Pharmacokinetic Bioanalysis Experiments Design and Exploration
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Documentation for package ‘PKbioanalysis’ version 0.5.0
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 |