Package: avoncap 0.0.0.9029

Rob Challen

avoncap: AvonCap Study Analysis

A WIP set of functions allowing data load, wrangling of the AvonCap data set.

Authors:Rob Challen [aut, cre]

avoncap_0.0.0.9029.tar.gz
avoncap_0.0.0.9029.zip(r-4.7)avoncap_0.0.0.9029.zip(r-4.6)avoncap_0.0.0.9029.zip(r-4.5)
avoncap_0.0.0.9029.tgz(r-4.6-any)avoncap_0.0.0.9029.tgz(r-4.5-any)
avoncap_0.0.0.9029.tar.gz(r-4.7-any)avoncap_0.0.0.9029.tar.gz(r-4.6-any)
avoncap_0.0.0.9029.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
avoncap/json (API)

# Install 'avoncap' in R:

install.packages('avoncap', repos = c('https://bristol-vaccine-centre.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/bristol-vaccine-centre/avoncap/issues

Pkgdown/docs site:https://bristol-vaccine-centre.github.io

Datasets:

denom_by_age_by_day - The avoncap denominator dataset
frameworks - Frameworks
icb_surgeries - GP surgeries in the Bristol ICB area
imd_to_townsend - High level IMD to Townsend score map
key_dates - Key dates:
phe_serotypes - Pneumococcal UAD serotypes
serotype_data - Pneumococcal UAD serotype groups and crossmaps
serotype_pcv_map - Pneumococcal serotype PCV groups
serotype_uad_map - Serotype UAD mappings
uad_groups - UAD serotype groups
uad_pcv_map - UAD PCV map
year_week_number_lookup - Year and week number lookup table

On CRAN:

1.74 score 11 scripts 85 exports 72 dependencies

Last updated from:c072ab40c1. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	164
source / vignettes	OK	267
linux-release-x86_64	OK	155
macos-release-arm64	OK	141
macos-oldrel-arm64	OK	88
windows-devel	OK	106
windows-release	OK	104
windows-oldrel	OK	99
wasm-release	OK	131

Exports:%>%all_files augment_data augment_generic binomial_proportion_points cut_integer default_column_names derive_admission_episode derive_aLRTD_categories derive_antiviral_status derive_catchment_status derive_completed_vaccination_status derive_continuous_categories derive_continuous_categories_pneumo derive_covid_status derive_diagnosis_categories derive_effective_vaccination_status derive_genomic_variant derive_gp_linkage derive_haematology_categories derive_hospital_burden_outcomes derive_infective_classification derive_invasive_status derive_nosocomial_covid_status derive_nosocomial_status derive_pandemic_timings derive_patient_identifier derive_pcv_groupings derive_phe_pcv_group derive_pneumo_clinical_syndrome derive_pneumo_polyfill derive_pneumo_uad_panel derive_pneumo_uad_status derive_pneumococcal_categories derive_pneumococcal_high_risk derive_pneumococcal_risk_category derive_polyfill_central derive_polyfill_ed derive_presumed_diagnosis_categories derive_qcovid derive_quintile_category derive_severe_disease_outcomes derive_simpler_comorbidities derive_survival_censoring derive_survival_times_avoncap derive_survival_times_pneumo derive_template derive_vaccination_timings derive_vaccine_combinations derive_WHO_outcome_score extract_dependencies find_new_field_names get_value_sets input km_plot load_data map_avoncap_central map_avoncap_consent map_avoncap_ed map_avoncap_ed_consent map_avoncap_haem map_avoncap_micro map_avoncap_pneumococcal map_avoncap_radio map_avoncap_virol map_urine_antigens map_urine_binax most_recent_files normalise_data original_field_names readable_label readable_label_mapping relevel_serotypes save_data_source_info scale_fill_serotype set_input spline_term_plot stacked_barplot start_date_of_week study_week upset_plot valid_inputs validate_data write_issues xglimpse

Dependencies:askpass assertthat base64enc binom bit bit64 cli clipr colorspace cpp11 crayon curl data.tree digest dplyr dtrackr farver fastmap forcats fs generics ggplot2 ggstance glue gtable hms htmltools isoband jsonlite labeling lattice lifecycle lubridate magrittr Matrix nplyr patchwork pdftools pillar pkgconfig plyr png prettyunits progress purrr qpdf R6 rappdirs RColorBrewer Rcpp readr rlang rsvg S7 scales stringi stringr survival sys tibble tidyr tidyselect timechange tzdb utf8 V8 vctrs viridisLite vroom withr writexl yaml

