| addObsPoints | INTERNAL PACKAGE USE: Add observed data points to a... |
| add_sims | Add simulations to an R object |
| AllCompounds | All possible compound IDs, suffixes, etc. |
| AllExpDetails | All possible experimental details for 'extractExpDetails' |
| AllPKParameters | All possible PK parameters for 'extractPK' (version for... |
| AllStats | All names for statistics used in the package |
| AllTissues | All possible tissues and tissue subtypes |
| annotateDetails | Annotate Simcyp Simulator experimental details |
| blueGreens | Create a vector of blues fading into greens |
| blues | Create a vector of blues |
| BufForestData | Example output from 'extractForestData' |
| BufForestData_20mg | Example output from 'extractForestData' |
| BufObsForestData | Example observed PK data for working with 'forest_plot' |
| calc_dosenumber | Calculate the dose number for each time in a set of... |
| calcKi | Calculate the Ki of an inhibitor with the Cheng-Prusoff... |
| calc_PK | Calculate basic PK parameters for concentration-time data |
| calc_PK_ratios | Calculate the ratio of PK parameters between two simulations |
| calc_PK_ratios_mult | Calculate the ratio of PK parameters between multiple pairs... |
| centerBin | Cut a set of numeric data into bins based on the middle value... |
| change_xml_path | Set the user name in the path of observed data overlay XML... |
| chartreuse | Create a vector of yellow-greens |
| check_doseint | Check whether an AUC interval ends on a dosing interval |
| check_file_name | Checks a file name for naming standards using the criteria... |
| check_include_dose_num | INTERNAL PACKAGE USE ONLY. Check on whether to include the... |
| check_simulator_initialized | check whether the Simcyp Simulator has been initialized |
| checkSS | Create a graph of simulated concentrations to check for... |
| clean_obs_data | Tidy up messy observed concentration-time data. UNDER... |
| confInt | Calculate the X percent confidence interval |
| convert_conc_units | Convert the concentration units in a data.frame of... |
| convert_days_to_hours | Convert times in days to times in hours |
| convert_time_units | Convert the time units in a data.frame of concentration-time... |
| convert_units | Convert concentration and time units as needed |
| countWords | Count the number of words in each item in a vector or list |
| create_doses | Create a csv file of dosing rows for XML files |
| create_doses_from_file | Create a csv file of dosing rows for XML files using a study... |
| ct_plot | Concentration-time plots to match Consultancy template |
| ct_plot_1stlast | Make concentration-time plots of the 1st and last doses only |
| ct_plot3 | Concentration-time plots of the full time range, first dose,... |
| ct_plot_mult | Make graphs for multiple Simulator output files at once |
| ct_plot_obs | Plot observed concentration-time data |
| ct_plot_overlay | Overlay multiple data sets onto a single concentration-time... |
| ct_x_axis | Set up x axis in a conc-time plot |
| ct_y_axis | Set up y axis in a conc-time plot |
| cutNumeric | Cut numeric data into bins with vector output |
| CYP3A4_gut | CYP3A4 enzyme-abundance data in the gut |
| CYP3A4_liver | CYP3A4 enzyme-abundance data in the liver |
| dateConv | Convert dates from numbers to Date |
| deannotateDetails | De-annotate a data.frame of experimental details that was... |
| demog_plot_sim | Make plots for comparing populations across simulations |
| demog_plot_SO | Make a set of plots showing the demographics used in a set of... |
| demog_table | Make a table of demographics for a set of simulations |
| detect_file_timestamp | Figure out what date/time stamps on Excel results files would... |
| determine_myperpetrator | Determine the (optionally pretty) name of all perpetrators... |
| difftime_sim | Calculate the time difference between two times formatted as... |
| dissolution_profile_plot | Make a graph of the dissolution profiles of a compound |
| dosing_regimen_plot | Plot the dosing regimens used in simulations |
| draft_methods_text | Create some draft text to insert into the methods section of... |
| draft_results_text | Create some draft text to insert into the results section of... |
| draft_text_mult | Create some draft text to insert into the methods and results... |
| eCT_harmonize | Harmonize the compound names on sim_data_xl to made finding... |
| eCT_pulldata | Pull the appropriate data from the harmonized Excel tab |
| eCT_readxl | Read into memory an Excel sheet for extracting conc-time... |
| elimFit | Calculate the elimination rate(s) for a concentration-time... |
| enz_plot | Plots of enzyme abundance changes over time to match... |
