Showing 43 of total 43 results (show query)
oxfordihtm
codigo:Interface to the International Classification of Diseases (ICD) API
The International Classification of Diseases (ICD) serves a broad range of uses globally and provides critical knowledge on the extent, causes and consequences of human disease and death worldwide via data that is reported and coded with the ICD. ICD API allows programmatic access to the ICD. It is an HTTP based REST API. This package provides functions that interface with the ICD API.
Maintained by Ernest Guevarra. Last updated 5 months ago.
72.4 match 4 stars 3.68 score 6 scripts 1 dependents
edonnachie
ICD10gm:Metadata Processing for the German Modification of the ICD-10 Coding System
Provides convenient access to the German modification of the International Classification of Diagnoses, 10th revision (ICD-10-GM). It provides functionality to aid in the identification, specification and historisation of ICD-10 codes. Its intended use is the analysis of routinely collected data in the context of epidemiology, medical research and health services research. The underlying metadata are released by the German Institute for Medical Documentation and Information <https://www.dimdi.de>, and are redistributed in accordance with their license.
Maintained by Ewan Donnachie. Last updated 1 years ago.
bfarmcharlsoncomorbiditiesdiagnosesdimdiicd-10metadataroutinedatenversorgungsforschung
49.9 match 10 stars 5.30 score 20 scriptsoxfordihtm
codeditr:Implementing Cause-of-Death Data Checks Based on the WHO CoDEdit Tool
The World Health Organization's CoDEdit electronic tool is intended to help producers of cause-of-death statistics in strengthening their capacity to perform routine checks on their data. This package ports the original tool built using Microsoft Access into R so as to leverage the utility and function of the original tool into a usable application program interface that can be used for building more universal tools or for creating programmatic scientific workflows aimed at routine, automated, and large-scale monitoring of cause-of-death data.
Maintained by Ernest Guevarra. Last updated 4 months ago.
54.7 match 3 stars 4.65 score 6 scripts
ellessenne
comorbidity:Computing Comorbidity Scores
Computing comorbidity indices and scores such as the weighted Charlson score (Charlson, 1987 <doi:10.1016/0021-9681(87)90171-8>) and the Elixhauser comorbidity score (Elixhauser, 1998 <doi:10.1097/00005650-199801000-00004>) using ICD-9-CM or ICD-10 codes (Quan, 2005 <doi:10.1097/01.mlr.0000182534.19832.83>). Australian and Swedish modifications of the Charlson Comorbidity Index are available as well (Sundararajan, 2004 <doi:10.1016/j.jclinepi.2004.03.012> and Ludvigsson, 2021 <doi:10.2147/CLEP.S282475>), together with different weighting algorithms for both the Charlson and Elixhauser comorbidity scores.
Maintained by Alessandro Gasparini. Last updated 8 months ago.
25.9 match 83 stars 9.36 score 98 scripts
hanjunwei-lab
ICDS:Identification of Cancer Dysfunctional Subpathway with Omics Data
Identify Cancer Dysfunctional Sub-pathway by integrating gene expression, DNA methylation and copy number variation, and pathway topological information. 1)We firstly calculate the gene risk scores by integrating three kinds of data: DNA methylation, copy number variation, and gene expression. 2)Secondly, we perform a greedy search algorithm to identify the key dysfunctional sub-pathways within the pathways for which the discriminative scores were locally maximal. 3)Finally, the permutation test was used to calculate statistical significance level for these key dysfunctional sub-pathways.
Maintained by Junwei Han. Last updated 8 months ago.
50.0 match 3.54 score 3 scripts
eribul
decoder:Decode Coded Variables to Plain Text and the Other Way Around
Main function "decode" is used to decode coded key values to plain text. Function "code" can be used to code plain text to code if there is a 1:1 relation between the two. The concept relies on 'keyvalue' objects used for translation. There are several 'keyvalue' objects included in the areas of geographical regional codes, administrative health care unit codes, diagnosis codes and more. It is also easy to extend the use by arbitrary code sets.
