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-4.7-any)PheCAP_1.2.2.zip(r-4.6-any)PheCAP_1.2.2.zip(r-4.5-any)
PheCAP_1.2.2.tgz(r-4.6-any)PheCAP_1.2.2.tgz(r-4.5-any)
PheCAP_1.2.2.tar.gz(r-4.7-any)PheCAP_1.2.2.tar.gz(r-4.6-any)
PheCAP_1.2.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
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
Pkgdown/docs site:https://celehs.github.io
Datasets:
- ehr_data - A Synthetic EHR Dataset
Last updated from:7c18179625. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 148 | ||
| source / vignettes | OK | 473 | ||
| linux-release | OK | 139 | ||
| macos-release | OK | 140 | ||
| macos-oldrel | OK | 203 | ||
| windows-devel | OK | 86 | ||
| windows-release | OK | 105 | ||
| windows-oldrel | OK | 106 | ||
| wasm-release | OK | 114 |
Exports:phecap_generate_dictionary_filephecap_perform_majority_votingphecap_plot_roc_curvesphecap_predict_phenotypephecap_run_feature_extractionphecap_train_phenotyping_modelphecap_validate_phenotyping_modelPhecapDataPhecapSurrogate
Dependencies:codetoolsDBIforeachglmnetiteratorslatticeMatrixRcppRcppEigenRMySQLshapesurvival
Running NLP using NILE
Last update: 2020-09-17
Started: 2019-03-29
Example 1: Simulated Data
Last update: 2020-09-17
Started: 2019-03-29
Example 2: Real EHR Data
Last update: 2020-09-17
Started: 2019-03-29
Main Steps
Last update: 2020-09-17
Started: 2019-03-19
NER using MetaMAP
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 |