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/test_data_from_UBA_2014.html | 62 +++++++++++++++++++++-------- 1 file changed, 45 insertions(+), 17 deletions(-) (limited to 'docs/reference/test_data_from_UBA_2014.html') diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html index f9032c84..a30161a2 100644 --- a/docs/reference/test_data_from_UBA_2014.html +++ b/docs/reference/test_data_from_UBA_2014.html @@ -62,7 +62,7 @@ mkin - 0.9.47.3 + 0.9.47.4 @@ -146,35 +146,63 @@

Examples

- 
  
# NOT RUN {
-  # This is a level P-II evaluation of the dataset according to the FOCUS kinetics
+    
  
  # This is a level P-II evaluation of the dataset according to the FOCUS kinetics
   # guidance. Due to the strong correlation of the parameter estimates, the
   # covariance matrix is not returned. Note that level P-II evaluations are
   # generally considered deprecated due to the frequent occurrence of such
   # large parameter correlations, among other reasons (e.g. the adequacy of the
   # model).
   m_ws <- mkinmod(parent_w = mkinsub("SFO", "parent_s"),
-                  parent_s = mkinsub("SFO", "parent_w"))
-  f_river <- mkinfit(m_ws, test_data_from_UBA_2014[[1]]$data, quiet = TRUE)
-  plot_sep(f_river)
-
-  summary(f_river)$bpar
-  mkinerrmin(f_river)
-
+                  parent_s = mkinsub("SFO", "parent_w"))
#> Successfully compiled differential equation model from auto-generated C code.
  f_river <- mkinfit(m_ws, test_data_from_UBA_2014[[1]]$data, quiet = TRUE)
+  plot_sep(f_river)

+  summary(f_river)$bpar
#>                         Estimate se_notrans      t value       Pr(>t) Lower
+#> parent_w_0          9.598567e+01 2.33959800 4.102657e+01 9.568967e-19    NA
+#> k_parent_w_sink     3.603743e-01 0.03497750 1.030303e+01 4.989002e-09    NA
+#> k_parent_w_parent_s 6.031371e-02 0.01746024 3.454346e+00 1.514723e-03    NA
+#> k_parent_s_sink     5.108539e-11 0.10382001 4.920572e-10 5.000000e-01    NA
+#> k_parent_s_parent_w 7.419672e-02 0.11338240 6.543936e-01 2.608069e-01    NA
+#>                     Upper
+#> parent_w_0             NA
+#> k_parent_w_sink        NA
+#> k_parent_w_parent_s    NA
+#> k_parent_s_sink        NA
+#> k_parent_s_parent_w    NA
  mkinerrmin(f_river)
#>             err.min n.optim df
+#> All data 0.09246946       5  6
+#> parent_w 0.06377096       3  3
+#> parent_s 0.20882324       2  3

   # This is the evaluation used for the validation of software packages
   # in the expertise from 2014
   m_soil <- mkinmod(parent = mkinsub("SFO", c("M1", "M2")),
                     M1 = mkinsub("SFO", "M3"),
                     M2 = mkinsub("SFO", "M3"),
                     M3 = mkinsub("SFO"),
-                    use_of_ff = "max")
-
+                    use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.

   f_soil <- mkinfit(m_soil, test_data_from_UBA_2014[[3]]$data, quiet = TRUE)
-  plot_sep(f_soil, lpos = c("topright", "topright", "topright", "bottomright"))
-  summary(f_soil)$bpar
-  mkinerrmin(f_soil)
-
-# }

+  plot_sep(f_soil, lpos = c("topright", "topright", "topright", "bottomright"))
  summary(f_soil)$bpar
#>                   Estimate  se_notrans    t value       Pr(>t)        Lower
+#> parent_0       76.55425584 0.943443794 81.1434198 4.422336e-30 74.602593773
+#> k_parent        0.12081956 0.004815515 25.0896457 1.639665e-18  0.111257517
+#> k_M1            0.84258651 0.930121548  0.9058886 1.871938e-01  0.085876516
+#> k_M2            0.04210878 0.013729902  3.0669396 2.729137e-03  0.021450630
+#> k_M3            0.01122919 0.008044865  1.3958206 8.804912e-02  0.002550984
+#> f_parent_to_M1  0.32240199 0.278620579  1.1571363 1.295467e-01           NA
+#> f_parent_to_M2  0.16099854 0.030548888  5.2701931 1.196190e-05           NA
+#> f_M1_to_M3      0.27921500 0.314732842  0.8871492 1.920908e-01  0.015016983
+#> f_M2_to_M3      0.55641333 0.650246995  0.8556954 2.004966e-01  0.005360555
+#>                      Upper
+#> parent_0       78.50591790
+#> k_parent        0.13120341
+#> k_M1            8.26712661
+#> k_M2            0.08266188
+#> k_M3            0.04942981
+#> f_parent_to_M1          NA
+#> f_parent_to_M2          NA
+#> f_M1_to_M3      0.90777163
+#> f_M2_to_M3      0.99658633
  mkinerrmin(f_soil)
#>             err.min n.optim df
+#> All data 0.09649963       9 20
+#> parent   0.04721283       2  6
+#> M1       0.26551209       2  5
+#> M2       0.20327575       2  5
+#> M3       0.05196549       3  4