diff options
Diffstat (limited to 'man/mkinfit.Rd')
| -rw-r--r-- | man/mkinfit.Rd | 28 |
1 files changed, 14 insertions, 14 deletions
diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd index 2d8d3726..93df5be1 100644 --- a/man/mkinfit.Rd +++ b/man/mkinfit.Rd @@ -237,36 +237,36 @@ fit <- mkinfit("FOMC", FOCUS_2006_C) summary(fit) # One parent compound, one metabolite, both single first order. +# Use mkinsub for convenience in model formulation. Pathway to sink included per default. SFO_SFO <- mkinmod( - parent = list(type = "SFO", to = "m1", sink = TRUE), - m1 = list(type = "SFO")) + parent = mkinsub("SFO", "m1"), + m1 = mkinsub("SFO")) # Fit the model to the FOCUS example dataset D using defaults -system.time(fit <- mkinfit(SFO_SFO, FOCUS_2006_D, - solution_type = "eigen")) +print(system.time(fit <- mkinfit(SFO_SFO, FOCUS_2006_D, + solution_type = "eigen"))) coef(fit) endpoints(fit) \dontrun{ -system.time(fit.deSolve <- mkinfit(SFO_SFO, FOCUS_2006_D, - solution_type = "deSolve")) +# deSolve is slower when ccSolve is not installed and set up +print(system.time(fit.deSolve <- mkinfit(SFO_SFO, FOCUS_2006_D, + solution_type = "deSolve"))) coef(fit.deSolve) endpoints(fit.deSolve) } # Use stepwise fitting, using optimised parameters from parent only fit, FOMC \dontrun{ -FOMC <- mkinmod(parent = list(type = "FOMC")) FOMC_SFO <- mkinmod( - parent = list(type = "FOMC", to = "m1", sink = TRUE), - m1 = list(type = "SFO")) + parent = mkinsub("FOMC", "m1"), + m1 = mkinsub("SFO")) # Fit the model to the FOCUS example dataset D using defaults fit.FOMC_SFO <- mkinfit(FOMC_SFO, FOCUS_2006_D) # Use starting parameters from parent only FOMC fit -fit.FOMC = mkinfit(FOMC, FOCUS_2006_D, plot=TRUE) +fit.FOMC = mkinfit("FOMC", FOCUS_2006_D, plot=TRUE) fit.FOMC_SFO <- mkinfit(FOMC_SFO, FOCUS_2006_D, parms.ini = fit.FOMC$bparms.ode, plot=TRUE) # Use stepwise fitting, using optimised parameters from parent only fit, SFORB -SFORB <- mkinmod(parent = list(type = "SFORB")) SFORB_SFO <- mkinmod( parent = list(type = "SFORB", to = "m1", sink = TRUE), m1 = list(type = "SFO")) @@ -274,14 +274,14 @@ SFORB_SFO <- mkinmod( fit.SFORB_SFO <- mkinfit(SFORB_SFO, FOCUS_2006_D) fit.SFORB_SFO.deSolve <- mkinfit(SFORB_SFO, FOCUS_2006_D, solution_type = "deSolve") # Use starting parameters from parent only SFORB fit (not really needed in this case) -fit.SFORB = mkinfit(SFORB, FOCUS_2006_D) +fit.SFORB = mkinfit("SFORB", FOCUS_2006_D) fit.SFORB_SFO <- mkinfit(SFORB_SFO, FOCUS_2006_D, parms.ini = fit.SFORB$bparms.ode) } \dontrun{ # Weighted fits, including IRLS -SFO_SFO.ff <- mkinmod(parent = list(type = "SFO", to = "m1"), - m1 = list(type = "SFO"), use_of_ff = "max") +SFO_SFO.ff <- mkinmod(parent = mkinsub("SFO", "m1"), + m1 = mkinsub("SFO"), use_of_ff = "max") f.noweight <- mkinfit(SFO_SFO.ff, FOCUS_2006_D) summary(f.noweight) f.irls <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, reweight.method = "obs") |