Package: epidm 1.0.6

Alex Bhattacharya

epidm: UK Epidemiological Data Management

Contains utilities and functions for the cleaning, processing and management of patient level public health data for surveillance and analysis held by the UK Health Security Agency, UKHSA.

Authors:Alex Bhattacharya [aut, cre], Alice Graham [aut], Harshana Liyanage [aut], Frederick Sloots [aut], Emma Parker [aut]

epidm_1.0.6.tar.gz
epidm_1.0.6.zip(r-4.7)epidm_1.0.6.zip(r-4.6)epidm_1.0.6.zip(r-4.5)
epidm_1.0.6.tgz(r-4.6-any)epidm_1.0.6.tgz(r-4.5-any)
epidm_1.0.6.tar.gz(r-4.7-any)epidm_1.0.6.tar.gz(r-4.6-any)
epidm_1.0.6.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
epidm/json (API)

# Install 'epidm' in R:

install.packages('epidm', repos = c('https://ukhsa-collaboration.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ukhsa-collaboration/epidm/issues

Datasets:

genus_gram_stain - Bacterial Genus Gram Stain Lookup Table
group_ecds_discharge_destination - A&E attendance discharge destination
group_inpatient_admission_method - Inpatient admission methods
group_inpatient_discharge_destination - Inpatient discharge destination
lab_data - Synthetic Lab Data for epidm
respeciate_organism - Respeciated organisms
specimen_type_grouping - Specimen type grouping

On CRAN:

6.22 score 6 stars 7 scripts 380 downloads 14 exports 76 dependencies

Last updated from:e0d0ac04a1. Checks:7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	NOTE	180
source / vignettes	OK	209
linux-release-x86_64	NOTE	146
macos-release-arm64	NOTE	131
macos-oldrel-arm64	NOTE	199
windows-devel	NOTE	129
windows-release	NOTE	109
windows-oldrel	NOTE	114
wasm-release	OK	172

Exports:cip_spells csv_from_zip group_time inpatient_codes link_ae_inpatient lookup_recode proxy_episode_dates respeciate_generic sql_clean sql_connect sql_read sql_write uk_patient_id valid_nhs

Dependencies:base64enc BH bit bit64 blob bslib cachem cli clipr cpp11 crayon data.table DBI DiagrammeR digest dplyr evaluate farver fastmap fontawesome fs generics ggplot2 glue gtable highr hms htmltools htmlwidgets igraph isoband jquerylib jsonlite knitr labeling lattice lifecycle lubridate magrittr Matrix memoise mime odbc phonics pillar pkgconfig prettyunits progress purrr R6 rappdirs RColorBrewer Rcpp readr rlang rmarkdown rstudioapi S7 sass scales stringi stringr tibble tidyr tidyselect timechange tinytex tzdb utf8 vctrs viridisLite visNetwork vroom withr xfun yaml

Guide: Staged Patient Matching and Time-based Episode Grouping with EpiDM

Rendered fromepidm-function-usage.Rmdusingknitr::rmarkdown

Last update: 2026-02-16
Started: 2026-02-06

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Continuous Inpatient (CIP) Spells	cip_spells
Download a csv from a zip	csv_from_zip
Bacterial Genus Gram Stain Lookup Table	genus_gram_stain
A&E attendance discharge destination	group_ecds_discharge_destination
Inpatient admission methods	group_inpatient_admission_method
Inpatient discharge destination	group_inpatient_discharge_destination
Grouping of intervals or events that occur close together in time	group_time
Hospital IN/OUT dates	hospital_in_out_dates
Inpatient Codes cleanup	inpatient_codes
Synthetic Lab Data for epidm	lab_data
Lookup table switch handler	lookup_recode
Clean and Impute HES/SUS Episode Start and End Dates	proxy_episode_dates
Respeciate unspecified samples	respeciate_generic
Respeciated organisms	respeciate_organism
Specimen type grouping	specimen_type_grouping
Clean and Read a SQL query	sql_clean
Connect to a SQL database	sql_connect
Read a table from a SQL database	sql_read
Write a table to a SQL database	sql_write
Patient ID record grouping	uk_patient_id
NHS Number Validity Check	valid_nhs