Man pages for Thaliehln/timci
Data management and visualisation for the TIMCI project
| allocate_screening_facility | Allocate the screening facility |
| allocate_screening_facility2 | Allocate the screening facility (copy to allow for a list... |
| anonymise_dataframe | Anonymise a dataframe by hashing selected columns |
| calculate_antibio_has_been_prescribed | Create derived variable rx_has_been_prescribed... |
| calculate_antibio_has_been_recorded | Create derived variable rx_has_been_recorded (TIMCI-specific... |
| calendar_heatmap | Calendar Heatmap |
| check_name_consistency | Check name consistency (TIMCI-specific function) |
| clean_followup_for_rate_estimation | Clean follow-up data for estimating rough follow-up rate... |
| combine_columns | Combine 2 columns - function in progress (to be tested) |
| combine_dataframes | Combine two dataframes in one |
| concatenate_names | Concatenate names for fuzzy-matching scoring (TIMCI-specific... |
| convert_age2ctg | Convert age in days to age categories (TIMCI-specific... |
| convert_yi_age2ctg | Convert age in days to age categories (TIMCI-specific... |
| correct_day0_all | Edit Day 0 data for all errors that were detected by quality... |
| correct_day0_drug_data | Edit drug data in Day 0 data entries (TIMCI-specific function... |
| correct_day0_inconsistent_facilities | Edit non-valid facilities in Day 0 data entries... |
| correct_day0_non_valid_facilities | Edit non-valid facilities in Day 0 data entries... |
| correct_day28_all | Edit Day 28 follow-up data for all errors that were detected... |
| correct_day28_duplicates | Correct Day 28 duplicates (TIMCI-specific function) |
| correct_day7_all | Edit Day 7 follow-up data for all errors that were detected... |
| correct_day7_duplicates | Correct Day 7 duplicates (TIMCI-specific function) |
| correct_device_ids | Edit non-valid facilities in Day 0 data entries... |
| correct_hospit_ids | Correct hospital follow-up IDs (TIMCI-specific function) |
| correct_repeat_ids | Correct repeat follow-up visit IDs (TIMCI-specific function) |
| correct_spa_sco_all | Edit SPA sick child observation data for all errors that were... |
| correct_spa_sco_fids | Edit non-valid facilities in SPA sick child observation data... |
| correct_spa_sco_hcp_ids | Edit incorrect healthcare provider (HCP) IDs in SPA sick... |
| correct_spo2_values | Correct hospital follow-up IDs (TIMCI-specific function) |
| correct_tf_inconsistent_facilities | Edit non-valid facilities in time-flow data entries... |
| count_baseline_vs_repeat | Count the occurrence of baseline versus repeat visits... |
| count_noneligibility | Count the occurrence of non-eligibility reasons... |
| count_screening | Count the occurrence of non-enrolment causes during screening... |
| count_submissions | Count submissions (TIMCI-specific) |
| create_day0_qc_flowchart | Create a Flowchart Illustrating Cleaning Process for Day 0... |
| create_day28fu_outcome_qc_flowchart | Create cleaning flowchart for successful Day 28 follow-up... |
| create_day28fu_qc_flowchart | Create cleaning flowchart for Day 28 follow-up data... |
| create_day7fu_outcome_qc_flowchart | Create a Flowchart Illustrating Cleaning Process for... |
| create_day7fu_qc_flowchart | Create cleaning flowchart for Day 7 follow-up data... |
| create_drug_qc_flowchart | Create a flowchart summarizing the cleaning of drug re-entry... |
| create_hospit_qc_flowchart | Create a Flowchart Illustrating Cleaning Process for... |
| create_odkc_draft_form | Create an ODK Central draft form See reference ODK API... |
| create_repeat_qc_flowchart | Create a Flowchart Illustrating Cleaning Process for Repeat... |
| create_screening_qc_flowchart | This function generates a flowchart to visualize the cleaning... |
| create_withdrawal_qc_flowchart | Create a Flowchart Illustrating Cleaning Process for... |
| csv_download_server | CSV data download module server-side processing |
| csv_download_ui | CSV data download module user interface |
| dataset_export | Export datasets |
| data_table_server | Data table module server-side processing |
