From 91c5db736a4d3f2290a0cc5698fb4e35ae7bda59 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 18 May 2022 21:26:17 +0200 Subject: Remove outdated comment in FOCUS L vignette, update docs This also adds the first benchmark results obtained on my laptop system --- docs/articles/web_only/NAFTA_examples.html | 154 ++++++++++++++--------------- 1 file changed, 75 insertions(+), 79 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 996e5d49..df1e06db 100644 --- a/docs/articles/web_only/NAFTA_examples.html +++ b/docs/articles/web_only/NAFTA_examples.html @@ -43,7 +43,7 @@ Functions and data
  • - vignettes/web_only/NAFTA_examples.rmd @@ -161,7 +161,7 @@ ## 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 2.26e-12 5.00e-01 0.0000 Inf +## k2 2.95e-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 ## @@ -170,7 +170,7 @@ ## 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 5.59e+11 3.07e+11 +## DFOP 55.5 4.28e+11 2.35e+11 ## ## Representative half-life: ## [1] 321.51 @@ -212,7 +212,7 @@ ## 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 8.63e-12 5.00e-01 0.0000 Inf +## k2 9.41e-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 ## @@ -221,7 +221,7 @@ ## 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 1.32e+11 8.04e+10 +## DFOP 83.6 1.21e+11 7.36e+10 ## ## Representative half-life: ## [1] 215.87 @@ -263,7 +263,7 @@ ## 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 3.22e-11 5.00e-01 0.0000 Inf +## k2 4.40e-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 ## @@ -272,7 +272,7 @@ ## 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 1.01e+10 2.15e+10 +## DFOP 34.1 7.43e+09 1.58e+10 ## ## Representative half-life: ## [1] 53.17 @@ -314,7 +314,7 @@ ## 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 3.63e-10 5.00e-01 0.0000 Inf +## k2 2.81e-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 ## @@ -323,7 +323,7 @@ ## 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 3.77e+09 1.91e+09 +## DFOP 96.4 4.87e+09 2.46e+09 ## ## Representative half-life: ## [1] 454.55 @@ -434,7 +434,7 @@ ## 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 7.69e+11 +## DFOP 10.5 1.38e+12 7.68e+11 ## ## Representative half-life: ## [1] 101.43 @@ -445,17 +445,12 @@ 
     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 
@@ -482,8 +477,8 @@
 ##          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
 ## 
 ## 
@@ -500,7 +495,7 @@
 
    
 
    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
    
@@ -508,10 +503,10 @@
 ## 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(p10)
    
 
    
-
    +
     print(p10)
    
 
    ## Sums of squares:
 ##      SFO     IORE     DFOP 
@@ -537,8 +532,8 @@
 ## $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
+## k1         0.0495 6.32e-03  0.0241   0.1018
+## k2         0.0495 2.41e-03  0.0272   0.0901
 ## g          0.4487 5.00e-01      NA       NA
 ## sigma      8.0152 2.50e-04  4.5886  11.4418
 ## 
@@ -560,14 +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 
@@ -594,7 +589,7 @@
 ##          Estimate   Pr(>t)    Lower    Upper
 ## parent_0 1.05e+02 9.47e-13  99.9990 109.1224
 ## k1       4.41e-02 5.95e-03   0.0296   0.0658
-## k2       9.94e-13 5.00e-01   0.0000      Inf
+## k2       9.93e-13 5.00e-01   0.0000      Inf
 ## g        3.22e-01 1.45e-03   0.2814   0.3650
 ## sigma    3.22e+00 3.52e-04   1.8410   4.5906
 ## 
@@ -606,7 +601,7 @@
 ## DFOP 3.07e+11 1.93e+12 6.98e+11
 ## 
 ## Representative half-life:
-## [1] 41148170
    
+## [1] 41148171
    
 
    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.
    
 
    
 
    
@@ -617,21 +612,19 @@
 
    
 
    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 
@@ -655,12 +648,12 @@
 ## sigma             3.965     NA    NA    NA
 ## 
 ## $DFOP
-##          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
+##          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           0.793     NA    NA    NA
+## sigma       7.048     NA    NA    NA
 ## 
 ## 
 ## DTx values:
@@ -675,18 +668,17 @@
 
    
 
    Example on page 12, lower panel
 
    
-
    +
     p12b <- nafta(NAFTA_SOP_Attachment[["p12b"]])
    
 
    ## 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
    
 
    ## 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 
@@ -730,14 +722,18 @@
 
    
 
    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 
@@ -763,9 +759,9 @@
 ## $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
-## g         0.16452     NA 0.00e+00  1.00000
+## k1        0.00258     NA 4.24e-04  0.01573
+## k2        0.00258     NA 1.76e-03  0.00379
+## g         0.16452     NA       NA       NA
 ## sigma     3.41172     NA 2.02e+00  4.79960
 ## 
 ## 
@@ -782,7 +778,7 @@
 
    
 
    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
    
@@ -790,10 +786,10 @@
 ## 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 
@@ -820,7 +816,7 @@
 ##          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       6.08e-12 5.00e-01  0.00000      Inf
+## k2       5.03e-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
 ## 
@@ -829,7 +825,7 @@
 ##          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 3.05e+10 2.95e+11 1.14e+11
+## DFOP 3.69e+10 3.57e+11 1.38e+11
 ## 
 ## Representative half-life:
 ## [1] 6697.44
    
@@ -838,14 +834,18 @@
 
    
 
    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)
    
 
    
-
    +
     print(p15a)
    
 
    ## Sums of squares:
 ##      SFO     IORE     DFOP 
@@ -871,9 +871,9 @@
 ## $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
 ## 
 ## 
@@ -885,18 +885,14 @@
 ## 
 ## 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
    
 
    ## 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 
@@ -916,15 +912,15 @@
 ##                Estimate   Pr(>t)    Lower  Upper
 ## 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
+## N_parent           0.00 5.00e-01 -1.07695   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
+## k1       4.86e-03     NA 8.62e-04 2.74e-02
 ## k2       4.86e-03     NA 3.21e-03 7.35e-03
-## g        1.88e-01     NA       NA       NA
+## g        1.88e-01     NA 0.00e+00 1.00e+00
 ## sigma    2.76e+00     NA 1.58e+00 3.94e+00
 ## 
 ## 
@@ -941,16 +937,16 @@
 
    
 
    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 
@@ -1026,7 +1022,7 @@
 
 
    
   
    
-
    Site built with pkgdown 2.0.2.
    
+
    Site built with pkgdown 2.0.3.
    
 
    
 
       
-- 
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