From a77a10ea6c607346778ba0700b3b66ac393101a2 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 27 May 2020 06:06:08 +0200 Subject: Create up to date pkgdown docs in development mode --- docs/dev/reference/test_data_from_UBA_2014.html | 251 ++++++++++++++++++++++++ 1 file changed, 251 insertions(+) create mode 100644 docs/dev/reference/test_data_from_UBA_2014.html (limited to 'docs/dev/reference/test_data_from_UBA_2014.html') diff --git a/docs/dev/reference/test_data_from_UBA_2014.html b/docs/dev/reference/test_data_from_UBA_2014.html new file mode 100644 index 00000000..291e3959 --- /dev/null +++ b/docs/dev/reference/test_data_from_UBA_2014.html @@ -0,0 +1,251 @@ + + + + + + + + +Three experimental datasets from two water sediment systems and one soil — test_data_from_UBA_2014 • mkin + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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Three experimental datasets from two water sediment systems and one soil

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The datasets were used for the comparative validation of several kinetic evaluation + software packages (Ranke, 2014).

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test_data_from_UBA_2014
+ + +

Format

+ +

A list containing three datasets as an R6 class defined by mkinds. + Each dataset has, among others, the following components

+
title

The name of the dataset, e.g. UBA_2014_WS_river

+
data

A data frame with the data in the form expected by mkinfit

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Source

+ +

Ranke (2014) Prüfung und Validierung von Modellierungssoftware als Alternative + zu ModelMaker 4.0, Umweltbundesamt Projektnummer 27452

+ +

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"))
#> Successfully compiled differential equation model from auto-generated C code.
  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
#> Warning: Could not calculate correlation; no covariance matrix
#>                           Estimate se_notrans t value Pr(>t) Lower Upper
+#> parent_w_0             95.91998116         NA      NA     NA    NA    NA
+#> k_parent_w              0.41145375         NA      NA     NA    NA    NA
+#> k_parent_s              0.04663944         NA      NA     NA    NA    NA
+#> 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)
#>            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")
#> Successfully compiled differential equation model from auto-generated C code.

+  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
#>                   Estimate  se_notrans    t value       Pr(>t)        Lower
+#> parent_0       76.55425584 0.859186419 89.1008681 1.113862e-26 74.755958720
+#> k_parent        0.12081956 0.004601919 26.2541703 1.077361e-16  0.111561576
+#> k_M1            0.84258629 0.806165149  1.0451783 1.545282e-01  0.113778910
+#> k_M2            0.04210878 0.017083049  2.4649452 1.170195e-02  0.018013823
+#> k_M3            0.01122919 0.007245870  1.5497364 6.885076e-02  0.002909418
+#> f_parent_to_M1  0.32240193 0.240785518  1.3389590 9.819221e-02           NA
+#> f_parent_to_M2  0.16099854 0.033691991  4.7785404 6.531224e-05           NA
+#> f_M1_to_M3      0.27921506 0.269425582  1.0363346 1.565282e-01  0.022977955
+#> f_M2_to_M3      0.55641331 0.595121774  0.9349571 1.807710e-01  0.008002320
+#> sigma           1.14005399 0.149696423  7.6157731 1.727024e-07  0.826735778
+#>                      Upper
+#> parent_0       78.35255297
+#> k_parent        0.13084582
+#> k_M1            6.23974738
+#> k_M2            0.09843271
+#> k_M3            0.04334017
+#> f_parent_to_M1          NA
+#> f_parent_to_M2          NA
+#> f_M1_to_M3      0.86450905
+#> f_M2_to_M3      0.99489911
+#> sigma           1.45337221
  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
  # }
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+ + + + + + + + -- cgit v1.2.1