From e5d1df9a9b1f0951d7dfbaf24eee4294470b73e2 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 17 Nov 2022 14:54:20 +0100 Subject: Complete update of online docs for v1.2.0 --- docs/reference/test_data_from_UBA_2014.html | 75 ++++++++++++++++------------- 1 file changed, 42 insertions(+), 33 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 327e8ae9..a76f23ab 100644 --- a/docs/reference/test_data_from_UBA_2014.html +++ b/docs/reference/test_data_from_UBA_2014.html @@ -18,7 +18,7 @@ mkin - 1.1.0 + 1.2.0 @@ -45,11 +45,14 @@ Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models
  • - Example evaluation of FOCUS Example Dataset Z + Short demo of the multistart method
  • Performance benefit by using compiled model definitions in mkin
    • +
  • + Example evaluation of FOCUS Example Dataset Z +
  • Calculation of time weighted average concentrations with mkin
    • @@ -57,7 +60,10 @@ Example evaluation of NAFTA SOP Attachment examples
  • - Some benchmark timings + Benchmark timings for mkin +
    • +
  • + Benchmark timings for saem.mmkin
  • @@ -89,7 +95,7 @@
    - 
    test_data_from_UBA_2014
    + 
    test_data_from_UBA_2014
    @@ -111,21 +117,23 @@

    Examples

    - 
      # \dontrun{
-  # 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"))
+    
      # \dontrun{
+  # 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"))
 #> Temporary DLL for differentials generated and loaded
-  f_river <- mkinfit(m_ws, test_data_from_UBA_2014[[1]]$data, quiet = TRUE)
-  plot_sep(f_river)
+  f_river <- mkinfit(m_ws, test_data_from_UBA_2014[[1]]$data, quiet = TRUE)
+#> Warning: Observations with value of zero were removed from the data
+  plot_sep(f_river)
 
-
-  summary(f_river)$bpar
+
+  summary(f_river)$bpar
+#> Warning: Could not calculate correlation; no covariance matrix
 #>                           Estimate se_notrans t value Pr(>t) Lower Upper
 #> parent_w_0             95.91998118         NA      NA     NA    NA    NA
 #> k_parent_w              0.41145375         NA      NA     NA    NA    NA
@@ -133,25 +141,26 @@
 #> f_parent_w_to_parent_s  0.12467894         NA      NA     NA    NA    NA
 #> f_parent_s_to_parent_w  0.50000000         NA      NA     NA    NA    NA
 #> sigma                   3.13612618         NA      NA     NA    NA    NA
-  mkinerrmin(f_river)
+  mkinerrmin(f_river)
 #>            err.min n.optim df
 #> All data 0.1090929       5  6
 #> parent_w 0.0817436       3  3
 #> parent_s 0.1619965       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")
+
+  # 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")
 #> Temporary DLL for differentials generated and loaded
-
-  f_soil <- mkinfit(m_soil, test_data_from_UBA_2014[[3]]$data, quiet = TRUE)
-  plot_sep(f_soil, lpos = c("topright", "topright", "topright", "bottomright"))
+
+  f_soil <- mkinfit(m_soil, test_data_from_UBA_2014[[3]]$data, quiet = TRUE)
+#> Warning: Observations with value of zero were removed from the data
+  plot_sep(f_soil, lpos = c("topright", "topright", "topright", "bottomright"))
 
-  summary(f_soil)$bpar
+  summary(f_soil)$bpar
 #>                   Estimate  se_notrans    t value       Pr(>t)        Lower
 #> parent_0       76.55425650 0.859186399 89.1008710 1.113861e-26 74.755959418
 #> k_parent        0.12081956 0.004601918 26.2541722 1.077359e-16  0.111561575
@@ -174,14 +183,14 @@
 #> f_M1_to_M3      0.86450775
 #> f_M2_to_M3      0.99489895
 #> sigma           1.45337221
-  mkinerrmin(f_soil)
+  mkinerrmin(f_soil)
 #>             err.min n.optim df
 #> All data 0.09649963       9 20
 #> parent   0.04721283       2  6
 #> M1       0.26551208       2  5
 #> M2       0.20327575       2  5
 #> M3       0.05196550       3  4
-  # }
+  # }
    @@ -196,7 +205,7 @@
    -

    Site built with pkgdown 2.0.2.

    +

    Site built with pkgdown 2.0.6.

    -- cgit v1.2.1