| enz_plot_overlay | Overlay multiple data sets onto a single enzyme-abundance... |
| ExpDetailDefinitions | All possible experimental details for 'extractExpDetails' |
| ExpDetailDefinitions_Discovery | All possible experimental details for 'extractExpDetails' |
| ExpDetailListItems | The names of the items that should be in the list output from... |
| extractAUCXtab | FOR INTERNAL USE ONLY: Extract PK data from a generic AUC... |
| extractConcTime | Extract concentration-time data from a simulator output Excel... |
| extractConcTime_DB | Extract concentration-time data from a Simcyp Simulator... |
| extractConcTime_mult | Pull concentration-time data from multiple Simcyp Simulator... |
| extractDemog | Extract simulated demographic data from the "Demographic... |
| extractEnzAbund | Extract enzyme abundance data from a simulator output Excel... |
| extractEnzAbund_mult | Pull enzyme-abundance data from multiple Simcyp Simulator... |
| extractExpDetails | Extract details about the experimental design |
| extractExpDetails_DB | Extract simulation experimental details from a database file |
| extractExpDetails_mult | Extract experimental details for multiple files at once |
| extractExpDetails_XML | Extract experimental details for multiple Simcyp Simulator... |
| extractFmFe | Extract fm and fe valuesthat change with time from a... |
| extractForestData | Extract pertinent data from Simulator output files for... |
| extract_fu | Extract fu,plasma values that change with time from a... |
| extractObsConcTime | Extract observed concentration-time data from an Excel file |
| extractObsConcTime_mult | Extract observed concentration-time data from multiple Excel... |
| extractObsConcTime_xlsx | INTERNAL - Extract observed conc-time data from an xlsx file |
| extractObsConcTime_XML | INTERNAL - Extract observed conc-time data from an xml file |
| extractPK | Extract PK data for specific parameters from a simulator... |
| extractPK_DB | Extract PK from a Simcyp Simulator database file |
| filter_sims | Selectively include or omit specific simulations from an R... |
| fm_plot | Create a plot of how fm or fe values change over time |
| fm_treemap | For comparing fm values, make a treemap as opposed to the... |
| forest_plot | Create a forest plot |
| format_obs_for_XML | Format generic observed data for making an XML overlay file |
| format_scripts | Format common PBPK model parameters to have appropriate... |
| formatTable_Simcyp | Format tables according to Simcyp Consultancy Team... |
| format_table_simple | Format a table rather simply to look nice in a Word file |
| get_obs_PK | INTERNAL - For use w/pksummary_table. |
| getReferences | Pull references from a "DataRec" folder |
| gm_conf | Calculate the geometric X percent confidence interval |
| gm_CV | Calculate the geometric coefficient of variation (CV) |
| gm_mean | Calculate the geometric mean |
| gm_sd | Calculate the geometric standard deviation |
| graph_boxplot | Make boxplots or boxplots overlaid with individual points |
| greens | Create a vector of greens |
| green_to_red | Make a vector of colors that match the "green to red" option... |
| guess_col_widths | INTERNAL guess appropriate column widths |
| harmonize_details | FOR INTERNAL PACKAGE USE. Take as input an existing... |
| harmonize_dosing | INTERNAL - Harmonize the dosing information for an object... |
| harmonize_PK_names | Harmonize user input for PK parameters |
| IndData | Example induction data for use with the inductFit function |
| inductFit | Fit induction data to calculate EC50, Emax, and/or slope |
| insert_copyright | Insert the standard Certara UK Limited copyright box that... |
| launch_package_index | Launch the shiny app for showing an annotated index of what... |
| list_interactions | Find all the possible drug-drug interactions between... |
| LMVct | Plasma concentration-time data for a simulation of letermovir |
| log10_breaks | Create nice breaks for graphs of log-transformed data |
| make_color_set | Create a set of colors for use in graphs |
| make_ct_caption | INTERNAL - make caption for conc-time plots |
| make_example_PK_input | Examples for supplying PK parameters to the pk_table or... |
| make_gmr_highlight_key | Make a key for highlighted geometric mean ratios for DDIs in... |
| make_log_breaks | Make pretty breaks and labels for a log axis |
| make_Simcyp_inputs_table | Summarize a PBPK model using parameters pulled from... |
| make_simulation_directory | Make a directory of simulations indicating which simulation... |
| make_so_highlight_key | Make a key for highlighted S/O values in a table or graph |
| make_table_annotations | Make table headings and captions for use internally when... |
