{
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  "Type": "Package",
  "Package": "PKbioanalysis",
  "Title": "Pharmacokinetic Bioanalysis Experiments Design and Exploration",
  "Version": "0.5.0",
  "Authors@R": "c(\nperson(\"Omar\", \"Elashkar\", email = \"omar.i.elashkar@gmail.com\",\nrole = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-5505-778X\"))\n)",
  "Maintainer": "Omar Elashkar <omar.i.elashkar@gmail.com>",
  "Description": "Automate pharmacokinetic/pharmacodynamic bioanalytical\nprocedures based on best practices and regulatory\nrecommendations. The package impose regulatory constrains and\nsanity checking for common bioanalytical procedures.\nAdditionally, 'PKbioanalysis' provides a relational\ninfrastructure for plate management and injection sequence.",
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  "Collate": "'PKbioanalysis-package.R' 'calc.R' 'chrom_anomaly_plots.R'\n'chrom_app.R' 'chrom_parsers.R' 'chrom_utils.R' 'generics.R'\n'class.R' 'chromatogram.R' 'config.R' 'dil_map.R'\n'estim_residuals.R' 'genAI.R' 'gen_studydesign.R'\n'generate_test_set.R' 'injec_list.R' 'linearitycheck.R'\n'method_file.R' 'peak_integerate.R' 'plate.R' 'plate_expr.R'\n'plates_class.R' 'process_chroms.R' 'quant_app.R'\n'quant_misc.R' 'quant_object.R' 'quant_parsers.R'\n'samples_profiles.R' 'study_app.R' 'suitability_utils.R'\n'utils.R' 'writers.R' 'zzz.R'",
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  "Packaged": {
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  "Author": "Omar Elashkar [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-5505-778X>)",
  "Config/pak/sysreqs": "python3",
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  "_exports": [
    "add_blank",
    "add_cs_curve",
    "add_DB",
    "add_DQC",
    "add_QC",
    "add_samples",
    "add_samples_db",
    "add_suitability",
    "area_report.PeakRes",
    "build_injec_seq",
    "calc_var_summary",
    "chrom_app",
    "combine_injec_lists",
    "combine_plates",
    "create_new_study",
    "cv",
    "download_sample_list",
    "estim_dil_limit",
    "estim_lloq",
    "export_integration",
    "export_pk_profiles",
    "export_run",
    "fill_scheme",
    "filter_chrom",
    "fit_var",
    "formated_print",
    "generate_96",
    "get_compound_ID",
    "get_sample_ID",
    "get_sample_names",
    "has_default_bounds",
    "install_py_dep",
    "integrate",
    "is_integrated",
    "is_smoothed",
    "make_calibration_study",
    "make_metabolic_study",
    "nca_table",
    "plate_metadata",
    "plate_tree",
    "plot_chrom",
    "plot_peak_areas.PeakRes",
    "plot_RT.PeakRes",
    "plot_var_pattern",
    "precision_per_vial",
    "prefilter_precision_data",
    "quant_app",
    "read_chrom",
    "read_experiment_results",
    "register_plate",
    "reverse_predict",
    "run_summary",
    "smooth_chrom",
    "study_app",
    "update_RT",
    "write_injec_seq"
  ],
  "_help": [
    {
      "page": "sub-sub-MultiPlate-method",
      "title": "Subsetting method for MultiPlate",
      "topics": [
        "[[,MultiPlate-method"
      ]
    },
    {
      "page": "add_blank",
      "title": "Add blank to the plate Can be either double blank (DB), CS0IS+ or CS+IS0",
      "topics": [
        "add_blank"
      ]
    },
    {
      "page": "add_cs_curve",
      "title": "Add calibration curve to the plate",
      "topics": [
        "add_cs_curve"
      ]
    },
    {
      "page": "add_DB",
      "title": "Add double blank (DB) to a plate",
      "topics": [
        "add_DB"
      ]
    },
    {
      "page": "add_DQC",
      "title": "Add dilution quality control (DQC) to the plate",
      "topics": [
        "add_DQC"
      ]
    },
    {
      "page": "add_QC",
      "title": "Add quality control samples to the plate",
      "topics": [
        "add_QC"
      ]
    },
    {
      "page": "add_samples",
      "title": "Add samples to plate with pharmacokinetic attributes",
      "topics": [
        "add_samples"
      ]
    },
    {
      "page": "add_samples_db",
      "title": "Add samples from the sample log to the plate",
