Files in shirewoman2/Consultancy

Standardized tools for using R within the Simcyp Consultancy Team

R/addObsPoints.R R/add_sims.R R/annotateDetails.R R/calcKi.R R/calc_PK.R R/calc_PK_ratios.R R/calc_PK_ratios_mult.R R/calc_dosenumber.R R/centerBin.R R/change_xml_path.R R/checkSS.R R/check_doseint.R R/check_file_name.R R/check_include_dose_num.R R/check_simulator_initialized.R R/clean_obs_data.R R/colorVectors.R R/convert_days_to_hours.R R/convert_units.R R/countWords.R R/create_doses.R R/create_doses_from_file.R R/ct_plot.R R/ct_plot3.R R/ct_plot_1stlast.R R/ct_plot_mult.R R/ct_plot_obs.R R/ct_plot_overlay.R R/ct_x_axis.R R/ct_y_axis.R R/cutNumeric.R R/data.R R/dateConv.R R/deannotateDetails.R R/demog_plot_SO.R R/demog_plot_sim.R R/demog_table.R R/detect_file_timestamp.R R/determine_myperpetrator.R R/difftime_sim.R R/dissolution_profile_plot.R R/dosing_regimen_plot.R R/draft_methods_text.R R/draft_results_text.R R/draft_text_mult.R R/eCT_harmonize.R R/eCT_pulldata.R R/eCT_readxl.R R/elimFit.R R/enz_plot.R R/enz_plot_overlay.R R/extractAUCXtab.R R/extractConcTime.R R/extractConcTime_DB.R R/extractConcTime_mult.R R/extractDemog.R R/extractEnzAbund.R R/extractEnzAbund_mult.R R/extractExpDetails.R R/extractExpDetails_DB.R R/extractExpDetails_XML.R R/extractExpDetails_mult.R R/extractFmFe.R R/extractForestData.R R/extractObsConcTime.R R/extractObsConcTime_XML.R R/extractObsConcTime_mult.R R/extractObsConcTime_xlsx.R R/extractPK.R R/extractPK_DB.R R/extract_fu.R R/filter_sims.R R/fm_plot.R R/fm_treemap.R R/forest_plot.R R/formatTable_Simcyp.R R/format_obs_for_XML.R R/format_scripts.R R/format_table_simple.R R/getReferences.R R/get_obs_PK.R R/gm_mean.R R/graph_boxplot.R R/guess_col_widths.R R/harmonize_PK_names.R R/harmonize_details.R R/harmonize_dosing.R R/inductFit.R R/insert_copyright.R R/launch_package_index.R R/list_interactions.R R/log10_breaks.R R/make_Simcyp_inputs_table.R R/make_color_set.R R/make_ct_caption.R R/make_example_PK_input.R R/make_log_breaks.R R/make_simulation_directory.R R/make_table_annotations.R R/make_text_legos.R R/make_trial_design_table.R R/make_xml_path_mine.R R/match_obs_to_sim.R R/move_asterisks.R R/noncompAUC.R R/ontogeny_plot.R R/pdf_to_csv.R R/pk_table.R R/pk_table_subfun.R R/pksummary_mult.R R/pksummary_table.R R/prettify_column_names.R R/prettify_compound_name.R R/qc_sims.R R/recalc_PK.R R/release_profile_plot.R R/remove_file_timestamp.R R/renameStats.R R/round_opt.R R/rounding.R R/runShiny.R R/save_table_to_Excel.R R/save_table_to_Word.R R/scale_x_time.R R/scale_x_time_setup.R R/sensitivity_plot.R R/set_aesthet.R R/set_boundary_colors.R R/show_code_example.R R/so_graph.R R/sort_sims.R R/str_comma.R R/theme_consultancy.R R/tidyPop.R R/tidy_PKparameters_names.R R/tidy_input_PK.R R/timeConv.R R/trapRule.R R/trial_means_plot.R R/wrapn.R README.Rmd