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bartisan: Generalized Bayesian Additive Regression Trees

Overview

Bayesian additive regression trees (BART) estimate a regression function as a sum of small trees, so nonlinearity and interactions are found rather than specified. bartisan does that for response distributions that standard BART cannot reach, using the Laplace-approximation reversible-jump sampler of Linero (2025), which relaxes the requirement that the leaf parameters be integrable in closed form. That requirement ties standard BART to a Gaussian likelihood. Relaxing it generalizes BART much as a generalized linear model extends linear regression: the analyst can choose the response distribution.

Models are specified with a formula, a data frame, and a family, just as in glm(). bartisan accepts standard stats::family objects without modification. Beyond them come the families that have no glm() counterpart: negative binomial, ordinal, multinomial, beta and ordered beta, zero-inflated counts, a Tweedie compound Poisson, accelerated failure time and proportional hazards models for right-censored times, location-scale regression, a Dirichlet process mixture for the error distribution, and a log density written as an R function. Decision rules are smooth by default, in the manner of Linero and Yang (2018), which fits a smoother function than the step functions of standard BART.

bartisan supports varying-coefficient models, where the effect of a predictor receives its own forest, a special case of which is the Bayesian causal forest (BCF) model for estimating treatment effects. Along with this is an interface for estimating average treatment effects from BART and BCF models. In addition, bartisan supports random intercepts BART models.

Integration is provided with the future and progressr packages for parallel processing and progress bars.

Installation

You can install the current stable version of bartisan from CRAN with:

install.packages("bartisan")

You can install the development version of bartisan from GitHub with:

# install.packages("pak")
pak::pak("ngreifer/bartisan")

Installing from source, which the development version always requires, compiles C++ and so needs a C++17 toolchain.

Example

The rhc dataset in bartisan holds 1500 critically ill patients from the SUPPORT study, recording whether each was given right heart catheterization on admission to intensive care, whether they died during follow-up, and thirteen covariates measured beforehand (Connors et al. 1996). Fitting a model to it takes one call, and the family is the one glm() would be given:

library(bartisan)

data("rhc")
set.seed(123)

fit <- bartisan(death ~ rhc + age + sex + race + edu + pafi + 
                  paco2 + crea + surv2m + card,
                data = rhc, family = binomial())

fit
#> Generalized BART
#> 
#> Call:
#> bartisan(formula = death ~ rhc + age + sex + race + edu + pafi + 
#>     paco2 + crea + surv2m + card, data = rhc, family = binomial())
#> 
#> Family: "binomial" with the "logit" link
#> Observations: 1500
#> Structure: 1 forest of 50 trees, soft decision rules
#> Draws: 800 kept after 200 warmup

Calling summary() on the fit gives a quick check of convergence and the predictors used most often to split the trees, and points to the functions that examine each of these in full:

summary(fit)
#> Convergence and mixing
#> 
#> Log likelihood: R-hat 1.039, bulk ESS 98, tail ESS 185, over 1 chain
#> 
#> ℹ Use diagnose() (`?bartisan::diagnose`) to examine convergence and mixing
#>   diagnostics.
#> 
#> Variable importance
#> 
#> Predictors ranked by use; 5 of 10 shown.
#>  variable prop_used prop_splits splits
#>    surv2m         1       0.141   10.6
#>       age         1       0.109    8.3
#>     paco2         1       0.109    8.2
#>       edu         1       0.095    7.2
#>       sex         1       0.093    7.0
#> 
#> ℹ Use variable_importance() (`?bartisan::variable_importance`) to examine
#>   variable importance.
#> 
#> Further tools
#> 
#> ℹ Use loo() (`?bartisan::loo.bartisan_fit`) to compare this fit with others, or
#>   kfold() (`?bartisan::kfold.bartisan_fit`) if `loo()` reports many Pareto k
#>   values above 0.7.
#> ℹ Use partial_dependence() (`?bartisan::partial_dependence`) and plot()
#>   (`?bartisan::plot.bartisan_fit`) to view the partial dependence of the
#>   predictions on a predictor.

Nothing had to be specified about which predictors matter, which are curved, or which interact. plot() after partial_dependence() shows what the model made of one of them, here the study’s own estimate of each patient’s chance of surviving two months:

partial_dependence(fit, ~ surv2m) |>
  plot() +
  ggplot2::labs(x = "Estimated probability of surviving two months",
                y = "Fitted probability of death")

A forest has no coefficients, so an effect is a contrast between what the model predicts under one value of a predictor and under another, averaged over the sample. Every posterior draw goes through that contrast, so what comes back is a credible interval rather than a standard error:

estimate_effect(fit, treat = "rhc")
#> Average treatment effect (difference)
#> 
#> Treatment: `rhc`
#> Averaged over 1500 units
#> 
#>     contrast estimate  lower upper    n
#>  Y[1] - Y[0]    0.064 0.0143  0.11 1500
#> 
#> Average potential outcomes
#> 
#>  quantity estimate lower upper
#>      Y[0]    0.631 0.602 0.659
#>      Y[1]    0.695 0.656 0.732
#> 
#> ℹ estimate is the posterior mean; lower and upper bound the 95% equal-tailed
#>   credible interval.
#> ℹ Y[a] is the average response with `rhc` set to "a".

To examine effect heterogeneity, one can generate a plot of conditional effect estimates for all units:

estimate_effect(fit, treat = "rhc", estimand = "CATE") |>
  plot()

Learning More

vignette("bartisan") is the place to start. It carries one analysis from the formula through to the estimates, and each of its sections points at the guide that takes that step further:

A fitted model also works with the packages that already read Bayesian fits: marginaleffects for a wider range of estimands, loo for model comparison, bayesplot and posterior for the draws themselves, and performance for fit statistics. Load one and call its functions on the fit; there is nothing to set up.

Citing bartisan

bartisan implements the sampler of Linero (2025), and its MCMC engine is adapted from that paper’s FlexBart reference implementation. Please cite the method and the package both, the latter with its version number, which citation("bartisan") supplies. The smooth decision rules are those of Linero and Yang (2018). Both papers are listed under References below.

Questions and Bug Reports

Please file an issue at https://github.com/ngreifer/bartisan/issues, with a reproducible example where the report concerns a fit.

References

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.