# Pharmacokinetic Bioanalysis Experiments Design and Exploration

## Documentation for package ‘PKbioanalysis’ version 0.5.0

- DESCRIPTION file
- Package NEWS
- Package README

## Help Pages

add_blank | Add blank to the plate Can be either double blank (DB), CS0IS+ or CS+IS0
add_cs_curve | Add calibration curve to the plate
add_DB | Add double blank (DB) to a plate
add_DQC | Add dilution quality control (DQC) to the plate
add_QC | Add quality control samples to the plate
add_samples | Add samples to plate with pharmacokinetic attributes
add_samples_db | Add samples from the sample log to the plate
add_samples_db2 | Add samples from the sample log to the plate with multiplication
add_suitability | Add suitability sample to the plate
area_report.PeakRes | gt table of areas
calc_var_summary | Calculate Summary Statistics for Each Concentration Level For Either Concentration, Area, or Area Ratio
check_chrom_cmpds | Check Matching of Compound and Transitions in chrom_res and method database
chrom_app | chrom_apps
combine_injec_lists | Create Sample List with rigorous design
combine_plates | Combine plates in MultiPlate object
config_suitability | Configure suitability runs
create_new_study | Create a new study in the database
cv | Calculate Coefficient of variation
download_sample_list | Download sample list from database to local spreadsheet with vendor specific format
estim_dil_limit | Estimate Dilution Limit Based on Additive and Proportional Errors and LLOQ
estim_lloq | Estimate LLOQ From Existing Additive and Proportional errors
export_integration | Export Expected RT
export_pk_profiles | Export PK profiles for a given compound in a specified format Currently supports "nonmem" format. The exported file will include a CSV with the PK data and an Excel file with the codebook.
export_run | Export run
extract_peak_bounds | Extract Peak Boundaries
fill_scheme | Filling orientation of the plate
filter_chrom | title Filter Chromatogram Peaks
fit_var | Estimate Additive and proportional errors from calibration data
formated_print | Format and print the results of fit_var
generate_96 | Generate 96 well plate
get_compound_ID | Find Compound ID from compound Name
get_sample_ID | Find Sample ID from sample Name
get_sample_names | Find sample names for all samples
has_default_bounds | check if default expected RT is set for a compound
install_py_dep | Install Python dependencies for PKbioanalysis
integrate | integrate Peak with trapzoid method given start and end
is_integrated | Check if peak was integrated for a specific compound
is_integrated-method | Check if peak was integrated for a specific compound
is_smoothed | Return an indicator if the chromatogram is smoothed
length-method | Length method for MultiPlate
make_calibration_study | Create a calibration study with calibration standards and QCs
make_metabolic_study | Create a metabolic study layout
nca_table | Calculate Cmax, Tmax and AUC for each subject given a compound's PK profiles
pkmerge | Merge PK profiles into QuantRes object
plate_metadata | Set plate description
plate_tree | Plot the design of the plate
plot.PlateObj | Plotting 96 well plate
plot_chrom | Plot Chromatogram per Sample for Selected transitions
plot_peak_areas.PeakRes | Plot peak areas
plot_RT.ChromRes | Plotting RT intervals of chromatogram
plot_RT.PeakRes | Plot RT
plot_var_pattern | Plot Relationship Between Concentration and CV/SD
precision_per_vial | Precision per vial
prefilter_precision_data | Filter data
prefilter_precision_data-method | Filter data
quant_app | Quantification App
read_chrom | Read Chromatogram Files
read_experiment_results | Read experiment results
register_plate | This will save the plate to the database
response_to_conc | Convert response to concentration
reverse_predict | Reverse predict concentration from response
run_summary | Get Summary of an object
run_summary.PeakRes | Get Summary of an object
smooth_chrom | Smooth Chromatogram Peaks
study_app | bioanalytic_app
update_RT | Manually Update Observed RT for either all compounds, all next samples, or single compound and sample
write_injec_seq | Write injection sequence to database
[[-method | Subsetting method for MultiPlate