knitr::opts_chunk$set( collapse = TRUE, comment = "#>" )

library(here) library(brms) library(brmstools) library(dplyr)

Forest plots display estimated parameters from multiple sources (studies, participants, etc.) in one figure. They are most commonly used in meta-analysis, where individual studies are used to inform an average, or meta-analytic, overall estimate. However, they can be seamlessly applied to other types of multilevel models--models in which parameters are assumed to vary among units. **brmstools**' `forest()`

function draws forest plots from `brmsfit`

objects. They should be most useful for meta-analytic models, but can be produced from any `brmsfit`

with one or more varying parameters.

The `forest()`

function uses the fantastic ggridges R package in the backend, and assumes you've installed it. If you haven't, `forest()`

will return an error.

We illustrate using a data set from the metafor package.

data("dat.bangertdrowns2004", package = "metafor") dat <- dat.bangertdrowns2004 %>% mutate(study = paste0(author, " (", year, ")"), sei = sqrt(vi)) %>% select(study, yi, sei) %>% slice(1:15)

brms allows flexible specification of meta-analytic models.

fit_rem <- brm( yi | se(sei) ~ 1 + (1|study), data = dat, cores = 4, control=list(adapt_delta = .99) )

# Save time by using locally saved models save(fit_rem, file = here("vignettes/forest-plots/fit_rem.rda"))

load(here("vignettes/forest-plots/fit_rem.rda"))

Use `forest()`

to draw the forest plot:

forest(fit_rem)

There are various options (see `?forest`

)

forest(fit_rem, level = .80, av_name = "Meta-Analytic\nEstimate", col_ridge = "purple", fill_ridge = "grey90")

Data points can also be shown (note this probably only makes sense with a meta-analytic model):

forest(fit_rem, show_data = T)

The `forest()`

function can be seamlessly applied to any multilevel model.

We use example data from the lme4 package.

data(sleepstudy, package = "lme4") head(sleepstudy)

A multilevel model with varying intercepts and slopes (effect of `Days`

):

fit_ml <- brm( Reaction ~ Days + (Days|Subject), data = sleepstudy, cores = 4 )

save(fit_ml, file = here("vignettes/forest-plots/fit_ml.rda"))

load(here("vignettes/forest-plots/fit_ml.rda"))

If there are multiple varying parameters, users can input a variable name:

forest(fit_ml, pars = "Days")

Or let the function automatically draw a plot with all the variables:

```
forest(fit_ml, digits=0)
```

You can also turn off the ridgeline plots (densities)

forest(fit_ml, density = F, digits=0)

mvuorre/brmstools documentation built on July 10, 2018, 7:49 a.m.

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