,14 @@
 

 

 Example on page 6

-
p6 <- nafta(NAFTA_SOP_Attachment[["p6"]])

+
p6 <- nafta(NAFTA_SOP_Attachment[["p6"]])

+
## Warning in summary.mkinfit(x): Could not estimate covariance matrix;
+## singular system.

 
## 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)

+
print(p6)

 
## Sums of squares:
 ##       SFO      IORE      DFOP 
 ## 188.45361  51.00699  42.46931 
@@ -215,22 +221,22 @@
 ## 
 ## Parameters:
 ## $SFO
-##                  Estimate       Pr(>t)       Lower       Upper
-## parent_0      94.77587412 1.246335e-24 92.25575879 97.29598945
-## k_parent_sink  0.01794259 2.347664e-16  0.01660595  0.01938682
+##               Estimate   Pr(>t)   Lower   Upper
+## parent_0       94.7759 1.25e-24 92.2558 97.2960
+## k_parent_sink   0.0179 2.35e-16  0.0166  0.0194
 ## 
 ## $IORE
-##                         Estimate       Pr(>t)        Lower        Upper
-## parent_0            97.124460863 5.616271e-27 95.493434421 98.755487305
-## k__iore_parent_sink  0.002517728 3.535472e-03  0.001263771  0.005015906
-## N_parent             1.495871465 6.129227e-13  1.323799338  1.667943591
+##                     Estimate   Pr(>t)    Lower    Upper
+## parent_0            97.12446 5.62e-27 95.49343 98.75549
+## k__iore_parent_sink  0.00252 3.54e-03  0.00126  0.00502
+## N_parent             1.49587 6.13e-13  1.32380  1.66794
 ## 
 ## $DFOP
-##              Estimate       Pr(>t) Lower Upper
-## parent_0 9.662275e+01 4.174516e-26    NA    NA
-## k1       2.547327e-02 2.115246e-05    NA    NA
-## k2       3.087623e-11 5.000000e-01    NA    NA
-## g        8.613785e-01 2.097173e-05    NA    NA
+##          Estimate   Pr(>t) Lower Upper
+## parent_0 9.66e+01 4.17e-26    NA    NA
+## k1       2.55e-02 2.12e-05    NA    NA
+## k2       3.09e-11 5.00e-01    NA    NA
+## g        8.61e-01 2.10e-05    NA    NA
 ## 
 ## 
 ## DTx values:
@@ -245,12 +251,14 @@
 

 

 Example on page 7

-
p7 <- nafta(NAFTA_SOP_Attachment[["p7"]])

+
p7 <- nafta(NAFTA_SOP_Attachment[["p7"]])

+
## Warning in summary.mkinfit(x): Could not estimate covariance matrix;
+## singular system.

 
## 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)

+
print(p7)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
 ## 3661.661 3195.030 3174.145 
@@ -260,22 +268,22 @@
 ## 
 ## Parameters:
 ## $SFO
-##                   Estimate       Pr(>t)        Lower        Upper
-## parent_0      96.417960406 1.520951e-53 93.295541980 99.540378832
-## k_parent_sink  0.007350054 3.592731e-21  0.006413446  0.008423441
+##               Estimate   Pr(>t)    Lower    Upper
+## parent_0      96.41796 1.52e-53 93.29554 99.54038
+## k_parent_sink  0.00735 3.59e-21  0.00641  0.00842
 ## 
 ## $IORE
-##                         Estimate       Pr(>t)        Lower        Upper
-## parent_0            9.915322e+01 7.332574e-49 9.534934e+01 1.029571e+02
-## k__iore_parent_sink 1.600884e-05 3.472978e-01 9.982484e-08 2.567328e-03
-## N_parent            2.446000e+00 6.141482e-05 1.260173e+00 3.631827e+00
+##                     Estimate   Pr(>t)    Lower    Upper
+## parent_0            9.92e+01 7.33e-49 9.53e+01 1.03e+02
+## k__iore_parent_sink 1.60e-05 3.47e-01 9.98e-08 2.57e-03
+## N_parent            2.45e+00 6.14e-05 1.26e+00 3.63e+00
 ## 
 ## $DFOP
-##              Estimate       Pr(>t) Lower Upper
-## parent_0 9.886065e+01 8.134302e-48    NA    NA
-## k1       1.805928e-02 2.198367e-01    NA    NA
-## k2       3.279731e-10 5.000000e-01    NA    NA
-## g        6.063177e-01 2.601365e-01    NA    NA
+##          Estimate   Pr(>t) Lower Upper
+## parent_0 9.89e+01 8.13e-48    NA    NA
+## k1       1.81e-02 2.20e-01    NA    NA
+## k2       3.28e-10 5.00e-01    NA    NA
+## g        6.06e-01 2.60e-01    NA    NA
 ## 
 ## 
 ## DTx values:
@@ -295,12 +303,17 @@
 

