From 9d6a975a0e3850a36889a18b5d9929d27b901ab3 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 4 Mar 2019 14:09:45 +0100 Subject: Make some example output more reproducible In order to avoid some unnecessary documentation rebuilds --- docs/reference/mccall81_245T.html | 229 +++++++++----------------------------- 1 file changed, 50 insertions(+), 179 deletions(-) (limited to 'docs/reference/mccall81_245T.html') diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 5fbbc962..47fa6482 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -161,189 +161,60 @@ 
  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.
  
    fit.1 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"), quiet = TRUE)
-    summary(fit.1, data = FALSE)
#> Warning: Could not estimate covariance matrix; singular system.
#> mkin version used for fitting:    0.9.48.1 
-#> R version used for fitting:       3.5.2 
-#> Date of fit:     Mon Mar  4 10:08:00 2019 
-#> Date of summary: Mon Mar  4 10:08:00 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 3.762 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:
-#> 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 ...
+    summary(fit.1)$bpar
#> Warning: Could not estimate covariance matrix; singular system.
#>                      Estimate   se_notrans      t value       Pr(>t) Lower
+#> T245_0           1.038550e+02 2.4256088519 4.281607e+01 7.235908e-20    NA
+#> k_T245_sink      1.636106e-02 0.0183803090 8.901408e-01 1.925667e-01    NA
+#> k_T245_phenol    2.700936e-02 0.0179604385 1.503825e+00 7.498498e-02    NA
+#> k_phenol_sink    1.286034e-11 0.2810970202 4.575054e-11 5.000000e-01    NA
+#> k_phenol_anisole 4.050581e-01 0.1608928349 2.517564e+00 1.075371e-02    NA
+#> k_anisole_sink   6.678742e-03 0.0008199239 8.145563e+00 9.469402e-08    NA
+#>                  Upper
+#> T245_0              NA
+#> k_T245_sink         NA
+#> k_T245_phenol       NA
+#> k_phenol_sink       NA
+#> k_phenol_anisole    NA
+#> k_anisole_sink      NA
    endpoints(fit.1)
#> $ff
+#>      T245_sink    T245_phenol    phenol_sink phenol_anisole   anisole_sink 
+#>   3.772401e-01   6.227599e-01   3.174937e-11   1.000000e+00   1.000000e+00 
+#> 
+#> $SFORB
+#> logical(0)
+#> 
+#> $distimes
+#>               DT50      DT90
+#> T245     15.982025  53.09114
+#> phenol    1.711229   5.68458
+#> anisole 103.784093 344.76330
+#> 
    # 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:    0.9.48.1 
-#> R version used for fitting:       3.5.2 
-#> Date of fit:     Mon Mar  4 10:08:02 2019 
-#> Date of summary: Mon Mar  4 10:08:02 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 1.598 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
+ summary(fit.2)$bpar
#> Estimate se_notrans t value Pr(>t) Lower +#> T245_0 1.038550e+02 2.3517950656 44.159900 6.461715e-21 98.932670927 +#> k_T245_sink 1.636106e-02 0.0021685502 7.544701 1.978480e-07 0.012397413 +#> k_T245_phenol 2.700936e-02 0.0013511301 19.990199 1.606634e-14 0.024324422 +#> k_phenol_anisole 4.050581e-01 0.1238660786 3.270129 2.013627e-03 0.213574853 +#> k_anisole_sink 6.678742e-03 0.0007468908 8.942059 1.543812e-08 0.005284957 +#> Upper +#> T245_0 1.087774e+02 +#> k_T245_sink 2.159195e-02 +#> k_T245_phenol 2.999066e-02 +#> k_phenol_anisole 7.682180e-01 +#> k_anisole_sink 8.440105e-03
endpoints(fit.1)
#> $ff +#> T245_sink T245_phenol phenol_sink phenol_anisole anisole_sink +#> 3.772401e-01 6.227599e-01 3.174937e-11 1.000000e+00 1.000000e+00 +#> +#> $SFORB +#> logical(0) +#> +#> $distimes +#> DT50 DT90 +#> T245 15.982025 53.09114 +#> phenol 1.711229 5.68458 +#> anisole 103.784093 344.76330 +#>