From 6653ff2507f45eae909f491a9af3f1eb5358a600 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 1 Mar 2018 14:32:46 +0100 Subject: Static documentation rebuilt using current pkgdown::build_site() --- docs/reference/mccall81_245T.html | 124 ++++++++------------------------------ 1 file changed, 24 insertions(+), 100 deletions(-) (limited to 'docs/reference/mccall81_245T.html') diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 0111deb3..ec7f8ccd 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -18,12 +18,21 @@ + + + + + + + @@ -69,6 +78,9 @@
  • Example evaluation of FOCUS Laboratory Data L1 to L3
    • +
  • + Example evaluation of FOCUS Example Dataset Z +
  • Performance benefit by using compiled model definitions in mkin
    • @@ -83,12 +95,7 @@ @@ -127,108 +134,25 @@

    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

    + 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.
    
+                         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"), quiet = TRUE)
-    summary(fit.1, data = FALSE)
    #> mkin version:    0.9.46 
-#> R version:       3.4.1 
-#> Date of fit:     Sat Jul 29 15:14:14 2017 
-#> Date of summary: Sat Jul 29 15:14:14 2017 
-#> 
-#> 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 612 model solutions performed in 3.558 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    -26.8400         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 7.499e-02    NA    NA
-#> k_phenol_sink    2.212e-12 7.870e-12 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    5.462e-12
-#> 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, data = FALSE)
+
+# }
      # 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:    0.9.46 
-#> R version:       3.4.1 
-#> Date of fit:     Sat Jul 29 15:14:15 2017 
-#> Date of summary: Sat Jul 29 15:14:15 2017 
+  summary(fit.2, data = FALSE)
    #> mkin version used for fitting:    0.9.47.1 
+#> R version used for fitting:       3.4.3 
+#> Date of fit:     Thu Mar  1 14:26:15 2018 
+#> Date of summary: Thu Mar  1 14:26:15 2018 
 #> 
 #> Equations:
 #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -238,7 +162,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 246 model solutions performed in 1.431 s
+#> Fitted with method Port using 246 model solutions performed in 1.359 s
 #> 
 #> Weighting: none
 #> 
@@ -340,7 +264,7 @@
 
    
 
 
    
-  
    Site built with pkgdown.
    
+  
    Site built with pkgdown.
    
 
    
 
       
-- 
cgit v1.2.1