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

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.

AuthorPatrick McCormick [aut, cre], Thomas Joseph [aut]
Date of publication2016-01-24 15:45:31
MaintainerPatrick McCormick <patrick.mccormick@alum.mit.edu>
LicenseGPL-3 | file LICENSE
Version1.2
https://github.com/patrickmdnet/medicalrisk

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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