Maintained by Erik Bulow. Last updated 5 years ago.
38.8 match 3.98 score 16 scripts 1 dependents
cran
icd.data:International Classifcation of Diseases (ICD) Data
Data from the United States Center for Medicare and Medicaid Services (CMS) is included in this package. There are ICD-9 and ICD-10 diagnostic and procedure codes, and lists of the chapter and sub-chapter headings and the ranges of ICD codes they encompass. There are also two sample datasets. These data are used by the 'icd' package for finding comorbidities.
Maintained by Jack O. Wasey. Last updated 7 years ago.
85.2 match 1.70 score
kenhanscombe
ukbtools:Manipulate and Explore UK Biobank Data
A set of tools to create a UK Biobank <http://www.ukbiobank.ac.uk/> dataset from a UKB fileset (.tab, .r, .html), visualize primary demographic data for a sample subset, query ICD diagnoses, retrieve genetic metadata, read and write standard file formats for genetic analyses.
Maintained by Ken Hanscombe. Last updated 2 years ago.
20.9 match 101 stars 6.78 score 118 scripts
bioc
gpuMagic:An openCL compiler with the capacity to compile R functions and run the code on GPU
The package aims to help users write openCL code with little or no effort. It is able to compile an user-defined R function and run it on a device such as a CPU or a GPU. The user can also write and run their openCL code directly by calling .kernel function.
Maintained by Jiefei Wang. Last updated 5 months ago.
22.5 match 10 stars 5.60 score 1 scripts
wenjie2wang
touch:Tools of Utilization and Cost in Healthcare
R implementation of the software tools developed in the H-CUP (Healthcare Cost and Utilization Project) <https://www.hcup-us.ahrq.gov> and AHRQ (Agency for Healthcare Research and Quality) <https://www.ahrq.gov>. It currently contains functions for mapping ICD-9 codes to the AHRQ comorbidity measures and translating ICD-9 (resp. ICD-10) codes to ICD-10 (resp. ICD-9) codes based on GEM (General Equivalence Mappings) from CMS (Centers for Medicare and Medicaid Services).
Maintained by Wenjie Wang. Last updated 3 years ago.
ahrqcomorbiditycrosswalkhealthcareicd-10icd-9cpp
22.3 match 13 stars 4.58 score 29 scripts
cud2v
pccc:Pediatric Complex Chronic Conditions
An implementation of the pediatric complex chronic conditions (CCC) classification system using R and C++.
Maintained by Seth Russell. Last updated 5 months ago.
17.1 match 5 stars 5.93 score 38 scripts
celehs
phecodemap:Visualization for Phecode Mapping with ICD-9 and ICD-10-cm Codes
Phecodemap builds a shiny app to visualize the hierarchy of Phecode Mapping with ICD. The same Phecode hierarchy is displayed in two ways: as a sunburst plot and as a tree.
Maintained by Parse Health. Last updated 1 years ago.
12.9 match 3 stars 5.07 score 13 scripts
rmgpanw
trud:Query the 'NHS TRUD API'
A convenient R interface to the 'National Health Service (NHS) Technology Reference Update Distribution (TRUD) API'. Retrieve available releases for items that you are subscribed to and download these with ease. For more information on the API, see <https://isd.digital.nhs.uk/trud/users/guest/filters/0/api>.
Maintained by Alasdair Warwick. Last updated 6 months ago.
11.0 match 3 stars 4.61 score 3 scripts
dajuntian
InjurySeverityScore:Translate ICD-9 into Injury Severity Score
Calculate the injury severity score (ISS) based on the dictionary in 'ICDPIC' from <https://ideas.repec.org/c/boc/bocode/s457028.html>. The original code was written in 'STATA 11'. The original 'STATA' code was written by David Clark, Turner Osler and David Hahn. I implement the same logic for easier access. Ref: David E. Clark & Turner M. Osler & David R. Hahn, 2009. "ICDPIC: Stata module to provide methods for translating International Classification of Diseases (Ninth Revision) diagnosis codes into standard injury categories and/or scores," Statistical Software Components S457028, Boston College Department of Economics, revised 29 Oct 2010.
