Throughout the invitroTKstats
R package, there is
standardized notation used to describe the data processing pipeline.
This appendix serves as an overview for users to understand the data
structure at each processing step.
The minimum information required to pipeline data through
invitroTKstats
can be found in each of the vignettes titled
“<Assay>” where “<Assay>” can be replaced with the following
assays represented in the invitroTKstats
package:
L0 - Compiled raw data files generated by the laboratory containing mass spectrometry results
L1 - L0 data with standardized column names
L2 - L1 data with added “Verification” column
L3 - Frequentist point estimates of desired chemical-specific toxicokinetic (TK) parameters
L4 - Bayesian estimates of desired chemical-specific toxicokinetic (TK) parameters
In the function notations, “<assay>” can be replaced with the following:
build_mydata_<assay> - function used to create data objects necessary for Bayesian modeling
calc_<assay>_point - function used to calculate frequentist estimates from L2 file
calc_<assay> - function used to calculate Bayesian estimates from L2 file
create_catalog - function used to create catalog of raw data (L0) files to be merged with “merge_level0” function
create_chem_table - function used to create chemical ID mapping table
create_method_table - function used to create chemical analysis method mapping table from L1 or L2 file
format_<assay> - function used to create L1 file from L0 file
Heaviside - function used to calculate Heaviside step function at desired values
initfunction_<assay> - function used to set initial values for Bayesian modeling
merge_level0 - function used to compile many raw data (L0) files into a single comprehensive L0 file
plot_clint - function used to plot response vs. time plot for Clint estimates
plot_fup_uc - function used to plot response vs. sample type for fup estimates collected used ultracentrifugation (UC)
sample_verification - function used to create L2 file from L1 file, i.e. add sample verification or exclusion criteria notes
summarize_table - function used to summarize L2 files