PharmUse is a database compiling information on prescription drug consumption, physicochemical properties, and literature-reported toxicity values for 290 pharmaceuticals. PharmUse integrates data from the 2020 Agency for Healthcare Research & Quality Medical Expenditure Panel Survey (MEPS) Prescribed Medicines File, accessible from here, with the Environmental Protection Agency's CompTox Chemicals Dashboard. Notably, the MEPS survey is from a nationally representative sample of United States citizens. In the associated scripts, the MEPS data are downloaded directly from the provided website and converted to a text file, which is used in the script pharmuse_constructor.R. The physicochemical properties and toxicity values are downloaded directly from CompTox by conducting a batch search for Chemical Name, SMILES, InChi String, InChiKey, Molecular Formula, Average Mass, ToxValDB Details, and Physicochemical Property Values.
PharmFlush is a binomial distribution model that predicts the concentration profile of the 290 pharmaceuticals in a sewershed of a given size, compares sewersheds of different sizes, and compares the predicted concentration profile to literature-reported concentrations. It uses data provided by PharmUse to run. PharmFlush is run using pharmflush.R.
The script ensemble_exploration.R uses csv files generated in pharmuse_constructor.R and pharmflush.R to compare literature-reported, predicted, and No Observed Effect Concentrations.
To run pharmuse_constructor.R, first run the following in your console:
install.packages("dplyr")
install.packages("readxl")
install.packages("stringr")
install.packages("tidyr")
install.packages("purrr")
Alternatively, these packages can be installed at once by running:
install.packages("tidyverse")
Additionally, the functions library pharmuse_constructor_functions.R, the MEPS data file MEPS_data_2020.txt, drugs_to_remove.xlsx, and comptox_search.xlsx must be in the working directory to run this script.
To run pharmflush.R, first run the following in your console:
install.packages("tidyverse")
install.packages("viridis")
install.packages("svglite")
install.packages("patchwork")
Additionally, pharmuse.csv, lit_values_all.csv, and lit_values_summary.csv must be in the working directory to run this script.
To run ensemble_exploration.R, first run the following in your console:
install.packages("tidyverse")
install.packages("ggforce")
Additionally, all_ensembles_100.csv, all_ensembles_1000.csv, all_ensembles_100k.csv, all_ensembles_1mil.csv, lit_values_all.csv, noec_vert.csv, noec_invert.csv, and noec_human.csv must be in the working directory to run this script.