Package: emcAdr 1.3

Jules Bangard

emcAdr: Evolutionary Version of the Metropolis-Hastings Algorithm

Provides computational methods for detecting adverse high-order drug interactions from individual case safety reports using statistical techniques, allowing the exploration of higher-order interactions among drug cocktails.

Authors:Jules Bangard [aut, cre]

emcAdr_1.3.tar.gz
emcAdr_1.3.tar.gz(r-4.7-arm64)emcAdr_1.3.tar.gz(r-4.7-x86_64)emcAdr_1.3.tar.gz(r-4.6-arm64)emcAdr_1.3.tar.gz(r-4.6-x86_64)
emcAdr_1.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
emcAdr/json (API)

# Install 'emcAdr' in R:

install.packages('emcAdr', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Uses libs:

c++– GNU Standard C++ Library v3
openmp– GCC OpenMP (GOMP) support library

Datasets:

ATC_Tree_UpperBound_2024 - ATC Tree Upper Bound 2024
FAERS_myopathy - FAERS Myopathy Dataset

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

cpp openmp

2.70 score 1 scripts 162 downloads 32 exports 89 dependencies

Last updated from:98805d9518. Checks:5 OK, 1 ERROR. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	158
linux-devel-x86_64	OK	164
source / vignettes	ERROR	359
linux-release-arm64	OK	179
linux-release-x86_64	OK	181
wasm-release	OK	161

Exports:ATCtoNumeric calculate_divergence clustering_genetic_algorithm combination_data_frame compute_hypergeom_cocktail compute_hypergeom_on_list compute_RR_on_list computeMetrics_size2 csv_to_population DistributionApproximation GeneticAlgorithm get_dissimilarity_from_cocktail_list get_dissimilarity_from_genetic_results get_dissimilarity_from_txt_file hclust_genetic_solution histogramToDitribution hyperparam_test_genetic_algorithm int_cocktail_to_string_cocktail OutsandingScoreToDistribution p_value_cocktails p_value_csv_file p_value_genetic_results p_value_on_sampled plot_evolution plot_frequency print_csv qq_plot_output remove_higher_cocktails run_firth_regression string_list_to_int_cocktails trueDistributionDrugs trueDistributionSizeTwoCocktail

Dependencies:askpass backports bit bit64 boot broom cli clipr codetools cpp11 crayon dbscan dplyr farver forcats foreach formula.tools generics ggplot2 glmnet glue gtable haven here hms isoband iterators jomo jsonlite labeling lattice lifecycle lme4 logistf magrittr MASS Matrix mgcv mice minqa mitml nlme nloptr nnet numDeriv openssl operator.tools ordinal pan pillar pkgconfig png prettyunits progress purrr R6 rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen RcppTOML Rdpack readr reformulas reticulate rlang rpart rprojroot RSpectra S7 scales shape stringi stringr survival sys tibble tidyr tidyselect tzdb ucminf umap utf8 vctrs viridisLite vroom withr

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

emcAdr : Evolutionary Markov Chain for Adverse Drug Reaction

Aim | Data | Score distribution estimation | Visualize and compare the results | Find cocktails with higher score

Rendered frombase.Rmdusingknitr::rmarkdown

Last update: 2025-02-27
Started: 2025-02-27

Citation

Readme and manuals

Help Manual

Help page	Topics
Evolutionary Version of the Metropolis-Hastings Algorithm	emcAdr-package emcAdr
ATC Tree Upper Bound 2024	ATC_Tree_UpperBound_2024
Convert ATC Code for each patients to the corresponding DFS number of the ATC tree	ATCtoNumeric
Calculate the divergence between 2 distributions (the true Distribution and the learned one)	calculate_divergence
Clustering of the solutions of the genetic algorithm using the hclust algorithm	clustering_genetic_algorithm
Generate Matrix for Drug Combinations	combination_data_frame
Function used to compute the Hypergeometric score on a cocktail	compute_hypergeom_cocktail
Function used to compute the Hypergeometric score on a list of cocktails	compute_hypergeom_on_list
Function used to compute the Relative Risk on a list of cocktails	compute_RR_on_list
Function used in the reference article to compare diverse Disproportionality Analysis metrics	computeMetrics_size2
Function used to convert your genetic algorithm results that are stored into a .csv file to a Data structure that can be used by the clustering algorithm	csv_to_population
The MCMC method that runs the random walk on a single cocktail in order to estimate the distribution of score among cocktails of size Smax.	DistributionApproximation
FAERS Myopathy Dataset	FAERS_myopathy
Genetic algorithm, trying to reach riskiest cocktails (the ones which maximize the fitness function, Hypergeometric score in our case)	GeneticAlgorithm
Recover the square matrix of distance between cocktails where the index (i,j) of the matrix is the distance between cocktails i and j in an arbitrary cocktail list	get_dissimilarity_from_cocktail_list
Recover the square matrix of distance between cocktails where the index (i,j) of the matrix is the distance between cocktails i and j in the genetic_results list.	get_dissimilarity_from_genetic_results
Recover the square matrix of distance between cocktails where the index (i,j) of the matrix is the distance between cocktails i and j in the csv file containing results of genetic algorithm	get_dissimilarity_from_txt_file
Clustering of the solutions of the genetic algorithm using the hclust algorithm	hclust_genetic_solution
Convert the histogram returned by the DistributionApproximation function, to a real number distribution (that can be used in a test for example)	histogramToDitribution
This function can be used in order to try different set of parameters for the genetic algorithm in a convenient way. This will run each combination of mutation_rate, nb_elite and alphas possible nb_test_desired times. For each sets of parameters, results will be saved in a file named according to the set of parameter. One can regroup the results of each run in a csv file by using the print_csv function specifying the names of each file that needs to be treated and the number of performed runs on each parameter set	hyperparam_test_genetic_algorithm
Function used to convert integer cocktails (like the one outputed by the distributionApproximation function) to string cocktail in order to make them more readable	int_cocktail_to_string_cocktail
Output the outstanding score (Outstanding_score) outputed by the MCMC algorithm in a special format	OutsandingScoreToDistribution
Used to add the p_value to each cocktail of cocktail list	p_value_cocktails
Used to add the p_value to each cocktail of a csv_file that is an output of the genetic algorithm	p_value_csv_file
Used to add the p_value to each cocktail of an output of the genetic algorithm	p_value_genetic_results
Calculate p-value of sampled value	p_value_on_sampled
Plot the evolution of the mean and the best value of the population used by the GeneticAlgorithm	plot_evolution
Plot the histogram of the approximation of the RR distribution	plot_frequency
Print every cocktails found during the genetic algorithm when used with the hyperparam_test_genetic_algorithm function. This enables to condense the solutions found in each files by collapsing similar cocktail in a single row by cocktail.	print_csv
Make a Quantile-Quantile diagram from the output of the MCMC algorithm (DistributionAproximation) and the algorithm that exhaustively calculates the distribution	qq_plot_output
Filter out drug cocktails with high-level ATC classifications	remove_higher_cocktails
Firth Penalized Logistic Regression for Drug Cocktails	run_firth_regression
Function used to convert a string vector of drugs in form "drug1:drug2" to a vector of index of the ATC tree ex: c(ATC_index(drug1), ATC_index(drugs2))	string_list_to_int_cocktails
The true distribution of the score among every single nodes of the ATC	trueDistributionDrugs
The true distribution of the score among every size-two cocktails	trueDistributionSizeTwoCocktail

Package: emcAdr 1.3

emcAdr: Evolutionary Version of the Metropolis-Hastings Algorithm

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)