From 396e40d2c45d81a8e74c41a2f632665021e980a1 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 26 Feb 2019 20:28:15 +0100 Subject: NAFTA SOP Attachment vignette Also: - Change rounding in print.nafta - Add dots argument to nafta() - Use cores=1 in examples - Restrict N in IORE model to values > 0 --- docs/reference/AIC.mmkin.html | 4 +- docs/reference/Extract.mmkin.html | 12 +- docs/reference/NAFTA_SOP_2015.html | 13 +- docs/reference/NAFTA_SOP_Attachment-1.png | Bin 0 -> 42277 bytes docs/reference/NAFTA_SOP_Attachment.html | 217 ++++++++++++++++++++++++++++++ docs/reference/index.html | 4 +- docs/reference/mccall81_245T.html | 12 +- docs/reference/mkinfit.html | 44 +++--- docs/reference/mkinmod.html | 2 +- docs/reference/mkinpredict.html | 4 +- docs/reference/mmkin.html | 4 +- docs/reference/nafta.html | 19 ++- docs/reference/plot.nafta.html | 12 +- docs/reference/print.nafta.html | 8 +- docs/reference/summary.mkinfit.html | 6 +- docs/reference/transform_odeparms.html | 24 ++-- 16 files changed, 310 insertions(+), 75 deletions(-) create mode 100644 docs/reference/NAFTA_SOP_Attachment-1.png create mode 100644 docs/reference/NAFTA_SOP_Attachment.html (limited to 'docs/reference') diff --git a/docs/reference/AIC.mmkin.html b/docs/reference/AIC.mmkin.html index 69552d5f..2a4a6de4 100644 --- a/docs/reference/AIC.mmkin.html +++ b/docs/reference/AIC.mmkin.html @@ -160,8 +160,8 @@

Examples

f <- mmkin(c("SFO", "FOMC", "DFOP"), list("FOCUS A" = FOCUS_2006_A, - "FOCUS C" = FOCUS_2006_C)) - AIC(f[1, "FOCUS A"]) # We get a single number for a single fit
#> [1] 55.32452
+ "FOCUS C" = FOCUS_2006_C), cores = 1, quiet = TRUE)
#> Warning: Optimisation by method Port did not converge: +#> false convergence (8)
AIC(f[1, "FOCUS A"]) # We get a single number for a single fit
#> [1] 55.32452
# For FOCUS A, the models fit almost equally well, so the higher the number # of parameters, the higher (worse) the AIC AIC(f[, "FOCUS A"])
#> df AIC diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 873d75bd..f10805a0 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -280,7 +280,7 @@ #> #> $time #> User System verstrichen -#> 0.195 0.000 0.195 +#> 0.071 0.000 0.071 #> #> $mkinmod #> <mkinmod> model generated with @@ -469,8 +469,8 @@ #> } #> return(mC) #> } -#> <bytecode: 0x55555925ca08> -#> <environment: 0x55555b668200> +#> <bytecode: 0x55555bb55ad0> +#> <environment: 0x55555c4dcf70> #> #> $cost_notrans #> function (P) @@ -492,8 +492,8 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <bytecode: 0x55555a590818> -#> <environment: 0x55555b668200> +#> <bytecode: 0x55555c537298> +#> <environment: 0x55555c4dcf70> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -560,7 +560,7 @@ #> 99.17407 #> #> $date -#> [1] "Tue Feb 26 09:27:10 2019" +#> [1] "Tue Feb 26 20:23:09 2019" #> #> $version #> [1] "0.9.48.1" diff --git a/docs/reference/NAFTA_SOP_2015.html b/docs/reference/NAFTA_SOP_2015.html index 4a2c71a9..f4d89222 100644 --- a/docs/reference/NAFTA_SOP_2015.html +++ b/docs/reference/NAFTA_SOP_2015.html @@ -152,7 +152,8 @@

