Files in Thaliehln/timci
Data management and visualisation for the TIMCI project

.Rbuildignore
.gitignore
.zenodo.json
CODE_OF_CONDUCT.md
DESCRIPTION
LICENSE
NAMESPACE
R/check_drugs.R R/check_duplicates.R R/check_gps_coordinates.R R/check_missing_info.R R/check_screening_facility.R R/check_timci_quality.R R/clean_timci_data.R R/count_submissions.R R/create_cleaning_flowcharts.R R/deidentify.R R/display_data_info_module.R R/display_data_table_module.R R/display_utils.R R/download_data_modules.R R/format_odk_data.R R/format_timci_data.R R/format_timci_fa_data.R R/format_timci_fu_data.R R/format_timci_hospitfu_data.R R/format_timci_qual_data.R R/format_timci_spatf_data.R R/generate_folder_structure.R R/generate_fu_logs.R R/generate_research_cdsa_report.R R/globals.R R/heatmaps.R R/load_timci_odk_data.R R/pie_chart_module.R R/plots.R R/process_location_data.R R/query_odkapi.R R/rmarkwdown_utils.R R/run_app.R R/run_rmarkdown.R R/select_list_item_module.R R/send_email.R R/stat_utils.R R/utils.R README.md
inst/extdata/cleaning/day0_childID_correction_inconsistent_facility_check1_tanzania.csv
inst/extdata/cleaning/day0_childID_correction_inconsistent_facility_check2_tanzania.csv
inst/extdata/cleaning/day0_deviceid_correction_from_field_tanzania.csv
inst/extdata/cleaning/day0_duplicate_correction_india.csv
inst/extdata/cleaning/day0_duplicate_correction_kenya.csv
inst/extdata/cleaning/day0_duplicate_correction_senegal.csv
inst/extdata/cleaning/day0_duplicate_correction_tanzania.csv
inst/extdata/cleaning/day0_facility_correction1_india.csv
inst/extdata/cleaning/day0_facility_correction1_kenya.csv
inst/extdata/cleaning/day0_facility_correction1_senegal.csv
inst/extdata/cleaning/day0_facility_correction1_tanzania.csv
inst/extdata/cleaning/day0_facility_correction2_tanzania.csv
inst/extdata/cleaning/day0_facility_correction3_senegal.csv
inst/extdata/cleaning/day0_non_valid_facility_correction_kenya.csv
inst/extdata/cleaning/day0_non_valid_facility_correction_tanzania.csv
inst/extdata/cleaning/day0_repeat_correction_different_id_tanzania.csv
inst/extdata/cleaning/day0_repeat_correction_india.csv
inst/extdata/cleaning/day0_repeat_correction_kenya.csv
inst/extdata/cleaning/day0_repeat_correction_same_id_tanzania.csv
inst/extdata/cleaning/day0_repeat_correction_senegal.csv
inst/extdata/cleaning/day0_repeat_inconsistent_names_correction_tanzania.csv
inst/extdata/cleaning/day0_repeat_inconsistent_names_deletion_kenya.csv
inst/extdata/cleaning/day0_repeat_inconsistent_names_deletion_senegal.csv
inst/extdata/cleaning/day0_repeat_inconsistent_names_deletion_tanzania.csv
inst/extdata/cleaning/day0_repeat_non_valid_pid_correction_tanzania.csv
inst/extdata/cleaning/day0_spo2_meas1_india.csv
inst/extdata/cleaning/day0_spo2_meas2_india.csv
inst/extdata/cleaning/day0_training_deletion_tanzania.csv
inst/extdata/cleaning/day0_true_duplicate_deletion_india.csv
inst/extdata/cleaning/day0_true_duplicate_deletion_kenya.csv
inst/extdata/cleaning/day0_true_duplicate_deletion_senegal.csv
inst/extdata/cleaning/day0_true_duplicate_deletion_tanzania.csv
inst/extdata/cleaning/day28_inconsistent_names_correction_india.xlsx
inst/extdata/cleaning/day28_inconsistent_names_correction_tanzania.csv
inst/extdata/cleaning/day28_inconsistent_names_deletion_india.csv
inst/extdata/cleaning/day28_inconsistent_names_deletion_tanzania.csv
