From c4a35c0e141a4bb05ba508914bebdc2884109e76 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 14 Sep 2018 11:38:43 +0200 Subject: Exclude more example code from CRAN checks to avoid NOTES about long execution times. Static documentation rebuilt by pkgdown with run_dont_run = TRUE --- docs/reference/mccall81_245T.html | 111 ++++++++++++++++++++++++++++++++------ 1 file changed, 96 insertions(+), 15 deletions(-) (limited to 'docs/reference/mccall81_245T.html') diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index cea92155..ac2adf1e 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -63,7 +63,7 @@ mkin - 0.9.47.3 + 0.9.47.4 @@ -155,19 +155,11 @@

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"), quiet = TRUE)
-    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 used for fitting:    0.9.47.3 
+                         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:    0.9.47.4 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 06:39:07 2018 
-#> Date of summary: Fri Sep 14 06:39:07 2018 
+#> Date of fit:     Fri Sep 14 11:34:50 2018 
+#> Date of summary: Fri Sep 14 11:34:50 2018 
 #> 
 #> Equations:
 #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -177,7 +169,96 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 246 model solutions performed in 1.423 s
+#> Fitted with method Port using 574 model solutions performed in 3.33 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)
+    summary(fit.2, data = FALSE)
#> mkin version used for fitting:    0.9.47.4 
+#> R version used for fitting:       3.5.1 
+#> Date of fit:     Fri Sep 14 11:34:51 2018 
+#> Date of summary: Fri Sep 14 11:34:51 2018 
+#> 
+#> 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 1.417 s
 #> 
 #> Weighting: none
 #> 
@@ -257,7 +338,7 @@
 #>            DT50    DT90
 #> T245     15.982  53.091
 #> phenol    1.711   5.685
-#> anisole 103.784 344.763
+#> anisole 103.784 344.763