Maintained by Dajun Tian. Last updated 6 years ago.
17.2 match 1 stars 2.70 score 2 scripts
totajuliusd
topr:Create Custom Plots for Viewing Genetic Association Results
A collection of functions for visualizing,exploring and annotating genetic association results.Association results from multiple traits can be viewed simultaneously along with gene annotation, over the entire genome (Manhattan plot) or in the more detailed regional view.
Maintained by Thorhildur Juliusdottir. Last updated 5 months ago.
6.9 match 57 stars 6.38 score 30 scripts
entjos
TreeMineR:Tree-Based Scan Statistics
Implementation of unconditional Bernoulli Scan Statistic developed by Kulldorff et al. (2003) <doi:10.1111/1541-0420.00039> for hierarchical tree structures. Tree-based Scan Statistics are an exploratory method to identify event clusters across the space of a hierarchical tree.
Maintained by Joshua P. Entrop. Last updated 7 months ago.
12.1 match 3.40 score 2 scripts
hugheylab
phers:Calculate Phenotype Risk Scores
Use phenotype risk scores based on linked clinical and genetic data to study Mendelian disease and rare genetic variants. See Bastarache et al. 2018 <doi:10.1126/science.aal4043>.
Maintained by Jake Hughey. Last updated 2 years ago.
12.8 match 3.00 score 1 scripts
darwin-eu
CodelistGenerator:Identify Relevant Clinical Codes and Evaluate Their Use
Generate a candidate code list for the Observational Medical Outcomes Partnership (OMOP) common data model based on string matching. For a given search strategy, a candidate code list will be returned.
Maintained by Edward Burn. Last updated 25 days ago.
3.5 match 13 stars 9.87 score 165 scripts 4 dependents
aprilnguyen1
icdcomorbid:Mapping ICD Codes to Comorbidity
Provides tools for mapping International Classification of Diseases codes to comorbidity, enabling the identification and analysis of various medical conditions within healthcare data.
Maintained by April Nguyen. Last updated 7 months ago.
9.9 match 2.70 score
marianschmidt
msSPChelpR:Helper Functions for Second Primary Cancer Analyses
A collection of helper functions for analyzing Second Primary Cancer data, including functions to reshape data, to calculate patient states and analyze cancer incidence.
Maintained by Marian Eberl. Last updated 1 years ago.
4.9 match 2 stars 4.18 score 15 scripts
irods
rirods:R Client for 'iRODS'
The open sourced data management software 'Integrated Rule-Oriented Data System' ('iRODS') offers solutions for the whole data life cycle (<https://irods.org/>). The loosely constructed and highly configurable architecture of 'iRODS' frees the user from strict formatting constraints and single-vendor solutions. This package provides an interface to the 'iRODS' HTTP API, allowing you to manage your data and metadata in 'iRODS' with R. Storage of annotated files and R objects in 'iRODS' ensures findability, accessibility, interoperability, and reusability of data.
Maintained by Martin Schobben. Last updated 1 years ago.
3.3 match 7 stars 6.04 score 31 scripts
ablack3
icdpicr:'ICD' Programs for Injury Categorization in R
Categorization and scoring of injury severity typically involves trained personnel with access to injured persons or their medical records. 'icdpicr' contains a function that provides automated calculation of Abbreviated Injury Scale ('AIS') and Injury Severity Score ('ISS') from International Classification of Diseases ('ICD') codes and may be a useful substitute to manual injury severity scoring. 'ICDPIC' was originally developed in 'Stata', and 'icdpicr' is an open-access update that accepts both 'ICD-9' and 'ICD-10' codes.
Maintained by Adam Black. Last updated 3 years ago.