| make_text_legos | INTERNAL - Assemble pieces of text for headings, captions and... |
| make_trial_design_table | Create a table describing a simulation trial design. |
| make_xml_path_mine | Make the user name in the path of observed data overlay XML... |
| match_obs_to_sim | Match observed concentration-time data to the correct... |
| MDZct | Plasma concentration-time data for multiple simulations of... |
| MDZdetails | Example output from 'extractExpDetails_mult' |
| MDZ_Keto | Plasma concentration-time data for midazolam and ketoconazole |
| move_asterisks | INTERNAL - Move asterisks around so that you can put... |
| noncompAUC | Calculate the AUC using the trapezoidal rule |
| ObsColNames | Column names for observed concentration-time data by... |
| ObsDVoptions | Observed data DV options |
| OntogenyEquations | Equations used for calculating drug-metabolizing enzyme and... |
| ontogeny_plot | Graph the ontogenies of drug-metabolizing enzymes and... |
| pdf_to_csv | Convert a page from a pdf file to a csv file |
| PKexamples | Examples for specifying PK parameters with pk_table |
| PKexamples_ratios | Examples for specifying PK parameters with calc_PK_ratios and... |
| PKexpressions | Formatted PK parameter labels for use with graphs |
| PKParameterDefinitions | All possible PK parameters for 'extractPK' |
| pksummary_mult | Make a summary PK table for a report or slide deck - THIS... |
| pksummary_table | Make a summary PK table for a report or slide deck - THIS... |
| pk_table | Make tables of PK values from Simulator output Excel files |
| pk_table_subfun | Subfunction for pk_table. FOR INTERNAL PACKAGE USE. |
| prettify_column_names | Convert the column names in a table of PK parameters into... |
| prettify_compound_name | Make a compound name prettier and more human readable |
| purples | Create a vector of purples |
| qc_sims | Make an Excel file for QCing simulations |
| rainbow | Create a vector of a rainbow of colors |
| recalc_PK | Recalculate the PK for specific concentration-time profiles... |
| reds | Create a vector of reds |
| release_profile_plot | Make a graph of the release profiles of a compound |
| remove_file_timestamp | Remove date/time stamps from Excel results files created by... |
| renameStats | INTERNAL: Rename the statistics listed in Simulator output to... |
| ReportInputForm | Report input forms to be used in conjunction with... |
| round_consultancy | Rounding to match the SimcypConsultancy report template... |
| round_down | Round a number or vector of numbers up or down to nice... |
| round_down_unit | Round a number or vector of numbers up or down to nice... |
| round_opt | INTERNAL: Rounding function |
| round_unit | Round a number or vector of numbers up or down to nice... |
| round_up | Round a number or vector of numbers up or down to nice... |
| round_up_nice | Round a number or vector of numbers up or down to nice... |
| round_up_unit | Round a number or vector of numbers up or down to nice... |
| runShiny | Launch the shiny app for making PK summary tables and... |
| save_table_to_Excel | Save a data.frame or tibble to Excel with some standard... |
| save_table_to_Word | Save a bespoke PK table to Word using the pk_table rmarkdown... |
| scale_x_time | Automatically scale a ggplot graph x axis for time |
| scale_x_time_setup | Get the information needed to automatically scale a ggplot... |
| sensitivity_plot | Make graphs of sensitivity analysis results |
| set_aesthet | Set up certain aesthetics a conc-time plot |
| set_boundary_colors | INTERNAL: Create a set of boundary colors based on the color... |
| show_code_example | IN PROGRESS - Show some examples for the code to use for... |
| SimcypColors | Simcyp colors used in the PowerPoint template |
| SOdata | Example simulated vs. observed PK data for use with the... |
| so_graph | Graph of simulated vs. observed PK |
| sort_sims | Sort the simulation file order in an object |
| str_comma | Collapse a vector of character strings into one readable... |
| theme_consultancy | Apply the standard Consultancy Team graphing styles to your... |
| tidy_input_PK | Tidy input PK data as needed |
| tidy_PKparameters_names | INTERNAL USE. tidy the column names of PKparameters supplied... |
| tidyPop | Tidying Simcyp simulator population names for reports, etc. |
| timeConv | Convert times from numbers to POSIXct |
| trapRule | Calculate the AUC using the trapezoidal rule |
| trial_means_plot | Make graphs comparing the center statistic and variability in... |
| wrapn | INTERNAL PACKAGE USE. Wrap warning text and add a carriage... |
| yellow_to_red | Make a vector of colors that match the "yellow to red" option... |
