From d0a358a8f4fd03c95536409523e492eb15726f44 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 4 Mar 2019 10:12:43 +0100 Subject: Review tests and examples based on winbuilder results Static documentation rebuilt by pkgdown --- docs/reference/Extract.mmkin.html | 12 ++++---- docs/reference/NAFTA_SOP_2015.html | 30 +++++++++---------- docs/reference/NAFTA_SOP_Attachment.html | 26 ++++++++-------- docs/reference/logLik.mkinfit.html | 4 +-- docs/reference/mccall81_245T.html | 18 +++++------ docs/reference/mkinfit.html | 46 ++++++++++++++--------------- docs/reference/mkinmod.html | 2 +- docs/reference/mkinpredict.html | 2 +- docs/reference/mmkin.html | 4 +-- docs/reference/nafta.html | 30 +++++++++---------- docs/reference/print.nafta.html | 6 +++- docs/reference/summary.mkinfit.html | 6 ++-- docs/reference/test_data_from_UBA_2014.html | 2 +- docs/reference/transform_odeparms.html | 24 +++++++-------- 14 files changed, 108 insertions(+), 104 deletions(-) (limited to 'docs/reference') diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 93be7412..96b9f218 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -283,7 +283,7 @@ #> #> $time #> User System verstrichen -#> 0.071 0.000 0.071 +#> 0.069 0.000 0.069 #> #> $mkinmod #> <mkinmod> model generated with @@ -472,8 +472,8 @@ #> } #> return(mC) #> } -#> <bytecode: 0x55555c80a350> -#> <environment: 0x55555b478bb8> +#> <bytecode: 0x55555c1f3208> +#> <environment: 0x555555c27dc0> #> #> $cost_notrans #> function (P) @@ -495,8 +495,8 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <bytecode: 0x55555c522e40> -#> <environment: 0x55555b478bb8> +#> <bytecode: 0x55555b84fce8> +#> <environment: 0x555555c27dc0> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -563,7 +563,7 @@ #> 99.17407 #> #> $date -#> [1] "Tue Feb 26 21:07:19 2019" +#> [1] "Mon Mar 4 10:07:37 2019" #> #> $version #> [1] "0.9.48.1" diff --git a/docs/reference/NAFTA_SOP_2015.html b/docs/reference/NAFTA_SOP_2015.html index c8b97493..d56c0ca3 100644 --- a/docs/reference/NAFTA_SOP_2015.html +++ b/docs/reference/NAFTA_SOP_2015.html @@ -165,29 +165,29 @@ #> #> Parameters: #> $SFO -#> Estimate Pr(>t) Lower Upper -#> parent_0 83.755751519 8.076390e-15 76.928220975 90.583282063 -#> k_parent_sink 0.001703321 7.452357e-05 0.001108568 0.002617164 +#> Estimate Pr(>t) Lower Upper +#> parent_0 83.7558 8.08e-15 76.92822 90.58328 +#> k_parent_sink 0.0017 7.45e-05 0.00111 0.00262 #> #> $IORE -#> Estimate Pr(>t) Lower Upper -#> parent_0 9.685291e+01 NA 8.752855e+01 1.061773e+02 -#> k__iore_parent_sink 8.403401e-14 NA 1.092058e-19 6.466429e-08 -#> N_parent 6.684457e+00 NA 3.538510e+00 9.830404e+00 +#> Estimate Pr(>t) Lower Upper +#> parent_0 9.69e+01 NA 8.75e+01 1.06e+02 +#> k__iore_parent_sink 8.40e-14 NA 1.09e-19 6.47e-08 +#> N_parent 6.68e+00 NA 3.54e+00 9.83e+00 #> #> $DFOP -#> Estimate Pr(>t) Lower Upper -#> parent_0 9.755655e+01 4.439930e-13 8.884447e+01 1.062686e+02 -#> k1 4.240633e-02 3.554769e-02 1.414189e-02 1.271610e-01 -#> k2 8.237928e-04 2.060933e-02 3.172784e-04 2.138925e-03 -#> g 2.881037e-01 1.313715e-04 1.783967e-01 4.299694e-01 +#> Estimate Pr(>t) Lower Upper +#> parent_0 9.76e+01 4.44e-13 8.88e+01 1.06e+02 +#> k1 4.24e-02 3.55e-02 1.41e-02 1.27e-01 +#> k2 8.24e-04 2.06e-02 3.17e-04 2.14e-03 +#> g 2.88e-01 1.31e-04 1.78e-01 4.30e-01 #> #> #> DTx values: #> DT50 DT90 DT50_rep -#> SFO 407 1350 407 -#> IORE 541 5190000 1560000 -#> DFOP 429 2380 841 +#> SFO 407 1352 407 +#> IORE 541 5192060 1562966 +#> DFOP 429 2383 841 #> #> Representative half-life: #> [1] 841.4096
plot(nafta_evaluation)
diff --git a/docs/reference/NAFTA_SOP_Attachment.html b/docs/reference/NAFTA_SOP_Attachment.html index 373da052..22d9c9fd 100644 --- a/docs/reference/NAFTA_SOP_Attachment.html +++ b/docs/reference/NAFTA_SOP_Attachment.html @@ -152,7 +152,7 @@