3.9 match 6 stars 4.48 score 10 scriptscelehs
MAP:Multimodal Automated Phenotyping
Electronic health records (EHR) linked with biorepositories are a powerful platform for translational studies. A major bottleneck exists in the ability to phenotype patients accurately and efficiently. Towards that end, we developed an automated high-throughput phenotyping method integrating International Classification of Diseases (ICD) codes and narrative data extracted using natural language processing (NLP). Specifically, our proposed method, called MAP (Map Automated Phenotyping algorithm), fits an ensemble of latent mixture models on aggregated ICD and NLP counts along with healthcare utilization. The MAP algorithm yields a predicted probability of phenotype for each patient and a threshold for classifying subjects with phenotype yes/no (See Katherine P. Liao, et al. (2019) <doi:10.1093/jamia/ocz066>.).
Maintained by Thomas Charlon. Last updated 2 months ago.
1.9 match 6 stars 8.58 score 177 scripts 1 dependents
canmod
iidda:Processing Infectious Disease Datasets in IIDDA.
Part of an open toolchain for processing infectious disease datasets available through the IIDDA data repository.
Maintained by Steve Walker. Last updated 4 months ago.
2.3 match 6.07 score 133 scripts 3 dependents
patrickmdnet
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.
Maintained by Patrick McCormick. Last updated 5 years ago.
3.6 match 4 stars 3.75 score 28 scriptscran
Rdiagnosislist:Manipulate SNOMED CT Diagnosis Lists
Functions and methods for manipulating 'SNOMED CT' concepts. The package contains functions for loading the 'SNOMED CT' release into a convenient R environment, selecting 'SNOMED CT' concepts using regular expressions, and navigating the 'SNOMED CT' ontology. It provides the 'SNOMEDconcept' S3 class for a vector of 'SNOMED CT' concepts (stored as 64-bit integers) and the 'SNOMEDcodelist' S3 class for a table of concepts IDs with descriptions. The package can be used to construct sets of 'SNOMED CT' concepts for research (<doi:10.1093/jamia/ocac158>). For more information about 'SNOMED CT' visit <https://www.snomed.org/>.
Maintained by Anoop D. Shah. Last updated 2 months ago.
2.8 match 1 stars 3.60 score
verbal-autopsy-software
InSilicoVA:Probabilistic Verbal Autopsy Coding with 'InSilicoVA' Algorithm
Computes individual causes of death and population cause-specific mortality fractions using the 'InSilicoVA' algorithm from McCormick et al. (2016) <DOI:10.1080/01621459.2016.1152191>. It uses data derived from verbal autopsy (VA) interviews, in a format similar to the input of the widely used 'InterVA' method. This package provides general model fitting and customization for 'InSilicoVA' algorithm and basic graphical visualization of the output.
Maintained by Zehang Richard Li. Last updated 1 months ago.
1.7 match 3 stars 5.67 score 35 scripts 1 dependents
martonkolossvary
parseRPDR:Parse and Manipulate Research Patient Data Registry ('RPDR') Text Queries
Functions to load Research Patient Data Registry ('RPDR') text queries from Partners Healthcare institutions into R. The package also provides helper functions to manipulate data and execute common procedures such as finding the closest radiological exams considering a given timepoint, or creating a DICOM header database from the downloaded images. All functionalities are parallelized for fast and efficient analyses.
Maintained by Marton Kolossvary. Last updated 2 months ago.
1.7 match 11 stars 4.61 score 37 scripts
jkhaukka
codeCollection:Collection of Codes with Labels
Includes several classifications such as International Statistical Classification of Diseases and Related Health Problems 10th Revision (ICD10), Anatomical Therapeutic Chemical (ATC) Classification, The International Classification of Diseases for Oncology (ICD-O-3), and International Classification of Primary Care (ICPC). Includes function that adds descriptive label to code value. Depending on classification following languages are available: English, Finnish, Swedish, and Latin.
Maintained by Jari Haukka. Last updated 2 years ago.
