Man pages for LisaHopcroft/CTutils
Helpful Functions for Clinical Trial Data Analysis at SCTRU (Public Health Scotland)
| add_dependency_to_fields | Add an additional dependency to certain columns |
| all_files_exist | Do all the files listed actually exist? |
| calculate_BMI | Given weight and height, returns BMI |
| calculate_dose_modification | Modify dose according to protocol schedule |
| calculate_missing_data | CAlculate how much data is missing for each patient, visit... |
| calculate_mode | Find the mode in a list of values (i.e., the most common... |
| calculate_number_of_instances | Calculate number of instances |
| calculate_RECIST_response | Calculates whether data indicates a complete response by... |
| check_all_files_exist | Check whether all files in a list exist |
| check_extract_date | Check whether the date recorded for the extract matches the... |
| convert_dates_to_EudraCT_age_categories | Given Date of Birth and Date of Registration, annotate the... |
| create_dummy_dataset | Create dummy CT data |
| create_SSR_structure | Create a new SSR directory |
| create_testresult_string | Return possible test results (repeated symbols) |
| CTutilsproject | CTutilsproject |
| do | Utility/wrapper function to DO the default things |
| do_count | Tabulate Yes/No entries in one or more columns. |
| do_count_comparison | Tabulate two separate Yes/No counts and merge together. |
| do_list_comparison | Tabulate two separate list occurence counts and merge... |
| do_list_extraction | Count the occurence of items in a list |
| do_summary | Summarise numerical data into a table and boxplot |
| example_trial.data | Example Trial Data |
| example_trial.glossary | Glossary for example Trial Data |
| example_trial.vocabulary | Vocabulary for example Trial Data |
| expand_dependency_locations_in_glossary | Expand dependency locations in glossary |
| expand_glossary | Expand glossary |
| expand_trial_data | Expand trial data (internal) |
| extract_complex_dependencies | Extract complex dependencies. |
| extract_simple_dependencies | #' Extract simple dependencies. |
| find_mode | Find the mode in the list of values (i.e., the most frequent... |
| fit_flextable_to_page | Fit flextable object to the width of the page |
| generate_visit_label | Generate a label for each visit for display purposes |
| get_random_dates | Generate a random sample of dates in a given range |
| initialise_RECIST_VALUES | Initialise RECIST values as global variables |
| parse_MACRO_DSD_file | Parse information from DSD (MACRO) document |
| parse_MACRO_DSD_file_for_glossary_and_dependencies | Parse information from DSD (MACRO) document |
| plot_attendance_data | CAlculate how much data is missing for each patient, visit... |
| plot_missing_data | Calculate how much data is missing for each patient, visit... |
| plot_missing_data_detailed | Plot the missing data, for specified test batteries and... |
| print_data_queries_message | Print data queries summary message. |
| print_error | Print an error message |
| print_file_loading_info | Print information about which files were loaded. |
| print_flextable | Print the labetests data |
| print_labtests_flextable | Print the labetests data |
| print_M0M1_flextable | Print the M0/M1 data |
| print_message | Print a message |
| print_signsandsyptoms_flextable | Print the signs and symptoms data |
| print_warning | Print a warning message |
| read_EudraCT_vocabulary | Provide necessary EudraCT and RMS vocabulary for use when... |
| read_report_YAML | Read in values from YAML and load them into the global... |
| RECIST_COMPLETE | RECIST_COMPLETE |
| RECIST_PARTIAL | RECIST_PARTIAL |
| RECIST_PARTIAL_calculation | RECIST_PARTIAL calculation |
| RECIST_PROGRESSIVE | RECIST_PROGRESSIVE |
| RECIST_PROGRESSIVEabs_calculation | RECIST PROGRESSIVE absolute increase calculation |
| RECIST_PROGRESSIVEperc_calculation | RECIST PROGRESSIVE percentage increase calculation |
| record_data_query | Record a data query |
| refactor_variable | Change the levels of a factor to use an explicit list |
| rejig_panel_dimensions | Rejig panel dimensions |
| rejig_panel_widths | Rejig panel widths |
| replace_func | Replace NAs with another value |
| replace_infinite_numbers | Replace infinite numbers with NA |
| replace_missing_number | Replace missing numeric value with another number. |
| replace_missing_string | Replace missing values with another string. |
| resolve_individual_filter_statement | Resolves a dependency, so that it can be used as a filter... |
| save_image | Save CT data to file. |
| subchunkify | Print a figure at a different width/height than the chunk it... |
| test_fn | Print a name |
| tidy_logical_expression | Tidy/reformat a dependency |
