From 3eefecf0adfbb30b8fb895c244dea6903bcb3e9c Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 31 Jan 2019 16:55:20 +0100 Subject: Restore NAMESPACE which was accidentally overwritten by pkgdown -> roxygen --- docs/reference/mccall81_245T.html | 183 +++++++++++++++++++++++++++++++++++++- 1 file changed, 181 insertions(+), 2 deletions(-) (limited to 'docs/reference/mccall81_245T.html') diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 86ba7566..93d7f197 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -157,11 +157,190 @@

Examples

  SFO_SFO_SFO <- mkinmod(T245 = list(type = "SFO", to = "phenol"),
                          phenol = list(type = "SFO", to = "anisole"),
-                         anisole = list(type = "SFO"))
#> Error in mkinmod(T245 = list(type = "SFO", to = "phenol"), phenol = list(type = "SFO",     to = "anisole"), anisole = list(type = "SFO")): konnte Funktion "mkinmod" nicht finden
  
    fit.1 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"), quiet = TRUE)
#> Error in mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"),     quiet = TRUE): konnte Funktion "mkinfit" nicht finden
    summary(fit.1, data = FALSE)
#> Error in summary(fit.1, data = FALSE): Objekt 'fit.1' nicht gefunden
    # No convergence, no covariance matrix ...
+                         anisole = list(type = "SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
  
    fit.1 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"), quiet = TRUE)
+    summary(fit.1, data = FALSE)
#> mkin version used for fitting:    0.9.47.6 
+#> R version used for fitting:       3.5.2 
+#> Date of fit:     Thu Jan 31 16:51:05 2019 
+#> Date of summary: Thu Jan 31 16:51:05 2019 
+#> 
+#> 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 574 model solutions performed in 3.87 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_sink      0.1002 deparm
+#> k_phenol_anisole   0.1003 deparm
+#> k_anisole_sink     0.1004 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_sink     -2.300587  -Inf   Inf
+#> log_k_phenol_anisole  -2.299590  -Inf   Inf
+#> log_k_anisole_sink    -2.298593  -Inf   Inf
+#> 
+#> Fixed parameter values:
+#>           value  type
+#> phenol_0      0 state
+#> anisole_0     0 state
+#> 
+#> Optimised, transformed parameters with symmetric confidence intervals:
+#>                      Estimate Std. Error Lower Upper
+#> T245_0               103.9000         NA    NA    NA
+#> log_k_T245_sink       -4.1130         NA    NA    NA
+#> log_k_T245_phenol     -3.6120         NA    NA    NA
+#> log_k_phenol_sink    -25.0800         NA    NA    NA
+#> log_k_phenol_anisole  -0.9037         NA    NA    NA
+#> log_k_anisole_sink    -5.0090         NA    NA    NA
+#> 
+#> Parameter correlation:
#> Warning: Could not estimate covariance matrix; singular system:
#> Could not estimate covariance matrix; singular system:
+#> 
+#> Residual standard error: 2.78 on 18 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 4.282e+01 7.236e-20    NA    NA
+#> k_T245_sink      1.636e-02 8.901e-01 1.926e-01    NA    NA
+#> k_T245_phenol    2.701e-02 1.504e+00 7.498e-02    NA    NA
+#> k_phenol_sink    1.286e-11 4.575e-11 5.000e-01    NA    NA
+#> k_phenol_anisole 4.051e-01 2.518e+00 1.075e-02    NA    NA
+#> k_anisole_sink   6.679e-03 8.146e+00 9.469e-08    NA    NA
+#> 
+#> Chi2 error levels in percent:
+#>          err.min n.optim df
+#> All data  10.070       6 16
+#> T245       7.908       3  5
+#> phenol   106.445       2  5
+#> anisole    5.379       1  6
+#> 
+#> Resulting formation fractions:
+#>                       ff
+#> T245_sink      3.772e-01
+#> T245_phenol    6.228e-01
+#> phenol_sink    3.175e-11
+#> phenol_anisole 1.000e+00
+#> anisole_sink   1.000e+00
+#> 
+#> Estimated disappearance times:
+#>            DT50    DT90
+#> T245     15.982  53.091
+#> phenol    1.711   5.685
+#> anisole 103.784 344.763
    # 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)
#> Error in mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"),     parms.ini = c(k_phenol_sink = 0), fixed_parms = "k_phenol_sink",     quiet = TRUE): konnte Funktion "mkinfit" nicht finden
    summary(fit.2, data = FALSE)
#> Error in summary(fit.2, data = FALSE): Objekt 'fit.2' nicht gefunden
+ fixed_parms = "k_phenol_sink", quiet = TRUE) + summary(fit.2, data = FALSE)
#> mkin version used for fitting: 0.9.47.6 +#> R version used for fitting: 3.5.2 +#> Date of fit: Thu Jan 31 16:51:07 2019 +#> Date of summary: Thu Jan 31 16:51:07 2019 +#> +#> 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 1.618 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