Examples

-
nafta_evaluation <- nafta(NAFTA_SOP_Appendix_D)
#> 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
print(nafta_evaluation)
#> Sums of squares: +
nafta_evaluation <- nafta(NAFTA_SOP_Appendix_D, cores = 1)
#> Warning: Calculation of the Jacobian failed for the cost function of the untransformed model. +#> No t-test results will be available
#> 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
print(nafta_evaluation)
#> Sums of squares: #> SFO IORE DFOP #> 1378.6832 615.7730 517.8836 #> @@ -168,8 +169,8 @@ #> $IORE #> Estimate Pr(>t) Lower Upper #> parent_0 9.685291e+01 NA 8.752855e+01 1.061773e+02 -#> k__iore_parent_sink 8.403374e-14 NA 1.092054e-19 6.466412e-08 -#> N_parent 6.684458e+00 NA 3.538511e+00 9.830405e+00 +#> k__iore_parent_sink 8.403401e-14 NA 1.092058e-19 6.466429e-08 +#> N_parent 6.684457e+00 NA 3.538510e+00 9.830404e+00 #> #> $DFOP #> Estimate Pr(>t) Lower Upper @@ -181,9 +182,9 @@ #> #> DTx values: #> DT50 DT90 DT50_rep -#> SFO 407 1352 407 -#> IORE 541 5192066 1562968 -#> DFOP 429 2383 841 +#> SFO 407 1350 407 +#> IORE 541 5190000 1560000 +#> DFOP 429 2380 841 #> #> Representative half-life: #> [1] 841.4096
plot(nafta_evaluation)
diff --git a/docs/reference/NAFTA_SOP_Attachment-1.png b/docs/reference/NAFTA_SOP_Attachment-1.png new file mode 100644 index 00000000..d781cdb0 Binary files /dev/null and b/docs/reference/NAFTA_SOP_Attachment-1.png differ diff --git a/docs/reference/NAFTA_SOP_Attachment.html b/docs/reference/NAFTA_SOP_Attachment.html new file mode 100644 index 00000000..63b47855 --- /dev/null +++ b/docs/reference/NAFTA_SOP_Attachment.html @@ -0,0 +1,217 @@ + + + + + + + + +Example datasets from Attachment 1 to the NAFTA SOP published 2015 — NAFTA_SOP_Attachment • mkin + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+
+ + + +
+ +
+
+ + +
+ +

Data taken from from Attachment 1 of the SOP.

+ +
+ +
NAFTA_SOP_Attachment
+ +

Format

+ +

Additionally, a list (NAFTA_SOP_Attachment) containing 16 datasets suitable + for the evaluation with nafta

+ +

Source

+ +

NAFTA (2011) Guidance for evaluating and calculating degradation kinetics + in environmental media. NAFTA Technical Working Group on Pesticides + https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation + accessed 2019-02-22

+

US EPA (2015) Standard Operating Procedure for Using the NAFTA Guidance to + Calculate Representative Half-life Values and Characterizing Pesticide + Degradation + https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance

+ + +

Examples

+
nafta_att_p5a <- nafta(NAFTA_SOP_Attachment[["p5a"]], cores = 1)
#> 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
print(nafta_att_p5a)
#> Sums of squares: +#> SFO IORE DFOP +#> 465.21753 56.27506 32.06401 +#> +#> Critical sum of squares for checking the SFO model: +#> [1] 64.4304 +#> +#> 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 +#> +#> $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 +#> +#> $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 +#> +#> +#> DTx values: +#> 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 5.84e+11 3.21e+11 +#> +#> Representative half-life: +#> [1] 321.5119
plot(nafta_att_p5a)
+
+ +
+ +
+ + +
+

Site built with pkgdown 1.3.0.9000.

+
+
+
+ + + + + + diff --git a/docs/reference/index.html b/docs/reference/index.html index a251dc33..4e57fd3d 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -338,7 +338,9 @@

plot(<nafta>)

-

Plot the results of the three models used in the NAFTA scheme

+

Plot the results of the three models used in the NAFTA scheme. The plots + are ordered with increasing complexity of the model in this function + (SFO, then IORE, then DFOP).

diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 1845a31c..2e5f0ac2 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -160,8 +160,8 @@ anisole = list(type = "SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
fit.1 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"), quiet = TRUE) summary(fit.1, data = FALSE)
#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Tue Feb 26 09:27:31 2019 -#> Date of summary: Tue Feb 26 09:27:31 2019 +#> Date of fit: Tue Feb 26 20:23:32 2019 +#> Date of summary: Tue Feb 26 20:23:32 2019 #> #> Equations: #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -171,7 +171,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 574 model solutions performed in 3.812 s +#> Fitted with method Port using 574 model solutions performed in 3.765 s #> #> Weighting: none #> @@ -249,8 +249,8 @@ fixed_parms = "k_phenol_sink", quiet = TRUE) summary(fit.2, data = FALSE)
#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Tue Feb 26 09:27:33 2019 -#> Date of summary: Tue Feb 26 09:27:33 2019 +#> Date of fit: Tue Feb 26 20:23:34 2019 +#> Date of summary: Tue Feb 26 20:23:34 2019 #> #> Equations: #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -260,7 +260,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 246 model solutions performed in 1.597 s +#> Fitted with method Port using 246 model solutions performed in 1.601 s #> #> Weighting: none #> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 53f46988..84c0fc49 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -438,15 +438,15 @@ fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE) summary(fit)
#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Tue Feb 26 09:27:36 2019 -#> Date of summary: Tue Feb 26 09:27:36 2019 +#> Date of fit: Tue Feb 26 20:23:36 2019 +#> Date of summary: Tue Feb 26 20:23:36 2019 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent #> #> Model predictions using solution type analytical #> -#> Fitted with method Port using 64 model solutions performed in 0.163 s +#> Fitted with method Port using 64 model solutions performed in 0.161 s #> #> Weighting: none #> @@ -515,7 +515,7 @@ m1 = mkinsub("SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
# Fit the model to the FOCUS example dataset D using defaults print(system.time(fit <- mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "eigen", quiet = TRUE)))
#> User System verstrichen -#> 1.008 0.000 1.008
coef(fit)
#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 1.081 0.000 1.081
coef(fit)
#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink #> 99.59848 -3.03822 -2.98030 -5.24750
#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 @@ -590,7 +590,7 @@ #> Model cost at call 146 : 371.2134 #> Optimisation by method Port successfully terminated. #> User System verstrichen -#> 0.812 0.000 0.813
coef(fit.deSolve)
#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 0.812 0.000 0.812
coef(fit.deSolve)
#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink #> 99.59848 -3.03822 -2.98030 -5.24750
endpoints(fit.deSolve)
#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 @@ -628,8 +628,8 @@ m1 = mkinsub("SFO"), use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.
f.noweight <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE) summary(f.noweight)
#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Tue Feb 26 09:27:48 2019 -#> Date of summary: Tue Feb 26 09:27:48 2019 +#> Date of fit: Tue Feb 26 20:23:48 2019 +#> Date of summary: Tue Feb 26 20:23:48 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -637,7 +637,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 186 model solutions performed in 0.845 s +#> Fitted with method Port using 186 model solutions performed in 0.852 s #> #> Weighting: none #> @@ -745,8 +745,8 @@ #> 120 m1 33.31 28.78984 4.520e+00
f.irls <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, reweight.method = "obs", quiet = TRUE) summary(f.irls)
#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Tue Feb 26 09:27:50 2019 -#> Date of summary: Tue Feb 26 09:27:50 2019 +#> Date of fit: Tue Feb 26 20:23:51 2019 +#> Date of summary: Tue Feb 26 20:23:51 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -754,7 +754,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 551 model solutions performed in 2.523 s +#> Fitted with method Port using 551 model solutions performed in 2.6 s #> #> Weighting: none #> @@ -867,8 +867,8 @@ #> 120 m1 33.31 28.80898 4.501e+00 2.722
f.w.mean <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, weight = "mean", quiet = TRUE) summary(f.w.mean)
#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Tue Feb 26 09:27:51 2019 -#> Date of summary: Tue Feb 26 09:27:51 2019 +#> Date of fit: Tue Feb 26 20:23:52 2019 +#> Date of summary: Tue Feb 26 20:23:52 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -876,7 +876,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 155 model solutions performed in 0.705 s +#> Fitted with method Port using 155 model solutions performed in 0.704 s #> #> Weighting: mean #> @@ -985,8 +985,8 @@ quiet = TRUE) summary(f.w.value)
#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Tue Feb 26 09:27:52 2019 -#> Date of summary: Tue Feb 26 09:27:52 2019 +#> Date of fit: Tue Feb 26 20:23:53 2019 +#> Date of summary: Tue Feb 26 20:23:53 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -994,7 +994,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 174 model solutions performed in 0.8 s +#> Fitted with method Port using 174 model solutions performed in 0.796 s #> #> Weighting: manual #> @@ -1105,8 +1105,8 @@ f.w.man <- mkinfit(SFO_SFO.ff, dw, err = "err.man", quiet = TRUE) summary(f.w.man)
#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Tue Feb 26 09:27:54 2019 -#> Date of summary: Tue Feb 26 09:27:54 2019 +#> Date of fit: Tue Feb 26 20:23:54 2019 +#> Date of summary: Tue Feb 26 20:23:54 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -1223,8 +1223,8 @@ reweight.method = "obs") summary(f.w.man.irls)
#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Tue Feb 26 09:27:57 2019 -#> Date of summary: Tue Feb 26 09:27:57 2019 +#> Date of fit: Tue Feb 26 20:23:58 2019 +#> Date of summary: Tue Feb 26 20:23:58 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -1232,7 +1232,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 692 model solutions performed in 3.246 s +#> Fitted with method Port using 692 model solutions performed in 3.182 s #> #> Weighting: manual #> diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index bcf39e7f..a6dd68c5 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -231,7 +231,7 @@ For the definition of model types and their parameters, the equations given SFO_SFO <- mkinmod( parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"), verbose = TRUE)
#> Compilation argument: -#> /usr/lib/R/bin/R CMD SHLIB file4a116f6acbf1.c 2> file4a116f6acbf1.c.err.txt +#> /usr/lib/R/bin/R CMD SHLIB file240f6aec3e43.c 2> file240f6aec3e43.c.err.txt #> Program source: #> 1: #include <R.h> #> 2: diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index a38de769..bab6deb8 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -325,7 +325,7 @@ c(parent = 100, m1 = 0), seq(0, 20, by = 0.1), solution_type = "eigen")[201,]))
#> time parent m1 #> 201 20 4.978707 27.46227
#> User System verstrichen -#> 0.004 0.000 0.004
system.time( +#> 0.003 0.000 0.004
system.time( print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01), c(parent = 100, m1 = 0), seq(0, 20, by = 0.1), solution_type = "deSolve")[201,]))
#> time parent m1 @@ -335,7 +335,7 @@ c(parent = 100, m1 = 0), seq(0, 20, by = 0.1), solution_type = "deSolve", use_compiled = FALSE)[201,]))
#> time parent m1 #> 201 20 4.978707 27.46227
#> User System verstrichen -#> 0.040 0.000 0.039
+#> 0.039 0.000 0.040
# Predict from a fitted model f <- mkinfit(SFO_SFO, FOCUS_2006_C)
#> Model cost at call 1 : 552.5739 #> Model cost at call 3 : 552.5739 diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index 6613f35c..0078baed 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -191,8 +191,8 @@ time_1 <- system.time(fits.4 <- mmkin(models, datasets, cores = 1, quiet = TRUE)) time_default
#> User System verstrichen -#> 0.052 0.024 7.037
time_1
#> User System verstrichen -#> 22.463 0.000 22.476
+#> 0.059 0.021 6.916
time_1
#> User System verstrichen +#> 22.506 0.000 22.518
endpoints(fits.0[["SFO_lin", 2]])
#> $ff #> parent_M1 parent_sink M1_M2 M1_sink #> 0.7340480 0.2659520 0.7505686 0.2494314 diff --git a/docs/reference/nafta.html b/docs/reference/nafta.html index b1d45272..9b879786 100644 --- a/docs/reference/nafta.html +++ b/docs/reference/nafta.html @@ -133,7 +133,7 @@
-
nafta(ds, title = NA, quiet = FALSE)
+
nafta(ds, title = NA, quiet = FALSE, …)

