From c6086d1dd97ad2d6420625de7b8009b1b0f85d06 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 18 Nov 2016 15:01:53 +0100 Subject: Static documentation rebuilt by pkgdown::build_site(run_dont_run = TRUE) Using branch 'jranke' on jranke/pkgdown, fixing issues hadley/pgkdown#178 and hadley/pkgdown#213 Remove plot=TRUE from mkinfit calls also in dontrun sections of examples to avoid a flood png files documenting the progress of the fit. --- docs/reference/mccall81_245T.html | 250 ++++++++++++++++++++++++++++++++++++-- 1 file changed, 242 insertions(+), 8 deletions(-) (limited to 'docs/reference/mccall81_245T.html') diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 4314c84e..7b294129 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -111,19 +111,253 @@

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)
-#   
-## ---------------------------------------------
+                         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"))
#> Model cost at call  1 :  13655.2 
+#> Model cost at call  2 :  13655.2 
+#> Model cost at call  8 :  9191.59 
+#> Model cost at call  16 :  5663.584 
+#> Model cost at call  17 :  5663.582 
+#> Model cost at call  18 :  5663.566 
+#> Model cost at call  19 :  5663.55 
+#> Model cost at call  23 :  3035.567 
+#> Model cost at call  24 :  3035.566 
+#> Model cost at call  26 :  3035.561 
+#> Model cost at call  27 :  3035.559 
+#> Model cost at call  28 :  3035.558 
+#> Model cost at call  30 :  2252.97 
+#> Model cost at call  31 :  2252.965 
+#> Model cost at call  32 :  2252.965 
+#> Model cost at call  36 :  2252.958 
+#> Model cost at call  37 :  1220.201 
+#> Model cost at call  38 :  1220.2 
+#> Model cost at call  39 :  1220.199 
+#> Model cost at call  41 :  1220.183 
+#> Model cost at call  45 :  507.1358 
+#> Model cost at call  48 :  507.1353 
+#> Model cost at call  52 :  198.5695 
+#> Model cost at call  55 :  198.5694 
+#> Model cost at call  60 :  175.8239 
+#> Model cost at call  63 :  175.8239 
+#> Model cost at call  67 :  170.6316 
+#> Model cost at call  69 :  170.6316 
+#> Model cost at call  74 :  165.881 
+#> Model cost at call  77 :  165.881 
+#> Model cost at call  81 :  161.6423 
+#> Model cost at call  84 :  161.6423 
+#> Model cost at call  88 :  158.2953 
+#> Model cost at call  91 :  158.2953 
+#> Model cost at call  95 :  156.7311 
+#> Model cost at call  97 :  156.731 
+#> Model cost at call  103 :  155.998 
+#> Model cost at call  106 :  155.998 
+#> Model cost at call  110 :  155.6263 
+#> Model cost at call  113 :  155.6262 
+#> Model cost at call  116 :  155.6262 
+#> Model cost at call  117 :  155.1202 
+#> Model cost at call  120 :  155.1202 
+#> Model cost at call  124 :  154.4133 
+#> Model cost at call  125 :  153.8489 
+#> Model cost at call  126 :  152.7413 
+#> Model cost at call  129 :  152.7413 
+#> Model cost at call  132 :  152.7413 
+#> Model cost at call  133 :  150.3995 
+#> Model cost at call  134 :  148.7256 
+#> Model cost at call  135 :  147.2618 
+#> Model cost at call  137 :  147.2618 
+#> Model cost at call  139 :  147.2618 
+#> Model cost at call  142 :  145.115 
+#> Model cost at call  144 :  145.115 
+#> Model cost at call  145 :  145.115 
+#> Model cost at call  146 :  145.115 
+#> Model cost at call  147 :  145.115 
+#> Model cost at call  150 :  143.7878 
+#> Model cost at call  157 :  142.8531 
+#> Model cost at call  160 :  142.8531 
+#> Model cost at call  164 :  142.7325 
+#> Model cost at call  167 :  142.7325 
+#> Model cost at call  169 :  142.7325 
+#> Model cost at call  172 :  141.8393 
+#> Model cost at call  173 :  141.8393 
+#> Model cost at call  174 :  141.8393 
+#> Model cost at call  179 :  141.3446 
+#> Model cost at call  180 :  141.3446 
+#> Model cost at call  181 :  141.3446 
+#> Model cost at call  186 :  141.1111 
+#> Model cost at call  193 :  140.7786 
+#> Model cost at call  200 :  140.451 
+#> Model cost at call  207 :  140.1395 
+#> Model cost at call  214 :  139.7903 
+#> Model cost at call  221 :  139.5476 
+#> Model cost at call  228 :  139.4441 
+#> Model cost at call  235 :  139.3204 
+#> Model cost at call  242 :  139.2508 
+#> Model cost at call  249 :  139.1891 
