mkin 0.9.42

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

Usage

mccall81_245T

Description

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.

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)
#   ## End(Not run)
  # 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:    0.9.42 
R version:       3.2.4 
Date of fit:     Wed Mar 23 18:10:44 2016 
Date of summary: Wed Mar 23 18:10:44 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 1.482 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 log_k_phenol_anisole log_k_anisole_sink
T245_0                1.00000         0.63761           -0.1742             -0.05948            -0.1621
log_k_T245_sink       0.63761         1.00000           -0.3831              0.08745            -0.6047
log_k_T245_phenol    -0.17416        -0.38313            1.0000             -0.30470             0.5227
log_k_phenol_anisole -0.05948         0.08745           -0.3047              1.00000            -0.1774
log_k_anisole_sink   -0.16208        -0.60469            0.5227             -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