Package: PheCAP 1.2.2
PheCAP: High-Throughput Phenotyping with EHR using a Common Automated Pipeline
Implement surrogate-assisted feature extraction (SAFE) and common machine learning approaches to train and validate phenotyping models. Background and details about the methods can be found at Zhang et al. (2019) <doi:10.1038/s41596-019-0227-6>, Yu et al. (2017) <doi:10.1093/jamia/ocw135>, and Liao et al. (2015) <doi:10.1136/bmj.h1885>.
Authors:
PheCAP_1.2.2.tar.gz
PheCAP_1.2.2.zip(r-4.5)PheCAP_1.2.2.zip(r-4.4)PheCAP_1.2.2.zip(r-4.3)
PheCAP_1.2.2.tgz(r-4.4-any)PheCAP_1.2.2.tgz(r-4.3-any)
PheCAP_1.2.2.tar.gz(r-4.5-noble)PheCAP_1.2.2.tar.gz(r-4.4-noble)
PheCAP_1.2.2.tgz(r-4.4-emscripten)PheCAP_1.2.2.tgz(r-4.3-emscripten)
PheCAP.pdf |PheCAP.html✨
PheCAP/json (API)
# Install 'PheCAP' in R: |
install.packages('PheCAP', repos = c('https://celehs.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/celehs/phecap/issues
- ehr_data - A Synthetic EHR Dataset
Last updated 4 years agofrom:7c18179625. Checks:OK: 7. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 04 2024 |
R-4.5-win | OK | Nov 04 2024 |
R-4.5-linux | OK | Nov 04 2024 |
R-4.4-win | OK | Nov 04 2024 |
R-4.4-mac | OK | Nov 04 2024 |
R-4.3-win | OK | Nov 04 2024 |
R-4.3-mac | OK | Nov 04 2024 |
Exports:phecap_generate_dictionary_filephecap_perform_majority_votingphecap_plot_roc_curvesphecap_predict_phenotypephecap_run_feature_extractionphecap_train_phenotyping_modelphecap_validate_phenotyping_modelPhecapDataPhecapSurrogate
Dependencies:codetoolsDBIforeachglmnetiteratorslatticeMatrixRcppRcppEigenRMySQLshapesurvival
Example 1: Simulated Data
Rendered fromexample1.Rmd
usingknitr::rmarkdown
on Nov 04 2024.Last update: 2020-09-17
Started: 2019-03-29
Example 2: Real EHR Data
Rendered fromexample2.Rmd
usingknitr::rmarkdown
on Nov 04 2024.Last update: 2020-09-17
Started: 2019-03-29
Main Steps
Rendered frommain.Rmd
usingknitr::rmarkdown
on Nov 04 2024.Last update: 2020-09-17
Started: 2019-03-19
NER using MetaMAP
Rendered fromNER-MetaMAP.Rmd
usingknitr::rmarkdown
on Nov 04 2024.Last update: 2020-09-17
Started: 2019-03-29
Running NLP using NILE
Rendered fromNLP-NILE.Rmd
usingknitr::rmarkdown
on Nov 04 2024.Last update: 2020-09-17
Started: 2019-03-29
Readme and manuals
Help Manual
Help page | Topics |
---|---|
High-Throughput Phenotyping with EHR using a Common Automated Pipeline | PheCAP-package PheCAP |
A Synthetic EHR Dataset | ehr_data |
Generate a Dictionary File for Note Parsing | phecap_generate_dictionary_file |
Perform Majority Voting on the CUIs from Multiple Knowledge Sources | phecap_perform_majority_voting |
Plot ROC and Related Curves for Phenotyping Models | phecap_plot_roc_curves |
Predict Phenotype | phecap_predict_phenotype |
Run Surrogate-Assisted Feature Extraction (SAFE) | phecap_run_feature_extraction |
Train Phenotyping Model using the Training Labels | phecap_train_phenotyping_model |
Validate the Phenotyping Model using the Validation Labels | phecap_validate_phenotyping_model |
Define or Read Datasets for Phenotyping | PhecapData |
Define a Surrogate Variable used in Surrogate-Assisted Feature Extraction (SAFE) | PhecapSurrogate |