Package: avoncap 0.0.0.9028

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_0.0.0.9028.tar.gz
avoncap_0.0.0.9028.zip(r-4.5)avoncap_0.0.0.9028.zip(r-4.4)avoncap_0.0.0.9028.zip(r-4.3)
avoncap_0.0.0.9028.tgz(r-4.4-any)avoncap_0.0.0.9028.tgz(r-4.3-any)
avoncap_0.0.0.9028.tar.gz(r-4.5-noble)avoncap_0.0.0.9028.tar.gz(r-4.4-noble)
avoncap_0.0.0.9028.tgz(r-4.4-emscripten)avoncap_0.0.0.9028.tgz(r-4.3-emscripten)
avoncap.pdf |avoncap.html✨
avoncap/json (API)

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

Peer review:

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

Datasets:

On CRAN:

2.38 score 12 scripts 85 exports 76 dependencies

Last updated 30 days agofrom:8b2fc0b36b. Checks:OK: 5 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 06 2024
R-4.5-winOKNov 06 2024
R-4.5-linuxOKNov 06 2024
R-4.4-winNOTENov 06 2024
R-4.4-macNOTENov 06 2024
R-4.3-winOKNov 06 2024
R-4.3-macOKNov 06 2024

Exports:%>%all_filesaugment_dataaugment_genericbinomial_proportion_pointscut_integerdefault_column_namesderive_admission_episodederive_aLRTD_categoriesderive_antiviral_statusderive_catchment_statusderive_completed_vaccination_statusderive_continuous_categoriesderive_continuous_categories_pneumoderive_covid_statusderive_diagnosis_categoriesderive_effective_vaccination_statusderive_genomic_variantderive_gp_linkagederive_haematology_categoriesderive_hospital_burden_outcomesderive_infective_classificationderive_invasive_statusderive_nosocomial_covid_statusderive_nosocomial_statusderive_pandemic_timingsderive_patient_identifierderive_pcv_groupingsderive_phe_pcv_groupderive_pneumo_clinical_syndromederive_pneumo_polyfillderive_pneumo_uad_panelderive_pneumo_uad_statusderive_pneumococcal_categoriesderive_pneumococcal_high_riskderive_pneumococcal_risk_categoryderive_polyfill_centralderive_polyfill_edderive_presumed_diagnosis_categoriesderive_qcovidderive_quintile_categoryderive_severe_disease_outcomesderive_simpler_comorbiditiesderive_survival_censoringderive_survival_times_avoncapderive_survival_times_pneumoderive_templatederive_vaccination_timingsderive_vaccine_combinationsderive_WHO_outcome_scoreextract_dependenciesfind_new_field_namesget_value_setsinputkm_plotload_datamap_avoncap_centralmap_avoncap_consentmap_avoncap_edmap_avoncap_ed_consentmap_avoncap_haemmap_avoncap_micromap_avoncap_pneumococcalmap_avoncap_radiomap_avoncap_virolmap_urine_antigensmap_urine_binaxmost_recent_filesnormalise_dataoriginal_field_namesreadable_labelreadable_label_mappingrelevel_serotypessave_data_source_infoscale_fill_serotypeset_inputspline_term_plotstacked_barplotstart_date_of_weekstudy_weekupset_plotvalid_inputsvalidate_datawrite_issuesxglimpse

Dependencies:askpassassertthatbase64encbinombitbit64clicliprcolorspacecpp11crayoncurldata.treedigestdplyrdtrackrfansifarverfastmapforcatsfsgenericsggplot2ggstancegluegtablehmshtmltoolsisobandjsonlitelabelinglatticelifecyclelubridatemagrittrMASSMatrixmgcvmunsellnlmenplyrpatchworkpdftoolspillarpkgconfigplyrpngprettyunitsprogresspurrrqpdfR6rappdirsRColorBrewerRcppreadrrlangrsvgscalesstringistringrsurvivalsystibbletidyrtidyselecttimechangetzdbutf8V8vctrsviridisLitevroomwithrwritexlyaml

