Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Improved meta-analysis forest plotting #272

Open
bwiernik opened this issue Mar 4, 2023 · 0 comments
Open

Improved meta-analysis forest plotting #272

bwiernik opened this issue Mar 4, 2023 · 0 comments
Labels
Enhancement 💥 New feature or request

Comments

@bwiernik
Copy link
Contributor

bwiernik commented Mar 4, 2023

Related to easystats/insight#726

We should plot the aggregate results from a meta-analysis using a diamond for the confidence interval using geom_polygon() and also include the prediction interval.

Example:

library(tidyverse)
library(metafor)

delta <- .5
tau <- .2
diamond_height <- .3

studies <- tibble(
  study = LETTERS,
  ni = round(runif(n = length(study), min = 100, max = 200)),
  true_i = delta + rnorm(n = length(study), mean = 0, sd = tau),
  yi = rnorm(n = length(study), mean = true_i, sd = sqrt(psychmeta::var_error_d(d = true_i, n1 = ni, n2 = ni))),
  se = sqrt(psychmeta::var_error_d(d = yi, n1 = ni, n2 = ni)),
  ci.lb = yi - qnorm(.975) * se,
  ci.ub = yi + qnorm(.975) * se
)

plot_dat <- bind_rows(
  Studies = studies,
  Aggregate = rma(yi ~ 1, sei = se, data = studies, method = "REML", test = "knha") |> 
    predict() |> 
    as.data.frame() |> 
    rename(yi = pred) |> 
    mutate(study = "Random effects"),
  .id = "type"
) |> 
  mutate(type = as_factor(type), study = as_factor(study), ypos = datawizard::reverse(as.integer(study)))

ggplot(plot_dat) +
  aes(y = forcats::fct_rev(study), x = yi, xmin = ci.lb, xmax = ci.ub) +
  geom_linerange(data = \(x) filter(x, type == "Studies")) +
  geom_point(data = \(x) filter(x, type == "Studies")) +
  geom_linerange(
    aes(xmin = pi.lb, xmax = pi.ub),
    data = \(x) filter(x, type == "Aggregate"),
    linetype = "twodash"
  ) +
  geom_polygon(
    aes(x = x.diamond, y = y.diamond, group = study),
    data = \(x) filter(x, type == "Aggregate") |> 
      group_by(study) |> 
      reframe(
        x.diamond = c(ci.ub, yi, ci.lb, yi),
        y.diamond = ypos + c(0, diamond_height, 0, -diamond_height)
      ),
    inherit.aes = FALSE
  ) +
  labs(y = NULL, x = "Standardized mean difference") +
  scale_y_discrete(drop = FALSE) + # this one is key!
  see::theme_modern() +
  theme(strip.background = element_blank(), strip.text = element_blank())
@IndrajeetPatil IndrajeetPatil added the Enhancement 💥 New feature or request label Mar 15, 2023
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
Enhancement 💥 New feature or request
Projects
None yet
Development

No branches or pull requests

2 participants