Evolutionary Version of the Metropolis-Hastings Algorithm

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Documentation for package ‘emcAdr’ version 1.2

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

emcAdr-package	Evolutionary Version of the Metropolis-Hastings Algorithm
ATCtoNumeric	Convert ATC Code for each patients to the corresponding DFS number of the ATC tree
ATC_Tree_UpperBound_2024	ATC Tree Upper Bound 2024
calculate_divergence	Calculate the divergence between 2 distributions (the true Distribution and the learned one)
clustering_genetic_algorithm	Clustering of the solutions of the genetic algorithm using the hclust algorithm
computeMetrics_size2	Function used in the reference article to compare diverse Disproportionality Analysis metrics
compute_hypergeom_on_list	Function used to compute the Hypergeometric score on a list of cocktails
compute_RR_on_list	Function used to compute the Relative Risk on a list of cocktails
csv_to_population	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
DistributionApproximation	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.
emcAdr	Evolutionary Version of the Metropolis-Hastings Algorithm
FAERS_myopathy	FAERS Myopathy Dataset
GeneticAlgorithm	Genetic algorithm, trying to reach riskiest cocktails (the ones which maximize the fitness function, Hypergeometric score in our case)
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 an arbitrary cocktail 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 genetic_results list.
get_dissimilarity_from_txt_file	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
hclust_genetic_solution	Clustering of the solutions of the genetic algorithm using the hclust algorithm
histogramToDitribution	Convert the histogram returned by the DistributionApproximation function, to a real number distribution (that can be used in a test for example)
hyperparam_test_genetic_algorithm	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
int_cocktail_to_string_cocktail	Function used to convert integer cocktails (like the one outputed by the distributionApproximation function) to string cocktail in order to make them more readable
OutsandingScoreToDistribution	Output the outstanding score (Outstanding_score) outputed by the MCMC algorithm in a special format
plot_evolution	Plot the evolution of the mean and the best value of the population used by the GeneticAlgorithm
plot_frequency	Plot the histogram of the approximation of the RR distribution
print_csv	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.
p_value_cocktails	Used to add the p_value to each cocktail of cocktail list
p_value_csv_file	Used to add the p_value to each cocktail of a csv_file that is an output of the genetic algorithm
p_value_genetic_results	Used to add the p_value to each cocktail of an output of the genetic algorithm
p_value_on_sampled	Calculate p-value of sampled value
qq_plot_output	Make a Quantile-Quantile diagram from the output of the MCMC algorithm (DistributionAproximation) and the algorithm that exhaustively calculates the distribution
string_list_to_int_cocktails	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))
trueDistributionDrugs	The true distribution of the score among every single nodes of the ATC
trueDistributionSizeTwoCocktail	The true distribution of the score among every size-two cocktails