Introduction | Installation | Pharmacovigilance Analysis using FAERS | Check metadata of FAERS | Download and Parse quarterly data files from FAERS | Standardize and De-duplication | Pharmacovigilance analysis | sessionInfo
Package: faers 1.8.0
Yun Peng
faers: R interface for FDA Adverse Event Reporting System
The FDA Adverse Event Reporting System (FAERS) is a database used for the spontaneous reporting of adverse events and medication errors related to human drugs and therapeutic biological products. faers pacakge serves as the interface between the FAERS database and R. Furthermore, faers pacakge offers a standardized approach for performing pharmacovigilance analysis.
Authors:
faers_1.8.0.tar.gz
faers_1.8.0.zip(r-4.7)faers_1.8.0.zip(r-4.6)faers_1.8.0.zip(r-4.5)
faers_1.8.0.tgz(r-4.6-any)faers_1.8.0.tgz(r-4.5-any)
faers_1.8.0.tar.gz(r-4.7-any)faers_1.8.0.tar.gz(r-4.6-any)
faers_1.8.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
faers/json (API)
| # Install 'faers' in R: |
| install.packages('faers', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/wanglabcsu/faers/issues
On BioConductor:faers-1.9.0(bioc 3.24)faers-1.8.0(bioc 3.23)
softwaredataimportbiomedicalinformaticspharmacogenomicsadverse-eventsdrug-safetyfaersfaers-procedurepharmacovigilancesignal-detection
Last updated from:0a111c637b (on RELEASE_3_23). Checks:2 ERROR, 8 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 160 | ||
| linux-devel-x86_64 | ERROR | 187 | ||
| source / vignettes | OK | 233 | ||
| linux-release-x86_64 | OK | 220 | ||
| macos-release-arm64 | OK | 87 | ||
| macos-oldrel-arm64 | OK | 108 | ||
| windows-devel | OK | 130 | ||
| windows-release | OK | 103 | ||
| windows-oldrel | OK | 115 | ||
| wasm-release | OK | 133 |
Exports:athenafaersfaers_availablefaers_before_periodfaers_clearcachefaers_combinefaers_countsfaers_datafaers_dedupfaers_deleted_casesfaers_downloadfaers_filterfaers_getfaers_headerfaers_keepfaers_loadfaers_meddrafaers_mergefaers_metafaers_mgetfaers_modifyfaers_parsefaers_periodfaers_phv_signalfaers_phv_tablefaers_primaryidfaers_quarterfaers_standardizefaers_yearfda_drugsmeddrameddra_hierarchymeddra_smqmeddra_versionphv_bcpnn_mcmcphv_bcpnn_normphv_chisqphv_ebgmphv_fisherphv_obsexp_shrinkphv_prrphv_rorphv_signalshow
Dependencies:askpassBHBiocParallelbitbit64brioclicodacodetoolscpp11crayoncurldata.tablefarverformatRfutile.loggerfutile.optionsggplot2gluegtablehmshttrhttr2isobandjsonlitelabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixModelsmcmcMCMCpackmimeopenEBGMopensslpillarpkgconfigprettyunitsprogressquantregR6rappdirsRColorBrewerrlangrvestS7scalesselectrsnowSparseMsurvivalsystibbletidyselecttzdbutf8vctrsviridisLitevroomwithrxml2
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Read and Parse ATHENA VOCABULARIES data | athena |
| Download and parse FAERS Quarterly Data files | faers |
| Check if FAERS year | faers_available |
| Test whether years and quarters are before specified period | faers_before_period |
| Remove caches | faers_clearcache |
| Combine FAERS objects from different Quarterly files. | faers_combine |
| Counting the number of unique case for each event | faers_counts faers_counts,FAERSascii-method |
| Tidy up FAERS Quarterly Data with duplicate records removed | faers_dedup faers_dedup,ANY-method faers_dedup,FAERSascii-method faers_dedup,FAERSxml-method |
| Download FAERS data | faers_download |
| Methods for FAERS class | $,FAERSascii-method faers_filter faers_filter,FAERSascii-method faers_get faers_get,FAERSascii-method faers_keep faers_keep,FAERSascii-method faers_mget faers_mget,FAERSascii-method faers_modify faers_modify,FAERSascii-method faers_primaryid faers_primaryid,FAERSascii-method [,FAERSascii,ANY,ANY,ANY-method [,FAERSascii-method [[,FAERSascii-method |
| Load data attached in faers package | faers_load |
| Merge all FAERS field data into one | faers_merge faers_merge,ANY-method faers_merge,FAERSascii-method faers_merge,FAERSxml-method |
| List of FAERS data | faers_meta |
| Parse FAERS Quarterly Data | faers_parse |
| Create contingency table and run disproportionality analysis | faers_phv_signal faers_phv_signal,FAERSascii-method faers_phv_table faers_phv_table,FAERSascii,FAERSascii,missing-method faers_phv_table,FAERSascii,missing,FAERSascii-method |
| Standardize FAERS Quarterly Data for Preferred Term and drug names | faers_standardize faers_standardize,FAERSascii-method |
| FAERS class | FAERS FAERS-class FAERSascii FAERSascii-class FAERSxml FAERSxml-class faers_data faers_data,FAERS-method faers_deleted_cases faers_deleted_cases,FAERSascii-method faers_field faers_header faers_header,FAERSxml-method faers_meddra faers_meddra,FAERS-method faers_period faers_period,FAERS-method faers_quarter faers_quarter,FAERS-method faers_year faers_year,FAERS-method show,FAERS-method show,FAERSascii-method |
| Read and Parse Drugs@FDA data | fda_drugs |
| MedDRA class | MedDRA meddra MedDRA-class meddra_hierarchy meddra_hierarchy,MedDRA-method meddra_smq meddra_smq,MedDRA-method meddra_version meddra_version,MedDRA-method show,MedDRA-method |
| Pharmacovigilance Analysis | phv_bcpnn_mcmc phv_bcpnn_norm phv_chisq phv_ebgm phv_fisher phv_obsexp_shrink phv_prr phv_ror phv_signal |