      "topics": [
        "add_samples_db"
      ]
    },
    {
      "page": "add_samples_db2",
      "title": "Add samples from the sample log to the plate with multiplication",
      "topics": [
        "add_samples_db2"
      ]
    },
    {
      "page": "add_suitability",
      "title": "Add suitability sample to the plate",
      "topics": [
        "add_suitability"
      ]
    },
    {
      "page": "area_report.PeakRes",
      "title": "gt table of areas",
      "topics": [
        "area_report.PeakRes"
      ]
    },
    {
      "page": "calc_var_summary",
      "title": "Calculate Summary Statistics for Each Concentration Level For Either Concentration, Area, or Area Ratio",
      "topics": [
        "calc_var_summary"
      ]
    },
    {
      "page": "check_chrom_cmpds",
      "title": "Check Matching of Compound and Transitions in chrom_res and method database",
      "topics": [
        "check_chrom_cmpds"
      ]
    },
    {
      "page": "chrom_app",
      "title": "chrom_apps",
      "topics": [
        "chrom_app"
      ]
    },
    {
      "page": "combine_injec_lists",
      "title": "Create Sample List with rigorous design",
      "topics": [
        "combine_injec_lists"
      ]
    },
    {
      "page": "combine_plates",
      "title": "Combine plates in MultiPlate object",
      "topics": [
        "combine_plates"
      ]
    },
    {
      "page": "config_suitability",
      "title": "Configure suitability runs",
      "topics": [
        "config_suitability"
      ]
    },
    {
      "page": "create_new_study",
      "title": "Create a new study in the database",
      "topics": [
        "create_new_study"
      ]
    },
    {
      "page": "cv",
      "title": "Calculate Coefficient of variation",
      "topics": [
        "cv"
      ]
    },
    {
      "page": "download_sample_list",
      "title": "Download sample list from database to local spreadsheet with vendor specific format",
      "topics": [
        "download_sample_list"
      ]
    },
    {
      "page": "estim_dil_limit",
      "title": "Estimate Dilution Limit Based on Additive and Proportional Errors and LLOQ",
      "topics": [
        "estim_dil_limit"
      ]
    },
    {
      "page": "estim_lloq",
      "title": "Estimate LLOQ From Existing Additive and Proportional errors",
      "topics": [
        "estim_lloq"
      ]
    },
    {
      "page": "export_integration",
      "title": "Export Expected RT",
      "topics": [
        "export_integration"
      ]
    },
    {
      "page": "export_pk_profiles",
      "title": "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.",
      "topics": [
        "export_pk_profiles"
      ]
    },
    {
      "page": "export_run",
      "title": "Export run",
      "topics": [
        "export_run"
      ]
    },
    {
      "page": "extract_peak_bounds",
      "title": "Extract Peak Boundaries",
      "topics": [
        "extract_peak_bounds"
      ]
    },
    {
      "page": "fill_scheme",
      "title": "Filling orientation of the plate",
      "topics": [
        "fill_scheme"
      ]
    },
    {
      "page": "filter_chrom",
      "title": "title Filter Chromatogram Peaks",
      "topics": [
        "filter_chrom"
      ]
    },
    {
      "page": "fit_var",
      "title": "Estimate Additive and proportional errors from calibration data",
      "topics": [
        "fit_var"
      ]
    },
    {
      "page": "formated_print",
      "title": "Format and print the results of fit_var",
      "topics": [
        "formated_print"
      ]
    },
    {
      "page": "generate_96",
      "title": "Generate 96 well plate",
      "topics": [
        "generate_96"
      ]
    },
    {
      "page": "get_compound_ID",
      "title": "Find Compound ID from compound Name",
      "topics": [
        "get_compound_ID"
      ]
    },
    {
      "page": "get_sample_ID",
      "title": "Find Sample ID from sample Name",
      "topics": [
        "get_sample_ID"
      ]
    },
    {
      "page": "get_sample_names",
      "title": "Find sample names for all samples",
