# Comorbidity Calculations and Tools for ICD-9 and ICD-10 Codes

## Documentation for package ‘icd’ version 3.3

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A C D F G I L N P S U V W misc

icd-package | icd: Comorbidity Calculations and Tools for ICD-9 and ICD-10 Codes
icd10-package | icd: Comorbidity Calculations and Tools for ICD-9 and ICD-10 Codes
icd9-package | icd: Comorbidity Calculations and Tools for ICD-9 and ICD-10 Codes

## -- A --

ahrq | AHRQ comorbidities
as.decimal_diag | Get or set whether ICD codes have have an attribute indicating 'short' or 'decimal' format
as.icd_decimal_diag | Get or set whether ICD codes have have an attribute indicating 'short' or 'decimal' format
as.icd_long_data | Convert between and identify 'long' and 'wide' patient data formats
as.icd_short_diag | Get or set whether ICD codes have have an attribute indicating 'short' or 'decimal' format
as.icd_wide_data | Convert between and identify 'long' and 'wide' patient data formats
as.short_diag | Get or set whether ICD codes have have an attribute indicating 'short' or 'decimal' format

## -- C --

c.icd10 | combine ICD codes
c.icd9 | combine ICD codes
categorize_simple | Categorize codes according to a mapping
charlson | Calculate Charlson Comorbidity Index (Charlson Score)
charlson.data.frame | Calculate Charlson Comorbidity Index (Charlson Score)
charlson_from_comorbid | Calculate Charlson scores from precomputed Charlson comorbidities
children | Get children of ICD codes
children.character | Get children of ICD codes
children.icd10 | Get children of ICD codes
children.icd10cm | Get children of ICD codes
children.icd9 | Get children of ICD codes
children.icd9cm | Get children of ICD codes
combine | combine ICD codes
comorbid | Find comorbidities from ICD-9 codes.
comorbid_ahrq | Find comorbidities from ICD-9 codes.
comorbid_ccs | Find comorbidities from ICD-9 codes.
comorbid_charlson | Find comorbidities from ICD-9 codes.
comorbid_df_to_mat | convert comorbidity matrix to data frame
comorbid_elix | Find comorbidities from ICD-9 codes.
comorbid_hcc | Get Hierarchical Condition Codes (HCC)
comorbid_mat_to_df | convert comorbidity data frame from matrix
comorbid_pccc_dx | Calculate pediatric complex chronic conditions (PCCC) comorbidities
comorbid_pccc_pcs | Calculate pediatric complex chronic conditions (PCCC) comorbidities
comorbid_quan_deyo | Find comorbidities from ICD-9 codes.
comorbid_quan_elix | Find comorbidities from ICD-9 codes.
convert | Convert ICD9 codes between formats and structures.
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

## -- D --

diff_comorbid | show the difference between two comorbidity mappings
diff_comorbid.list | show the difference between two comorbidity mappings

## -- F --

filter_invalid | Filter ICD codes by validity.
filter_poa | Filters data frame based on present-on-arrival flag
filter_poa_no | Filters data frame based on present-on-arrival flag
filter_poa_not_no | Filters data frame based on present-on-arrival flag
filter_poa_not_yes | Filters data frame based on present-on-arrival flag
filter_poa_yes | Filters data frame based on present-on-arrival flag
filter_valid | Filter ICD codes by validity.

