physiology.data {httk} | R Documentation |
Species-specific physiology parameters
Description
This data set contains values from Davies and Morris (1993) necessary to paramaterize a toxicokinetic model for human, mouse, rat, dog, or rabbit. The temperature for each species are taken from Reece (2015), Jordon (1995), and Stammers (1926). Mean residence time for the small intestine is from Grandoni et al. (2019). Human small intestine radius is from Yu et al. (1999). Rat small intestine radius is from Griffin and O'Driscoll (2008).
Usage
physiology.data
Format
A data.frame containing 18 rows and 7 columns.
Author(s)
John Wambaugh and Nisha Sipes
References
Davies B, Morris T (1993). “Physiological parameters in laboratory animals and humans.” Pharmaceutical research, 10(7), 1093–1095. doi:10.1023/A:1018943613122.
Brown RP, Delp MD, Lindstedt SL, Rhomberg LR, Beliles RP (1997). “Physiological parameter values for physiologically based pharmacokinetic models.” Toxicology and industrial health, 13(4), 407–484. doi:10.1177/074823379701300401.
Birnbaum L, Brown R, Bischoff K, Foran J, Blancato J, Clewell H, Dedrick R (1994). “Physiological parameter values for PBPK models.” International Life Sciences Institute, Risk Science Institute, Washington, DC.
Reece WO (2015). “14 Body Temperature and Its Regulation.” Dukes' physiology of domestic animals, 149.
Stammers AD (1926). “The blood count and body temperature in normal rats.” The Journal of Physiology, 61(3), 329. doi:10.1113/jphysiol.1926.sp002297.
Jordan D (1995). “Temperature regulation in laboratory rodents.” Journal of anatomy, 186(Pt 1), 228.
Grandoni S, Cesari N, Brogin G, Puccini P, Magni P (2019). “Building in-house PBPK modelling tools for oral drug administration from literature information.” ADMET and DMPK, 7(1), 4–21. doi:10.5599/admet.638.
Griffin B, O'Driscoll C (2008). “Models of the Small Intestine.” In Ehrhardt C, Kim K (eds.), Drug Absorption Studies: In Situ, In Vitro and In Silico Models, chapter 2, 34–76. Springer US, Boston, MA. ISBN 978-0-387-74901-3, doi:10.1007/978-0-387-74901-3_2.
Examples
# We can add a new species (for example, wolverines) by adding new information
# to the physiology.data and tissue.data tables. It can be convenient to start by
# by replicating the data from another species and adjusting as appropriate:
# Copy physiology data from rabbit:
new.species <- physiology.data[,"Rabbit"]
names(new.species) <- physiology.data[,"Parameter"]
rabbit.BW <- new.species["Average BW"]
# Rausch and Pearson (1972) https://doi.org/10.2307/3799057 :
new.species["Average BW"] <- 31.2
# Thiel et al. (2019) https://doi.org/10.1186/s12983-019-0319-8 :
new.species["Average Body Temperature"] <- 38.5
# Add new physiology data column to physiology.data table"
physiology.data <- cbind(physiology.data, new.species)
colnames(physiology.data)[length(colnames(physiology.data))] <- "Wolverine"
# Copy tissue data from rabbit:
new.tissue.data <- subset(tissue.data,Species=="Rabbit")
new.tissue.data$Species <- "Wolverine"
# Add new tissue data rows to tissue.data table:
tissue.data <- rbind(tissue.data, new.tissue.data)
# Species is now available for calculations:
calc_mc_css(chem.cas="80-05-7",
species="wolverine",
parameterize.args.list =list(default.to.human=TRUE),
suppress.messages=TRUE,
samples = 100)