From 70591022c07f0e8fb4dd67789b7c8d78af8ebc18 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 2 May 2019 13:17:05 +0200 Subject: Better initials for error model parameters - Also make it possible to specify initial values for error model parameters. - Run tests - Rebuild docs --- docs/reference/AIC.mmkin.html | 4 +- docs/reference/Extract.mmkin.html | 2 +- docs/reference/NAFTA_SOP_2015-1.png | Bin 41450 -> 41438 bytes docs/reference/NAFTA_SOP_2015.html | 2 +- docs/reference/NAFTA_SOP_Attachment-1.png | Bin 42277 -> 42265 bytes docs/reference/NAFTA_SOP_Attachment.html | 2 +- docs/reference/add_err-1.png | Bin 89854 -> 89823 bytes docs/reference/add_err-3.png | Bin 52620 -> 52617 bytes docs/reference/mccall81_245T.html | 20 +-- docs/reference/mkinfit.html | 226 ++++++++++++++------------- docs/reference/mkinmod.html | 2 +- docs/reference/mkinparplot-1.png | Bin 16555 -> 16555 bytes docs/reference/mkinpredict.html | 56 +++---- docs/reference/mmkin-1.png | Bin 97714 -> 97607 bytes docs/reference/mmkin-2.png | Bin 88254 -> 88227 bytes docs/reference/mmkin-3.png | Bin 85751 -> 85742 bytes docs/reference/mmkin-4.png | Bin 63345 -> 63315 bytes docs/reference/mmkin-5.png | Bin 57629 -> 57623 bytes docs/reference/mmkin.html | 4 +- docs/reference/nafta-1.png | Bin 41450 -> 41438 bytes docs/reference/nafta.html | 2 +- docs/reference/plot.mkinfit-3.png | Bin 43743 -> 43718 bytes docs/reference/plot.mkinfit-4.png | Bin 59806 -> 59800 bytes docs/reference/plot.mmkin-1.png | Bin 34400 -> 34389 bytes docs/reference/plot.mmkin-2.png | Bin 34840 -> 34829 bytes docs/reference/plot.mmkin-3.png | Bin 25445 -> 25441 bytes docs/reference/schaefer07_complex_case.html | 10 +- docs/reference/summary.mkinfit.html | 12 +- docs/reference/test_data_from_UBA_2014-1.png | Bin 53400 -> 53388 bytes docs/reference/test_data_from_UBA_2014-2.png | Bin 69202 -> 69105 bytes docs/reference/test_data_from_UBA_2014.html | 16 +- 31 files changed, 183 insertions(+), 175 deletions(-) (limited to 'docs/reference') diff --git a/docs/reference/AIC.mmkin.html b/docs/reference/AIC.mmkin.html index d5386145..c797567c 100644 --- a/docs/reference/AIC.mmkin.html +++ b/docs/reference/AIC.mmkin.html @@ -169,10 +169,10 @@ # of parameters, the higher (worse) the AIC AIC(f[, "FOCUS A"])
#> df AIC #> SFO 3 55.28197 -#> FOMC 4 57.28198 +#> FOMC 4 57.28202 #> DFOP 5 59.28197
AIC(f[, "FOCUS A"], k = 0) # If we do not penalize additional parameters, we get nearly the same
#> df AIC #> SFO 3 49.28197 -#> FOMC 4 49.28198 +#> FOMC 4 49.28202 #> DFOP 5 49.28197
# For FOCUS C, the more complex models fit better AIC(f[, "FOCUS C"])
#> df AIC diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 77eff52e..3b7209b1 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -189,7 +189,7 @@ fits[["FOMC", "B"]] )
#> $par #> parent_0 log_alpha log_beta sigma -#> 99.666193 2.549849 5.050586 1.890202 +#> 99.666193 2.549850 5.050586 1.890202 #> #> $objective #> [1] 28.58291 diff --git a/docs/reference/NAFTA_SOP_2015-1.png b/docs/reference/NAFTA_SOP_2015-1.png index c4f9f048..bcf5d12c 100644 Binary files a/docs/reference/NAFTA_SOP_2015-1.png and b/docs/reference/NAFTA_SOP_2015-1.png differ diff --git a/docs/reference/NAFTA_SOP_2015.html b/docs/reference/NAFTA_SOP_2015.html index 513cb128..84341a17 100644 --- a/docs/reference/NAFTA_SOP_2015.html +++ b/docs/reference/NAFTA_SOP_2015.html @@ -192,7 +192,7 @@ #> DFOP 429 2380 841 #> #> Representative half-life: -#> [1] 841.4094
plot(nafta_evaluation)
+#> [1] 841.41
plot(nafta_evaluation)
plot(nafta_att_p5a)
+#> [1] 321.51
plot(nafta_att_p5a)
plot(nafta_evaluation)
#> Successfully compiled differential equation model from auto-generated C code.
