scratchpad/run_through.R

In meghapsimatrix/wildmeta: Cluster Wild Bootstrapping for Meta-Analysis

library(clubSandwich)
library(robumeta)
library(metafor)
library(tidyverse)

devtools::load_all()

source("R/helpers.R")
source("R/run_cwb.R")
source("R/plot_wildmeta.R") #why won't this get loaded?

# robumeta ----------------------------------------------------------------

full_model <- robu(d ~ 0 + study_type + hrs + test,
                   studynum = study,
                   var.eff.size = V,
                   small = FALSE,
                   data = SATcoaching)

C_mat <- constrain_equal(1:3, coefs = full_model$b.r)

null_model <- estimate_null(full_model,
                            C_mat)

cluster_id <- null_model$data.full$study


boots <- run_cwb(null_model,
                 cluster = cluster_id,
                 R = 12,
                 simplify = FALSE)

boots

boots <- run_cwb(null_model,
                 cluster = cluster_id,
                 R = 12,
                 f = get_boot_F)

sapply(boots,
       FUN = get_boot_F,
       full_model = full_model,
       C_mat = C_mat)


boot_mod <- update_robu(full_model,
            y = boots[[1]])

cov_mat <- clubSandwich::vcovCR(boot_mod, type = "CR1")

res <- clubSandwich::Wald_test(boot_mod,
                               constraints = C_mat,
                               vcov = cov_mat,
                               test = "Naive-F")

res <- res$Fstat


res <- Wald_test_cwb(full_model = full_model,
              constraint_matrix = C_mat,
              R = 12)

# need to do the whole print thing

res

res$p_val
res$test

str(res)

attributes(res)$bootstraps
attributes(res)$original

plot_cwb(res, fill = "darkred", alpha = 0.5)

Wald_test_cwb(full_model = full_model,
              constraint_matrix = C_mat,
              R = 12,
              adjust = "CR2")


# metafor -----------------------------------------------------------------


full_model <- rma.mv(yi = d ~ 0 + study_type + hrs + test,
                     V = V,
                     random = ~ study_type| study,
                     data = SATcoaching)

C_mat <- constrain_equal(1:3, coefs = coef(full_model))

res <- Wald_test_cwb(full_model = full_model,
                     constraint_matrix = C_mat,
                     R = 12)

res

plot_cwb(res)
str(res)