| data_table_ui | Data table module user interface |
| deidentify_data | Deidentify data (TIMCI-specific function) |
| deidentify_spa_data | De-identify SPA data (TIMCI-specific Function) |
| deidentify_spa_rx_data | De-identify SPA treatment data (TIMCI-specific Function) |
| delete_day0_records | Drop incorrect child IDs in Day 0 data entries... |
| delete_repeat_records | Drop incorrect child IDs in repeat data entries... |
| detect_blank_value | Detect blank ("") value (TIMCI-specific function) |
| detect_drug | Detect specific string in free text entries where structured... |
| detect_id_duplicates | Detect ID duplicates (TIMCI-specific function) |
| detect_inconsistent_dates | Detect inconsistent dates (TIMCI-specific function) |
| detect_inconsistent_names_between_visits | Detect inconsistent participant names between follow-up and... |
| detect_missing_clinical_presentation | Detect missing clinical presentation (TIMCI-specific... |
| detect_missing_diagnosis | Detect missing diagnosis (TIMCI-specific function) |
| detect_missing_referral | Detect missing referral reported by caregiver at the exit of... |
| detect_missing_treatment | Detect missing treatment (TIMCI-specific function) |
| detect_missing_value | Detect missing (NA) value (TIMCI-specific function) |
| detect_namedob_duplicates | Detect participant duplicates (TIMCI-specific function)... |
| detect_name_duplicates | Detect name duplicates (TIMCI-specific function) Search for... |
| detect_negative_value | Detect negative value (TIMCI-specific function) |
| detect_non_timely_completion | Detect non-timely completion of a submission, i.e.... |
| detect_non_timely_submission | Detect non-timely submissions, i.e. submissions not sent to... |
| detect_participant_duplicates | Detect participant duplicates (TIMCI-specific function)... |
| display_weekly_fa_data_per_facility | Display weekly facility assessment data per facility... |
| edit_day0_child_ids | Edit incorrect child IDs in Day 0 data entries... |
| edit_day0_child_ids_spa_sco | Edit incorrect child IDs based on Day 0 data correction in... |
| edit_day0_to_repeat | Edit incorrect child IDs in Day 0 data entries... |
| export_cost_studies | Run Rmarkdown files |
| export_df2csv | Write dataframe to a CSV file format, with a filename... |
| export_df2csvxlsx | Write dataframe to both CSV and Excel spreadsheet formats,... |
| export_df2rds | Write dataframe to an RDS file format, with a filename... |
| export_df2sqlite | Write dataframe to an SQLite file, with a filename consisting... |
| export_df2xlsx | Write dataframe to an Excel spreadsheet, with a filename... |
| extract_additional_data_from_odk_zip | Unzip and extract additional data from ODK zip |
| extract_all_visits | Extract visits (TIMCI-specific function) |
| extract_baseline_visits | Extract baseline visits (TIMCI-specific function) |
| extract_complex_data_from_odk_server | Extract complex data from ODK server to a a list of... |
| extract_daily_facility_for_deviceid | Extract main device ID used in a facility at a given date |
| extract_data_from_odk_server | Extract data from ODK server to a formatted dataframe. This... |
| extract_data_from_odk_zip | Unzip and extract ODK data from ODK zip |
| extract_enrolled_participants | Extract enrolled participants (TIMCI-specific function) |
| extract_hypoxaemia | Extract hypoxaemia (TIMCI-specific function) |
| extract_last_fa_data | Extract last available facility assessment data... |
| extract_main_facility_for_deviceid | Extract main device ID used in a facility |
| extract_noneligible | Extract non-enrolled participants (TIMCI-specific function) |
| extract_pii | Extract personally identifiable information (TIMCI-specific... |
| extract_referrals | Extract referrals (TIMCI-specific function) |
| extract_repeat_visits | Extract repeat visits (TIMCI-specific function) |
| extract_screening_data | Extract screening data (TIMCI-specific function) |
| extract_tf_data | Extract Time-Flow Data (TIMCI-specific function) |