## -- G --

get_defined | Select only defined ICD codes

## -- I --

icd | icd: Comorbidity Calculations and Tools for ICD-9 and ICD-10 Codes
icd10cm2016 | ICD-10-CM
icd10_chapters | ICD-10 chapters
icd10_comorbid | Find comorbidities from ICD-9 codes.
icd10_comorbid_ahrq | Find comorbidities from ICD-9 codes.
icd10_comorbid_ccs | Find comorbidities from ICD-9 codes.
icd10_comorbid_charlson | Find comorbidities from ICD-9 codes.
icd10_comorbid_elix | Find comorbidities from ICD-9 codes.
icd10_comorbid_hcc | Get Hierarchical Condition Codes (HCC)
icd10_comorbid_pccc_dx | Calculate pediatric complex chronic conditions (PCCC) comorbidities
icd10_comorbid_pccc_pcs | Calculate pediatric complex chronic conditions (PCCC) comorbidities
icd10_comorbid_quan_deyo | Find comorbidities from ICD-9 codes.
icd10_comorbid_quan_elix | Find comorbidities from ICD-9 codes.
icd10_filter_invalid | Filter ICD codes by validity.
icd10_filter_valid | Filter ICD codes by validity.
icd10_map_ahrq | AHRQ comorbidities
icd10_map_ahrq_pcs | AHRQ ICD-10-PCS categories
icd10_map_cc | Medicare Hierarchical Condition Categories
icd10_map_ccs | Clinical Classifications Software (CCS) for ICD9/10-CM
icd10_map_charlson | Quan adaptation of Deyo/Charlson comorbidities
icd10_map_elix | Elixhauser comorbidities
icd10_map_pccc_dx | Pediatric Complex Chronic Conditions
icd10_map_pccc_pcs | Pediatric Complex Chronic Conditions
icd10_map_quan_deyo | Quan adaptation of Deyo/Charlson comorbidities
icd10_map_quan_elix | Quan adaptation of Elixhauser comorbidities
icd10_pcs | ICD-10-CM Procedure Codes
icd10_sub_chapters | ICD-10 sub-chapters
icd9Billable | list of annual versions of billable leaf nodes of ICD-9-CM
icd9cm_billable | list of annual versions of billable leaf nodes of ICD-9-CM
icd9cm_hierarchy | Latest ICD-9-CM diagnosis codes, in flat 'data.frame' format
icd9_chapters | ICD-9 chapters
icd9_comorbid | Find comorbidities from ICD-9 codes.
icd9_comorbid_ahrq | Find comorbidities from ICD-9 codes.
icd9_comorbid_ccs | Find comorbidities from ICD-9 codes.
icd9_comorbid_charlson | Find comorbidities from ICD-9 codes.
icd9_comorbid_elix | Find comorbidities from ICD-9 codes.
icd9_comorbid_hcc | Get Hierarchical Condition Codes (HCC)
icd9_comorbid_pccc_dx | Calculate pediatric complex chronic conditions (PCCC) comorbidities
icd9_comorbid_pccc_pcs | Calculate pediatric complex chronic conditions (PCCC) comorbidities
icd9_comorbid_quan_deyo | Find comorbidities from ICD-9 codes.
icd9_comorbid_quan_elix | Find comorbidities from ICD-9 codes.
icd9_filter_invalid | Filter ICD codes by validity.
icd9_filter_valid | Filter ICD codes by validity.
icd9_majors | ICD-9 chapters
icd9_map_ahrq | AHRQ comorbidities
icd9_map_cc | Medicare Hierarchical Condition Categories
icd9_map_charlson | Quan adaptation of Deyo/Charlson comorbidities
icd9_map_elix | Elixhauser comorbidities
icd9_map_hcc | Medicare Hierarchical Condition Categories
icd9_map_multi_ccs | Clinical Classifications Software (CCS) for ICD9/10-CM
icd9_map_pccc | Pediatric Complex Chronic Conditions
icd9_map_pccc_dx | Pediatric Complex Chronic Conditions
icd9_map_pccc_pcs | 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
icd9_sub_chapters | ICD-9 chapters
icd_charlson | Calculate Charlson Comorbidity Index (Charlson Score)
icd_charlson.data.frame | Calculate Charlson Comorbidity Index (Charlson Score)
icd_charlson_from_comorbid | Calculate Charlson scores from precomputed Charlson comorbidities
icd_children | Get children of ICD codes
icd_children.character | Get children of ICD codes
icd_children.icd10 | Get children of ICD codes
icd_children.icd10cm | Get children of ICD codes
icd_children.icd9 | Get children of ICD codes
icd_children_defined | Get children of ICD codes
icd_children_defined.icd10cm | Get children of ICD codes
icd_comorbid | Find comorbidities from ICD-9 codes.
icd_comorbid_ahrq | Find comorbidities from ICD-9 codes.
icd_comorbid_df_to_mat | convert comorbidity matrix to data frame
icd_comorbid_elix | Find comorbidities from ICD-9 codes.
icd_comorbid_hcc | Find comorbidities from ICD-9 codes.
icd_comorbid_mat_to_df | convert comorbidity matrix to data frame
icd_comorbid_quan_deyo | Find comorbidities from ICD-9 codes.
icd_comorbid_quan_elix | Find comorbidities from ICD-9 codes.
icd_count_codes | Count ICD codes or comorbidities for each patient
icd_count_codes_wide | Count ICD codes given in wide format
icd_count_comorbid | Count ICD codes or comorbidities for each patient
icd_diff_comorbid | show the difference between two comorbidity mappings
icd_diff_comorbid.list | show the difference between two comorbidity mappings
icd_filter_invalid | Filter ICD codes by validity.
icd_filter_poa | Filters data frame based on present-on-arrival flag
icd_filter_poa_no | Filters data frame based on present-on-arrival flag
icd_filter_poa_not_no | Filters data frame based on present-on-arrival flag
icd_filter_poa_not_yes | Filters data frame based on present-on-arrival flag
icd_filter_poa_yes | Filters data frame based on present-on-arrival flag
icd_filter_valid | Filter ICD codes by validity.
icd_get_defined | Select only defined ICD codes
icd_get_defined.icd9 | Select only defined ICD codes
icd_long_data | Convert between and identify 'long' and 'wide' patient data formats
icd_long_to_wide | Convert ICD data from long to wide format
icd_map_cc_hcc | Medicare Hierarchical Condition Categories
icd_names_ahrq | Comorbidity names
icd_names_ahrq_abbrev | Comorbidity names
icd_names_ahrq_htn | Comorbidity names
icd_names_ahrq_htn_abbrev | Comorbidity names
icd_names_cc | Comorbidity names
icd_names_charlson | Comorbidity names
icd_names_charlson_abbrev | Comorbidity names
icd_names_elix | Comorbidity names
icd_names_elix_abbrev | Comorbidity names
icd_names_elix_htn | Comorbidity names
icd_names_elix_htn_abbrev | Comorbidity names
icd_names_quan_elix | Comorbidity names
icd_names_quan_elix_abbrev | Comorbidity names
icd_names_quan_elix_htn | Comorbidity names
icd_names_quan_elix_htn_abbrev | Comorbidity names
icd_poa_choices | Present-on-admission flags
icd_van_walraven | Calculate van Walraven Elixhauser Score
icd_van_walraven.data.frame | Calculate van Walraven Elixhauser Score
icd_van_walraven_from_comorbid | Calculate van Walraven Elixhauser Score
icd_wide_data | Convert between and identify 'long' and 'wide' patient data formats
icd_wide_to_long | Convert ICD data from wide to long format
is.comorbidity_map | test ICD-related classes
is.decimal_diag | Get or set whether ICD codes have have an attribute indicating 'short' or 'decimal' format
is.icd10 | test ICD-related classes
is.icd10cm | test ICD-related classes
is.icd9 | test ICD-related classes
is.icd9cm | test ICD-related classes
is.icd_comorbidity_map | test ICD-related classes
is.icd_decimal_diag | Get or set whether ICD codes have have an attribute indicating 'short' or 'decimal' format
is.icd_long_data | Convert between and identify 'long' and 'wide' patient data formats
is.icd_short_diag | Get or set whether ICD codes have have an attribute indicating 'short' or 'decimal' format
is.icd_wide_data | Convert between and identify 'long' and 'wide' patient data formats
is.short_diag | Get or set whether ICD codes have have an attribute indicating 'short' or 'decimal' format