7.8 match 1.00 score 2 scriptscran
LTASR:Functions to Replicate the Center for Disease Control and Prevention's 'LTAS' Software in R
A suite of functions for reading in a rate file in XML format, stratify a cohort, and calculate 'SMRs' from the stratified cohort and rate file.
Maintained by Stephen Bertke. Last updated 7 months ago.
1.8 match 4.11 score 32 scripts
giancarlodigi
cancerR:Classification of Cancer Using Administrative Data
Classifies the type of cancer using routinely collected data commonly found in cancer registries from pathology reports. The package implements the International Classification of Diseases for Oncology, 3rd Edition site (topography), histology (morphology), and behaviour codes of neoplasms to classify cancer type <https://www.who.int/standards/classifications/other-classifications/international-classification-of-diseases-for-oncology>. Classification in children utilize the International Classification of Childhood Cancer by Steliarova-Foucher et al. (2005) <doi:10.1002/cncr.20910>. Adolescent and young adult cancer classification is based on Barr et al. (2020) <doi:10.1002/cncr.33041>.
Maintained by Giancarlo Di Giuseppe. Last updated 6 months ago.
1.8 match 1 stars 4.00 score 2 scripts
radivot
SEERaBomb:SEER and Atomic Bomb Survivor Data Analysis Tools
Creates SEER (Surveillance, Epidemiology and End Results) and A-bomb data binaries from ASCII sources and provides tools for estimating SEER second cancer risks. Methods are described in <doi:10.1038/leu.2015.258>.
Maintained by Tomas Radivoyevitch. Last updated 5 years ago.
1.8 match 2.85 score 176 scripts
patrickroocks
rPref:Database Preferences and Skyline Computation
Routines to select and visualize the maxima for a given strict partial order. This especially includes the computation of the Pareto frontier, also known as (Top-k) Skyline operator (see Börzsönyi, et al. (2001) <doi:10.1109/ICDE.2001.914855>), and some generalizations known as database preferences (see Kießling (2002) <doi:10.1016/B978-155860869-6/50035-4>).
Maintained by Patrick Roocks. Last updated 2 years ago.
0.5 match 2 stars 5.14 score 115 scripts 4 dependents
celehs
PheNorm:Unsupervised Gold-Standard Label Free Phenotyping Algorithm for EHR Data
The algorithm combines the most predictive variable, such as count of the main International Classification of Diseases (ICD) codes, and other Electronic Health Record (EHR) features (e.g. health utilization and processed clinical note data), to obtain a score for accurate risk prediction and disease classification. In particular, it normalizes the surrogate to resemble gaussian mixture and leverages the remaining features through random corruption denoising. Background and details about the method can be found at Yu et al. (2018) <doi:10.1093/jamia/ocx111>.
Maintained by Clara-Lea Bonzel. Last updated 4 years ago.
0.5 match 5 stars 4.70 score 7 scripts
wyattbensken
socialrisk:Identifying Patient Social Risk from Administrative Health Care Data
Social risks are increasingly becoming a critical component of health care research. One of the most common ways to identify social needs is by using ICD-10-CM "Z-codes." This package identifies social risks using varying taxonomies of ICD-10-CM Z-codes from administrative health care data. The conceptual taxonomies come from: Centers for Medicare and Medicaid Services (2021) <https://www.cms.gov/files/document/zcodes-infographic.pdf>, Reidhead (2018) <https://web.mhanet.com/>, A Arons, S DeSilvey, C Fichtenberg, L Gottlieb (2018) <https://sirenetwork.ucsf.edu/tools-resources/resources/compendium-medical-terminology-codes-social-risk-factors>.
Maintained by Wyatt Bensken. Last updated 2 years ago.
0.8 match 2.70 score 2 scriptscran
tmpm:Trauma Mortality Prediction Model
Trauma Mortality prediction for ICD-9, ICD-10, and AIS lexicons in long or wide format based on Dr. Alan Cook's tmpm mortality model.
Maintained by Cody Moore. Last updated 9 years ago.
0.8 match 1.00 score