Index

_

__init__() (nccidxclean.figures.categorical.CategoricalField method)

A

add_dicom_update() (in module nccidxclean.clean.enrich_with_dcm) allocate_hospital_codes() (in module nccidxclean.figures.prepare_dataframes) analyse_age() (in module nccidxclean.num_analysis.categorical)

analyse_pmh_cvs() (in module nccidxclean.num_analysis.categorical) analyse_pmh_htn() (in module nccidxclean.num_analysis.categorical) analyse_sex() (in module nccidxclean.num_analysis.categorical)

B

binarise_lung_csv() (in module nccidxclean.clean.binary_and_cat)

C

categorical_fields_analysis() (in module nccidxclean.num_analysis.categorical) CategoricalField (class in nccidxclean.figures.categorical) check_new_centres() (in module nccidxclean.clean.remap_hospitals) clean_numeric() (in module nccidxclean.clean.numeric) clean_raw_data() (in module nccidxclean.figures.numeric) clip_numeric() (in module nccidxclean.clean.numeric) column_shift() (in module nccidxclean.clean.geh_col_shift)

count_dates() (in module nccidxclean.num_analysis.dates) count_missing() (in module nccidxclean.num_analysis.num_analysis) create_error_report() (in module nccidxclean.clean.utils) create_numeric_results_fig() (in module nccidxclean.figures.numeric) create_xclean_id() (in module nccidxclean.clean.utils) creatinine_analysis() (in module nccidxclean.num_analysis.numeric) cvs_map_values() (nccidxclean.figures.categorical.CategoricalField method)

D

date_field_analysis() (in module nccidxclean.num_analysis.dates)

dates_summary() (in module nccidxclean.num_analysis.dates) ddimer_analysis() (in module nccidxclean.num_analysis.numeric)

E

excel_dates() (in module nccidxclean.num_analysis.dates) extract_day_and_month() (in module nccidxclean.figures.dates)

extract_dcm_metadata() (in module nccidxclean.clean.enrich_with_dcm) extract_old_data() (in module nccidxclean.clean.utils)

F

fio2_analysis() (in module nccidxclean.num_analysis.numeric)

fix_headers() (in module nccidxclean.clean.fix_headers_and_order)

G

get_gov_data() (in module nccidxclean.figures.dates)

get_min_gap() (in module nccidxclean.figures.dates) get_total_missing() (in module nccidxclean.figures.overall_numbers)

I

incorrect_date_format() (in module nccidxclean.num_analysis.dates) inferences() (in module nccidxclean.clean.inferences)

info_by_center() (in module nccidxclean.num_analysis.tables) is_float() (in module nccidxclean.figures.numeric)

M

main() (in module nccidxclean.analysis) (in module nccidxclean.nccidxclean) make_figure_1() (in module nccidxclean.figures.overall_numbers) make_figure_2() (in module nccidxclean.figures.categorical) make_figure_3() (in module nccidxclean.figures.dates) make_figure_4() (in module nccidxclean.figures.numeric) make_figure_5() (in module nccidxclean.figures.numeric) make_figure_6() (in module nccidxclean.figures.categorical) make_figure_7() (in module nccidxclean.figures.dates) make_figure_8() (in module nccidxclean.figures.numeric) make_figures_and_numeric_analysis() (in module nccidxclean.analysis) map_values() (nccidxclean.figures.categorical.CategoricalField method) merge_checks_with_cleaned_df() (in module nccidxclean.clean.utils) merge_pcr_and_study_dates() (in module nccidxclean.figures.dates) methods_hist_by_hosp() (nccidxclean.figures.categorical.CategoricalField method) module nccidxclean.analysis nccidxclean.clean.binary_and_cat nccidxclean.clean.dicts_and_maps nccidxclean.clean.enrich_with_dcm nccidxclean.clean.ethnicity_and_sex nccidxclean.clean.fix_headers_and_order nccidxclean.clean.geh_col_shift nccidxclean.clean.inferences nccidxclean.clean.numeric nccidxclean.clean.parse_dates nccidxclean.clean.remap_hospitals nccidxclean.clean.sense_check nccidxclean.clean.utils nccidxclean.figures.categorical nccidxclean.figures.dates nccidxclean.figures.numeric nccidxclean.figures.overall_numbers nccidxclean.figures.prepare_dataframes nccidxclean.figures.sns_settings nccidxclean.nccidxclean nccidxclean.num_analysis.categorical nccidxclean.num_analysis.dates nccidxclean.num_analysis.num_analysis nccidxclean.num_analysis.numeric nccidxclean.num_analysis.tables