inst/extdata/cleaning/day28_non_valid_pid_correction_india.csv
inst/extdata/cleaning/day28_non_valid_pid_correction_tanzania.csv
inst/extdata/cleaning/day7_duplicate_correction_india.csv
inst/extdata/cleaning/day7_inconsistent_names_correction_india.csv
inst/extdata/cleaning/day7_inconsistent_names_correction_kenya.csv
inst/extdata/cleaning/day7_inconsistent_names_correction_senegal.csv
inst/extdata/cleaning/day7_inconsistent_names_correction_tanzania.csv
inst/extdata/cleaning/day7_inconsistent_names_deletion_india.csv
inst/extdata/cleaning/day7_inconsistent_names_deletion_kenya.csv
inst/extdata/cleaning/day7_inconsistent_names_deletion_senegal.csv
inst/extdata/cleaning/day7_inconsistent_names_deletion_tanzania.csv
inst/extdata/cleaning/day7_non_valid_pid_correction_india.csv
inst/extdata/cleaning/day7_non_valid_pid_correction_kenya.csv
inst/extdata/cleaning/day7_non_valid_pid_correction_senegal.csv
inst/extdata/cleaning/day7_non_valid_pid_correction_tanzania.csv
inst/extdata/cleaning/hospit_non_valid_pid_correction_india.csv
inst/extdata/cleaning/hospit_non_valid_pid_correction_tanzania.csv
inst/extdata/cleaning/spa_sco_child_correction_kenya.csv
inst/extdata/cleaning/spa_sco_facility_correction_kenya.csv
inst/extdata/cleaning/spa_sco_facility_correction_senegal.csv
inst/extdata/cleaning/spa_sco_facility_correction_tanzania.csv
inst/extdata/cleaning/spa_sco_hcp_correction_kenya.csv
inst/extdata/cleaning/tf_facility_correction_kenya.csv
inst/extdata/cleaning/tf_facility_correction_senegal.csv
inst/extdata/cleaning/tf_facility_correction_tanzania.csv
inst/extdata/day28_dict.xlsx
inst/extdata/day7_dict.xlsx
inst/extdata/drug_dict.xlsx
inst/extdata/hospit_dict.xlsx
inst/extdata/main_dict.xlsx
inst/extdata/main_dict_tanzania_pilot_baseline.xlsx
inst/extdata/maps/India/gadm36_IND_2.cpg
inst/extdata/maps/India/gadm36_IND_2.dbf
inst/extdata/maps/India/gadm36_IND_2.prj
inst/extdata/maps/India/gadm36_IND_2.shp
inst/extdata/maps/India/gadm36_IND_2.shx
inst/extdata/maps/India/license.txt
inst/extdata/maps/Kenya/gadm36_KEN_1.cpg
inst/extdata/maps/Kenya/gadm36_KEN_1.dbf
inst/extdata/maps/Kenya/gadm36_KEN_1.prj
inst/extdata/maps/Kenya/gadm36_KEN_1.shp
inst/extdata/maps/Kenya/gadm36_KEN_1.shx
inst/extdata/maps/Kenya/license.txt
inst/extdata/maps/Senegal/gadm36_SEN_1.cpg
inst/extdata/maps/Senegal/gadm36_SEN_1.dbf
inst/extdata/maps/Senegal/gadm36_SEN_1.prj
inst/extdata/maps/Senegal/gadm36_SEN_1.shp
inst/extdata/maps/Senegal/gadm36_SEN_1.shx
inst/extdata/maps/Senegal/license.txt
inst/extdata/qrcode_python/QR_code India Septembre 2021.ipynb
inst/extdata/qrcode_python/QR_code Kenya July 2021.ipynb
inst/extdata/qrcode_python/QR_code Senegal Feb 2021.ipynb
inst/extdata/qrcode_python/QR_code Tanzania May 2021.ipynb
inst/extdata/qrcode_python/QR_code Tanzania May 2022.ipynb
inst/extdata/spa_cgei_dict.xlsx
inst/extdata/spa_hcpi_dict.xlsx
inst/extdata/spa_sco_dict.xlsx
inst/extdata/tf_dict.xlsx
inst/extdata/wfa_dict.xlsx
inst/extdata/~$main_dict_kenya.xlsx
inst/rmarkdown/banner.png
