Extract all fitted models from a tuned pvEBayes Object — extract_all_fitted

This function retrieves the list of all fitted models from a pvEBayes_tuned object, which is the output of the pvEBayes_tune() function.

Usage

extract_all_fitted_models(object)

Arguments

object: An object of class pvEBayes_tuned, usually returned by pvEBayes_tune. This function will throw an error if the input is not of the correct class.

Value

A list containing the results of each model fitted during the tuning process.

Examples


valid_matrix <- matrix(c(1, 2, 3, 4, 5, 6, 7, 8), nrow = 2)
rownames(valid_matrix) <- c("AE_1", "AE_2")
colnames(valid_matrix) <- c("drug_1", "drug_2", "drug_3", "drug_4")

tuned_object <- pvEBayes_tune(valid_matrix,
  model = "general-gamma",
  return_all_fit = TRUE
)
#> The alpha value selected under AIC is 0.3,
#> The alpha value selected under BIC is 0.3.
#>   alpha      AIC      BIC num_mixture
#> 1   0.0      NaN      NaN           7
#> 2   0.1 32.16579 32.40411           1
#> 3   0.3 32.16579 32.40411           1
#> 4   0.5 32.16579 32.40411           1
#> 5   0.7 32.16579 32.40411           1
#> 6   0.9 44.16579 44.88076           3
extract_all_fitted_models(tuned_object)
#> $best_model_AIC
#> Object of class 'pvEBayes'
#> 
#> General-gamma model with hyperparameter alpha = 0.3.
#> Estimated prior is a mixture of 1 gamma distributions.
#> 
#> Running time of the general-gamma model fitting: 0.0019 seconds.
#> No posterior draws were generated.
#> 
#> Extract estimated prior parameters, discovered signals
#> and signal strength posterior draws using `summary()`.
#> 
#> $best_model_BIC
#> Object of class 'pvEBayes'
#> 
#> General-gamma model with hyperparameter alpha = 0.3.
#> Estimated prior is a mixture of 1 gamma distributions.
#> 
#> Running time of the general-gamma model fitting: 0.0019 seconds.
#> No posterior draws were generated.
#> 
#> Extract estimated prior parameters, discovered signals
#> and signal strength posterior draws using `summary()`.
#> 
#> $all_fit
#> $all_fit[[1]]
#> Object of class 'pvEBayes'
#> 
#> General-gamma model with hyperparameter alpha = 0.
#> Estimated prior is a mixture of 7 gamma distributions.
#> 
#> Running time of the general-gamma model fitting: 0.0076 seconds.
#> No posterior draws were generated.
#> 
#> Extract estimated prior parameters, discovered signals
#> and signal strength posterior draws using `summary()`.
#> 
#> $all_fit[[2]]
#> Object of class 'pvEBayes'
#> 
#> General-gamma model with hyperparameter alpha = 0.1.
#> Estimated prior is a mixture of 1 gamma distributions.
#> 
#> Running time of the general-gamma model fitting: 0.002 seconds.
#> No posterior draws were generated.
#> 
#> Extract estimated prior parameters, discovered signals
#> and signal strength posterior draws using `summary()`.
#> 
#> $all_fit[[3]]
#> Object of class 'pvEBayes'
#> 
#> General-gamma model with hyperparameter alpha = 0.3.
#> Estimated prior is a mixture of 1 gamma distributions.
#> 
#> Running time of the general-gamma model fitting: 0.0019 seconds.
#> No posterior draws were generated.
#> 
#> Extract estimated prior parameters, discovered signals
#> and signal strength posterior draws using `summary()`.
#> 
#> $all_fit[[4]]
#> Object of class 'pvEBayes'
#> 
#> General-gamma model with hyperparameter alpha = 0.5.
#> Estimated prior is a mixture of 1 gamma distributions.
#> 
#> Running time of the general-gamma model fitting: 0.002 seconds.
#> No posterior draws were generated.
#> 
#> Extract estimated prior parameters, discovered signals
#> and signal strength posterior draws using `summary()`.
#> 
#> $all_fit[[5]]
#> Object of class 'pvEBayes'
#> 
#> General-gamma model with hyperparameter alpha = 0.7.
#> Estimated prior is a mixture of 1 gamma distributions.
#> 
#> Running time of the general-gamma model fitting: 0.0021 seconds.
#> No posterior draws were generated.
#> 
#> Extract estimated prior parameters, discovered signals
#> and signal strength posterior draws using `summary()`.
#> 
#> $all_fit[[6]]
#> Object of class 'pvEBayes'
#> 
#> General-gamma model with hyperparameter alpha = 0.9.
#> Estimated prior is a mixture of 3 gamma distributions.
#> 
#> Running time of the general-gamma model fitting: 0.0025 seconds.
#> No posterior draws were generated.
#> 
#> Extract estimated prior parameters, discovered signals
#> and signal strength posterior draws using `summary()`.
#> 
#> 
#> $all_AIC
#> [1]      NaN 32.16579 32.16579 32.16579 32.16579 44.16579
#> 
#> $all_BIC
#> [1]      NaN 32.40411 32.40411 32.40411 32.40411 44.88076
#>