N

nccidxclean.analysis module nccidxclean.clean.binary_and_cat module nccidxclean.clean.dicts_and_maps module nccidxclean.clean.enrich_with_dcm module nccidxclean.clean.ethnicity_and_sex module nccidxclean.clean.fix_headers_and_order module nccidxclean.clean.geh_col_shift module nccidxclean.clean.inferences module nccidxclean.clean.numeric module nccidxclean.clean.parse_dates module nccidxclean.clean.remap_hospitals module nccidxclean.clean.sense_check module nccidxclean.clean.utils module

nccidxclean.figures.categorical module nccidxclean.figures.dates module nccidxclean.figures.numeric module nccidxclean.figures.overall_numbers module nccidxclean.figures.prepare_dataframes module nccidxclean.figures.sns_settings module nccidxclean.nccidxclean module nccidxclean.num_analysis.categorical module nccidxclean.num_analysis.dates module nccidxclean.num_analysis.num_analysis module nccidxclean.num_analysis.numeric module nccidxclean.num_analysis.tables module numeric_analysis() (in module nccidxclean.num_analysis.num_analysis) numeric_fields_analysis() (in module nccidxclean.num_analysis.numeric)

O

order_columns() (in module nccidxclean.clean.fix_headers_and_order)

P

pao2_analysis() (in module nccidxclean.num_analysis.numeric) parse_binary_and_cat() (in module nccidxclean.clean.binary_and_cat) parse_date_columns() (in module nccidxclean.clean.parse_dates)

pcr_imaging_gaps() (in module nccidxclean.num_analysis.dates) prepare_dataframe_dates() (in module nccidxclean.figures.dates) prepare_dataframes_for_comparison() (in module nccidxclean.figures.prepare_dataframes) print_df_as_latex() (in module nccidxclean.analysis)

R

read_in_clinical_data() (in module nccidxclean.clean.utils) remap_column_names() (nccidxclean.figures.categorical.CategoricalField method) remap_ethnicity() (in module nccidxclean.clean.ethnicity_and_sex) remap_hospitals() (in module nccidxclean.clean.remap_hospitals) remap_melted_date_names() (in module nccidxclean.figures.dates)

remap_sex() (in module nccidxclean.clean.ethnicity_and_sex) rename_field() (nccidxclean.figures.categorical.CategoricalField method) rescale_fio2() (in module nccidxclean.clean.numeric) results_hist_by_dataset() (nccidxclean.figures.categorical.CategoricalField method) round_sig() (in module nccidxclean.num_analysis.numeric)

S

save_dcm_updates() (in module nccidxclean.clean.enrich_with_dcm) select_output_cols() (in module nccidxclean.clean.fix_headers_and_order)

sense_check() (in module nccidxclean.clean.sense_check) sense_check_dicom_dates() (in module nccidxclean.clean.sense_check) summary_table() (in module nccidxclean.num_analysis.tables)

T

troponin_analysis() (in module nccidxclean.num_analysis.numeric)

U

update_with_prev_changes() (in module nccidxclean.clean.utils)

V

value_counts_with_percentage() (in module nccidxclean.num_analysis.numeric)

X

xclean_nccid() (in module nccidxclean.nccidxclean)