Package: coder 0.13.10

Erik Bulow

coder: Deterministic Categorization of Items Based on External Code Data

Fast categorization of items based on external code data identified by regular expressions. A typical use case considers patient with medically coded data, such as codes from the International Classification of Diseases ('ICD') or the Anatomic Therapeutic Chemical ('ATC') classification system. Functions of the package relies on a triad of objects: (1) case data with unit id:s and possible dates of interest; (2) external code data for corresponding units in (1) and with optional dates of interest and; (3) a classification scheme ('classcodes' object) with regular expressions to identify and categorize relevant codes from (2). It is easy to introduce new classification schemes ('classcodes' objects) or to use default schemes included in the package. Use cases includes patient categorization based on 'comorbidity indices' such as 'Charlson', 'Elixhauser', 'RxRisk V', or the 'comorbidity-polypharmacy' score (CPS), as well as adverse events after hip and knee replacement surgery.

Authors:Erik Bulow [aut, cre], Emely C Zabore [rev], David Robinson [rev]

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coder/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/ropensci/coder/issues

Datasets:
  • charlson - Classcodes for Charlson comorbidity based on ICD-codes
  • cps - Classcodes for the comorbidity-polypharmacy score (CPS) based on ICD-10 codes
  • elixhauser - Classcodes for Elixhauser based on ICD-codes
  • ex_atc - Example data for random ATC codes
  • ex_icd10 - Example data for random codes assigned to random people
  • ex_people - Example data for random people
  • hip_ae - Classcodes for adverse events after knee and hip arthroplasty
  • hip_ae_hailer - Classcodes for infection and dislocation after hip arthroplasty
  • knee_ae - Classcodes for adverse events after knee and hip arthroplasty
  • rxriskv - Classcodes for RxRisk V based on ATC codes

On CRAN:

classificationicd-10

12 exports 22 stars 2.19 score 14 dependencies 263 downloads

Last updated 1 years agofrom:957d87186c11f55b6df0406684bc787b86b74d39 (via master)

Exports:%>%all_classcodesas.classcodescategorizeclassifycodebookcodebookscodifyindexis.classcodesset_classcodesvisualize

Dependencies:clidata.tabledecoderfansigenericsgluelifecyclemagrittrpillarpkgconfigrlangtibbleutf8vctrs

Classcodes

Rendered fromclasscodes.Rmdusingknitr::rmarkdownon Jun 06 2024.

Last update: 2020-11-19
Started: 2020-04-22

coder

Rendered fromcoder.Rmdusingknitr::rmarkdownon Jun 06 2024.

Last update: 2021-01-12
Started: 2018-10-04

Example data

Rendered fromex_data.Rmdusingknitr::rmarkdownon Jun 06 2024.

Last update: 2020-11-20
Started: 2020-11-19

Interpret regular expressions

Rendered fromInterpret_regular_expressions.Rmdusingknitr::rmarkdownon Jun 06 2024.

Last update: 2020-11-19
Started: 2020-11-19

Readme and manuals

Help Manual

Help pageTopics
Classcodes for adverse events after knee and hip arthroplastyae hip_ae knee_ae
Summary data for all default classcodes object in the packageall_classcodes
Convert output from classify() to matrix/data.frame/data.tableas.data.frame.classified as.data.table.classified as.matrix.classified
Make keyvalue object from classcodes objectas.keyvalue.classcodes
Categorize cases based on external data and classification schemecategorize categorize.codified categorize.data.frame categorize.data.table categorize.tbl_df
Classcodes for Charlson comorbidity based on ICD-codescharlson
Classcodes methodsas.classcodes as.classcodes.classcodes as.classcodes.data.frame classcodes is.classcodes
Classify codified dataclassify classify.codified classify.data.frame classify.data.table classify.default
codebook(s) for classcodes objectcodebook codebooks print.codebook
Codify case data with external code data (within specified time frames)codify codify.data.frame codify.data.table print.codified
Classcodes for the comorbidity-polypharmacy score (CPS) based on ICD-10 codescps
Classcodes for Elixhauser based on ICD-codeselixhauser
Example data for random ATC codesex_atc
Example data for random codes assigned to random peopleex_icd10
Example data for random peopleex_people
Classcodes for infection and dislocation after hip arthroplastyhip_ae_hailer
Calculate index based on classification schemeindex index.data.frame index.matrix index_fun
Print classcodes objectprint.classcodes
Printing classified dataprint.classified
Classcodes for RxRisk V based on ATC codesrxriskv
Set classcodes objectset_classcodes
Summarizing a classcodes objectprint.summary.classcodes summary.classcodes
Visualize classification scheme in web browservisualize.classcodes