 Example on page 8

 
For this dataset, the IORE fit does not converge when the default starting values used by mkin for the IORE model are used. Therefore, a lower value for the rate constant is used here.

-
p8 <- nafta(NAFTA_SOP_Attachment[["p8"]], parms.ini = c(k__iore_parent_sink = 1e-3))

+
p8 <- nafta(NAFTA_SOP_Attachment[["p8"]], parms.ini = c(k__iore_parent_sink = 1e-3))

+
## Warning in summary.mkinfit(x): Could not estimate covariance matrix;
+## singular system.
+
+## Warning in summary.mkinfit(x): Could not estimate covariance matrix;
+## singular system.

 
## 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)

+
print(p8)

 
## Sums of squares:
 ##       SFO      IORE      DFOP 
 ## 1996.9408  444.9237  547.5616 
@@ -310,31 +323,31 @@
 ## 
 ## Parameters:
 ## $SFO
-##                         Estimate Pr(>t) Lower Upper
-## parent_0            88.165489334     NA    NA    NA
-## k__iore_parent_sink  0.001000000     NA    NA    NA
-## k_parent_sink        0.008032303     NA    NA    NA
+##                     Estimate Pr(>t) Lower Upper
+## parent_0            88.16549     NA    NA    NA
+## k__iore_parent_sink  0.00100     NA    NA    NA
+## k_parent_sink        0.00803     NA    NA    NA
 ## 
 ## $IORE
-##                         Estimate       Pr(>t)        Lower        Upper
-## parent_0            9.771060e+01 1.048016e-35 9.442778e+01 1.009934e+02
-## k__iore_parent_sink 6.141041e-05 2.763666e-02 2.205805e-05 1.709688e-04
-## N_parent            2.271648e+00 5.996684e-19 2.015215e+00 2.528080e+00
+##                     Estimate   Pr(>t)    Lower    Upper
+## parent_0            9.77e+01 1.05e-35 9.44e+01 1.01e+02
+## k__iore_parent_sink 6.14e-05 2.76e-02 2.21e-05 1.71e-04
+## N_parent            2.27e+00 6.00e-19 2.02e+00 2.53e+00
 ## 
 ## $DFOP
-##                         Estimate Pr(>t) Lower Upper
-## parent_0            95.706193520     NA    NA    NA
-## k__iore_parent_sink  0.001000000     NA    NA    NA
-## k1                   0.024995243     NA    NA    NA
-## k2                   0.002734623     NA    NA    NA
-## g                    0.588349874     NA    NA    NA
+##                     Estimate Pr(>t) Lower Upper
+## parent_0            95.70619     NA    NA    NA
+## k__iore_parent_sink  0.00100     NA    NA    NA
+## k1                   0.02500     NA    NA    NA
+## k2                   0.00273     NA    NA    NA
+## g                    0.58835     NA    NA    NA
 ## 
 ## 
 ## DTx values:
 ##      DT50 DT90 DT50_rep
 ## SFO  86.3  287     86.3
 ## IORE 53.4  668    201.0
-## DFOP 55.6  517    253.0
+## DFOP 55.6  517    253.5
 ## 
 ## Representative half-life:
 ## [1] 201.0316

@@ -346,12 +359,14 @@
 

 

 Example on page 9, upper panel

-
p9a <- nafta(NAFTA_SOP_Attachment[["p9a"]])

+
p9a <- nafta(NAFTA_SOP_Attachment[["p9a"]])

+
## Warning in summary.mkinfit(x): Could not estimate covariance matrix;
+## singular system.