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Clear data from the passthrough cache for complex or long running operations	.cache_clear
Delete stale files in a cache	.cache_delete_stale
Download a file into a local cache.	.cache_download
A simple pass-through cache for complex or long running operations	.cached
Scans the input directory and returns csv or xlsx files in that directory	all_files
Sanitise AvonCap data columns	augment_data
Applies a set of functions to the whole dataframe	augment_generic
Dodged bar and whiskers proportions	binomial_proportion_points
Cut and label an integer valued quantity	cut_integer
default column naming mappings	default_column_names
The avoncap denominator dataset	denom_by_age_by_day
Create a counter in the event of repeated admissions	derive_admission_episode
The aLRTD incidence paper classifications	derive_aLRTD_categories
Create a flag for patients who have been given antivirals	derive_antiviral_status
Identify patients who are in the BNSSG ICB based on their GP practice name	derive_catchment_status
Derive detailed vaccination status on admission	derive_completed_vaccination_status
Categorical scores for continuous variables	derive_continuous_categories
Age and CURB score categories	derive_continuous_categories_pneumo
Determine if an admission is proven SARS-CoV-2 PCR positive	derive_covid_status
Create 4 non exclusive diagnostic categories	derive_diagnosis_categories
A simple vaccination status on admission as an ordered number of doses	derive_effective_vaccination_status
Give a inferred Alpha, Delta or Omicron status based on time alone.	derive_genomic_variant
Identify patients from the GP surgeries in linked primary care study	derive_gp_linkage
Binary outcomes for haematology data	derive_haematology_categories
Binary outcomes for hospital burden	derive_hospital_burden_outcomes
Determine if an admission is due to an infective cause	derive_infective_classification
Pneumococcal invasive status and binary test category	derive_invasive_status
Did the patient catch COVID in hospital	derive_nosocomial_covid_status
Identify patients who were admitted already prior to study entry	derive_nosocomial_status
Date columns	derive_pandemic_timings
Create a unique patient level id (if it does not already exist)	derive_patient_identifier
Group pneumo serotypes according to e.g. vaccine coverage	derive_pcv_groupings
Get vaccine coverage group for known serotype	derive_phe_pcv_group
Add in clinical syndrome indicator	derive_pneumo_clinical_syndrome
Make pneumo data compatible with AvonCAP	derive_pneumo_polyfill
Calculate UAD panel for test	derive_pneumo_uad_panel
Calculate summary status from UAD (or other serotype) panel results	derive_pneumo_uad_status
The pneumococcal incidence diagnostic classifications	derive_pneumococcal_categories
Determine if patient is in a high pneumococcal risk group	derive_pneumococcal_high_risk
Determine pneumococcal risk group	derive_pneumococcal_risk_category
Polyfill data	derive_polyfill_central
Polyfill ED data	derive_polyfill_ed
Create presumed diagnostic categories	derive_presumed_diagnosis_categories
Calculate a QCOVID2 score from AvonCap data source	derive_qcovid
Split a continuous variable into quintiles	derive_quintile_category
Binary outcomes for severe disease	derive_severe_disease_outcomes
Rationalise some of the more detailed comorbidities	derive_simpler_comorbidities
Survival outcomes	derive_survival_censoring
Survival analysis times	derive_survival_times_avoncap
Survival analysis times	derive_survival_times_pneumo
Derived data function template	derive_template
Derive times from vaccination to symptom onset	derive_vaccination_timings
Deprecated - Vaccine combinations are less relevant now	derive_vaccine_combinations
determine WHO outcome score	derive_WHO_outcome_score
Get provenance of data column	extract_dependencies
Get the transformed columns from original field names	find_new_field_names
Frameworks	frameworks
Get a value set list of a dataframe	get_value_sets
GP surgeries in the Bristol ICB area	icb_surgeries
High level IMD to Townsend score map	imd_to_townsend
Locate the input directory	input
Key dates:	key_dates
Faceted Kaplan-Meier plot	km_plot
Load data and check structure	load_data
Core avoncap normalisation	map_avoncap_central
Core avoncap consent	map_avoncap_consent
Avoncap ED normalisation	map_avoncap_ed
ED consent	map_avoncap_ed_consent
Normalise the avoncap data haematology data	map_avoncap_haem
Normalise the avoncap data microbiology data	map_avoncap_micro
Normalise the avoncap pneumococcal data	map_avoncap_pneumococcal
Normalise the avoncap data radiology data	map_avoncap_radio
Normalise the avoncap data virology data	map_avoncap_virol
Normalise the urinary antigen data	map_urine_antigens
Normalise the urinary antigen data (binax results)	map_urine_binax
find most recent files of a specific type	most_recent_files
Sanitise AvonCap data columns	normalise_data
Get the mapping of transformed columns back to original	original_field_names
Pneumococcal UAD serotypes	phe_serotypes
Get a label for a column	readable_label
Get a readable label for the AvonCap data as a named list (for ggplot)	readable_label_mapping readable_label_mapping.character readable_label_mapping.data.frame readable_label_mapping.default readable_label_mapping.list
Relevel serotype data into an factor based on PCV group status and serotype name.	relevel_serotypes
Write file source information out to a text files	save_data_source_info
A ggplot scale for pneumococcal serotypes that keeps PCV groups together	scale_fill_serotype
Pneumococcal UAD serotype groups and crossmaps	serotype_data
Pneumococcal serotype PCV groups	serotype_pcv_map
Serotype UAD mappings	serotype_uad_map
Sets the location of data for an analysis	set_input
Spline term marginal effects plot	spline_term_plot
Stacked bar plot	stacked_barplot
Convert a study week back into a date	start_date_of_week
Convert a study week back into a date	start_date_of_week_legacy
Convert a date to a study week	study_week
Convert a date to a study week	study_week_legacy
UAD serotype groups	uad_groups
UAD PCV map	uad_pcv_map
Upset plot with counts stratified by a categorical column	upset_plot
A valid set of types of file that can be loaded by 'load_data(...)'	valid_inputs
Validate AvonCap raw data	validate_data
Write out data quality issues	write_issues
Wrapper around 'table'	xglimpse
Year and week number lookup table	year_week_number_lookup