README.md inst/rmarkdown/templates/concentration-time-plots/skeleton/skeleton.Rmd inst/rmarkdown/templates/ctplotmult-qc/skeleton/skeleton.Rmd inst/rmarkdown/templates/draftsections/skeleton/skeleton.Rmd inst/rmarkdown/templates/enzabund/skeleton/skeleton.Rmd inst/rmarkdown/templates/enzyme-abundance-plot/skeleton/skeleton.Rmd inst/rmarkdown/templates/forestplot/skeleton/skeleton.Rmd inst/rmarkdown/templates/inductfit/skeleton/skeleton.Rmd inst/rmarkdown/templates/methodstext/skeleton/skeleton.Rmd inst/rmarkdown/templates/multctplot/skeleton/skeleton.Rmd inst/rmarkdown/templates/pairedci/skeleton/skeleton.Rmd inst/rmarkdown/templates/pk-summary-table/skeleton/skeleton.Rmd inst/rmarkdown/templates/pksummarymult/skeleton/skeleton.Rmd inst/rmarkdown/templates/pktable/skeleton/skeleton.Rmd inst/rmarkdown/templates/pktableindiv/skeleton/skeleton.Rmd inst/rmarkdown/templates/pktablesection/skeleton/skeleton.Rmd inst/rmarkdown/templates/resultstext/skeleton/skeleton.Rmd inst/rmarkdown/templates/savetable/skeleton/skeleton.Rmd inst/rmarkdown/templates/savetablesimcyp/skeleton/skeleton.Rmd inst/rmarkdown/templates/sensitivity-analysis-plot/skeleton/skeleton.Rmd inst/rmarkdown/templates/sograph/skeleton/skeleton.Rmd inst/rmarkdown/templates/trialmeansplot/skeleton/skeleton.Rmd inst/rmarkdown/templates/unpairedci/skeleton/skeleton.Rmd inst/shiny/SimcypConsultancy_index/app.R inst/shiny/pk_plot_table/global.R inst/shiny/pk_plot_table/server.R inst/shiny/pk_plot_table/ui.R man/AllCompounds.Rd man/AllExpDetails.Rd man/AllPKParameters.Rd man/AllStats.Rd man/AllTissues.Rd man/BufForestData.Rd man/BufForestData_20mg.Rd man/BufObsForestData.Rd man/CYP3A4_gut.Rd man/CYP3A4_liver.Rd man/ExpDetailDefinitions.Rd man/ExpDetailDefinitions_Discovery.Rd man/ExpDetailListItems.Rd man/IndData.Rd man/LMVct.Rd man/MDZ_Keto.Rd man/MDZct.Rd man/MDZdetails.Rd man/ObsColNames.Rd man/ObsDVoptions.Rd man/OntogenyEquations.Rd man/PKParameterDefinitions.Rd man/PKexamples.Rd man/PKexamples_ratios.Rd man/PKexpressions.Rd man/ReportInputForm.Rd man/SOdata.Rd man/SimcypColors.Rd man/addObsPoints.Rd man/add_sims.Rd man/annotateDetails.Rd man/blueGreens.Rd man/blues.Rd man/calcKi.Rd man/calc_PK.Rd man/calc_PK_ratios.Rd man/calc_PK_ratios_mult.Rd man/calc_dosenumber.Rd man/centerBin.Rd man/change_xml_path.Rd man/chartreuse.Rd man/checkSS.Rd man/check_doseint.Rd man/check_file_name.Rd man/check_include_dose_num.Rd man/check_simulator_initialized.Rd man/clean_obs_data.Rd man/confInt.Rd man/convert_conc_units.Rd man/convert_days_to_hours.Rd man/convert_time_units.Rd man/convert_units.Rd man/countWords.Rd man/create_doses.Rd man/create_doses_from_file.Rd man/ct_plot.Rd man/ct_plot3.Rd man/ct_plot_1stlast.Rd man/ct_plot_mult.Rd man/ct_plot_obs.Rd man/ct_plot_overlay.Rd man/ct_x_axis.Rd man/ct_y_axis.Rd man/cutNumeric.Rd