diff options
Diffstat (limited to 'vignettes')
| -rw-r--r-- | vignettes/FOCUS_Z.Rnw | 30 |
1 files changed, 9 insertions, 21 deletions
diff --git a/vignettes/FOCUS_Z.Rnw b/vignettes/FOCUS_Z.Rnw index 40ddfc44..23b229ab 100644 --- a/vignettes/FOCUS_Z.Rnw +++ b/vignettes/FOCUS_Z.Rnw @@ -108,24 +108,14 @@ The simplified model is obtained by setting the list component \texttt{sink} to <<FOCUS_2006_Z_fits_3, echo=TRUE, fig.height=4>>= Z.3 <- mkinmod(Z0 = list(type = "SFO", to = "Z1", sink = FALSE), - Z1 = list(type = "SFO")) + Z1 = list(type = "SFO"), use_of_ff = "max") m.Z.3 <- mkinfit(Z.3, FOCUS_2006_Z_mkin, quiet = TRUE) plot(m.Z.3) summary(m.Z.3, data = FALSE) @ -This model definition is not supported when formation fractions -are used, but the formation fraction can be fixed to unity. - -<<FOCUS_2006_Z_fits_3.ff, echo=TRUE, fig.height=4>>= -Z.3.ff <- mkinmod(Z0 = list(type = "SFO", to = "Z1"), - Z1 = list(type = "SFO"), use_of_ff = "max") -m.Z.3.ff <- mkinfit(Z.3.ff, FOCUS_2006_Z_mkin, - parms.ini = c(f_Z0_to_Z1 = 1), - fixed_parms = "f_Z0_to_Z1", - quiet = TRUE) -summary(m.Z.3.ff, data = FALSE) -@ +As there is only one transformation product for Z0 and no pathway +to sink, the formation fraction is internally fixed to unity. \section{Including metabolites Z2 and Z3} @@ -172,17 +162,15 @@ mkinresplot(m.Z.FOCUS, "Z3", lpos = "bottomright") We can also investigate the confidence interval for the formation fraction from Z1 to Z2 by specifying the model using formation -fractions, and fixing only the formation fraction from Z0 to Z1 -to unity. +fractions. <<FOCUS_2006_Z_fits_6_ff, echo=TRUE, fig.height=4>>= -Z.FOCUS.ff <- mkinmod(Z0 = list(type = "SFO", to = "Z1"), - Z1 = list(type = "SFO", to = "Z2"), +Z.FOCUS.ff <- mkinmod(Z0 = list(type = "SFO", to = "Z1", sink = FALSE), + Z1 = list(type = "SFO", to = "Z2", sink = FALSE), Z2 = list(type = "SFO", to = "Z3"), - Z3 = list(type = "SFO"), use_of_ff = "max") -m.Z.FOCUS.ff <- mkinfit(Z.FOCUS.ff, FOCUS_2006_Z_mkin, - parms.ini = c(f_Z0_to_Z1 = 1), - fixed_parms = c("f_Z0_to_Z1"), quiet = TRUE) + Z3 = list(type = "SFO"), + use_of_ff = "max") +m.Z.FOCUS.ff <- mkinfit(Z.FOCUS.ff, FOCUS_2006_Z_mkin, quiet = TRUE) plot(m.Z.FOCUS.ff) summary(m.Z.FOCUS.ff, data = FALSE) @ |