Examples

- 
  nafta_att_p5a <- nafta(NAFTA_SOP_Attachment[["p5a"]], cores = 1)
#> The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
#> The half-life obtained from the IORE model may be used
  print(nafta_att_p5a)
#> Sums of squares:
+    
  nafta_att_p5a <- nafta(NAFTA_SOP_Attachment[["p5a"]], cores = 1)
#> Warning: Could not estimate covariance matrix; singular system.
#> The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
#> The half-life obtained from the IORE model may be used
  print(nafta_att_p5a)
#> Sums of squares:
 #>       SFO      IORE      DFOP 
 #> 465.21753  56.27506  32.06401 
 #> 
@@ -161,22 +161,22 @@
 #> 
 #> Parameters:
 #> $SFO
-#>                  Estimate       Pr(>t)        Lower       Upper
-#> parent_0      95.84012168 1.095639e-21 92.120517864 99.55972549
-#> k_parent_sink  0.01024015 1.710227e-12  0.008996874  0.01165524
+#>               Estimate   Pr(>t)  Lower   Upper
+#> parent_0       95.8401 1.10e-21 92.121 99.5597
+#> k_parent_sink   0.0102 1.71e-12  0.009  0.0117
 #> 
 #> $IORE
-#>                         Estimate       Pr(>t)        Lower        Upper
-#> parent_0            1.007532e+02 2.365797e-26 9.891170e+01 1.025947e+02
-#> k__iore_parent_sink 1.544192e-05 8.733384e-02 3.482391e-06 6.847393e-05
-#> N_parent            2.569877e+00 1.140446e-11 2.215298e+00 2.924456e+00
+#>                     Estimate   Pr(>t)    Lower    Upper
+#> parent_0            1.01e+02 2.37e-26 9.89e+01 1.03e+02
+#> k__iore_parent_sink 1.54e-05 8.73e-02 3.48e-06 6.85e-05
+#> N_parent            2.57e+00 1.14e-11 2.22e+00 2.92e+00
 #> 
 #> $DFOP
-#>              Estimate       Pr(>t) Lower Upper
-#> parent_0 9.994630e+01 4.330861e-27    NA    NA
-#> k1       2.674255e-02 3.171390e-05    NA    NA
-#> k2       2.161318e-12 5.000000e-01    NA    NA
-#> g        6.465276e-01 2.129114e-05    NA    NA
+#>          Estimate   Pr(>t) Lower Upper
+#> parent_0 9.99e+01 4.33e-27    NA    NA
+#> k1       2.67e-02 3.17e-05    NA    NA
+#> k2       2.16e-12 5.00e-01    NA    NA
+#> g        6.47e-01 2.13e-05    NA    NA
 #> 
 #> 
 #> DTx values:
diff --git a/docs/reference/logLik.mkinfit.html b/docs/reference/logLik.mkinfit.html
index 229f8b04..fc4193cb 100644
--- a/docs/reference/logLik.mkinfit.html
+++ b/docs/reference/logLik.mkinfit.html
@@ -195,7 +195,7 @@ In the case of iterative reweighting, the variances obtained by this
     
 
     
Examples

-    
  sfo_sfo <- mkinmod(
+    
  
  sfo_sfo <- mkinmod(
     parent = mkinsub("SFO", to = "m1"),
     m1 = mkinsub("SFO")
   )
#> Successfully compiled differential equation model from auto-generated C code.
  d_t <- FOCUS_2006_D
@@ -209,7 +209,7 @@ In the case of iterative reweighting, the variances obtained by this
 #> f_nw   5 204.4619
 #> f_obs  6 205.8727
 #> f_tc   6 143.8773
-#> f_man  4 291.8000

+#> f_man  4 291.8000
  

   

   
 
     
# S3 method for nafta
-print(x, quiet = TRUE, ...)

+print(x, quiet = TRUE, digits = 3, ...)

