medicalrisk: Medical Risk and Comorbidity Tools for ICD-9-CM Data

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Generates risk estimates and comorbidity flags from ICD-9-CM codes available in administrative medical datasets. The package supports the Charlson Comorbidity Index, the Elixhauser Comorbidity classification, the Revised Cardiac Risk Index, and the Risk Stratification Index. Methods are table-based, fast, and use the 'plyr' package, so parallelization is possible for large jobs. Also includes a sample of real ICD-9 data for 100 patients from a publicly available dataset.

Author
Patrick McCormick [aut, cre], Thomas Joseph [aut]
Date of publication
2016-01-24 15:45:31
Maintainer
Patrick McCormick <patrick.mccormick@alum.mit.edu>
License
GPL-3 | file LICENSE
Version
1.2
URLs

View on CRAN

Man pages

charlson_list
List of Charlson comorbidities
charlson_weights
Map of Charlson comorbidity categories to revised weights
charlson_weights_orig
Map of Charlson comorbidity categories to weights
elixhauser_list
List of Elixhauser comorbidities
generate_charlson_index_df
Calculate the Charlson Comorbidity Index
generate_comorbidity_df
Generate a comorbidity dataframe
icd9cm_charlson_deyo
Create Deyo map of ICD-9-CM to Charlson comorbidities
icd9cm_charlson_quan
Create Quan map of ICD-9-CM to Charlson comorbidities
icd9cm_charlson_romano
Create Romano map of ICD-9-CM to Charlson comorbidities
icd9cm_elixhauser_ahrq37
Create AHRQ v3.7 map of ICD-9-CM to Elixhauser comorbidities
icd9cm_elixhauser_quan
Create Quan map of ICD-9-CM to Elixhauser comorbidities
icd9cm_list
List of ICD-9-CM diagnostic and procedural codes
icd9cm_rcri
Create Map of ICD-9-CM to Revised Cardiac Risk Index classes
icd9cm_sessler_rsi
Returns composite Sessler risk stratification index, given a...
melt_icd9list
Convert ICD-9-CM code list to dataframe
merge_icd9_dx_and_procs
Merge ICD-9-CM diagnostic and procedure codes
rsi_beta_1yrpod
Values for calculating RSI for 1 year mortality
rsi_beta_30dlos
Values for calculating RSI for 30-day length of stay
rsi_beta_30dpod
Values for calculating RSI for 30-day mortality
rsi_beta_inhosp
Values for calculating RSI for in-hospital mortality.
rsi_sample_data
Sample data for validating RSI
rsi_sample_results
Sample results for validating RSI
sessler_get_single_beta
Returns the covariate coefficient for a particular diagnosis...
verify_sessler_rsi
Validates this Sessler RSI implementation against reference...
vt_inp_sample
First 100 patients and their ICD-9-CM codes from the Vermont...

Files in this package

medicalrisk
medicalrisk/inst
medicalrisk/inst/tests
medicalrisk/inst/tests/test-melt_icd9list.R
medicalrisk/inst/sql
medicalrisk/inst/sql/sql_example.sql
medicalrisk/inst/doc
medicalrisk/inst/doc/advanced.Rmd
medicalrisk/inst/doc/medicalrisk.Rmd
medicalrisk/inst/doc/advanced.R
medicalrisk/inst/doc/medicalrisk.R
medicalrisk/inst/doc/advanced.html
medicalrisk/inst/doc/medicalrisk.html
medicalrisk/tests
medicalrisk/tests/test-all.R
medicalrisk/NAMESPACE
medicalrisk/NEWS
medicalrisk/data
medicalrisk/data/elixhauser_list.rda
medicalrisk/data/rsi_beta_inhosp.rda
medicalrisk/data/rsi_beta_1yrpod.rda
medicalrisk/data/charlson_weights_orig.rda
medicalrisk/data/rsi_beta_30dpod.rda
medicalrisk/data/icd9cm_list.rda
medicalrisk/data/rsi_sample_data.rda
medicalrisk/data/charlson_weights.rda
medicalrisk/data/rsi_beta_30dlos.rda
medicalrisk/data/rsi_sample_results.rda
medicalrisk/data/vt_inp_sample.rda
medicalrisk/data/charlson_list.rda
medicalrisk/R
medicalrisk/R/data.R
medicalrisk/R/icd9cm.R
medicalrisk/R/calculate-rsi.R
medicalrisk/vignettes
medicalrisk/vignettes/advanced.Rmd
medicalrisk/vignettes/medicalrisk.Rmd
medicalrisk/vignettes/medicalrisk.bib
medicalrisk/README.md
medicalrisk/MD5
medicalrisk/build
medicalrisk/build/vignette.rds
medicalrisk/DESCRIPTION
medicalrisk/man
medicalrisk/man/charlson_weights.Rd
medicalrisk/man/melt_icd9list.Rd
medicalrisk/man/icd9cm_rcri.Rd
medicalrisk/man/icd9cm_sessler_rsi.Rd
medicalrisk/man/rsi_beta_30dpod.Rd
medicalrisk/man/icd9cm_elixhauser_quan.Rd
medicalrisk/man/icd9cm_elixhauser_ahrq37.Rd
medicalrisk/man/merge_icd9_dx_and_procs.Rd
medicalrisk/man/icd9cm_list.Rd
medicalrisk/man/vt_inp_sample.Rd
medicalrisk/man/generate_charlson_index_df.Rd
medicalrisk/man/icd9cm_charlson_quan.Rd
medicalrisk/man/generate_comorbidity_df.Rd
medicalrisk/man/rsi_sample_data.Rd
medicalrisk/man/verify_sessler_rsi.Rd
medicalrisk/man/rsi_beta_30dlos.Rd
medicalrisk/man/sessler_get_single_beta.Rd
medicalrisk/man/charlson_list.Rd
medicalrisk/man/rsi_sample_results.Rd
medicalrisk/man/rsi_beta_1yrpod.Rd
medicalrisk/man/charlson_weights_orig.Rd
medicalrisk/man/icd9cm_charlson_deyo.Rd
medicalrisk/man/icd9cm_charlson_romano.Rd
medicalrisk/man/elixhauser_list.Rd
medicalrisk/man/rsi_beta_inhosp.Rd
medicalrisk/LICENSE