From bc3825ae2d12c18ea3d3caf17eb23c93fef180b8 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 8 Oct 2020 09:31:35 +0200 Subject: Fix issues for release --- docs/dev/articles/FOCUS_D.html | 31 +++++++++++++++++++------------ 1 file changed, 19 insertions(+), 12 deletions(-) (limited to 'docs/dev/articles/FOCUS_D.html') diff --git a/docs/dev/articles/FOCUS_D.html b/docs/dev/articles/FOCUS_D.html index 7d5dd732..02701431 100644 --- a/docs/dev/articles/FOCUS_D.html +++ b/docs/dev/articles/FOCUS_D.html @@ -101,7 +101,7 @@

Example evaluation of FOCUS Example Dataset D

Johannes Ranke

2020-05-27

2020-10-08

Source: vignettes/FOCUS_D.rmd

FOCUS_D.rmd

@@ -171,18 +171,20 @@

fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)

## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE): Observations with value
 ## of zero were removed from the data

## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE): Shapiro-Wilk test for
+## standardized residuals: p = 0.0165

A plot of the fit including a residual plot for both observed variables is obtained using the plot_sep method for mkinfit objects, which shows separate graphs for all compounds and their residuals.

plot_sep(fit, lpos = c("topright", "bottomright"))

plot_sep(fit, lpos = c("topright", "bottomright"))

Confidence intervals for the parameter estimates are obtained using the mkinparplot function.

mkinparplot(fit)

mkinparplot(fit)

A comprehensive report of the results is obtained using the summary method for mkinfit objects.

summary(fit)

summary(fit)

## mkin version used for fitting:    0.9.50.3 
-## R version used for fitting:       4.0.0 
-## Date of fit:     Wed May 27 07:51:36 2020 
-## Date of summary: Wed May 27 07:51:37 2020 
+## R version used for fitting:       4.0.2 
+## Date of fit:     Thu Oct  8 09:14:03 2020 
+## Date of summary: Thu Oct  8 09:14:03 2020 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent * parent
@@ -190,7 +192,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 421 model solutions performed in 0.173 s
+## Fitted using 421 model solutions performed in 0.171 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -214,6 +216,11 @@
 ##      value  type
 ## m1_0     0 state
 ## 
+## 
+## Warning(s): 
+## Observations with value of zero were removed from the data
+## Shapiro-Wilk test for standardized residuals: p =  0.0165
+## 
 ## Results:
 ## 
 ##        AIC      BIC    logLik
@@ -229,11 +236,11 @@
 ## 
 ## Parameter correlation:
 ##                  parent_0 log_k_parent   log_k_m1 f_parent_ilr_1      sigma
-## parent_0        1.000e+00    5.174e-01 -1.688e-01     -5.471e-01 -3.190e-07
+## parent_0        1.000e+00    5.174e-01 -1.688e-01     -5.471e-01 -3.214e-07
 ## log_k_parent    5.174e-01    1.000e+00 -3.263e-01     -5.426e-01  3.168e-07
-## log_k_m1       -1.688e-01   -3.263e-01  1.000e+00      7.478e-01 -1.406e-07
-## f_parent_ilr_1 -5.471e-01   -5.426e-01  7.478e-01      1.000e+00 -1.587e-10
-## sigma          -3.190e-07    3.168e-07 -1.406e-07     -1.587e-10  1.000e+00
+## log_k_m1       -1.688e-01   -3.263e-01  1.000e+00      7.478e-01 -1.410e-07
+## f_parent_ilr_1 -5.471e-01   -5.426e-01  7.478e-01      1.000e+00  5.093e-10
+## sigma          -3.214e-07    3.168e-07 -1.410e-07      5.093e-10  1.000e+00
 ## 
 ## Backtransformed parameters:
 ## Confidence intervals for internally transformed parameters are asymmetric.
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