 
## 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)

+
print(p9a)

 
## Sums of squares:
 ##       SFO      IORE      DFOP 
 ## 839.35238  88.57064   9.93363 
@@ -361,22 +376,22 @@
 ## 
 ## Parameters:
 ## $SFO
-##                 Estimate       Pr(>t)       Lower       Upper
-## parent_0      88.1933161 1.117569e-12 79.76708923 96.61954288
-## k_parent_sink  0.0409019 9.501453e-08  0.03258829  0.05133639
+##               Estimate   Pr(>t)   Lower   Upper
+## parent_0       88.1933 1.12e-12 79.7671 96.6195
+## k_parent_sink   0.0409 9.50e-08  0.0326  0.0513
 ## 
 ## $IORE
-##                         Estimate       Pr(>t)        Lower        Upper
-## parent_0            9.891481e+01 5.163566e-17 9.497891e+01 1.028507e+02
-## k__iore_parent_sink 1.927824e-05 1.480158e-01 2.650455e-06 1.402214e-04
-## N_parent            2.910027e+00 3.738041e-09 2.428904e+00 3.391151e+00
+##                     Estimate   Pr(>t)    Lower    Upper
+## parent_0            9.89e+01 5.16e-17 9.50e+01 1.03e+02
+## k__iore_parent_sink 1.93e-05 1.48e-01 2.65e-06 1.40e-04
+## N_parent            2.91e+00 3.74e-09 2.43e+00 3.39e+00
 ## 
 ## $DFOP
-##              Estimate       Pr(>t) Lower Upper
-## parent_0 9.853112e+01 1.308505e-21    NA    NA
-## k1       1.382145e-01 3.630589e-09    NA    NA
-## k2       6.019228e-13 5.000000e-01    NA    NA
-## g        6.518659e-01 1.502543e-10    NA    NA
+##          Estimate   Pr(>t) Lower Upper
+## parent_0 9.85e+01 1.31e-21    NA    NA
+## k1       1.38e-01 3.63e-09    NA    NA
+## k2       6.02e-13 5.00e-01    NA    NA
+## g        6.52e-01 1.50e-10    NA    NA
 ## 
 ## 
 ## DTx values:
@@ -392,12 +407,14 @@
 

 

 Example on page 9, lower panel

-
p9b <- nafta(NAFTA_SOP_Attachment[["p9b"]])

+
p9b <- nafta(NAFTA_SOP_Attachment[["p9b"]])

+
## Warning in summary.mkinfit(x): Could not estimate covariance matrix;
+## singular system.

 
## 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)

+
print(p9b)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
 ## 35.64867 23.22334 35.64867 
@@ -407,22 +424,22 @@
 ## 
 ## Parameters:
 ## $SFO
-##                  Estimate       Pr(>t)      Lower       Upper
-## parent_0      94.71226787 2.207090e-20 93.0673253 96.35721040
-## k_parent_sink  0.03887215 1.482921e-14  0.0368549  0.04099981
+##               Estimate   Pr(>t)   Lower  Upper
+## parent_0       94.7123 2.21e-20 93.0673 96.357
+## k_parent_sink   0.0389 1.48e-14  0.0369  0.041
 ## 
 ## $IORE
-##                       Estimate       Pr(>t)       Lower      Upper
-## parent_0            93.8626223 2.911881e-19 92.29955547 95.4256890
-## k__iore_parent_sink  0.1271399 2.725876e-02  0.04570569  0.3536663
-## N_parent             0.7108771 3.130915e-05  0.46052920  0.9612249
+##                     Estimate   Pr(>t)   Lower  Upper
+## parent_0              93.863 2.91e-19 92.2996 95.426
+## k__iore_parent_sink    0.127 2.73e-02  0.0457  0.354
+## N_parent               0.711 3.13e-05  0.4605  0.961
 ## 
 ## $DFOP
-##             Estimate Pr(>t) Lower Upper
-## parent_0 94.71226786     NA    NA    NA
-## k1        0.03887215     NA    NA    NA
-## k2        0.03887215     NA    NA    NA
-## g         0.77417779     NA    NA    NA
+##          Estimate Pr(>t) Lower Upper
+## parent_0  94.7123     NA    NA    NA
+## k1         0.0389     NA    NA    NA
+## k2         0.0389     NA    NA    NA
+## g          0.7742     NA    NA    NA
 ## 
 ## 
 ## DTx values:
@@ -438,12 +455,14 @@
 