     
     
Arguments

     
@@ -150,6 +150,10 @@
       
+    
+      
+      
+    
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index 8d9e0287..e2f4d2e2 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -211,15 +211,15 @@
     
Examples
  summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Tue Feb 26 21:09:01 2019 
-#> Date of summary: Tue Feb 26 21:09:01 2019 
+#> Date of fit:     Mon Mar  4 10:09:19 2019 
+#> Date of summary: Mon Mar  4 10:09:19 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted with method Port using 35 model solutions performed in 0.084 s
+#> Fitted with method Port using 35 model solutions performed in 0.086 s
 #> 
 #> Weighting: none
 #> 
diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html
index 12904a1f..28e8b41c 100644
--- a/docs/reference/test_data_from_UBA_2014.html
+++ b/docs/reference/test_data_from_UBA_2014.html
@@ -160,7 +160,7 @@
   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)
   plot_sep(f_river)

-  summary(f_river)$bpar
#>                         Estimate se_notrans      t value       Pr(>t) Lower
+  summary(f_river)$bpar
#> Warning: Could not estimate covariance matrix; singular system.
#>                         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
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index 115ee0ca..3148f00b 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -205,8 +205,8 @@ The transformation of sets of formation fractions is fragile, as it supposes
 fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
 summary(fit, data=FALSE) # See transformed and backtransformed parameters
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Tue Feb 26 21:09:09 2019 
-#> Date of summary: Tue Feb 26 21:09:09 2019 
+#> Date of fit:     Mon Mar  4 10:09:27 2019 
+#> Date of summary: Mon Mar  4 10:09:27 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -214,7 +214,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 153 model solutions performed in 0.709 s
+#> Fitted with method Port using 153 model solutions performed in 0.699 s
 #> 
 #> Weighting: none
 #> 
@@ -281,8 +281,8 @@ The transformation of sets of formation fractions is fragile, as it supposes
 
fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE, quiet = TRUE)
 summary(fit.2, data=FALSE)
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Tue Feb 26 21:09:11 2019 
-#> Date of summary: Tue Feb 26 21:09:11 2019 
+#> Date of fit:     Mon Mar  4 10:09:29 2019 
+#> Date of summary: Mon Mar  4 10:09:29 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -290,7 +290,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 350 model solutions performed in 1.588 s
+#> Fitted with method Port using 350 model solutions performed in 1.584 s
 #> 
 #> Weighting: none
 #> 
@@ -369,8 +369,8 @@ The transformation of sets of formation fractions is fragile, as it supposes
 fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
 summary(fit.ff, data = FALSE)
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Tue Feb 26 21:09:12 2019 
-#> Date of summary: Tue Feb 26 21:09:12 2019 
+#> Date of fit:     Mon Mar  4 10:09:30 2019 
+#> Date of summary: Mon Mar  4 10:09:30 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -378,7 +378,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 186 model solutions performed in 0.849 s
+#> Fitted with method Port using 186 model solutions performed in 0.86 s
 #> 
 #> Weighting: none
 #> 
@@ -453,8 +453,8 @@ The transformation of sets of formation fractions is fragile, as it supposes
 fit.ff.2 <- mkinfit(SFO_SFO.ff.2, FOCUS_2006_D, quiet = TRUE)
 summary(fit.ff.2, data = FALSE)
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Tue Feb 26 21:09:13 2019 
-#> Date of summary: Tue Feb 26 21:09:13 2019 
+#> Date of fit:     Mon Mar  4 10:09:31 2019 
+#> Date of summary: Mon Mar  4 10:09:31 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -462,7 +462,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 104 model solutions performed in 0.47 s
+#> Fitted with method Port using 104 model solutions performed in 0.476 s
 #> 
 #> Weighting: none
 #> 
-- 
cgit v1.2.1


quiet
       
Should the evaluation text be shown?

     
digits
Number of digits to be used for printing parameters and dissipation times.

     

       …
       
Not used.