Package index
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bootstrap_ci() - Apply the Bayesian subsampled bootstrap to a fitted tinyvamp model
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bootstrap_lrt() - Apply a likelihod ratio test
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calculate_log_penalty() - Calculate barrier penalty to add to objective function inside barrier algorithm
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costea2017_metaphlan2_profiles - MetaPhlAn2 taxonomic profiles from the Costea 2017 study.
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costea2017_mock_composition - The composition of 10 spike-in taxa in 19 samples observed from flow cytometry.
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costea2017_sample_data - costea2017_sample_data
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dataframes_to_parameters() - Convert parameter values stored in data frame format to matrix format
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estimate_parameters() - Fit tinyvamp model to HTS microbiome data
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evaluate_criterion_lr() - Criterion Evaluation Function
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karstens_phyloseq - karstens_phyloseq
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meaninate() - Calculate the mean given parameters
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mu_d_P() - Calculate derivative of mu_ij with respect to an entry of P
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mu_d_beta() - Calculate derivative of mu_ij with respect to B
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mu_d_gamma() - Calculate derivative of mu_ij with respect to ith entry of gamma
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mu_d_gamma_tilde() - Calculate derivative of mu_ij with respect to an entry of gamma_tilde
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mu_d_rho_faster() - Calculate derivative of mu_ij with respect to a row of matrix-valued parameter rho
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mu_d_rho_tilde_faster() - Calculate derivative of mu_i with respect to a row of matrix-valued parameter rho_tilde.
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sum_of_logs() - Sum positive numbers via their logarithms Given x and y, this function returns log(exp(x) + exp(y)).