fit <- mkinfit(model, data, quiet = TRUE) plot(fit)
endpoints(fit)
#> $ff #> parent_A1 parent_B1 parent_C1 parent_sink A1_A2 A1_sink -#> 0.3809619 0.1954667 0.4235714 0.0000000 0.4479605 0.5520395 +#> 0.3809619 0.1954667 0.4235714 0.0000000 0.4479603 0.5520397 #> #> $SFORB #> logical(0) @@ -175,10 +175,10 @@ #> $distimes #> DT50 DT90 #> parent 13.95078 46.34350 -#> A1 49.75344 165.27734 -#> B1 37.26908 123.80520 -#> C1 11.23130 37.30958 -#> A2 28.50644 94.69634 +#> A1 49.75343 165.27733 +#> B1 37.26907 123.80518 +#> C1 11.23131 37.30959 +#> A2 28.50644 94.69635 #>
# Compare with the results obtained in the original publication print(schaefer07_complex_results)
#> compound parameter KinGUI ModelMaker deviation #> 1 parent degradation rate 0.0496 0.0506 2.0 diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index e5565990..1a08132f 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -210,19 +210,19 @@

Examples

  summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
#> mkin version used for fitting:    0.9.49.4 
-#> R version used for fitting:       3.5.3 
-#> Date of fit:     Wed Apr 10 10:11:15 2019 
-#> Date of summary: Wed Apr 10 10:11:15 2019 
+#> R version used for fitting:       3.6.0 
+#> Date of fit:     Thu May  2 12:40:14 2019 
+#> Date of summary: Thu May  2 12:40:14 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted with method using 131 model solutions performed in 0.284 s
+#> Fitted using 131 model solutions performed in 0.269 s
 #> 
 #> Error model:
-#> NULL
+#> Constant variance 
 #> 
 #> Starting values for parameters to be optimised:
 #>                    value   type
@@ -260,7 +260,7 @@
 #> k_parent_sink   0.03722   10.90 5.650e-05  0.0294   0.04712
 #> sigma           5.26600    4.00 5.162e-03  1.8820   8.64900
 #> 
-#> Chi2 error levels in percent:
+#> FOCUS Chi2 error levels in percent:
 #>          err.min n.optim df
 #> All data   8.385       2  6
 #> parent     8.385       2  6
diff --git a/docs/reference/test_data_from_UBA_2014-1.png b/docs/reference/test_data_from_UBA_2014-1.png
index 9157a6a1..a9aeea21 100644
Binary files a/docs/reference/test_data_from_UBA_2014-1.png and b/docs/reference/test_data_from_UBA_2014-1.png differ
diff --git a/docs/reference/test_data_from_UBA_2014-2.png b/docs/reference/test_data_from_UBA_2014-2.png
index 528f3987..f6c91bff 100644
Binary files a/docs/reference/test_data_from_UBA_2014-2.png and b/docs/reference/test_data_from_UBA_2014-2.png differ
diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html
index dfb49619..688baf32 100644
--- a/docs/reference/test_data_from_UBA_2014.html
+++ b/docs/reference/test_data_from_UBA_2014.html
@@ -184,25 +184,25 @@
                     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 0.859186614 89.1008479 1.113866e-26 74.755959751
-#> k_parent        0.12081956 0.004601922 26.2541548 1.077373e-16  0.111561582
-#> k_M1            0.84258651 0.806231481  1.0450925 1.545475e-01  0.113839756
+#> parent_0       76.55425583 0.859186612 89.1008482 1.113866e-26 74.755959748
+#> k_parent        0.12081956 0.004601921 26.2541551 1.077372e-16  0.111561582
+#> k_M1            0.84258650 0.806231456  1.0450926 1.545475e-01  0.113839804
 #> k_M2            0.04210878 0.017083049  2.4649452 1.170195e-02  0.018013807
 #> k_M3            0.01122919 0.007245890  1.5497322 6.885127e-02  0.002909463
-#> f_parent_to_M1  0.32240199 0.240803570  1.3388589 9.820821e-02           NA
+#> f_parent_to_M1  0.32240199 0.240803564  1.3388589 9.820820e-02           NA
 #> f_parent_to_M2  0.16099854 0.033691991  4.7785403 6.531225e-05           NA
-#> f_M1_to_M3      0.27921500 0.269443517  1.0362654 1.565440e-01  0.022992921
-#> f_M2_to_M3      0.55641333 0.595125456  0.9349513 1.807725e-01  0.008003316
+#> f_M1_to_M3      0.27921500 0.269443517  1.0362654 1.565440e-01  0.022992933
+#> f_M2_to_M3      0.55641333 0.595125466  0.9349513 1.807725e-01  0.008003317
 #> sigma           1.14005399 0.149696423  7.6157731 1.727024e-07  0.826735778
 #>                      Upper
 #> parent_0       78.35255192
 #> k_parent        0.13084582
-#> k_M1            6.23641562
+#> k_M1            6.23641283
 #> k_M2            0.09843279
 #> k_M3            0.04333950
 #> f_parent_to_M1          NA
 #> f_parent_to_M2          NA
-#> f_M1_to_M3      0.86443090
+#> f_M1_to_M3      0.86443084
 #> f_M2_to_M3      0.99489847
 #> sigma           1.45337221
  mkinerrmin(f_soil)
#>             err.min n.optim df
 #> All data 0.09649963       9 20
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