Package: pvLRT 0.5.1

pvLRT: Likelihood Ratio Test-Based Approaches to Pharmacovigilance

A suite of likelihood ratio test based methods to use in pharmacovigilance. Contains various testing and post-processing functions.

Authors:Saptarshi Chakraborty [aut, cre], Marianthi Markatou [aut], Anran Liu [ctb]

pvLRT_0.5.1.tar.gz
pvLRT_0.5.1.zip(r-4.5)pvLRT_0.5.1.zip(r-4.4)pvLRT_0.5.1.zip(r-4.3)
pvLRT_0.5.1.tgz(r-4.4-any)pvLRT_0.5.1.tgz(r-4.3-any)
pvLRT_0.5.1.tar.gz(r-4.5-noble)pvLRT_0.5.1.tar.gz(r-4.4-noble)
pvLRT_0.5.1.tgz(r-4.4-emscripten)pvLRT_0.5.1.tgz(r-4.3-emscripten)
pvLRT.pdf |pvLRT.html✨
pvLRT/json (API)

# Install 'pvLRT' in R:
install.packages('pvLRT', repos = c('https://c7rishi.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/c7rishi/pvlrt/issues

Datasets:
  • faers22q3raw - FDA FAERS dataset for 2022 Q3
  • gbca - FDA GBCA dataset with all observed 1707 adverse events
  • lovastatin - FDA lovastatin dataset
  • rv - FDA rotavirus vaccine dataset with 794 adverse events observed among combined old (age >= 1 year) and young (age < 1 year) individuals
  • rvold - FDA rotavirus vaccine dataset with 727 adverse events observed among "old" (non-infant; age >= 1 year) individuals
  • rvyoung - FDA rotavirus vaccine dataset with 346 adverse events observed among young (infant - 1 year) individuals
  • statin - FDA Statin dataset with 6039 adverse events
  • statin1491 - FDA Statin dataset with 1491 adverse events
  • statin46 - FDA Statin dataset with 46 adverse events

On CRAN:

19 exports 1 stars 0.74 score 48 dependencies 9 scripts 278 downloads

Last updated 2 years agofrom:69c93d5347. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 09 2024
R-4.5-winNOTESep 09 2024
R-4.5-linuxNOTESep 09 2024
R-4.4-winNOTESep 09 2024
R-4.4-macNOTESep 09 2024
R-4.3-winOKSep 09 2024
R-4.3-macOKSep 09 2024

Exports:%>%bubbleplot_pvlrtconvert_raw_to_contin_tableextract_AE_namesextract_Drug_namesextract_lrstat_matrixextract_n_matrixextract_p_value_matrixextract_run_timeextract_significant_pairsextract_zi_probabilityheatmap_pvlrtlrt_poissonlrt_vanilla_poissonlrt_zi_poissonpvlrtr_contin_table_zipset_AE_namesset_Drug_names

Dependencies:bitbit64clicolorspacecommonmarkcrayoncurldata.tablefansifarverggfittextggplot2gluegridtextgtablehmsisobandjpeglabelinglatticelifecyclemagrittrmarkdownMASSMatrixmgcvmunsellnlmepillarpkgconfigpngprettyunitsprogressR6RColorBrewerRcpprlangscalesshadesstringistringrtibbleutf8vctrsviridisLitewithrxfunxml2

Readme and manuals

Help Manual

Help pageTopics
'pvLRT': An R package implementing various Likelihood Ratio Test-based approaches to pharmacovigilancepvLRT-package
Test if two pvlrt objects are (Nearly) Equalall.equal.pvlrt
Casting a 'pvlrt' object as a matrix of log LR statisticsas.matrix.pvlrt
Convert raw AE-Drug incidence data into a contingency tableconvert_raw_to_contin_table
Extracting and setting AE and Drug names from a pvlrt objectextract_AE_names extract_Drug_names set_AE_names set_Drug_names
Extract various summary measures from a pvlrt objectextract_lrstat_matrix extract_n_matrix extract_p_value_matrix extract_run_time extract_significant_pairs extract_zi_probability
FDA FAERS dataset for 2022 Q3faers22q3raw
FDA GBCA dataset with all observed 1707 adverse eventsgbca
Heatmap, barplot and bubbleplot displaying likelihood ratio test results in a 'pvlrt' objectbarplot.pvlrt bubbleplot_pvlrt heatmap_pvlrt
Overall Log-likelihood for a pvlrt objectlogLik.pvlrt
FDA lovastatin datasetlovastatin
Likelihood Ratio Test under the (vanilla, non-zero-inflated) Poisson modellrt_poisson lrt_vanilla_poisson
Pseudo Likelihood Ratio Test under the zero-inflated Poisson model with relative reporting rate parametrizationlrt_zi_poisson
Plotting method for a pvlrt objectplot.pvlrt
Print method for pvlrt objectsprint.pvlrt
Pseudo Likelihood Ratio Test for determining significant AE-Drug pairs under Poisson and zero-inflated Poisson models for pharmacovigilancepvlrt
Generate random contingency tables for adverse event (across rows) and drug (across columns) combinations given row and column marginal totals, embedded signals, and possibly with zero inflationr_contin_table_zip
FDA rotavirus vaccine dataset with 794 adverse events observed among combined old (age >= 1 year) and young (age < 1 year) individualsrv
FDA rotavirus vaccine dataset with 727 adverse events observed among "old" (non-infant; age >= 1 year) individualsrvold
FDA rotavirus vaccine dataset with 346 adverse events observed among young (infant - 1 year) individualsrvyoung
FDA Statin dataset with 6039 adverse eventsstatin
FDA Statin dataset with 1491 adverse eventsstatin1491
FDA Statin dataset with 46 adverse eventsstatin46
Summary method for a pvlrt objectsummary.pvlrt