Arguments

@@ -153,6 +153,10 @@ + + + +
quiet

Should the evaluation text be shown?

Further arguments passed to mmkin.

Value

@@ -175,7 +179,8 @@

Examples

-
nafta_evaluation <- nafta(NAFTA_SOP_Appendix_D)
#> 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
print(nafta_evaluation)
#> Sums of squares: +
nafta_evaluation <- nafta(NAFTA_SOP_Appendix_D, cores = 1)
#> Warning: Calculation of the Jacobian failed for the cost function of the untransformed model. +#> No t-test results will be available
#> 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
print(nafta_evaluation)
#> Sums of squares: #> SFO IORE DFOP #> 1378.6832 615.7730 517.8836 #> @@ -191,8 +196,8 @@ #> $IORE #> Estimate Pr(>t) Lower Upper #> parent_0 9.685291e+01 NA 8.752855e+01 1.061773e+02 -#> k__iore_parent_sink 8.403374e-14 NA 1.092054e-19 6.466412e-08 -#> N_parent 6.684458e+00 NA 3.538511e+00 9.830405e+00 +#> k__iore_parent_sink 8.403401e-14 NA 1.092058e-19 6.466429e-08 +#> N_parent 6.684457e+00 NA 3.538510e+00 9.830404e+00 #> #> $DFOP #> Estimate Pr(>t) Lower Upper @@ -204,9 +209,9 @@ #> #> DTx values: #> DT50 DT90 DT50_rep -#> SFO 407 1352 407 -#> IORE 541 5192066 1562968 -#> DFOP 429 2383 841 +#> SFO 407 1350 407 +#> IORE 541 5190000 1560000 +#> DFOP 429 2380 841 #> #> Representative half-life: #> [1] 841.4096
plot(nafta_evaluation)
diff --git a/docs/reference/plot.nafta.html b/docs/reference/plot.nafta.html index 76da1ffa..7949d36c 100644 --- a/docs/reference/plot.nafta.html +++ b/docs/reference/plot.nafta.html @@ -6,7 +6,9 @@ -Plot the results of the three models used in the NAFTA scheme — plot.nafta • mkin +Plot the results of the three models used in the NAFTA scheme. The plots + are ordered with increasing complexity of the model in this function + (SFO, then IORE, then DFOP). — plot.nafta • mkin @@ -30,7 +32,9 @@ - + @@ -118,7 +122,9 @@
diff --git a/docs/reference/print.nafta.html b/docs/reference/print.nafta.html index ac276857..44f1f6e5 100644 --- a/docs/reference/print.nafta.html +++ b/docs/reference/print.nafta.html @@ -32,7 +32,9 @@ - + @@ -125,7 +127,9 @@
-

