Function reference • icd: Comorbidities and tools for ICD codes

Package overview
`icd-package`	icd: Comorbidity Calculations and Tools for ICD-9 and ICD-10 Codes
Comorbidity and risk score calculations
`comorbid()` `icd10_comorbid()` `icd9_comorbid()` `icd9_comorbid_ahrq()` `icd10_comorbid_ahrq()` `icd9_comorbid_elix()` `icd10_comorbid_elix()` `icd9_comorbid_quan_elix()` `icd10_comorbid_quan_elix()` `icd9_comorbid_quan_deyo()` `icd10_comorbid_quan_deyo()` `icd9_comorbid_charlson()` `icd10_comorbid_charlson()` `comorbid_ccs()` `icd9_comorbid_ccs()` `icd10_comorbid_ccs()` `comorbid_ahrq()` `comorbid_elix()` `comorbid_quan_elix()` `comorbid_quan_deyo()` `comorbid_charlson()` `comorbid_pccc_dx()` `comorbid_pccc_pcs()` `icd9_comorbid_pccc_dx()` `icd10_comorbid_pccc_dx()` `icd9_comorbid_pccc_pcs()` `icd10_comorbid_pccc_pcs()`	Find comorbidities from ICD-9 codes.
`comorbid_hcc()` `icd9_comorbid_hcc()` `icd10_comorbid_hcc()`	Get Hierarchical Condition Codes (HCC)
`charlson()`	Calculate Charlson Comorbidity Index (Charlson Score)
`charlson_from_comorbid()`	Calculate Charlson scores from precomputed Charlson comorbidities
`van_walraven()` `van_walraven_from_comorbid()`	Calculate van Walraven Elixhauser Score
`count_codes()`	Count ICD codes or comorbidities for each patient
`count_codes_wide()`	Count ICD codes given in wide format
`count_comorbid()`	Count number of comorbidities per patient
Comorbidity to ICD code maps
`icd9_map_ahrq`	AHRQ comorbidities
`icd9_map_elix`	Elixhauser comorbidities
`icd9_map_hcc`	Medicare Hierarchical Condition Categories
`icd9_map_pccc`	Pediatric Complex Chronic Conditions
`icd9_map_quan_deyo`	Quan adaptation of Deyo/Charlson comorbidities
`icd9_map_quan_elix`	Quan adaptation of Elixhauser comorbidities
`icd9_map_single_ccs`	Clinical Classifications Software (CCS) for ICD9/10-CM
`icd10_map_ahrq_pcs`	AHRQ ICD-10-PCS categories
`names_elix`	Comorbidity names
Transforming data Reshaping of typical healthcare data frames containing one or more ICD code columns. Convert comorbidity results between matrices and ‘tidy’ data frmes.
`comorbid_df_to_mat()`	convert comorbidity matrix to data frame
`comorbid_mat_to_df()`	convert comorbidity data frame from matrix
`long_to_wide()`	Convert ICD data from long to wide format
`wide_to_long()`	Convert ICD data from wide to long format
`convert`	Convert ICD data between formats and structures.
Metadata Optionally describe and check the type and structure of your data. This enables functions like ‘`is_valid`’ and ‘`explain_code`’ to look up codes in the appropriate version of ICD-9 or ICD-10.
`as.icd9()` `as.icd9cm()` `as.icd9cm_pc()` `as.icd10()` `as.icd10cm()` `as.icd10cm_pc()` `as.icd10who()` `as.icd10fr()` `as.icd10be()`	Construct ICD-9 and ICD-10 data types
`as.icd_long_data()` `as.icd_wide_data()` `icd_long_data()` `icd_wide_data()`	Set the ICD data structure class of a `matrix` or `data.frame`.
`as.decimal_diag()` `as.icd_decimal_diag()` `as.short_diag()` `as.icd_short_diag()` `is.decimal_diag()` `is.icd_decimal_diag()` `is.short_diag()` `is.icd_short_diag()`	Get or set whether ICD codes have have an attribute indicating 'short' or 'decimal' format
`as.comorbidity_map()`	Set the class of a named list to show it is a comorbidity map.
`is.icd9()` `is.icd9cm()` `is.icd9cm_pc()` `is.icd9who()` `is.icd10()` `is.icd10cm()` `is.icd10cm_pc()` `is.icd10who()` `is.icd10fr()` `is.icd10be()` `is.comorbidity_map()`	Test presence of ICD classes
`is.icd_long_data()` `is.icd_wide_data()`	Test for class describing patient data
`icd9_chapters`	ICD-9 chapters
`icd9_sub_chapters`	ICD-9 sub-chapters
`icd10_chapters`	ICD-10 chapters
`icd10_sub_chapters`	ICD-10 sub-chapters
`is_billable()`	Check whether a code is billable according to ICD-9-CM or ICD-10-CM
`get_billable()`	Get the subset of codes that are billable according to ICD-9-CM or ICD-10-CM
