From 194659fcaccdd1ee37851725b8c72e99daa3a8cf Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 10 Apr 2019 10:17:35 +0200 Subject: Adapt tests, vignettes and examples - Write the NEWS - Static documentation rebuilt by pkgdown - Adapt mkinerrmin - Fix (hopefully all) remaining problems in mkinfit --- docs/reference/summary.mkinfit.html | 64 ++++++++++++++++++++----------------- 1 file changed, 34 insertions(+), 30 deletions(-) (limited to 'docs/reference/summary.mkinfit.html') diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index f561e258..e5565990 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -32,10 +32,10 @@ - + @@ -66,7 +66,7 @@ mkin - 0.9.48.1 + 0.9.49.4 @@ -131,10 +131,10 @@
-

Lists model equations, the summary as returned by summary.modFit, - the chi2 error levels calculated according to FOCUS guidance (2006) as far - as defined therein, and optionally the data, consisting of observed, predicted - and residual values.

+

Lists model equations, initial parameter values, optimised parameters with some + uncertainty statistics, the chi2 error levels calculated according to FOCUS + guidance (2006) as defined therein, formation fractions, DT50 values and + optionally the data, consisting of observed, predicted and residual values.

@@ -178,8 +178,7 @@

Value

-

The summary function returns a list derived from - summary.modFit, with components, among others

+

The summary function returns a list with components, among others

version, Rversion

The mkin and R versions used

date.fit, date.summary

The dates where the fit and the summary were produced

use_of_ff

Was maximum or minimum use made of formation fractions

@@ -193,6 +192,7 @@
errmin

The chi2 error levels for each observed variable.

bparms.ode

All backtransformed ODE parameters, for use as starting parameters for related models.

+
errparms

Error model parameters.

ff

The estimated formation fractions derived from the fitted model.

distimes

The DT50 and DT90 values for each observed variable.

SFORB

If applicable, eigenvalues of SFORB components of the model.

@@ -209,52 +209,56 @@

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:     Mon Mar  4 14:06:25 2019 
-#> Date of summary: Mon Mar  4 14:06:25 2019 
+    
  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 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted with method Port using 35 model solutions performed in 0.085 s
+#> Fitted with method using 131 model solutions performed in 0.284 s
 #> 
-#> Weighting: none
+#> Error model:
+#> NULL
 #> 
 #> Starting values for parameters to be optimised:
-#>                value   type
-#> parent_0      101.24  state
-#> k_parent_sink   0.10 deparm
+#>                    value   type
+#> parent_0      101.240000  state
+#> k_parent_sink   0.100000 deparm
+#> sigma           5.265546  error
 #> 
 #> Starting values for the transformed parameters actually optimised:
 #>                        value lower upper
 #> parent_0          101.240000  -Inf   Inf
 #> log_k_parent_sink  -2.302585  -Inf   Inf
+#> sigma               5.265546     0   Inf
 #> 
 #> Fixed parameter values:
 #> None
 #> 
 #> Optimised, transformed parameters with symmetric confidence intervals:
 #>                   Estimate Std. Error  Lower   Upper
-#> parent_0           109.200     4.3910 98.410 119.900
-#> log_k_parent_sink   -3.291     0.1152 -3.573  -3.009
+#> parent_0           109.200    3.70400 99.630 118.700
+#> log_k_parent_sink   -3.291    0.09176 -3.527  -3.055
+#> sigma                5.266    1.31600  1.882   8.649
 #> 
 #> Parameter correlation:
-#>                   parent_0 log_k_parent_sink
-#> parent_0             1.000             0.575
-#> log_k_parent_sink    0.575             1.000
-#> 
-#> Residual standard error: 6.08 on 6 degrees of freedom
+#>                    parent_0 log_k_parent_sink     sigma
+#> parent_0          1.000e+00         5.428e-01 1.642e-07
+#> log_k_parent_sink 5.428e-01         1.000e+00 2.507e-07
+#> sigma             1.642e-07         2.507e-07 1.000e+00
 #> 
 #> Backtransformed parameters:
 #> Confidence intervals for internally transformed parameters are asymmetric.
 #> t-test (unrealistically) based on the assumption of normal distribution
 #> for estimators of untransformed parameters.
-#>                Estimate t value    Pr(>t)    Lower     Upper
-#> parent_0      109.20000  24.860 1.394e-07 98.41000 119.90000
-#> k_parent_sink   0.03722   8.679 6.457e-05  0.02807   0.04934
+#>                Estimate t value    Pr(>t)   Lower     Upper
+#> parent_0      109.20000   29.47 4.218e-07 99.6300 118.70000
+#> 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:
 #>          err.min n.optim df
-- 
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