inst/rmarkdown/calculations.Rmd inst/rmarkdown/caregiver_selection.Rmd inst/rmarkdown/compare_rctls_cdsa.Rmd inst/rmarkdown/context.Rmd inst/rmarkdown/context_facility_list.Rmd inst/rmarkdown/data_cleaning_day0.Rmd inst/rmarkdown/data_cleaning_day7fu.Rmd inst/rmarkdown/data_cleaning_spa.Rmd inst/rmarkdown/database_export.Rmd inst/rmarkdown/database_export_cgidi_sub.Rmd inst/rmarkdown/database_export_hcpidi_sub.Rmd inst/rmarkdown/database_export_hospitalcost_sub.Rmd inst/rmarkdown/database_export_medicalcost_sub.Rmd inst/rmarkdown/database_export_processmap_sub.Rmd inst/rmarkdown/database_export_sub_QC_child_multiple_enrolments.Rmd inst/rmarkdown/database_export_sub_bar_plot.Rmd inst/rmarkdown/database_export_sub_corrections.Rmd inst/rmarkdown/database_export_sub_cost.Rmd inst/rmarkdown/database_export_sub_facet_bar_plot.Rmd inst/rmarkdown/database_export_sub_facet_scatter_plot.Rmd inst/rmarkdown/database_export_sub_qual.Rmd inst/rmarkdown/database_export_sub_quality_check.Rmd inst/rmarkdown/database_export_sub_rctls_context.Rmd inst/rmarkdown/database_export_sub_rctls_day0.Rmd inst/rmarkdown/database_export_sub_rctls_day0_drug.Rmd inst/rmarkdown/database_export_sub_rctls_day0_drug_addon.Rmd inst/rmarkdown/database_export_sub_rctls_day0_drug_integration.Rmd inst/rmarkdown/database_export_sub_rctls_day28.Rmd inst/rmarkdown/database_export_sub_rctls_day28_outcome.Rmd inst/rmarkdown/database_export_sub_rctls_day7.Rmd inst/rmarkdown/database_export_sub_rctls_day7_outcome.Rmd inst/rmarkdown/database_export_sub_rctls_deaths.Rmd inst/rmarkdown/database_export_sub_rctls_facilities.Rmd inst/rmarkdown/database_export_sub_rctls_hospit.Rmd inst/rmarkdown/database_export_sub_rctls_repeats.Rmd inst/rmarkdown/database_export_sub_rctls_screening.Rmd inst/rmarkdown/database_export_sub_rctls_withdrawals.Rmd inst/rmarkdown/database_export_sub_spa.Rmd inst/rmarkdown/database_export_sub_spa_cgei.Rmd inst/rmarkdown/database_export_sub_spa_fa.Rmd inst/rmarkdown/database_export_sub_spa_hcpi.Rmd inst/rmarkdown/database_export_sub_spa_sco.Rmd inst/rmarkdown/database_export_timeflow_sub.Rmd inst/rmarkdown/database_summary.Rmd inst/rmarkdown/database_summary_by_facility.Rmd inst/rmarkdown/database_summary_yi.Rmd inst/rmarkdown/facility_report.Rmd inst/rmarkdown/fu_daily_log.Rmd inst/rmarkdown/fu_weekly_log.Rmd inst/rmarkdown/generate_maps.Rmd inst/rmarkdown/hospit_fu_log.Rmd
inst/rmarkdown/mapping.xlsx
inst/rmarkdown/maps.Rmd inst/rmarkdown/path_report.Rmd inst/rmarkdown/pmtf_monitoring_report.Rmd inst/rmarkdown/pmtf_monitoring_report_sub_pm.Rmd inst/rmarkdown/pmtf_monitoring_report_sub_tf.Rmd inst/rmarkdown/qual_monitoring_report.Rmd inst/rmarkdown/qual_monitoring_report_sub_cgidi.Rmd inst/rmarkdown/qual_monitoring_report_sub_hcpidi.Rmd inst/rmarkdown/qual_monitoring_report_sub_kii.Rmd inst/rmarkdown/qual_monitoring_report_sub_survey.Rmd inst/rmarkdown/qual_randomisation.Rmd inst/rmarkdown/qual_randomisation_India.Rmd inst/rmarkdown/qual_randomisation_Kenya.Rmd inst/rmarkdown/rct_monitoring_report.Rmd inst/rmarkdown/rct_monitoring_report_facility_sub.Rmd inst/rmarkdown/rct_monitoring_report_sub_day28.Rmd inst/rmarkdown/rct_monitoring_report_sub_day7.Rmd inst/rmarkdown/rct_monitoring_report_sub_hospit.Rmd inst/rmarkdown/read_encrypted_data.Rmd inst/rmarkdown/spa_monitoring_report.Rmd inst/rmarkdown/spa_monitoring_report_sub_cgei.Rmd inst/rmarkdown/spa_monitoring_report_sub_fa.Rmd inst/rmarkdown/spa_monitoring_report_sub_hcpi.Rmd inst/rmarkdown/spa_monitoring_report_sub_sco.Rmd
inst/rmarkdown/stat_example_day0.xlsx
inst/rmarkdown/stat_example_day28.xlsx