Readme and manuals

Help Manual

Help pageTopics
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 directoryall_files
Sanitise AvonCap data columnsaugment_data
Applies a set of functions to the whole dataframeaugment_generic
Dodged bar and whiskers proportionsbinomial_proportion_points
Cut and label an integer valued quantitycut_integer
default column naming mappingsdefault_column_names
The avoncap denominator datasetdenom_by_age_by_day
Create a counter in the event of repeated admissionsderive_admission_episode
The aLRTD incidence paper classificationsderive_aLRTD_categories
Create a flag for patients who have been given antiviralsderive_antiviral_status
Identify patients who are in the BNSSG ICB based on their GP practice namederive_catchment_status
Derive detailed vaccination status on admissionderive_completed_vaccination_status
Categorical scores for continuous variablesderive_continuous_categories
Age and CURB score categoriesderive_continuous_categories_pneumo
Determine if an admission is proven SARS-CoV-2 PCR positivederive_covid_status
Create 4 non exclusive diagnostic categoriesderive_diagnosis_categories
A simple vaccination status on admission as an ordered number of dosesderive_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 studyderive_gp_linkage
Binary outcomes for haematology dataderive_haematology_categories
Binary outcomes for hospital burdenderive_hospital_burden_outcomes
Determine if an admission is due to an infective causederive_infective_classification
Pneumococcal invasive status and binary test categoryderive_invasive_status
Did the patient catch COVID in hospitalderive_nosocomial_covid_status
Identify patients who were admitted already prior to study entryderive_nosocomial_status
Date columnsderive_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 coveragederive_pcv_groupings
Get vaccine coverage group for known serotypederive_phe_pcv_group
Add in clinical syndrome indicatorderive_pneumo_clinical_syndrome
Make pneumo data compatible with AvonCAPderive_pneumo_polyfill
Calculate UAD panel for testderive_pneumo_uad_panel
Calculate summary status from UAD (or other serotype) panel resultsderive_pneumo_uad_status
The pneumococcal incidence diagnostic classificationsderive_pneumococcal_categories
Determine if patient is in a high pneumococcal risk groupderive_pneumococcal_high_risk
Determine pneumococcal risk groupderive_pneumococcal_risk_category
Polyfill dataderive_polyfill_central
Polyfill ED dataderive_polyfill_ed
Create presumed diagnostic categoriesderive_presumed_diagnosis_categories
Calculate a QCOVID2 score from AvonCap data sourcederive_qcovid
Split a continuous variable into quintilesderive_quintile_category
Binary outcomes for severe diseasederive_severe_disease_outcomes
Rationalise some of the more detailed comorbiditiesderive_simpler_comorbidities
Survival outcomesderive_survival_censoring
Survival analysis timesderive_survival_times_avoncap
Survival analysis timesderive_survival_times_pneumo
Derived data function templatederive_template
Derive times from vaccination to symptom onsetderive_vaccination_timings
Deprecated - Vaccine combinations are less relevant nowderive_vaccine_combinations
determine WHO outcome scorederive_WHO_outcome_score
Get provenance of data columnextract_dependencies
Get the transformed columns from original field namesfind_new_field_names
Frameworksframeworks
Get a value set list of a dataframeget_value_sets
GP surgeries in the Bristol ICB areaicb_surgeries
High level IMD to Townsend score mapimd_to_townsend
Locate the input directoryinput
Key dates:key_dates
Faceted Kaplan-Meier plotkm_plot
Load data and check structureload_data
Core avoncap normalisationmap_avoncap_central
Core avoncap consentmap_avoncap_consent
Avoncap ED normalisationmap_avoncap_ed
ED consentmap_avoncap_ed_consent
Normalise the avoncap data haematology datamap_avoncap_haem
Normalise the avoncap data microbiology datamap_avoncap_micro
Normalise the avoncap pneumococcal datamap_avoncap_pneumococcal
Normalise the avoncap data radiology datamap_avoncap_radio
Normalise the avoncap data virology datamap_avoncap_virol
Normalise the urinary antigen datamap_urine_antigens
Normalise the urinary antigen data (binax results)map_urine_binax
find most recent files of a specific typemost_recent_files
Sanitise AvonCap data columnsnormalise_data
Get the mapping of transformed columns back to originaloriginal_field_names
Pneumococcal UAD serotypesphe_serotypes
Get a label for a columnreadable_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 filessave_data_source_info
A ggplot scale for pneumococcal serotypes that keeps PCV groups togetherscale_fill_serotype
Pneumococcal UAD serotype groups and crossmapsserotype_data
Pneumococcal serotype PCV groupsserotype_pcv_map
Serotype UAD mappingsserotype_uad_map
Sets the location of data for an analysisset_input
Spline term marginal effects plotspline_term_plot
Stacked bar plotstacked_barplot
Convert a study week back into a datestart_date_of_week
Convert a date to a study weekstudy_week
UAD serotype groupsuad_groups
UAD PCV mapuad_pcv_map
Upset plot with counts stratified by a categorical columnupset_plot
A valid set of types of file that can be loaded by 'load_data(...)'valid_inputs
Validate AvonCap raw datavalidate_data
Write out data quality issueswrite_issues
Wrapper around 'table'xglimpse