Print nafta objects.

+

Print nafta objects. The results for the three models + are printed in the order of increasing model complexity, + i.e. SFO, then IORE, and finally DFOP.

diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index ca0b1c4c..6ec72f80 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -208,15 +208,15 @@

Examples

summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Tue Feb 26 09:28:49 2019 -#> Date of summary: Tue Feb 26 09:28:49 2019 +#> Date of fit: Tue Feb 26 20:24:50 2019 +#> Date of summary: Tue Feb 26 20:24:50 2019 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent #> #> Model predictions using solution type analytical #> -#> Fitted with method Port using 35 model solutions performed in 0.085 s +#> Fitted with method Port using 35 model solutions performed in 0.084 s #> #> Weighting: none #> diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index bcfbe975..6e65f609 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -202,8 +202,8 @@ The transformation of sets of formation fractions is fragile, as it supposes fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE) summary(fit, data=FALSE) # See transformed and backtransformed parameters
#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Tue Feb 26 09:28:57 2019 -#> Date of summary: Tue Feb 26 09:28:57 2019 +#> Date of fit: Tue Feb 26 20:24:58 2019 +#> Date of summary: Tue Feb 26 20:24:58 2019 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent @@ -211,7 +211,7 @@ The transformation of sets of formation fractions is fragile, as it supposes #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 153 model solutions performed in 0.7 s +#> Fitted with method Port using 153 model solutions performed in 0.707 s #> #> Weighting: none #> @@ -278,8 +278,8 @@ The transformation of sets of formation fractions is fragile, as it supposes
fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE, quiet = TRUE) summary(fit.2, data=FALSE)
#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Tue Feb 26 09:28:59 2019 -#> Date of summary: Tue Feb 26 09:28:59 2019 +#> Date of fit: Tue Feb 26 20:25:00 2019 +#> Date of summary: Tue Feb 26 20:25:00 2019 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent @@ -287,7 +287,7 @@ The transformation of sets of formation fractions is fragile, as it supposes #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 350 model solutions performed in 1.59 s +#> Fitted with method Port using 350 model solutions performed in 1.584 s #> #> Weighting: none #> @@ -366,8 +366,8 @@ The transformation of sets of formation fractions is fragile, as it supposes fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE) summary(fit.ff, data = FALSE)
#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Tue Feb 26 09:29:00 2019 -#> Date of summary: Tue Feb 26 09:29:00 2019 +#> Date of fit: Tue Feb 26 20:25:01 2019 +#> Date of summary: Tue Feb 26 20:25:01 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -375,7 +375,7 @@ The transformation of sets of formation fractions is fragile, as it supposes #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 186 model solutions performed in 0.844 s +#> Fitted with method Port using 186 model solutions performed in 0.867 s #> #> Weighting: none #> @@ -450,8 +450,8 @@ The transformation of sets of formation fractions is fragile, as it supposes fit.ff.2 <- mkinfit(SFO_SFO.ff.2, FOCUS_2006_D, quiet = TRUE) summary(fit.ff.2, data = FALSE)
#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Tue Feb 26 09:29:01 2019 -#> Date of summary: Tue Feb 26 09:29:01 2019 +#> Date of fit: Tue Feb 26 20:25:02 2019 +#> Date of summary: Tue Feb 26 20:25:02 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -459,7 +459,7 @@ The transformation of sets of formation fractions is fragile, as it supposes #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 104 model solutions performed in 0.467 s +#> Fitted with method Port using 104 model solutions performed in 0.472 s #> #> Weighting: none #> -- cgit v1.2.1