load_pradeep2020 {httk}

Load CLint and Fup QSPR predictions predictions from Pradeep et al. 2020.

Description

This function returns an updated version of chem.physical_and_invitro.data that includes quantitative structure-property relationship (QSPR) predictions from Support Vector Machine and Random Forest models developed and presented in Pradeep et al. 2020, included in pradeep2020.

Usage

load_pradeep2020(overwrite = FALSE, target.env = .GlobalEnv)

Arguments

overwrite

Only matters if load.image=FALSE. If overwrite=TRUE then existing data in chem.physical_and_invitro.data will be replaced by any predictions in Pradeep et al. (2020) that is for the same chemical and property. If overwrite=FALSE (DEFAULT) then new data for the same chemical and property are ignored. Funbound.plasma values of 0 (below limit of detection) are overwritten either way.

target.env

The environment where the new chem.physical_and_invitro.data is loaded. Defaults to global environment.

Details

Because Clint and Fup are the only measurements required for many HTTK models, changing the number of chemicals for which a value is available will change the number of chemicals which are listed with the get_cheminfo command. Use the command reset_httk to return to the initial (measured only) chem.physical_and_invitro.data (for all parameters).

Value

data.frame

An updated version of chem.physical_and_invitro.data.

Author(s)

Sarah E. Davidson

References

Pradeep P, Patlewicz G, Pearce R, Wambaugh J, Wetmore B, Judson R (2020). “Using chemical structure information to develop predictive models for in vitro toxicokinetic parameters to inform high-throughput risk-assessment.” Computational Toxicology, 16, 100136. ISSN 2468-1113, doi:10.1016/j.comtox.2020.100136, https://www.sciencedirect.com/science/article/pii/S2468111320300463.

See Also

reset_httk

get_cheminfo

Examples

## Not run: 
# Count how many chemicals for which HTTK is available without the QSPR:
num.chems <- length(get_cheminfo())
print(num.chems)

# For chemicals with Pradeep et al. (2020) Clint and Fup QSPR predictions, 
# add them to our chemical information wherever measured values are 
# unavailable:
load_pradeep2020()

# Or, for chemicals with Pradeep et al. (2020) QSPR predictions, add them to
# our chemical information but overwrite measured values where we had them:
load_pradeep2020(overwrite=TRUE) 

# Let's see how many chemicals we have now with the Pradeep et al. (2020)
# predictions data loaded:
length(get_cheminfo())

# Now let us reset the chemical data to the initial version:
reset_httk()

# We should be back to our original number:
num.chems == length(get_cheminfo())

## End(Not run)