From bbb74d4f60033899cd5cdd36aa70f157bc52209e Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 1 Nov 2019 12:19:03 +0100 Subject: Fix bug in yesterdays release, add methods for BIC --- docs/articles/FOCUS_L.html | 117 ++++++++++++++++++++------------------------- 1 file changed, 52 insertions(+), 65 deletions(-) (limited to 'docs/articles/FOCUS_L.html') diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index 7b35beeb..4033beba 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -90,7 +90,7 @@

Example evaluation of FOCUS Laboratory Data L1 to L3

Johannes Ranke

-

2019-09-19

+

2019-11-01

@@ -116,8 +116,8 @@ summary(m.L1.SFO) 
## mkin version used for fitting:    0.9.49.6 
 ## R version used for fitting:       3.6.1 
-## Date of fit:     Thu Sep 19 09:52:57 2019 
-## Date of summary: Thu Sep 19 09:52:57 2019 
+## Date of fit:     Fri Nov  1 10:10:46 2019 
+## Date of summary: Fri Nov  1 10:10:46 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
@@ -131,16 +131,14 @@
 ## Error model algorithm: OLS 
 ## 
 ## Starting values for parameters to be optimised:
-##                   value   type
-## parent_0      89.850000  state
-## k_parent_sink  0.100000 deparm
-## sigma          2.779827  error
+##               value   type
+## parent_0      89.85  state
+## k_parent_sink  0.10 deparm
 ## 
 ## Starting values for the transformed parameters actually optimised:
 ##                       value lower upper
 ## parent_0          89.850000  -Inf   Inf
 ## log_k_parent_sink -2.302585  -Inf   Inf
-## sigma              2.779827     0   Inf
 ## 
 ## Fixed parameter values:
 ## None
@@ -214,12 +212,12 @@
 
summary(m.L1.FOMC, data = FALSE)

 
## Warning in sqrt(diag(covar)): NaNs wurden erzeugt

 
## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt

-
## Warning in cov2cor(ans$cov.unscaled): diag(.) had 0 or NA entries; non-
-## finite result is doubtful

+
## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite
+## result is doubtful

 
## mkin version used for fitting:    0.9.49.6 
 ## R version used for fitting:       3.6.1 
-## Date of fit:     Thu Sep 19 09:52:59 2019 
-## Date of summary: Thu Sep 19 09:52:59 2019 
+## Date of fit:     Fri Nov  1 10:10:48 2019 
+## Date of summary: Fri Nov  1 10:10:48 2019 
 ## 
 ## 
 ## Warning: Optimisation did not converge:
@@ -231,25 +229,23 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 899 model solutions performed in 1.908 s
+## Fitted using 899 model solutions performed in 1.91 s
 ## 
 ## Error model: Constant variance 
 ## 
 ## Error model algorithm: OLS 
 ## 
 ## Starting values for parameters to be optimised:
-##              value   type
-## parent_0 89.850000  state
-## alpha     1.000000 deparm
-## beta     10.000000 deparm
-## sigma     2.779871  error
+##          value   type
+## parent_0 89.85  state
+## alpha     1.00 deparm
+## beta     10.00 deparm
 ## 
 ## Starting values for the transformed parameters actually optimised:
 ##               value lower upper
 ## parent_0  89.850000  -Inf   Inf
 ## log_alpha  0.000000  -Inf   Inf
 ## log_beta   2.302585  -Inf   Inf
-## sigma      2.779871     0   Inf
 ## 
 ## Fixed parameter values:
 ## None
@@ -323,33 +319,31 @@
 
summary(m.L2.FOMC, data = FALSE)

 
## mkin version used for fitting:    0.9.49.6 
 ## R version used for fitting:       3.6.1 
-## Date of fit:     Thu Sep 19 09:53:00 2019 
-## Date of summary: Thu Sep 19 09:53:00 2019 
+## Date of fit:     Fri Nov  1 10:10:49 2019 
+## Date of summary: Fri Nov  1 10:10:49 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 239 model solutions performed in 0.49 s
+## Fitted using 239 model solutions performed in 0.489 s
 ## 
 ## Error model: Constant variance 
 ## 
 ## Error model algorithm: OLS 
 ## 
 ## Starting values for parameters to be optimised:
-##              value   type
-## parent_0 93.950000  state
-## alpha     1.000000 deparm
-## beta     10.000000 deparm
-## sigma     2.275722  error
+##          value   type
+## parent_0 93.95  state
+## alpha     1.00 deparm
+## beta     10.00 deparm
 ## 
 ## Starting values for the transformed parameters actually optimised:
 ##               value lower upper
 ## parent_0  93.950000  -Inf   Inf
 ## log_alpha  0.000000  -Inf   Inf
 ## log_beta   2.302585  -Inf   Inf
-## sigma      2.275722     0   Inf
 ## 
 ## Fixed parameter values:
 ## None
@@ -399,8 +393,8 @@
 
summary(m.L2.DFOP, data = FALSE)