      "topics": [
        "get_sample_names"
      ]
    },
    {
      "page": "has_default_bounds",
      "title": "check if default expected RT is set for a compound",
      "topics": [
        "has_default_bounds"
      ]
    },
    {
      "page": "install_py_dep",
      "title": "Install Python dependencies for PKbioanalysis",
      "topics": [
        "install_py_dep"
      ]
    },
    {
      "page": "integrate",
      "title": "integrate Peak with trapzoid method given start and end",
      "topics": [
        "integrate"
      ]
    },
    {
      "page": "is_integrated",
      "title": "Check if peak was integrated for a specific compound",
      "topics": [
        "is_integrated",
        "is_integrated,ChromRes-method",
        "is_integrated,ChromResBase-method"
      ]
    },
    {
      "page": "is_smoothed",
      "title": "Return an indicator if the chromatogram is smoothed",
      "topics": [
        "is_smoothed"
      ]
    },
    {
      "page": "length-MultiPlate-method",
      "title": "Length method for MultiPlate",
      "topics": [
        "length,MultiPlate-method"
      ]
    },
    {
      "page": "make_calibration_study",
      "title": "Create a calibration study with calibration standards and QCs",
      "topics": [
        "make_calibration_study"
      ]
    },
    {
      "page": "make_metabolic_study",
      "title": "Create a metabolic study layout",
      "topics": [
        "make_metabolic_study"
      ]
    },
    {
      "page": "nca_table",
      "title": "Calculate Cmax, Tmax and AUC for each subject given a compound's PK profiles",
      "topics": [
        "nca_table"
      ]
    },
    {
      "page": "pkmerge",
      "title": "Merge PK profiles into QuantRes object",
      "topics": [
        "pkmerge"
      ]
    },
    {
      "page": "plate_metadata",
      "title": "Set plate description",
      "topics": [
        "plate_metadata"
      ]
    },
    {
      "page": "plate_tree",
      "title": "Plot the design of the plate",
      "topics": [
        "plate_tree"
      ]
    },
    {
      "page": "plot_chrom",
      "title": "Plot Chromatogram per Sample for Selected transitions",
      "topics": [
        "plot_chrom"
      ]
    },
    {
      "page": "plot_peak_areas.PeakRes",
      "title": "Plot peak areas",
      "topics": [
        "plot_peak_areas.PeakRes"
      ]
    },
    {
      "page": "plot_RT.ChromRes",
      "title": "Plotting RT intervals of chromatogram",
      "topics": [
        "plot_RT.ChromRes"
      ]
    },
    {
      "page": "plot_RT.PeakRes",
      "title": "Plot RT",
      "topics": [
        "plot_RT.PeakRes"
      ]
    },
    {
      "page": "plot_var_pattern",
      "title": "Plot Relationship Between Concentration and CV/SD",
      "topics": [
        "plot_var_pattern"
      ]
    },
    {
      "page": "plot.PlateObj",
      "title": "Plotting 96 well plate",
      "topics": [
        "plot.PlateObj"
      ]
    },
    {
      "page": "precision_per_vial",
      "title": "Precision per vial",
      "topics": [
        "precision_per_vial"
      ]
    },
    {
      "page": "prefilter_precision_data",
      "title": "Filter data",
      "topics": [
        "prefilter_precision_data",
        "prefilter_precision_data,data.frame-method",
        "prefilter_precision_data,QuantRes-method"
      ]
    },
    {
      "page": "quant_app",
      "title": "Quantification App",
      "topics": [
        "quant_app"
      ]
    },
    {
      "page": "read_chrom",
      "title": "Read Chromatogram Files",
      "topics": [
        "read_chrom"
      ]
    },
    {
      "page": "read_experiment_results",
      "title": "Read experiment results",
      "topics": [
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      ]
    },
    {
      "page": "register_plate",
      "title": "This will save the plate to the database",
      "topics": [
        "register_plate"
      ]
    },
    {
      "page": "response_to_conc",
      "title": "Convert response to concentration",
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