 

 Example on page 10

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

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

+
## Warning in summary.mkinfit(x): Could not estimate covariance matrix;
+## singular system.

 
## 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)

+
print(p10)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
 ## 899.4089 336.4348 899.4089 
@@ -453,29 +472,29 @@
 ## 
 ## Parameters:
 ## $SFO
-##                   Estimate       Pr(>t)       Lower        Upper
-## parent_0      101.73153064 4.954950e-11 90.96832870 112.49473259
-## k_parent_sink   0.04952864 3.398569e-07  0.03930194   0.06241642
+##               Estimate   Pr(>t)   Lower    Upper
+## parent_0      101.7315 4.95e-11 90.9683 112.4947
+## k_parent_sink   0.0495 3.40e-07  0.0393   0.0624
 ## 
 ## $IORE
-##                      Estimate       Pr(>t)      Lower       Upper
-## parent_0            96.855416 2.706118e-12 89.8843855 103.8264461
-## k__iore_parent_sink  2.960977 1.308097e-01  0.4609504  19.0202303
-## N_parent             0.000000 5.000000e-01 -0.4728922   0.4728922
+##                     Estimate   Pr(>t)  Lower   Upper
+## parent_0               96.86 2.71e-12 89.884 103.826
+## k__iore_parent_sink     2.96 1.31e-01  0.461  19.020
+## N_parent                0.00 5.00e-01 -0.473   0.473
 ## 
 ## $DFOP
-##              Estimate Pr(>t) Lower Upper
-## parent_0 101.73153022     NA    NA    NA
-## k1         0.04952864     NA    NA    NA
-## k2         0.04952864     NA    NA    NA
-## g          0.66344649     NA    NA    NA
+##          Estimate Pr(>t) Lower Upper
+## parent_0 101.7315     NA    NA    NA
+## k1         0.0495     NA    NA    NA
+## k2         0.0495     NA    NA    NA
+## g          0.6634     NA    NA    NA
 ## 
 ## 
 ## DTx values:
 ##      DT50 DT90 DT50_rep
-## SFO  14.0 46.5    14.00
+## SFO  14.0 46.5    13.99
 ## IORE 16.4 29.4     8.86
-## DFOP 14.0 46.5    14.00
+## DFOP 14.0 46.5    13.99
 ## 
 ## Representative half-life:
 ## [1] 8.862193

@@ -488,12 +507,14 @@
 

 

 Example on page 11

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

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

+
## Warning in summary.mkinfit(x): Could not estimate covariance matrix;
+## singular system.