 
## mkin version used for fitting:    0.9.49.6 
 ## R version used for fitting:       3.6.1 
-## Date of fit:     Thu Sep 19 09:53:02 2019 
-## Date of summary: Thu Sep 19 09:53:02 2019 
+## Date of fit:     Fri Nov  1 10:10:51 2019 
+## Date of summary: Fri Nov  1 10:10:51 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -409,19 +403,18 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 572 model solutions performed in 1.204 s
+## Fitted using 572 model solutions performed in 1.218 s
 ## 
 ## Error model: Constant variance 
 ## 
 ## Error model algorithm: OLS 
 ## 
 ## Starting values for parameters to be optimised:
-##              value   type
-## parent_0 93.950000  state
-## k1        0.100000 deparm
-## k2        0.010000 deparm
-## g         0.500000 deparm
-## sigma     1.413899  error
+##          value   type
+## parent_0 93.95  state
+## k1        0.10 deparm
+## k2        0.01 deparm
+## g         0.50 deparm
 ## 
 ## Starting values for the transformed parameters actually optimised:
 ##              value lower upper
@@ -429,7 +422,6 @@
 ## log_k1   -2.302585  -Inf   Inf
 ## log_k2   -4.605170  -Inf   Inf
 ## g_ilr     0.000000  -Inf   Inf
-## sigma     1.413899     0   Inf
 ## 
 ## Fixed parameter values:
 ## None
@@ -499,8 +491,8 @@
 
summary(mm.L3[["DFOP", 1]])

 
## mkin version used for fitting:    0.9.49.6 
 ## R version used for fitting:       3.6.1 
-## Date of fit:     Thu Sep 19 09:53:04 2019 
-## Date of summary: Thu Sep 19 09:53:04 2019 
+## Date of fit:     Fri Nov  1 10:10:53 2019 
+## Date of summary: Fri Nov  1 10:10:53 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -509,19 +501,18 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 373 model solutions performed in 0.799 s
+## Fitted using 373 model solutions performed in 0.784 s
 ## 
 ## Error model: Constant variance 
 ## 
 ## Error model algorithm: OLS 
 ## 
 ## Starting values for parameters to be optimised:
-##              value   type
-## parent_0 97.800000  state
-## k1        0.100000 deparm
-## k2        0.010000 deparm
-## g         0.500000 deparm
-## sigma     1.017292  error
+##          value   type
+## parent_0 97.80  state
+## k1        0.10 deparm
+## k2        0.01 deparm
+## g         0.50 deparm
 ## 
 ## Starting values for the transformed parameters actually optimised:
 ##              value lower upper
@@ -529,7 +520,6 @@
 ## log_k1   -2.302585  -Inf   Inf
 ## log_k2   -4.605170  -Inf   Inf
 ## g_ilr     0.000000  -Inf   Inf
-## sigma     1.017292     0   Inf
 ## 
 ## Fixed parameter values:
 ## None
@@ -605,31 +595,29 @@
 
summary(mm.L4[["SFO", 1]], data = FALSE)

 
## mkin version used for fitting:    0.9.49.6 
 ## R version used for fitting:       3.6.1 
-## Date of fit:     Thu Sep 19 09:53:04 2019 
-## Date of summary: Thu Sep 19 09:53:05 2019 
+## Date of fit:     Fri Nov  1 10:10:53 2019 
+## Date of summary: Fri Nov  1 10:10:54 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 142 model solutions performed in 0.287 s
+## Fitted using 142 model solutions performed in 0.292 s
 ## 
 ## Error model: Constant variance 
 ## 
 ## Error model algorithm: OLS 
 ## 
 ## Starting values for parameters to be optimised:
-##                  value   type
-## parent_0      96.60000  state
-## k_parent_sink  0.10000 deparm
-## sigma          3.16181  error
+##               value   type
+## parent_0       96.6  state
+## k_parent_sink   0.1 deparm
 ## 
 ## Starting values for the transformed parameters actually optimised:
 ##                       value lower upper
 ## parent_0          96.600000  -Inf   Inf
 ## log_k_parent_sink -2.302585  -Inf   Inf
-## sigma              3.161810     0   Inf
 ## 
 ## Fixed parameter values:
 ## None
@@ -670,33 +658,31 @@
 
summary(mm.L4[["FOMC", 1]], data = FALSE)

 
## mkin version used for fitting:    0.9.49.6 
 ## R version used for fitting:       3.6.1 
-## Date of fit:     Thu Sep 19 09:53:05 2019 
-## Date of summary: Thu Sep 19 09:53:05 2019 
+## Date of fit:     Fri Nov  1 10:10:54 2019 
+## Date of summary: Fri Nov  1 10:10:54 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 224 model solutions performed in 0.48 s
+## Fitted using 224 model solutions performed in 0.455 s
 ## 
 ## Error model: Constant variance 
 ## 
 ## Error model algorithm: OLS 
 ## 
 ## Starting values for parameters to be optimised:
-##              value   type
-## parent_0 96.600000  state
-## alpha     1.000000 deparm
-## beta     10.000000 deparm
-## sigma     1.830055  error
+##          value   type
+## parent_0  96.6  state
+## alpha      1.0 deparm
+## beta      10.0 deparm
 ## 
 ## Starting values for the transformed parameters actually optimised:
 ##               value lower upper
 ## parent_0  96.600000  -Inf   Inf
 ## log_alpha  0.000000  -Inf   Inf
 ## log_beta   2.302585  -Inf   Inf
-## sigma      1.830055     0   Inf
 ## 
 ## Fixed parameter values:
 ## None
@@ -746,6 +732,7 @@