Package index • avoncap

Raw data mappings

Mappings converting raw data to normalised

map_avoncap_central(): Core avoncap normalisation

map_avoncap_consent(): Core avoncap consent

map_avoncap_ed(): Avoncap ED normalisation

map_avoncap_ed_consent(): ED consent

map_avoncap_haem(): Normalise the avoncap data haematology data

map_avoncap_micro(): Normalise the avoncap data microbiology data

map_avoncap_pneumococcal(): Normalise the avoncap pneumococcal data

map_avoncap_radio(): Normalise the avoncap data radiology data

map_avoncap_virol(): Normalise the avoncap data virology data

map_urine_antigens(): Normalise the urinary antigen data

map_urine_binax(): Normalise the urinary antigen data (binax results)

Derived data

Functions deriving new fields from normalised data

derive_WHO_outcome_score(): determine WHO outcome score

derive_aLRTD_categories(): The aLRTD incidence paper classifications

derive_admission_episode(): Create a counter in the event of repeated admissions

derive_antiviral_status(): Create a flag for patients who have been given antivirals

derive_catchment_status(): Identify patients who are in the BNSSG ICB based on their GP practice name

derive_completed_vaccination_status(): Derive detailed vaccination status on admission

derive_continuous_categories(): Categorical scores for continuous variables

derive_continuous_categories_pneumo(): Age and CURB score categories

derive_covid_status(): Determine if an admission is proven SARS-CoV-2 PCR positive

derive_diagnosis_categories(): Create 4 non exclusive diagnostic categories

derive_effective_vaccination_status(): A simple vaccination status on admission as an ordered number of doses

derive_genomic_variant(): Give a inferred Alpha, Delta or Omicron status based on time alone.

derive_gp_linkage(): Identify patients from the GP surgeries in linked primary care study

derive_haematology_categories(): Binary outcomes for haematology data

derive_hospital_burden_outcomes(): Binary outcomes for hospital burden

derive_infective_classification(): Determine if an admission is due to an infective cause

derive_invasive_status(): Pneumococcal invasive status and binary test category

derive_nosocomial_covid_status(): Did the patient catch COVID in hospital

derive_nosocomial_status(): Identify patients who were admitted already prior to study entry

derive_patient_identifier(): Create a unique patient level id (if it does not already exist)

derive_pcv_groupings(): Group pneumo serotypes according to e.g. vaccine coverage

derive_phe_pcv_group(): Get vaccine coverage group for known serotype

derive_pneumo_clinical_syndrome(): Add in clinical syndrome indicator

derive_pneumo_polyfill(): Make pneumo data compatible with AvonCAP

derive_pneumo_uad_panel(): Calculate UAD panel for test

derive_pneumo_uad_status(): Calculate summary status from UAD (or other serotype) panel results

derive_pneumococcal_categories(): The pneumococcal incidence diagnostic classifications

derive_pneumococcal_high_risk(): Determine if patient is in a high pneumococcal risk group

derive_pneumococcal_risk_category(): Determine pneumococcal risk group

derive_polyfill_central(): Polyfill data

derive_polyfill_ed(): Polyfill ED data

derive_presumed_diagnosis_categories(): Create presumed diagnostic categories

derive_qcovid(): Calculate a QCOVID2 score from AvonCap data source

derive_severe_disease_outcomes(): Binary outcomes for severe disease

derive_simpler_comorbidities(): Rationalise some of the more detailed comorbidities

derive_survival_censoring(): Survival outcomes

derive_survival_times_avoncap(): Survival analysis times

derive_survival_times_pneumo(): Survival analysis times

derive_vaccination_timings(): Derive times from vaccination to symptom onset

derive_vaccine_combinations(): Deprecated - Vaccine combinations are less relevant now

Other

Other functions

all_files(): Scans the input directory and returns csv or xlsx files in that directory

augment_data(): Sanitise AvonCap data columns

augment_generic(): Applies a set of functions to the whole dataframe

binomial_proportion_points(): Dodged bar and whiskers proportions

cut_integer(): Cut and label an integer valued quantity

default_column_names(): default column naming mappings

denom_by_age_by_day: The avoncap denominator dataset

derive_pandemic_timings(): Date columns

derive_quintile_category(): Split a continuous variable into quintiles

derive_template(): Derived data function template

.cache_clear(): Clear data from the passthrough cache for complex or long running operations

.cache_delete_stale(): Delete stale files in a cache

.cache_download(): Download a file into a local cache.

.cached(): A simple pass-through cache for complex or long running operations

extract_dependencies(): Get provenance of data column

find_new_field_names(): Get the transformed columns from original field names

frameworks: Frameworks

get_value_sets(): Get a value set list of a dataframe

icb_surgeries: GP surgeries in the Bristol ICB area

imd_to_townsend: High level IMD to Townsend score map

input(): Locate the input directory

key_dates: Key dates:

km_plot(): Faceted Kaplan-Meier plot

load_data(): Load data and check structure

most_recent_files(): find most recent files of a specific type

normalise_data(): Sanitise AvonCap data columns

original_field_names(): Get the mapping of transformed columns back to original

phe_serotypes: Pneumococcal UAD serotypes

readable_label(): Get a label for a column

readable_label_mapping(): Get a readable label for the AvonCap data as a named list (for ggplot)

relevel_serotypes(): Relevel serotype data into an factor based on PCV group status and serotype name.

save_data_source_info(): Write file source information out to a text files

scale_fill_serotype(): A ggplot scale for pneumococcal serotypes that keeps PCV groups together

serotype_data: Pneumococcal UAD serotype groups and crossmaps

serotype_pcv_map: Pneumococcal serotype PCV groups

serotype_uad_map: Serotype UAD mappings

set_input(): Sets the location of data for an analysis

spline_term_plot(): Spline term marginal effects plot

stacked_barplot(): Stacked bar plot

start_date_of_week(): Convert a study week back into a date

start_date_of_week_legacy(): Convert a study week back into a date

study_week(): Convert a date to a study week

study_week_legacy(): Convert a date to a study week

uad_groups: UAD serotype groups

uad_pcv_map: UAD PCV map

upset_plot(): Upset plot with counts stratified by a categorical column

valid_inputs(): A valid set of types of file that can be loaded by load_data(...)

validate_data(): Validate AvonCap raw data

write_issues(): Write out data quality issues

xglimpse(): Wrapper around table

year_week_number_lookup: Year and week number lookup table