ATC_Tree_UpperBound_2024
                        ATC Tree Upper Bound 2024
ATCtoNumeric            Convert ATC Code for each patients to the
                        corresponding DFS number of the ATC tree
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.
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)
OutsandingScoreToDistribution
                        Output the outstanding score
                        (Outstanding_score) outputed by the MCMC
                        algorithm in a special format
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
combination_data_frame
                        Generate Matrix for Drug Combinations
computeMetrics_size2    Function used in the reference article to
                        compare diverse Disproportionality Analysis
                        metrics
compute_RR_on_list      Function used to compute the Relative Risk on a
                        list of cocktails
compute_hypergeom_cocktail
                        Function used to compute the Hypergeometric
                        score on a cocktail
compute_hypergeom_on_list
                        Function used to compute the Hypergeometric
                        score 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
emcAdr-package          Evolutionary Version of the Metropolis-Hastings
                        Algorithm
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
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
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.
qq_plot_output          Make a Quantile-Quantile diagram from the
                        output of the MCMC algorithm
                        (DistributionAproximation) and the algorithm
                        that exhaustively calculates the distribution
remove_higher_cocktails
                        Filter out drug cocktails with high-level ATC
                        classifications
run_firth_regression    Firth Penalized Logistic Regression for Drug
                        Cocktails
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