| find_best_matched_names_between_fu_and_day0 | Detects matched names between follow-up and day 0 dataframes... |
| find_closest_facility | Find Closest Facility |
| format_day28_data | Process day 28 follow-up data (TIMCI-specific function) |
| format_day7_data | Process day 7 follow-up data (TIMCI-specific function) |
| format_hospital_data | Process hospital data (TIMCI-specific function) |
| format_multiselect_asws | Format multiple select answers so as to separate them |
| format_nrow | Format display number of rows |
| format_odk_metadata | Format ODK metadata The function removes ODK note columns... |
| formats2h1 | Format string to header of level H1 for printing in console |
| formats2h2 | Format string to header of level H2 for printing in console |
| formats2h3 | Format string to header of level H3 for printing in console |
| format_summary_table | Format summary table to have a global descriptive statistics... |
| format_text_fields | Replace commas by semicolons in text fields for CSV export |
| format_weekly_fa_data_for_export | Format weekly facility assessment data for export... |
| generate_calendar_heatmap | Generate a calendar heatmap |
| generate_calendar_heatmap2 | Generate a calendar heatmap |
| generate_cg_log | Generate caregiver recruitment log (TIMCI-specific function) |
| generate_day_bar_plot | Create a daily bar plot |
| generate_day_cumbar_plot | Create a cumulative daily bar plot |
| generate_enrolment_hist | Create a histogram that represents the distribution of values... |
| generate_folder_structure | Generate folder structure (TIMCI-specific function) |
| generate_fu_log | Generate follow-up log (TIMCI-specific function) |
| generate_fu_log_csv | Generate follow-up log CSV for upload on ODK Central... |
| generate_fu_logs | General follow-up logs |
| generate_hospital_log | Generate hospital follow-up log (TIMCI-specific function) |
| generate_ltfu_log | Generate lost to follow-up log (TIMCI-specific function) |
| generate_pdf_report | Generate a PDF report using Rmarkdown |
| generate_physical_fu_log_csv | Generate physical follow-up log CSV for upload on ODK Central... |
| generate_pie_chart | Create a pie chart plot |
| generate_research_cdsa_report | Generate a report comparing research and CDSA data |
| generate_time_hist_plot | Generate an histogram of day times |
| generate_week_bar_plot | Create a weekly bar plot |
| generate_week_bar_plot2 | Create a weekly bar plot by adding values from a specific... |
| generate_word_report | Generate a Microsoft Word report using Rmarkdown |
| get_summary_by_deviceid | Get summary statistics grouped by device ID (TIMCI-specific... |
| get_summary_by_fid | Get summary statistics grouped by facility ID (TIMCI-specific... |
| heatmap_wday_hourofday | Generates a heat map of the number of submissions per weekday... |
| identify_day0_duplicates | Identify repeat ID duplicates by dates (TIMCI-specific... |
| identify_day0_duplicates_and_fu | Identify day 0 ID duplicates wit names and corresponding Day... |
| identify_duplicates_by_dates | Identify ID duplicates by dates (TIMCI-specific function) |
| identify_duplicates_with_names | Identify ID duplicates with names (TIMCI-specific function) |
| identify_ids_outside_lock_range | Identify non-valid IDs in a dataframe based on IDs in another... |
| identify_multiple_enrolments | Identify multiple 28-disease episodes for the same children... |
| identify_nonvalid_ids | Identify non-valid IDs in a dataframe based on IDs in another... |
| identify_nonvalid_ids2 | Identify non-valid IDs in a dataframe based on IDs in another... |
| identify_nonvalid_ids_flagged | Identify Non-Valid IDs in a Dataframe Based on Reference IDs... |
| identify_nonvalid_ids_with_matched_names | Identify non-valid IDs in a dataframe based on IDs in another... |
| identify_repeat_duplicate | Identify repeat ID duplicates by dates (TIMCI-specific... |
| identify_true_duplicate | Identify true ID duplicates by dates (TIMCI-specific... |
| import_col_specifications | Import column-specifications from country-specific Excel... |
| import_country_specific_xls_dict | Import country-specific Excel dictionary |