man/dateConv.Rd man/deannotateDetails.Rd man/demog_plot_SO.Rd man/demog_plot_sim.Rd man/demog_table.Rd man/detect_file_timestamp.Rd man/determine_myperpetrator.Rd man/difftime_sim.Rd man/dissolution_profile_plot.Rd man/dosing_regimen_plot.Rd man/draft_methods_text.Rd man/draft_results_text.Rd man/draft_text_mult.Rd man/eCT_harmonize.Rd man/eCT_pulldata.Rd man/eCT_readxl.Rd man/elimFit.Rd man/enz_plot.Rd man/enz_plot_overlay.Rd man/extractAUCXtab.Rd man/extractConcTime.Rd man/extractConcTime_DB.Rd man/extractConcTime_mult.Rd man/extractDemog.Rd man/extractEnzAbund.Rd man/extractEnzAbund_mult.Rd man/extractExpDetails.Rd man/extractExpDetails_DB.Rd man/extractExpDetails_XML.Rd man/extractExpDetails_mult.Rd man/extractFmFe.Rd man/extractForestData.Rd man/extractObsConcTime.Rd man/extractObsConcTime_XML.Rd man/extractObsConcTime_mult.Rd man/extractObsConcTime_xlsx.Rd man/extractPK.Rd man/extractPK_DB.Rd man/extract_fu.Rd man/filter_sims.Rd man/fm_plot.Rd man/fm_treemap.Rd man/forest_plot.Rd man/formatTable_Simcyp.Rd man/format_obs_for_XML.Rd man/format_scripts.Rd man/format_table_simple.Rd man/getReferences.Rd man/get_obs_PK.Rd man/gm_CV.Rd man/gm_conf.Rd man/gm_mean.Rd man/gm_sd.Rd man/graph_boxplot.Rd man/green_to_red.Rd man/greens.Rd man/guess_col_widths.Rd man/harmonize_PK_names.Rd man/harmonize_details.Rd man/harmonize_dosing.Rd man/inductFit.Rd man/insert_copyright.Rd man/launch_package_index.Rd man/list_interactions.Rd man/log10_breaks.Rd man/make_Simcyp_inputs_table.Rd man/make_color_set.Rd man/make_ct_caption.Rd man/make_example_PK_input.Rd man/make_gmr_highlight_key.Rd man/make_log_breaks.Rd man/make_simulation_directory.Rd man/make_so_highlight_key.Rd man/make_table_annotations.Rd man/make_text_legos.Rd man/make_trial_design_table.Rd man/make_xml_path_mine.Rd man/match_obs_to_sim.Rd man/move_asterisks.Rd man/noncompAUC.Rd man/ontogeny_plot.Rd man/pdf_to_csv.Rd man/pk_table.Rd man/pk_table_subfun.Rd man/pksummary_mult.Rd man/pksummary_table.Rd man/prettify_column_names.Rd man/prettify_compound_name.Rd man/purples.Rd man/qc_sims.Rd man/rainbow.Rd man/recalc_PK.Rd man/reds.Rd man/release_profile_plot.Rd man/remove_file_timestamp.Rd man/renameStats.Rd man/round_consultancy.Rd man/round_down.Rd man/round_down_unit.Rd man/round_opt.Rd man/round_unit.Rd man/round_up.Rd man/round_up_nice.Rd man/round_up_unit.Rd man/runShiny.Rd man/save_table_to_Excel.Rd man/save_table_to_Word.Rd man/scale_x_time.Rd man/scale_x_time_setup.Rd man/sensitivity_plot.Rd man/set_aesthet.Rd man/set_boundary_colors.Rd man/show_code_example.Rd man/so_graph.Rd man/sort_sims.Rd man/str_comma.Rd man/theme_consultancy.Rd man/tidyPop.Rd man/tidy_PKparameters_names.Rd man/tidy_input_PK.Rd man/timeConv.Rd man/trapRule.Rd man/trial_means_plot.Rd man/wrapn.Rd man/yellow_to_red.Rd vignettes/ct_plot_vignette.Rmd