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qch (version 2.1.0)

Query Composite Hypotheses

Description

Provides functions for the joint analysis of Q sets of p-values obtained for the same list of items. This joint analysis is performed by querying a composite hypothesis, i.e. an arbitrary complex combination of simple hypotheses, as described in Mary-Huard et al. (2021) and De Walsche et al.(2023) . In this approach, the Q-uplet of p-values associated with each item is distributed as a multivariate mixture, where each of the 2^Q components corresponds to a specific combination of simple hypotheses. The dependence between the p-value series is considered using a Gaussian copula function. A p-value for the composite hypothesis test is derived from the posterior probabilities.

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Version

Install

install.packages('qch')

Monthly Downloads

209

Version

2.1.0

License

GPL-3

Maintainer

Tristan Mary-Huard

Last Published

July 4th, 2025

Functions in qch (2.1.0)

prior_update_arma_ptr_parallel

Update of the prior estimate in EM algo parallelized version
fHconfig_sum_update_ptr_parallel

Computation of the sum sum_c(w_c*psi_c) parallelized version
qch-package

qch: Query Composite Hypotheses
qch.fit

Infer posterior probabilities of \(H_0\)/\(H_1\) configurations.
gaussian_copula_density

Gaussian copula density
prior_update_gaussian_copula_ptr_parallel

Update of the prior estimate in EM algo using Gaussian copula, parallelized version
GetH1Equal

Specify the configurations corresponding to the composite \(H_1\) test "Equal".
EM_calibration_indep

EM calibration in the case of conditional independence
EM_calibration_gaussian_memory

EM calibration in the case of the Gaussian copula (unsigned) with memory management
FastKerFdr_unsigned

FastKerFdr unsigned
FastKerFdr_signed

FastKerFdr signed
Copula.Hconfig_gaussian_density

Gaussian copula density for each H-configuration.
GetH1AtLeast

Specify the configurations corresponding to the composite \(H_1\) test "AtLeast".
EM_calibration_indep_memory

EM calibration in the case of conditional independence with memory management (unsigned)
GetHconfig

Generate the \(H_0\)/\(H_1\) configurations.
EM_calibration_gaussian

EM calibration in the case of the Gaussian copula (unsigned)
R.MLE

Gaussian copula correlation matrix Maximum Likelihood estimator.
PvalSets

Synthetic example to illustrate the main qch functions
f1_separation_signed

Signed case function: Separate f1 into f+ and f-
R_MLE_update_gaussian_copula_ptr_parallel

Update the estimate of R correlation matrix of the gaussian copula, parallelized version
R.MLE.memory

Gaussian copula correlation matrix Maximum Likelihood estimator (memory handling)
fHconfig_sum_update_gaussian_copula_ptr_parallel

Computation of the sum sum_c(w_c*psi_c) using Gaussian copula parallelized version
PvalSets_cor

Synthetic example to illustrate the main qch functions using Gaussian copula
R.MLE.check

Check the Gaussian copula correlation matrix Maximum Likelihood estimator
qch.test

Perform composite hypothesis testing.