mccall81_245T.RdTime course of 2,4,5-trichlorophenoxyacetic acid, and the corresponding 2,4,5-trichlorophenol and 2,4,5-trichloroanisole as recovered in diethylether extracts.
mccall81_245T
A dataframe containing the following variables.
namethe name of the compound observed. Note that T245 is used as
an acronym for 2,4,5-T. T245 is a legitimate object name
in R, which is necessary for specifying models using
mkinmod.
timea numeric vector containing sampling times in days after treatment
valuea numeric vector containing concentrations in percent of applied radioactivity
soila factor containing the name of the soil
McCall P, Vrona SA, Kelley SS (1981) Fate of uniformly carbon-14 ring labeled 2,4,5-Trichlorophenoxyacetic acid and 2,4-dichlorophenoxyacetic acid. J Agric Chem 29, 100-107 http://dx.doi.org/10.1021/jf00103a026
SFO_SFO_SFO <- mkinmod(T245 = list(type = "SFO", to = "phenol"), phenol = list(type = "SFO", to = "anisole"), anisole = list(type = "SFO"))#>fit.1 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"), quiet = TRUE) summary(fit.1, data = FALSE)#> mkin version used for fitting: 0.9.47.6 #> R version used for fitting: 3.5.1 #> Date of fit: Mon Nov 26 09:45:54 2018 #> Date of summary: Mon Nov 26 09:45:54 2018 #> #> Equations: #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 #> d_phenol/dt = + k_T245_phenol * T245 - k_phenol_sink * phenol - #> k_phenol_anisole * phenol #> d_anisole/dt = + k_phenol_anisole * phenol - k_anisole_sink * anisole #> #> Model predictions using solution type deSolve #> #> Fitted with method Port using 574 model solutions performed in 3.641 s #> #> Weighting: none #> #> Starting values for parameters to be optimised: #> value type #> T245_0 100.9000 state #> k_T245_sink 0.1000 deparm #> k_T245_phenol 0.1001 deparm #> k_phenol_sink 0.1002 deparm #> k_phenol_anisole 0.1003 deparm #> k_anisole_sink 0.1004 deparm #> #> Starting values for the transformed parameters actually optimised: #> value lower upper #> T245_0 100.900000 -Inf Inf #> log_k_T245_sink -2.302585 -Inf Inf #> log_k_T245_phenol -2.301586 -Inf Inf #> log_k_phenol_sink -2.300587 -Inf Inf #> log_k_phenol_anisole -2.299590 -Inf Inf #> log_k_anisole_sink -2.298593 -Inf Inf #> #> Fixed parameter values: #> value type #> phenol_0 0 state #> anisole_0 0 state #> #> Optimised, transformed parameters with symmetric confidence intervals: #> Estimate Std. Error Lower Upper #> T245_0 103.9000 NA NA NA #> log_k_T245_sink -4.1130 NA NA NA #> log_k_T245_phenol -3.6120 NA NA NA #> log_k_phenol_sink -25.0800 NA NA NA #> log_k_phenol_anisole -0.9037 NA NA NA #> log_k_anisole_sink -5.0090 NA NA NA #> #> Parameter correlation:#> Warning: Could not estimate covariance matrix; singular system:#> Could not estimate covariance matrix; singular system: #> #> Residual standard error: 2.78 on 18 degrees of freedom #> #> Backtransformed parameters: #> Confidence intervals for internally transformed parameters are asymmetric. #> t-test (unrealistically) based on the assumption of normal distribution #> for estimators of untransformed parameters. #> Estimate t value Pr(>t) Lower Upper #> T245_0 1.039e+02 4.282e+01 7.236e-20 NA NA #> k_T245_sink 1.636e-02 8.901e-01 1.926e-01 NA NA #> k_T245_phenol 2.701e-02 1.504e+00 7.498e-02 NA NA #> k_phenol_sink 1.286e-11 4.575e-11 5.000e-01 NA NA #> k_phenol_anisole 4.051e-01 2.518e+00 1.075e-02 NA NA #> k_anisole_sink 6.679e-03 8.146e+00 9.469e-08 NA NA #> #> Chi2 error levels in percent: #> err.min n.optim df #> All data 10.070 6 16 #> T245 7.908 3 5 #> phenol 106.445 2 5 #> anisole 5.379 1 6 #> #> Resulting formation fractions: #> ff #> T245_sink 3.772e-01 #> T245_phenol 6.228e-01 #> phenol_sink 3.175e-11 #> phenol_anisole 1.000e+00 #> anisole_sink 1.000e+00 #> #> Estimated disappearance times: #> DT50 DT90 #> T245 15.982 53.091 #> phenol 1.711 5.685 #> anisole 103.784 344.763# No convergence, no covariance matrix ... # k_phenol_sink is really small, therefore fix it to zero fit.2 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"), parms.ini = c(k_phenol_sink = 0), fixed_parms = "k_phenol_sink", quiet = TRUE) summary(fit.2, data = FALSE)#> mkin version used for fitting: 0.9.47.6 #> R version used for fitting: 3.5.1 #> Date of fit: Mon Nov 26 09:45:56 2018 #> Date of summary: Mon Nov 26 09:45:56 2018 #> #> Equations: #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 #> d_phenol/dt = + k_T245_phenol * T245 - k_phenol_sink * phenol - #> k_phenol_anisole * phenol #> d_anisole/dt = + k_phenol_anisole * phenol - k_anisole_sink * anisole #> #> Model predictions using solution type deSolve #> #> Fitted with method Port using 246 model solutions performed in 1.627 s #> #> Weighting: none #> #> Starting values for parameters to be optimised: #> value type #> T245_0 100.9000 state #> k_T245_sink 0.1000 deparm #> k_T245_phenol 0.1001 deparm #> k_phenol_anisole 0.1002 deparm #> k_anisole_sink 0.1003 deparm #> #> Starting values for the transformed parameters actually optimised: #> value lower upper #> T245_0 100.900000 -Inf Inf #> log_k_T245_sink -2.302585 -Inf Inf #> log_k_T245_phenol -2.301586 -Inf Inf #> log_k_phenol_anisole -2.300587 -Inf Inf #> log_k_anisole_sink -2.299590 -Inf Inf #> #> Fixed parameter values: #> value type #> phenol_0 0 state #> anisole_0 0 state #> k_phenol_sink 0 deparm #> #> Optimised, transformed parameters with symmetric confidence intervals: #> Estimate Std. Error Lower Upper #> T245_0 103.9000 2.35200 98.930 108.8000 #> log_k_T245_sink -4.1130 0.13250 -4.390 -3.8350 #> log_k_T245_phenol -3.6120 0.05002 -3.716 -3.5070 #> log_k_phenol_anisole -0.9037 0.30580 -1.544 -0.2637 #> log_k_anisole_sink -5.0090 0.11180 -5.243 -4.7750 #> #> Parameter correlation: #> T245_0 log_k_T245_sink log_k_T245_phenol #> T245_0 1.00000 0.63761 -0.1742 #> log_k_T245_sink 0.63761 1.00000 -0.3831 #> log_k_T245_phenol -0.17416 -0.38313 1.0000 #> log_k_phenol_anisole -0.05948 0.08745 -0.3047 #> log_k_anisole_sink -0.16208 -0.60469 0.5227 #> log_k_phenol_anisole log_k_anisole_sink #> T245_0 -0.05948 -0.1621 #> log_k_T245_sink 0.08745 -0.6047 #> log_k_T245_phenol -0.30470 0.5227 #> log_k_phenol_anisole 1.00000 -0.1774 #> log_k_anisole_sink -0.17744 1.0000 #> #> Residual standard error: 2.706 on 19 degrees of freedom #> #> Backtransformed parameters: #> Confidence intervals for internally transformed parameters are asymmetric. #> t-test (unrealistically) based on the assumption of normal distribution #> for estimators of untransformed parameters. #> Estimate t value Pr(>t) Lower Upper #> T245_0 1.039e+02 44.160 6.462e-21 98.930000 108.80000 #> k_T245_sink 1.636e-02 7.545 1.978e-07 0.012400 0.02159 #> k_T245_phenol 2.701e-02 19.990 1.607e-14 0.024320 0.02999 #> k_phenol_anisole 4.051e-01 3.270 2.014e-03 0.213600 0.76820 #> k_anisole_sink 6.679e-03 8.942 1.544e-08 0.005285 0.00844 #> #> Chi2 error levels in percent: #> err.min n.optim df #> All data 9.831 5 17 #> T245 7.908 3 5 #> phenol 99.808 1 6 #> anisole 5.379 1 6 #> #> Resulting formation fractions: #> ff #> T245_sink 0.3772 #> T245_phenol 0.6228 #> phenol_anisole 1.0000 #> phenol_sink 0.0000 #> anisole_sink 1.0000 #> #> Estimated disappearance times: #> DT50 DT90 #> T245 15.982 53.091 #> phenol 1.711 5.685 #> anisole 103.784 344.763