inst/rmarkdown/stat_example_day7.xlsx
inst/rmarkdown/stat_random_export.Rmd inst/rmarkdown/technical_info.Rmd inst/rmarkdown/translations.Rmd
inst/rmarkdown/word_styles1.docx
inst/rmarkdown/word_styles2.docx
inst/shiny/mini/server.R inst/shiny/mini/ui.R inst/shiny/myapp/server.R inst/shiny/myapp/ui.R inst/test.Rmd
inst/test.docx
inst/test.html
man/allocate_screening_facility.Rd man/allocate_screening_facility2.Rd man/anonymise_dataframe.Rd man/calculate_antibio_has_been_prescribed.Rd man/calculate_antibio_has_been_recorded.Rd man/calendar_heatmap.Rd man/check_name_consistency.Rd man/clean_followup_for_rate_estimation.Rd man/combine_columns.Rd man/combine_dataframes.Rd man/concatenate_names.Rd man/convert_age2ctg.Rd man/convert_yi_age2ctg.Rd man/correct_day0_all.Rd man/correct_day0_drug_data.Rd man/correct_day0_inconsistent_facilities.Rd man/correct_day0_non_valid_facilities.Rd man/correct_day28_all.Rd man/correct_day28_duplicates.Rd man/correct_day7_all.Rd man/correct_day7_duplicates.Rd man/correct_device_ids.Rd man/correct_hospit_ids.Rd man/correct_repeat_ids.Rd man/correct_spa_sco_all.Rd man/correct_spa_sco_fids.Rd man/correct_spa_sco_hcp_ids.Rd man/correct_spo2_values.Rd man/correct_tf_inconsistent_facilities.Rd man/count_baseline_vs_repeat.Rd man/count_noneligibility.Rd man/count_screening.Rd man/count_submissions.Rd man/create_day0_qc_flowchart.Rd man/create_day28fu_outcome_qc_flowchart.Rd man/create_day28fu_qc_flowchart.Rd man/create_day7fu_outcome_qc_flowchart.Rd man/create_day7fu_qc_flowchart.Rd man/create_drug_qc_flowchart.Rd man/create_hospit_qc_flowchart.Rd man/create_odkc_draft_form.Rd man/create_repeat_qc_flowchart.Rd man/create_screening_qc_flowchart.Rd man/create_withdrawal_qc_flowchart.Rd man/csv_download_server.Rd man/csv_download_ui.Rd man/data_table_server.Rd man/data_table_ui.Rd man/dataset_export.Rd man/deidentify_data.Rd man/deidentify_spa_data.Rd man/deidentify_spa_rx_data.Rd man/delete_day0_records.Rd man/delete_repeat_records.Rd man/detect_blank_value.Rd man/detect_drug.Rd man/detect_id_duplicates.Rd man/detect_inconsistent_dates.Rd man/detect_inconsistent_names_between_visits.Rd man/detect_missing_clinical_presentation.Rd man/detect_missing_diagnosis.Rd man/detect_missing_referral.Rd man/detect_missing_treatment.Rd man/detect_missing_value.Rd man/detect_name_duplicates.Rd man/detect_namedob_duplicates.Rd man/detect_negative_value.Rd man/detect_non_timely_completion.Rd man/detect_non_timely_submission.Rd man/detect_participant_duplicates.Rd man/display_weekly_fa_data_per_facility.Rd man/edit_day0_child_ids.Rd man/edit_day0_child_ids_spa_sco.Rd man/edit_day0_to_repeat.Rd man/export_cost_studies.Rd man/export_df2csv.Rd man/export_df2csvxlsx.Rd man/export_df2rds.Rd man/export_df2sqlite.Rd man/export_df2xlsx.Rd man/extract_additional_data_from_odk_zip.Rd man/extract_all_visits.Rd man/extract_baseline_visits.Rd man/extract_complex_data_from_odk_server.Rd man/extract_daily_facility_for_deviceid.Rd man/extract_data_from_odk_server.Rd man/extract_data_from_odk_zip.Rd man/extract_enrolled_participants.Rd man/extract_hypoxaemia.Rd man/extract_last_fa_data.Rd man/extract_main_facility_for_deviceid.Rd man/extract_noneligible.Rd man/extract_pii.Rd man/extract_referrals.Rd man/extract_repeat_visits.Rd man/extract_screening_data.Rd man/extract_tf_data.Rd