# Power simulations using multiple approaches for internal validation

    library(graphicalMCP)

C:5n8420812d74b3d-validation.R

# Introduction

Multiple approaches are implemented in `graphicalMCP` to reject a hypothesis for different purposes and/or considerations. One approach is to calculate the adjusted p-value of this hypothesis and compare it with `alpha`. This approach is implemented in `adjusted_p` functions and `graph_test_closure()` (when `test_values = FALSE`). Another approach is to calculate the adjusted significance level of this hypothesis and compare it with its p-value. This approach is implemented in `adjusted_weights` functions, `graph_test_closure()` (when `test_values = TRUE`), and `graph_calculate_power()`. To further tailor this approach for different outputs, a different way of coding are used for `graph_test_closure()` (when `test_values = TRUE`). When implementing these approaches in `graph_calculate_power()`, variations are added to optimize computing speed. Thus, these approaches could be compared with each other for internal validation.

# Power simulations

A random graph will be generated and used for the comparison. A set of marginal power (without multiplicity adjustment) is randomly generated. Local power (with multiplicity adjustment) is calculated using `graph_calculate_power()`. In addition, p-values simulated from `graph_calculate_power()` are saved. These p-values are used to generate local power via `graph_test_shortcut()` and `graph_test_closure()` as the proportion of times every hypothesis can be rejected. We expect to observe matching results for 1000 random graphs.

## Bonferroni tests

We compare power simulations from `graph_calculate_power()` and those using `graph_test_shortcut()` via respectively the adjusted p-value approach and the adjusted significance level approach.

    out <- read.csv(here::here("vignettes/internal-validation_bonferroni.csv"))
    # Matching power using the adjusted p-value approach
    all.equal(out$adjusted_p, rep(TRUE, nrow(out)))
    #> [1] TRUE
    # Matching power using the adjusted significance level approach
    all.equal(out$adjusted_significance_level, rep(TRUE, nrow(out)))
    #> [1] TRUE

C:5n8420812d74b3d-validation.R

## Hochberg tests

We compare power simulations from `graph_calculate_power()` and those using `graph_test_closure()` via respectively the adjusted p-value approach and the adjusted significance level approach. Two test groups are used with randomly assigned hypotheses.

    out <- read.csv(here::here("vignettes/internal-validation_hochberg.csv"))
    # Matching power using the adjusted p-value approach
    all.equal(out$adjusted_p, rep(TRUE, nrow(out)))
    #> [1] TRUE
    # Matching power using the adjusted significance level approach
    all.equal(out$adjusted_significance_level, rep(TRUE, nrow(out)))
    #> [1] TRUE

C:5n8420812d74b3d-validation.R

## Simes tests

We compare power simulations from `graph_calculate_power()` and those using `graph_test_closure()` via respectively the adjusted p-value approach and the adjusted significance level approach. Two test groups are used with randomly assigned hypotheses.

    out <- read.csv(here::here("vignettes/internal-validation_simes.csv"))
    # Matching power using the adjusted p-value approach
    all.equal(out$adjusted_p, rep(TRUE, nrow(out)))
    #> [1] TRUE
    # Matching power using the adjusted significance level approach
    all.equal(out$adjusted_significance_level, rep(TRUE, nrow(out)))
    #> [1] TRUE

C:5n8420812d74b3d-validation.R

## Parametric tests

We compare power simulations from `graph_calculate_power()` and those using `graph_test_closure()` via respectively the adjusted p-value approach and the adjusted significance level approach. Two test groups are used with randomly assigned hypotheses.

    out <- read.csv(here::here("vignettes/internal-validation_parametric.csv"))
    # Matching power using the adjusted p-value approach
    all.equal(out$adjusted_p, rep(TRUE, nrow(out)))
    #> [1] TRUE
    # Matching power using the adjusted significance level approach
    all.equal(out$adjusted_significance_level, rep(TRUE, nrow(out)))
    #> [1] TRUE

C:5n8420812d74b3d-validation.R

## Mixed tests of Bonferroni, Hochberg and Simes

We compare power simulations from `graph_calculate_power()` and those using `graph_test_closure()` via respectively the adjusted p-value approach and the adjusted significance level approach. Two test groups are used with randomly assigned hypotheses. Two test types are randomly picked among Bonferroni, Hochberg and Simes tests.

    out <- read.csv(here::here("vignettes/internal-validation_mixed.csv"))
    # Matching power using the adjusted p-value approach
    all.equal(out$adjusted_p, rep(TRUE, nrow(out)))
    #> [1] TRUE
    # Matching power using the adjusted significance level approach
    all.equal(out$adjusted_significance_level, rep(TRUE, nrow(out)))
    #> [1] TRUE

C:5n8420812d74b3d-validation.R

## Mixed tests of parametric and one of Bonferroni, Hochberg and Simes

We compare power simulations from `graph_calculate_power()` and those using `graph_test_closure()` via respectively the adjusted p-value approach and the adjusted significance level approach. Two test groups are used with randomly assigned hypotheses. Parametric test type is assigned to the first test group and the test type for the second test group is randomly picked among Bonferroni, Hochberg and Simes tests.

    out <- read.csv(here::here("vignettes/internal-validation_parametric-mixed.csv"))
    # Matching power using the adjusted p-value approach
    all.equal(out$adjusted_p, rep(TRUE, nrow(out)))
    #> [1] TRUE
    # Matching power using the adjusted significance level approach
    all.equal(out$adjusted_significance_level, rep(TRUE, nrow(out)))
    #> [1] TRUE

C:5n8420812d74b3d-validation.R

# Conclusions

Multiple approaches are implemented in `graphicalMCP` to reject a hypothesis for different purposes and/or considerations. One approach is to calculate the adjusted p-value of this hypothesis and compare it with `alpha`. Another approach is to calculate the adjusted significance level of this hypothesis and compare it with its p-value. Based on 1000 random graphs, these two approaches produce matching power for all types of tests. Therefore, the internal validation is considered to be complete.