 
## 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)

+
print(p11)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
 ## 579.6805 204.7932 144.7783 
@@ -503,22 +524,22 @@
 ## 
 ## Parameters:
 ## $SFO
-##                   Estimate       Pr(>t)        Lower        Upper
-## parent_0      96.158200840 1.560217e-13 89.913728706 1.024027e+02
-## k_parent_sink  0.003208498 5.266271e-05  0.002183575 4.714497e-03
+##               Estimate   Pr(>t)    Lower    Upper
+## parent_0      96.15820 1.56e-13 89.91373 1.02e+02
+## k_parent_sink  0.00321 5.27e-05  0.00218 4.71e-03
 ## 
 ## $IORE
-##                         Estimate Pr(>t)        Lower        Upper
-## parent_0            1.045981e+02     NA 9.798102e+01 1.112151e+02
-## k__iore_parent_sink 3.110367e-17     NA 6.875825e-25 1.407014e-09
-## N_parent            8.360812e+00     NA 4.397006e+00 1.232462e+01
+##                     Estimate Pr(>t)    Lower    Upper
+## parent_0            1.05e+02     NA 9.80e+01 1.11e+02
+## k__iore_parent_sink 3.11e-17     NA 6.88e-25 1.41e-09
+## N_parent            8.36e+00     NA 4.40e+00 1.23e+01
 ## 
 ## $DFOP
-##              Estimate       Pr(>t) Lower Upper
-## parent_0 1.045607e+02 7.502642e-13    NA    NA
-## k1       4.414526e-02 3.343950e-02    NA    NA
-## k2       7.246905e-13 5.000000e-01    NA    NA
-## g        3.217737e-01 7.868540e-03    NA    NA
+##          Estimate   Pr(>t) Lower Upper
+## parent_0 1.05e+02 7.50e-13    NA    NA
+## k1       4.41e-02 3.34e-02    NA    NA
+## k2       7.25e-13 5.00e-01    NA    NA
+## g        3.22e-01 7.87e-03    NA    NA
 ## 
 ## 
 ## DTx values:
@@ -539,12 +560,14 @@
 

 

 Example on page 12, upper panel

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

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

+
## Warning in summary.mkinfit(x): Could not estimate covariance matrix;
+## singular system.

 
## 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)

+
print(p12a)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
 ## 695.4440 220.0685 695.4440 
@@ -554,22 +577,22 @@
 ## 
 ## Parameters:
 ## $SFO
-##                  Estimate       Pr(>t)      Lower       Upper
-## parent_0      100.5206988 5.606929e-12 91.6867692 109.3546284
-## k_parent_sink   0.1243142 7.235485e-08  0.1017305   0.1519113
+##               Estimate   Pr(>t)  Lower   Upper
+## parent_0       100.521 5.61e-12 91.687 109.355
+## k_parent_sink    0.124 7.24e-08  0.102   0.152
 ## 
 ## $IORE
-##                       Estimate       Pr(>t)       Lower       Upper
-## parent_0            96.8234045 1.242894e-13 91.56908085 102.0777281
-## k__iore_parent_sink  2.4360714 3.893118e-02  0.78536982   7.5562415
-## N_parent             0.2627157 3.639503e-02 -0.02875633   0.5541876
+##                     Estimate   Pr(>t)   Lower   Upper
+## parent_0              96.823 1.24e-13 91.5691 102.078
+## k__iore_parent_sink    2.436 3.89e-02  0.7854   7.556
+## N_parent               0.263 3.64e-02 -0.0288   0.554
 ## 
 ## $DFOP
-##             Estimate Pr(>t) Lower Upper
-## parent_0 100.5206988     NA    NA    NA
-## k1         0.1243142     NA    NA    NA
-## k2         0.1243142     NA    NA    NA
-## g          0.8772377     NA    NA    NA
+##          Estimate Pr(>t) Lower Upper
+## parent_0  100.521     NA    NA    NA
+## k1          0.124     NA    NA    NA
+## k2          0.124     NA    NA    NA
+## g           0.877     NA    NA    NA
 ## 
 ## 
 ## DTx values:
@@ -584,12 +607,14 @@
 

 

 Example on page 12, lower panel

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

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

+
## Warning in summary.mkinfit(x): Could not estimate covariance matrix;
+## singular system.