| is_not_empty | Check that a dataframe is not empty |
| load_qual_data | Load RCT/LS data |
| load_qual_data_and_generate_report | Load qualitative data and generate corresponding report |
| load_rctls_data | Load RCT/LS data |
| load_spapmtf_data | Load Service Provision Assessment (SPA), process mapping &... |
| match_from_day0_xls_dict | Match facility data using the Day 0 dictionary adapted for... |
| match_from_dict | Extract and match variable names using a dictionary |
| match_from_drug_xls_dict | Match facility data using the Drug dictionary adapted for... |
| match_from_filtered_xls_dict | Extract and match variable names using an external Excel... |
| match_from_tf_xls_dict | Match facility data using the Time-Flow dictionary adapted... |
| match_from_xls_dict | Extract and match variable names using an external Excel... |
| normalised_levenshtein_ratio | Calculate a normalised Levenshtein ratio between two strings |
| odk_data_info_server | ODK data info module server-side processing |
| odk_data_info_ui | ODK data info module user interface |
| pie_chart_server | Pie chart module server-side processing |
| pie_chart_ui | Pie chart module user interface |
| pivot_duplicates_to_columns | Pivot values of duplicated rows into new columns |
| plot_gauge | Create an enrolment gauge |
| plot_geom_bar_by_facility_over_time | Create facets with bar plots over time |
| plot_geom_bar_over_time | Plot Bar Chart over Time |
| plot_numeric_indicator | Create a numeric indicator |
| plot_scatter_by_facility_over_time | Create facets with scatters over time |
| process_facility_data | Process facility data (TIMCI-specific function) |
| process_gps_coordinates | Process GPS coordinates (TIMCI-specific function) |
| process_spa_hcpi_data | Process healthcare provider interview data (TIMCI-specific... |
| process_spa_sco_data | Process sick child observation data (TIMCI-specific function) |
| process_tanzania_facility_data | Process Tanzania facility data (TIMCI-specific function) |
| process_weekly_fa_data | Process weekly facility assessment data (TIMCI-specific... |
| publish_odkc_draft_form | Publish a draft form See reference ODK API documentation in... |
| quality_check_export | Write dataframe to an Excel file, with a filename consisting... |
| reactive_csv_download_server | Reactive CSV data download module server-side processing |
| reactive_data_table_server | Reactive data table module server-side processing |
| reactive_odk_data_info_server | Reactive ODK data info module server-side processing |
| reactive_xlsx_download_server | Reactive Excel data download module server-side processing |
| read_day0_xls_dict | Load the Day 0 dictionary - adapted for each country to... |
| read_tf_xls_dict | Load the Time-Flow Dictionary Adapted for Each Country... |
| remove_facilities_for_other_studies | Remove facilities in which data collection is conducted for... |
| report_download_server | Report download module server-side processing |
| report_download_ui | Report download module user interface |
| run_app | Run the TIMCI Shiny app |
| run_mini_app | Run a minimalist Shiny app example |
| run_rmarkdown_rctls | Run Rmarkdown files |
| run_rmarkdown_reportonly | Run Rmarkdown files |
| selective_multi_replace | Replace NA and 0 values in a data frame column with 1 if... |
| selective_replace | Replace NA and 0 values in a data frame column with 1 if... |
| select_list_item_server | List item selection module server-side processing |
| select_list_item_ui | List item selection module user interface |
| send_email | Send email |
| send_email_tls | Send email |
| send_weekly_email | Send email |
| set_language_settings | Set language settings |
| set_odkc_connection | Set the connection to ODK Central through ruODK |
| text_2_plot | Plot string in image |
| upload_odkc_csv_attachment | Upload the new CSV created as a form attachment See reference... |
| xlsx_download_server | Excel data download module server-side processing |
| xlsx_download_ui | Excel data download module user interface |
