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 labelled 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.
  # \dontrun{
    fit.1 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"), quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
    summary(fit.1)$bpar
#>                         Estimate  se_notrans   t value       Pr(>t)
#> T245_0              1.038550e+02 2.184707514 47.537272 4.472189e-18
#> k_T245              4.337042e-02 0.001898397 22.845818 2.276912e-13
#> k_phenol            4.050581e-01 0.298699428  1.356073 9.756994e-02
#> k_anisole           6.678742e-03 0.000802144  8.326114 2.623179e-07
#> f_T245_to_phenol    6.227599e-01 0.398534167  1.562626 6.949418e-02
#> f_phenol_to_anisole 1.000000e+00 0.671844168  1.488440 7.867794e-02
#> sigma               2.514628e+00 0.490755943  5.123989 6.233164e-05
#>                            Lower        Upper
#> T245_0              99.246061371 1.084640e+02
#> k_T245               0.039631621 4.746194e-02
#> k_phenol             0.218013878 7.525762e-01
#> k_anisole            0.005370739 8.305299e-03
#> f_T245_to_phenol     0.547559082 6.924813e-01
#> f_phenol_to_anisole  0.000000000 1.000000e+00
#> sigma                1.706607296 3.322649e+00
    endpoints(fit.1)
#> $ff
#>    T245_phenol      T245_sink phenol_anisole    phenol_sink 
#>   6.227599e-01   3.772401e-01   1.000000e+00   1.748047e-10 
#> 
#> $distimes
#>               DT50      DT90
#> T245     15.982025  53.09114
#> phenol    1.711229   5.68458
#> anisole 103.784092 344.76329
#> 
    # k_phenol_sink is really small, therefore fix it to zero
    fit.2 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"),
                   parms.ini = c(k_phenol_sink = 0),
                   fixed_parms = "k_phenol_sink", quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
#> Warning: Initial parameter(s) k_phenol_sink not used in the model
#> Error in data.frame(value = c(state.ini.fixed, parms.fixed)): row names contain missing values
    summary(fit.2)$bpar
#> Error in summary(fit.2): object 'fit.2' not found
    endpoints(fit.1)
#> $ff
#>    T245_phenol      T245_sink phenol_anisole    phenol_sink 
#>   6.227599e-01   3.772401e-01   1.000000e+00   1.748047e-10 
#> 
#> $distimes
#>               DT50      DT90
#> T245     15.982025  53.09114
#> phenol    1.711229   5.68458
#> anisole 103.784092 344.76329
#> 
    plot_sep(fit.2)
#> Error in identical(fit$err_mod, "const"): object 'fit.2' not found
  # }