 
## 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)

+
print(p12b)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
 ## 58.90242 19.06353 58.90242 
@@ -599,29 +624,29 @@
 ## 
 ## Parameters:
 ## $SFO
-##                 Estimate       Pr(>t)       Lower        Upper
-## parent_0      97.6840211 0.0000535970 86.32050115 109.04754103
-## k_parent_sink  0.0589177 0.0009869932  0.04320553   0.08034377
+##               Estimate   Pr(>t)   Lower    Upper
+## parent_0       97.6840 5.36e-05 86.3205 109.0475
+## k_parent_sink   0.0589 9.87e-04  0.0432   0.0803
 ## 
 ## $IORE
-##                       Estimate       Pr(>t)       Lower      Upper
-## parent_0            95.5232270 0.0003860431 84.09629121 106.950163
-## k__iore_parent_sink  0.3329365 0.1708863327  0.01026046  10.803285
-## N_parent             0.5677771 0.0548808046 -0.31606833   1.451622
+##                     Estimate   Pr(>t)   Lower  Upper
+## parent_0              95.523 0.000386 84.0963 106.95
+## k__iore_parent_sink    0.333 0.170886  0.0103  10.80
+## N_parent               0.568 0.054881 -0.3161   1.45
 ## 
 ## $DFOP
-##            Estimate Pr(>t) Lower Upper
-## parent_0 97.6840212     NA    NA    NA
-## k1        0.0589177     NA    NA    NA
-## k2        0.0589177     NA    NA    NA
-## g         0.6901929     NA    NA    NA
+##          Estimate Pr(>t) Lower Upper
+## parent_0  97.6840     NA    NA    NA
+## k1         0.0589     NA    NA    NA
+## k2         0.0589     NA    NA    NA
+## g          0.6902     NA    NA    NA
 ## 
 ## 
 ## DTx values:
 ##      DT50 DT90 DT50_rep
-## SFO  11.8 39.1    11.80
+## SFO  11.8 39.1    11.76
 ## IORE 12.9 31.4     9.46
-## DFOP 11.8 39.1    11.80
+## DFOP 11.8 39.1    11.76
 ## 
 ## Representative half-life:
 ## [1] 9.461912

@@ -629,12 +654,14 @@
 

 

 Example on page 13

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

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

+
## Warning in summary.mkinfit(x): Could not estimate covariance matrix;
+## singular system.

 
## 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)

+
print(p13)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
 ## 174.5971 142.3951 174.5971 
@@ -644,22 +671,22 @@
 ## 
 ## Parameters:
 ## $SFO
-##                   Estimate       Pr(>t)        Lower        Upper
-## parent_0      92.735003006 1.453426e-17 89.389064698 96.080941315
-## k_parent_sink  0.002581189 2.630396e-09  0.002198171  0.003030945
+##               Estimate   Pr(>t)   Lower    Upper
+## parent_0      92.73500 1.45e-17 89.3891 96.08094
+## k_parent_sink  0.00258 2.63e-09  0.0022  0.00303
 ## 
 ## $IORE
-##                        Estimate       Pr(>t)       Lower     Upper
-## parent_0            91.60158658 2.932498e-16 88.08710837 95.116065
-## k__iore_parent_sink  0.03960674 2.810573e-01  0.00102485  1.530656
-## N_parent             0.35408757 1.972378e-01 -0.51942545  1.227601
+##                     Estimate   Pr(>t)    Lower Upper
+## parent_0             91.6016 2.93e-16 88.08711 95.12
+## k__iore_parent_sink   0.0396 2.81e-01  0.00102  1.53
+## N_parent              0.3541 1.97e-01 -0.51943  1.23
 ## 
 ## $DFOP
-##              Estimate Pr(>t) Lower Upper
-## parent_0 92.735003208     NA    NA    NA
-## k1        0.002581186     NA    NA    NA
-## k2        0.002581188     NA    NA    NA
-## g         0.004422859     NA    NA    NA
+##          Estimate Pr(>t) Lower Upper
+## parent_0 92.73500     NA    NA    NA
+## k1        0.00258     NA    NA    NA
+## k2        0.00258     NA    NA    NA
+## g         0.00442     NA    NA    NA
 ## 
 ## 
 ## DTx values:
@@ -675,12 +702,14 @@
 

 

 DT50 not observed in the study and DFOP problems in PestDF

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

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

+
## Warning in summary.mkinfit(x): Could not estimate covariance matrix;
+## singular system.

