aboutsummaryrefslogtreecommitdiff
path: root/man
diff options
context:
space:
mode:
authorJohannes Ranke <jranke@uni-bremen.de>2020-05-29 15:03:04 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2020-05-29 15:03:04 +0200
commit510436646b1bdd5b8cfab70be29334bd3cc9c828 (patch)
tree4b3e26f658e822e18d09e2d939a5c89214566b6d /man
parent609bfe2fd7ecbdcad5f5d641f0db51541dcd6a4e (diff)
Warn if standardized residuals are unlikely normal
This revealed a bug in the data returned in mkinfit$data in the case of the d_3 algorithm, which also affected the residual plot - the data from the direct fitting was not returned even if this was the better method.
Diffstat (limited to 'man')
-rw-r--r--man/mkinfit.Rd63
1 files changed, 0 insertions, 63 deletions
diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd
index 5e6b242e..748dcb50 100644
--- a/man/mkinfit.Rd
+++ b/man/mkinfit.Rd
@@ -214,69 +214,6 @@ When using the "IORE" submodel for metabolites, fitting with
numerical ODE solver. In this situation it may help to switch off the
internal rate transformation.
}
-\examples{
-
-# Use shorthand notation for parent only degradation
-fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
-summary(fit)
-
-# One parent compound, one metabolite, both single first order.
-# Use mkinsub for convenience in model formulation. Pathway to sink included per default.
-SFO_SFO <- mkinmod(
- parent = mkinsub("SFO", "m1"),
- m1 = mkinsub("SFO"))
-# Fit the model to the FOCUS example dataset D using defaults
-print(system.time(fit <- mkinfit(SFO_SFO, FOCUS_2006_D,
- solution_type = "eigen", quiet = TRUE)))
-parms(fit)
-endpoints(fit)
-\dontrun{
-# deSolve is slower when no C compiler (gcc) was available during model generation
-print(system.time(fit.deSolve <- mkinfit(SFO_SFO, FOCUS_2006_D,
- solution_type = "deSolve")))
-parms(fit.deSolve)
-endpoints(fit.deSolve)
-}
-
-# Use stepwise fitting, using optimised parameters from parent only fit, FOMC
-\dontrun{
-FOMC_SFO <- mkinmod(
- parent = mkinsub("FOMC", "m1"),
- m1 = mkinsub("SFO"))
-# Fit the model to the FOCUS example dataset D using defaults
-fit.FOMC_SFO <- mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE)
-# Use starting parameters from parent only FOMC fit
-fit.FOMC = mkinfit("FOMC", FOCUS_2006_D, quiet = TRUE)
-fit.FOMC_SFO <- mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE,
- parms.ini = fit.FOMC$bparms.ode)
-
-# Use stepwise fitting, using optimised parameters from parent only fit, SFORB
-SFORB_SFO <- mkinmod(
- parent = list(type = "SFORB", to = "m1", sink = TRUE),
- m1 = list(type = "SFO"))
-# Fit the model to the FOCUS example dataset D using defaults
-fit.SFORB_SFO <- mkinfit(SFORB_SFO, FOCUS_2006_D, quiet = TRUE)
-fit.SFORB_SFO.deSolve <- mkinfit(SFORB_SFO, FOCUS_2006_D, solution_type = "deSolve",
- quiet = TRUE)
-# Use starting parameters from parent only SFORB fit (not really needed in this case)
-fit.SFORB = mkinfit("SFORB", FOCUS_2006_D, quiet = TRUE)
-fit.SFORB_SFO <- mkinfit(SFORB_SFO, FOCUS_2006_D, parms.ini = fit.SFORB$bparms.ode, quiet = TRUE)
-}
-
-\dontrun{
-# Weighted fits, including IRLS (error_model = "obs")
-SFO_SFO.ff <- mkinmod(parent = mkinsub("SFO", "m1"),
- m1 = mkinsub("SFO"), use_of_ff = "max")
-f.noweight <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
-summary(f.noweight)
-f.obs <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, error_model = "obs", quiet = TRUE)
-summary(f.obs)
-f.tc <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, error_model = "tc", quiet = TRUE)
-summary(f.tc)
-}
-
-
-}
\references{
Rocke DM and Lorenzato S (1995) A two-component model
for measurement error in analytical chemistry. \emph{Technometrics} 37(2), 176-184.

Contact - Imprint