Manipulation Working with codes and the ICD hierarchies
`children()`	Get children of ICD codes
`condense()` `icd9_condense_decimal()`	Condense ICD-9 code by replacing complete families with parent codes
`c(<icd9>)` `c(<icd10>)`	Combine ICD codes
`diff_comorbid()`	show the difference between two comorbidity mappings
`filter_poa()` `filter_poa_yes()` `filter_poa_no()` `filter_poa_not_no()` `filter_poa_not_yes()`	Filters data frame based on present-on-arrival flag
`filter_valid()` `filter_invalid()` `icd9_filter_valid()` `icd10_filter_valid()` `icd9_filter_invalid()` `icd10_filter_invalid()`	Filter ICD codes by validity.
`get_defined()`	Select only defined ICD codes
`[`(<icd9>) `[[`(<icd9>) `[`(<icd10>) `[[`(<icd10>)	extract subset(s) from ICD data
`icd9_map_ahrq`	AHRQ comorbidities
International and historic ICD editions
`set_icd_data_dir()` `get_icd_data_dir()`	Set up the data download cache, give permission to download data
`download_all_icd_data()`	Download all the additional data at once
`set_icd10cm_active_year()` `get_icd10cm_active_year()`	Get or set the annual version of ICD-10-CM to use
`get_icd10cm_version()` `get_icd10cm_active()`	Get the data for a given version (four-digit year) of ICD-10-CM
`get_icd10cm_available()`	Get the ICD-10-CM versions available in this package
`get_icd10cm_latest()` `get_icd10cm_latest()`	The latest available version of ICD-10-CM in this package
ICD data included in the package
`icd9cm2014_leaf`	The final ICD-9-CM list of leaf (‘billable’) codes
`icd10cm2019`	United States and Belgium ICD-10-CM
`vermont_dx`	Hospital discharge data from Vermont
`uranium_pathology`	United States Transuranium & Uranium Registries
Get ICD data This is needed for explaining codes, and checking validity. The package includes data for the most recent ICD-9-CM and ICD-10-CM. Some editions, like WHO, cannot be distributed in the package due to copyright. Others are also available for download on demand, or in bulk using `download_all_icd_data()`.
`with_icd10cm_version()`	Evaluate code with a particular version of ICD-10-CM
`get_icd10be2014`	Belgian ICD-10-BE
`get_icd10be2014_pc`	ICD-10-BE 2014 procedure codes
`get_icd10be2017`	ICD-10-BE 2017
`get_icd10be2017_pc`	ICD-10-BE 2017 procedure codes
`get_icd10cm2014`	ICD-10-CM 2014
`get_icd10cm2014_pc`	ICD-10-CM Procedure codes for 2014
`get_icd10cm2015`	ICD-10-CM 2015
`get_icd10cm2015_pc`	ICD-10-CM Procedure codes for 2015
`get_icd10cm2016`	ICD-10-CM 2016
`get_icd10cm2016_pc`	ICD-10-CM Procedure codes for 2016
`get_icd10cm2017`	ICD-10-CM 2017
`get_icd10cm2017_pc`	ICD-10-CM Procedure codes for 2017
`get_icd10cm2018`	ICD-10-CM 2018
`get_icd10cm2018_pc`	ICD-10-CM Procedure codes for 2018
`get_icd10cm2019`	ICD-10-CM 2019
`get_icd10cm2019_pc`	ICD-10-CM Procedure Codes
`get_icd10fr2019`	French ICD-10-FR modification of WHO ICD-10 used in France
`get_cim10fr2019()`	Localised synonym for `get_icd10fr2019`, with French column names
`get_icd10who2008fr`	2008 WHO ICD-10 data in French
`get_icd10who2016`	2016 WHO ICD-10 data
`icd9cm_hierarchy`	ICD-9-CM diagnosis codes including leaf nodes and branch names up to the three-digit codes.
`get_icd9cm2014_leaf`	ICD-9-CM, just billable/leaf codes
Other
`sort_icd()` `sort(<icd10>)` `sort(<icd10cm>)` `sort(<icd10be>)` `sort(<icd9>)` `order.icd9()` `order.icd10cm()` `order.icd10be()`	Sort or order ICD-9 or ICD-10 codes according to published sequence
`plot_comorbid()` `plot_comorbid_results()`	Basic ordered bar plot showing counts of each comorbidity
`poa_choices`	Present-on-admission flags
`print(<icd9>)` `print(<icd10>)`	Print ICD codes and comorbidity maps cleanly

Reference

Package overview

Comorbidity and risk score calculations

Comorbidity to ICD code maps

Transforming data

Metadata

Manipulation

International and historic ICD editions

ICD data included in the package

Get ICD data

Other