## -- L --

long_to_wide | Convert ICD data from long to wide format

## -- N --

names_ahrq | Comorbidity names
names_ahrq_abbrev | Comorbidity names
names_ahrq_htn | Comorbidity names
names_ahrq_htn_abbrev | Comorbidity names
names_cc | Comorbidity names
names_charlson | Comorbidity names
names_charlson_abbrev | Comorbidity names
names_elix | Comorbidity names
names_elix_abbrev | Comorbidity names
names_elix_htn | Comorbidity names
names_elix_htn_abbrev | Comorbidity names
names_quan_elix | Comorbidity names
names_quan_elix_abbrev | Comorbidity names
names_quan_elix_htn | Comorbidity names
names_quan_elix_htn_abbrev | Comorbidity names

## -- P --

package-icd | icd: Comorbidity Calculations and Tools for ICD-9 and ICD-10 Codes
package-icd10 | icd: Comorbidity Calculations and Tools for ICD-9 and ICD-10 Codes
package-icd9 | icd: Comorbidity Calculations and Tools for ICD-9 and ICD-10 Codes
poa_choices | Present-on-admission flags
print.comorbidity_map | Print a comorbidity map

## -- S --

subset_icd | extract subset from ICD data

## -- U --

unzip_single | unzip a single file from URL
uranium_pathology | United States Transuranium & Uranium Registries

## -- V --

van_walraven | Calculate van Walraven Elixhauser Score
van_walraven.data.frame | Calculate van Walraven Elixhauser Score
van_walraven_from_comorbid | Calculate van Walraven Elixhauser Score
vermont_dx | Hospital discharge data from Vermont

## -- W --

wide_to_long | Convert ICD data from wide to long format

## -- misc --

[.icd10 | extract subset from ICD data
[.icd9 | extract subset from ICD data
[[.comorbidity_map | Extract vector of codes from an ICD comorbidity map
[[.icd10 | extract subset from ICD data
[[.icd9 | extract subset from ICD data
_PACKAGE | icd: Comorbidity Calculations and Tools for ICD-9 and ICD-10 Codes