This function takes the parameters from predict_partitioning_schmitt and lumps the partition coefficients along with the volumes and flows based on the given tissue list. It is useful in Monte Carlo simulation of individual partition coefficients when calculating the rest of body partition coefficient.
lump_tissues(
Ktissue2pu.in,
parameters = NULL,
tissuelist = NULL,
species = "Human",
tissue.vols = NULL,
tissue.flows = NULL,
model = "pbtk",
suppress.messages = FALSE
)Ratio of concentration of chemical in red blood cells to unbound concentration in plasma.
Ratio of concentration of chemical in rest of body tissue to unbound concentration in plasma.
Volume of the rest of the body per kg body weight, L/kg BW.
Volume of the liver per kg body weight, L/kg BW.
Fraction of cardiac output flowing to the gut and liver, i.e. out of the liver.
Fraction of cardiac output flowing to the gut.
Fraction of cardiac output flowing to the kidneys.
List of partition coefficients from predict_partitioning_schmitt.
A list of physiological parameters including flows and
volumes for tissues in tissuelist
Manually specifies compartment names and tissues, which
override the standard compartment names and tissues that are usually
specified in a model's associated modelinfo file. Remaining tissues in the
model's associated alltissues listing are lumped in the rest of the body.
Species desired (either "Rat", "Rabbit", "Dog", "Mouse", or default "Human").
A list of volumes for tissues in tissuelist
A list of flows for tissues in tissuelist
Specify which model (and therefore which tissues) are being considered
Whether or not the output message is suppressed.
John Wambaugh and Robert Pearce
This function returns the flows, volumes, and partition coefficients for the lumped tissues specified in tissue list Ktissue2plasma -- tissue to free plasma concentration partition coefficients for every tissue specified by Schmitt (2008) (the tissue.data table) tissuelist -- a list of character vectors, the name of each entry in the list is its own compartment. The tissues in the alltissues vector are the Schmitt (2008) tissues that are to be considered in the lumping process. The tissuelist can also be manually specified for alternate lumping schemes: for example, tissuelist<-list(Rapid=c("Brain","Kidney")) specifies the flow.col and vol.col in the tissuedata.table.
Pearce, Robert G., et al. "Evaluation and calibration of high-throughput predictions of chemical distribution to tissues." Journal of pharmacokinetics and pharmacodynamics 44.6 (2017): 549-565.
pcs <- predict_partitioning_schmitt(chem.name='bisphenola')
tissuelist <- list(liver=c("liver"),kidney=c("kidney"),lung=c("lung"),gut=c("gut")
,muscle.bone=c('muscle','bone'))
lump_tissues(pcs,tissuelist=tissuelist)
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