Batch processing for hierarchical fits

- 'R/mhmkin.R': New method for performing multiple hierarchical mkin fits in one function call, optionally in parallel.

- 'R/saem.R': 'logLik' and 'update' methods for 'saem.mmkin' objects.

- 'R/illparms.R': Add methods for 'saem.mmkin' and 'mhmkin' objects.

tests: Use 2 cores on travis, should work according to docs

1 files changed, 6 insertions, 3 deletions

diff --git a/man/saem.Rd b/man/saem.Rd
index 0c066dd2..a202f52f 100644
--- a/man/saem.Rd
+++ b/man/saem.Rd
@@ -49,9 +49,9 @@ saemix_data(object, verbose = FALSE, ...)
 
 \item{transformations}{Per default, all parameter transformations are done
 in mkin. If this argument is set to 'saemix', parameter transformations
-are done in 'saemix' for the supported cases. Currently this is only
-supported in cases where the initial concentration of the parent is not fixed,
-SFO or DFOP is used for the parent and there is either no metabolite or one.}
+are done in 'saemix' for the supported cases, i.e. (as of version 1.1.2)
+SFO, FOMC, DFOP and HS without fixing \code{parent_0}, and SFO or DFOP with
+one SFO metabolite.}
 
 \item{degparms_start}{Parameter values given as a named numeric vector will
 be used to override the starting values obtained from the 'mmkin' object.}
@@ -120,6 +120,9 @@ f_mmkin_parent <- mmkin(c("SFO", "FOMC", "DFOP"), ds, quiet = TRUE)
 f_saem_sfo <- saem(f_mmkin_parent["SFO", ])
 f_saem_fomc <- saem(f_mmkin_parent["FOMC", ])
 f_saem_dfop <- saem(f_mmkin_parent["DFOP", ])
+illparms(f_saem_dfop)
+update(f_saem_dfop, covariance.model = diag(c(1, 1, 1, 0)))
+AIC(f_saem_dfop)
 
 # The returned saem.mmkin object contains an SaemixObject, therefore we can use
 # functions from saemix