mccall81_245T. mkin 0.9.44.9000

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)
+#   
+## ---------------------------------------------
+  # 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:     Sat Sep 10 05:53:00 2016 
+Date of summary: Sat Sep 10 05:53:00 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 1.45 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
+

+ +

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

Usage

Description

Format

Source

Examples