 
## 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)

+
print(p14)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
 ## 48.43249 28.67746 27.26248 
@@ -690,22 +719,22 @@
 ## 
 ## Parameters:
 ## $SFO
-##                   Estimate       Pr(>t)        Lower        Upper
-## parent_0      99.471243637 1.708290e-31 98.373131052 1.005694e+02
-## k_parent_sink  0.002789581 2.222078e-15  0.002554583 3.046197e-03
+##               Estimate   Pr(>t)    Lower    Upper
+## parent_0      99.47124 1.71e-31 98.37313 1.01e+02
+## k_parent_sink  0.00279 2.22e-15  0.00255 3.05e-03
 ## 
 ## $IORE
-##                         Estimate Pr(>t)        Lower        Upper
-## parent_0            1.003522e+02     NA 9.926773e+01 1.014366e+02
-## k__iore_parent_sink 9.443770e-08     NA 6.810412e-11 1.309536e-04
-## N_parent            3.308552e+00     NA 1.690051e+00 4.927053e+00
+##                     Estimate Pr(>t)    Lower    Upper
+## parent_0            1.00e+02     NA 9.93e+01 1.01e+02
+## k__iore_parent_sink 9.44e-08     NA 6.81e-11 1.31e-04
+## N_parent            3.31e+00     NA 1.69e+00 4.93e+00
 ## 
 ## $DFOP
-##              Estimate       Pr(>t) Lower Upper
-## parent_0 1.003398e+02 2.698790e-28    NA    NA
-## k1       9.532677e-03 3.394353e-01    NA    NA
-## k2       9.189935e-12 5.000000e-01    NA    NA
-## g        3.982564e-01 3.920847e-01    NA    NA
+##          Estimate   Pr(>t) Lower Upper
+## parent_0 1.00e+02 2.70e-28    NA    NA
+## k1       9.53e-03 3.39e-01    NA    NA
+## k2       9.19e-12 5.00e-01    NA    NA
+## g        3.98e-01 3.92e-01    NA    NA
 ## 
 ## 
 ## DTx values:
@@ -721,12 +750,14 @@
 

 

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

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

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

+
## Warning in summary.mkinfit(x): Could not estimate covariance matrix;
+## singular system.

 
## 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)

+
print(p15a)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
 ## 245.5248 135.0132 245.5248 
@@ -736,22 +767,22 @@
 ## 
 ## Parameters:
 ## $SFO
-##                   Estimate       Pr(>t)        Lower       Upper
-## parent_0      97.967511635 4.984358e-16 94.038286642 101.8967366
-## k_parent_sink  0.009522227 5.239115e-09  0.008126698   0.0111574
+##               Estimate   Pr(>t)    Lower    Upper
+## parent_0      97.96751 4.98e-16 94.03829 101.8967
+## k_parent_sink  0.00952 5.24e-09  0.00813   0.0112
 ## 
 ## $IORE
-##                       Estimate       Pr(>t)       Lower      Upper
-## parent_0            95.8736780 8.295860e-16 92.58018331 99.1671726
-## k__iore_parent_sink  0.6285106 2.386496e-01  0.03155477 12.5187302
-## N_parent             0.0000000 5.000000e-01 -0.72189225  0.7218923
+##                     Estimate   Pr(>t)   Lower  Upper
+## parent_0              95.874 8.30e-16 92.5802 99.167
+## k__iore_parent_sink    0.629 2.39e-01  0.0316 12.519
+## N_parent               0.000 5.00e-01 -0.7219  0.722
 ## 
 ## $DFOP
-##              Estimate Pr(>t) Lower Upper
-## parent_0 97.967516468     NA    NA    NA
-## k1        0.009522243     NA    NA    NA
-## k2        0.009522223     NA    NA    NA
-## g         0.172466840     NA    NA    NA
+##          Estimate Pr(>t) Lower Upper
+## parent_0 97.96752     NA    NA    NA
+## k1        0.00952     NA    NA    NA
+## k2        0.00952     NA    NA    NA
+## g         0.17247     NA    NA    NA
 ## 
 ## 
 ## DTx values:
@@ -762,12 +793,14 @@
 ## 
 ## Representative half-life:
 ## [1] 41.32749

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

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

+
## Warning in summary.mkinfit(x): Could not estimate covariance matrix;
+## singular system.

