mccall81_245T. mkin

+ +

Time 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

+ +

Format

+ +

A dataframe containing the following variables. +

name: the 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.
time: a numeric vector containing sampling times in days after + treatment
value: a numeric vector containing concentrations in percent of applied radioactivity
soil: a factor containing the name of the soil

+ +

Source

+ +

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

+ +

Examples

  SFO_SFO_SFO <- mkinmod(T245 = list(type = "SFO", to = "phenol"),
+                         phenol = list(type = "SFO", to = "anisole"),
+                         anisole = list(type = "SFO"))
Successfully compiled differential equation model from auto-generated C code.
  ## Not run: ------------------------------------
+#     fit.1 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"))
+#     summary(fit.1, data = FALSE)
+#   
+## ---------------------------------------------
+  # No covariance matrix and 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:    0.9.44.9000 
+#> R version:       3.3.1 
+#> Date of fit:     Thu Oct  6 09:17:57 2016 
+#> Date of summary: Thu Oct  6 09:17:57 2016 
+#> 
+#> Equations:
+#> d_T245 = - k_T245_sink * T245 - k_T245_phenol * T245
+#> d_phenol = + k_T245_phenol * T245 - k_phenol_sink * phenol -
+#>            k_phenol_anisole * phenol
+#> d_anisole = + k_phenol_anisole * phenol - k_anisole_sink * anisole
+#> 
+#> Model predictions using solution type deSolve 
+#> 
+#> Fitted with method Port using 246 model solutions performed in 1.508 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
+#>