man/find_best_matched_names_between_fu_and_day0.Rd man/find_closest_facility.Rd man/format_day28_data.Rd man/format_day7_data.Rd man/format_hospital_data.Rd man/format_multiselect_asws.Rd man/format_nrow.Rd man/format_odk_metadata.Rd man/format_summary_table.Rd man/format_text_fields.Rd man/format_weekly_fa_data_for_export.Rd man/formats2h1.Rd man/formats2h2.Rd man/formats2h3.Rd man/generate_calendar_heatmap.Rd man/generate_calendar_heatmap2.Rd man/generate_cg_log.Rd man/generate_day_bar_plot.Rd man/generate_day_cumbar_plot.Rd man/generate_enrolment_hist.Rd man/generate_folder_structure.Rd man/generate_fu_log.Rd man/generate_fu_log_csv.Rd man/generate_fu_logs.Rd man/generate_hospital_log.Rd man/generate_ltfu_log.Rd man/generate_pdf_report.Rd man/generate_physical_fu_log_csv.Rd man/generate_pie_chart.Rd man/generate_research_cdsa_report.Rd man/generate_time_hist_plot.Rd man/generate_week_bar_plot.Rd man/generate_week_bar_plot2.Rd man/generate_word_report.Rd man/get_summary_by_deviceid.Rd man/get_summary_by_fid.Rd man/heatmap_wday_hourofday.Rd man/identify_day0_duplicates.Rd man/identify_day0_duplicates_and_fu.Rd man/identify_duplicates_by_dates.Rd man/identify_duplicates_with_names.Rd man/identify_ids_outside_lock_range.Rd man/identify_multiple_enrolments.Rd man/identify_nonvalid_ids.Rd man/identify_nonvalid_ids2.Rd man/identify_nonvalid_ids_flagged.Rd man/identify_nonvalid_ids_with_matched_names.Rd man/identify_repeat_duplicate.Rd man/identify_true_duplicate.Rd man/import_col_specifications.Rd man/import_country_specific_xls_dict.Rd man/is_not_empty.Rd man/load_qual_data.Rd man/load_qual_data_and_generate_report.Rd man/load_rctls_data.Rd man/load_spapmtf_data.Rd man/match_from_day0_xls_dict.Rd man/match_from_dict.Rd man/match_from_drug_xls_dict.Rd man/match_from_filtered_xls_dict.Rd man/match_from_tf_xls_dict.Rd man/match_from_xls_dict.Rd man/normalised_levenshtein_ratio.Rd man/odk_data_info_server.Rd man/odk_data_info_ui.Rd man/pie_chart_server.Rd man/pie_chart_ui.Rd man/pivot_duplicates_to_columns.Rd man/plot_gauge.Rd man/plot_geom_bar_by_facility_over_time.Rd man/plot_geom_bar_over_time.Rd man/plot_numeric_indicator.Rd man/plot_scatter_by_facility_over_time.Rd man/process_facility_data.Rd man/process_gps_coordinates.Rd man/process_spa_hcpi_data.Rd man/process_spa_sco_data.Rd man/process_tanzania_facility_data.Rd man/process_weekly_fa_data.Rd man/publish_odkc_draft_form.Rd man/quality_check_export.Rd man/reactive_csv_download_server.Rd man/reactive_data_table_server.Rd man/reactive_odk_data_info_server.Rd man/reactive_xlsx_download_server.Rd man/read_day0_xls_dict.Rd man/read_tf_xls_dict.Rd man/remove_facilities_for_other_studies.Rd man/report_download_server.Rd man/report_download_ui.Rd man/run_app.Rd man/run_mini_app.Rd man/run_rmarkdown_rctls.Rd man/run_rmarkdown_reportonly.Rd man/select_list_item_server.Rd man/select_list_item_ui.Rd man/selective_multi_replace.Rd man/selective_replace.Rd man/send_email.Rd man/send_email_tls.Rd man/send_weekly_email.Rd man/set_language_settings.Rd man/set_odkc_connection.Rd man/text_2_plot.Rd man/upload_odkc_csv_attachment.Rd man/xlsx_download_server.Rd man/xlsx_download_ui.Rd
renv.lock
renv/.gitignore
renv/activate.R
renv/settings.dcf
timci.Rproj
Thaliehln/timci documentation built on April 8, 2024, 3:38 p.m.