 
## 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)

+
print(p15b)

 
## Sums of squares:
 ##       SFO      IORE      DFOP 
 ## 106.91629  68.55574 106.91629 
@@ -777,29 +810,29 @@
 ## 
 ## Parameters:
 ## $SFO
-##                   Estimate       Pr(>t)        Lower        Upper
-## parent_0      1.008816e+02 4.987925e-18 98.127607367 1.036355e+02
-## k_parent_sink 4.856586e-03 1.756208e-10  0.004316334 5.464459e-03
+##               Estimate   Pr(>t)    Lower    Upper
+## parent_0      1.01e+02 4.99e-18 98.12761 1.04e+02
+## k_parent_sink 4.86e-03 1.76e-10  0.00432 5.46e-03
 ## 
 ## $IORE
-##                       Estimate       Pr(>t)       Lower     Upper
-## parent_0            99.8268283 4.490292e-17 97.19753163 102.45613
-## k__iore_parent_sink  0.3799625 3.406003e-01  0.00206198  70.01593
-## N_parent             0.0000000 5.000000e-01 -1.20105017   1.20105
+##                     Estimate   Pr(>t)    Lower Upper
+## parent_0               99.83 4.49e-17 97.19753 102.5
+## k__iore_parent_sink     0.38 3.41e-01  0.00206  70.0
+## N_parent                0.00 5.00e-01 -1.20105   1.2
 ## 
 ## $DFOP
-##              Estimate Pr(>t) Lower Upper
-## parent_0 1.008816e+02     NA    NA    NA
-## k1       4.856586e-03     NA    NA    NA
-## k2       4.856586e-03     NA    NA    NA
-## g        1.496838e-01     NA    NA    NA
+##          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        1.50e-01     NA    NA    NA
 ## 
 ## 
 ## DTx values:
 ##      DT50 DT90 DT50_rep
-## SFO   143  474    143.0
+## SFO   143  474    142.7
 ## IORE  131  236     71.2
-## DFOP  143  474    143.0
+## DFOP  143  474    142.7
 ## 
 ## Representative half-life:
 ## [1] 71.18014

@@ -808,14 +841,14 @@
 

 

 The DFOP fraction parameter is greater than 1

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

+
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)

+
print(p16)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
 ## 3831.804 2062.008 1550.980 
@@ -825,22 +858,22 @@
 ## 
 ## Parameters:
 ## $SFO
-##                 Estimate       Pr(>t)      Lower      Upper
-## parent_0      71.9528227 3.923531e-14 61.0870510 82.8185944
-## k_parent_sink  0.1594518 2.271601e-06  0.1110583  0.2289327
+##               Estimate   Pr(>t)  Lower  Upper
+## parent_0        71.953 3.92e-14 61.087 82.819
+## k_parent_sink    0.159 2.27e-06  0.111  0.229
 ## 
 ## $IORE
-##                         Estimate       Pr(>t)        Lower        Upper
-## parent_0            8.738846e+01 1.739390e-16 7.706991e+01 97.707005461
-## k__iore_parent_sink 4.549683e-04 2.282721e-01 3.008533e-05  0.006880303
-## N_parent            2.696278e+00 1.869479e-08 1.966442e+00  3.426114200
+##                     Estimate   Pr(>t)    Lower    Upper
+## parent_0            8.74e+01 1.74e-16 7.71e+01 97.70701
+## k__iore_parent_sink 4.55e-04 2.28e-01 3.01e-05  0.00688
+## N_parent            2.70e+00 1.87e-08 1.97e+00  3.42611
 ## 
 ## $DFOP
-##             Estimate Pr(>t)       Lower      Upper
-## parent_0 88.53333334     NA 79.36733990 97.6993268
-## k1       18.55624337     NA  0.00000000        Inf
-## k2        0.07759679     NA  0.04709945  0.1278414
-## g         0.47333008     NA  0.31375096  0.6385506
+##          Estimate Pr(>t)   Lower  Upper
+## parent_0  88.5333     NA 79.3673 97.699
+## k1        18.5562     NA  0.0000    Inf
+## k2         0.0776     NA  0.0471  0.128
+## g          0.4733     NA  0.3138  0.639
 ## 
 ## 
 ## DTx values:
-- 
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