+#> Model cost at call  256 :  139.1561 
+#> Model cost at call  263 :  139.137 
+#> Model cost at call  270 :  139.1278 
+#> Model cost at call  271 :  139.1278 
+#> Model cost at call  279 :  139.1211 
+#> Model cost at call  280 :  139.1211 
+#> Model cost at call  281 :  139.1211 
+#> Model cost at call  282 :  139.1211 
+#> Model cost at call  286 :  139.1179 
+#> Model cost at call  287 :  139.1179 
+#> Model cost at call  291 :  139.1179 
+#> Model cost at call  294 :  139.1179 
+#> Model cost at call  298 :  139.1158 
+#> Model cost at call  299 :  139.1158 
+#> Model cost at call  302 :  139.1158 
+#> Model cost at call  310 :  139.1148 
+#> Model cost at call  311 :  139.1148 
+#> Model cost at call  315 :  139.1148 
+#> Model cost at call  322 :  139.1143 
+#> Model cost at call  323 :  139.1143 
+#> Model cost at call  326 :  139.1143 
+#> Model cost at call  334 :  139.114 
+#> Model cost at call  335 :  139.114 
+#> Model cost at call  338 :  139.114 
+#> Model cost at call  339 :  139.114 
+#> Model cost at call  346 :  139.1139 
+#> Model cost at call  347 :  139.1139 
+#> Model cost at call  350 :  139.1139 
+#> Model cost at call  351 :  139.1139 
+#> Model cost at call  358 :  139.1139 
+#> Model cost at call  359 :  139.1139 
+#> Model cost at call  362 :  139.1139 
+#> Model cost at call  363 :  139.1139 
+#> Model cost at call  370 :  139.1138 
+#> Model cost at call  382 :  139.1138 
+#> Model cost at call  390 :  139.1138 
+#> Model cost at call  395 :  139.1138 
+#> Model cost at call  403 :  139.1138 
+#> Model cost at call  408 :  139.1138 
+#> Model cost at call  416 :  139.1138 
+#> Model cost at call  421 :  139.1138 
+#> Model cost at call  429 :  139.1138 
+#> Model cost at call  434 :  139.1138 
+#> Model cost at call  442 :  139.1138 
+#> Model cost at call  447 :  139.1138 
+#> Model cost at call  455 :  139.1138 
+#> Model cost at call  460 :  139.1138 
+#> Model cost at call  468 :  139.1138 
+#> Model cost at call  473 :  139.1138 
+#> Model cost at call  481 :  139.1138 
+#> Model cost at call  486 :  139.1138 
+#> Model cost at call  494 :  139.1138 
+#> Model cost at call  499 :  139.1138 
+#> Model cost at call  507 :  139.1138 
+#> Model cost at call  512 :  139.1138 
+#> Model cost at call  519 :  139.1138 
+#> Model cost at call  520 :  139.1138 
+#> Model cost at call  525 :  139.1138 
+#> Model cost at call  538 :  139.1138 
+#> Model cost at call  545 :  139.1138 
+#> Model cost at call  546 :  139.1138 
+#> Model cost at call  551 :  139.1138 
+#> Model cost at call  558 :  139.1138 
+#> Model cost at call  559 :  139.1138 
+#> Model cost at call  564 :  139.1138 
+#> Model cost at call  571 :  139.1138 
+#> Model cost at call  580 :  139.1138 
+#> Model cost at call  588 :  139.1138 
#> Warning: Optimisation by method Port did not converge.
+#> Convergence code is 1
    summary(fit.1, data = FALSE)
#> mkin version:    0.9.44.9000 
+#> R version:       3.3.2 
+#> Date of fit:     Fri Nov 18 15:19:33 2016 
+#> Date of summary: Fri Nov 18 15:19:33 2016 
+#> 
+#> 
+#> Warning: Optimisation by method Port did not converge.
+#> Convergence code is 1 
+#> 
+#> 
+#> 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 590 model solutions performed in 3.45 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_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    -26.3900         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    3.457e-12 1.230e-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    8.534e-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 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:       3.3.2 
-#> Date of fit:     Thu Nov 17 22:56:55 2016 
-#> Date of summary: Thu Nov 17 22:56:55 2016 
+#> Date of fit:     Fri Nov 18 15:19:35 2016 
+#> Date of summary: Fri Nov 18 15:19:35 2016 
 #> 
 #> Equations:
 #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -133,7 +367,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 246 model solutions performed in 1.457 s
+#> Fitted with method Port using 246 model solutions performed in 1.477 s
 #> 
 #> Weighting: none
 #> 
-- 
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