Datasets on aerobic soil metabolism of 2,4,5-T in six soils

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"), quiet = TRUE)
    summary(fit.1, data = FALSE)

# }
  # 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:    0.9.47.1 
#> R version used for fitting:       3.4.4 
#> Date of fit:     Wed Mar 21 18:14:30 2018 
#> Date of summary: Wed Mar 21 18:14:30 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 1.403 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