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Getting started with ustats

Source: vignettes/ustats.Rmd
ustats.Rmd

ustats is a thin R interface to the Python package u-stats, which computes higher-order U-statistics efficiently using Einstein summation (numpy.einsum / torch.einsum). This vignette covers the one part of the package that needs a little care — setting up the Python environment — and then shows basic usage.

Quick start 

install.packages("ustats")
library(ustats)

H <- matrix(rnorm(100), 10, 10)
ustat(list(H, H), "ab,bc->")

That is all most users need: on the first call, reticulate (>= 1.41) automatically downloads a private Python together with the required packages (u-stats, numpy, torch) into a cached environment, and reuses it in later sessions.

How the Python environment is resolved

ustats declares its Python dependencies via reticulate::py_require() when the package is loaded. When Python is first needed, reticulate resolves these requirements as follows:

  1. If you have already configured a Python environment — via reticulate::use_virtualenv(), reticulate::use_condaenv(), or the RETICULATE_PYTHON environment variable — that environment is used. It must contain u-stats, numpy, and (recommended) torch.
  2. Otherwise, reticulate provisions an ephemeral, cached environment containing the declared packages automatically. Nothing is installed into your system Python.

There are therefore three ways to set things up, from least to most manual.

Do nothing. The first call that touches Python triggers the automatic setup:

library(ustats)
ustat(list(matrix(rnorm(100), 10, 10)), "ab->")

Two things to know:

  • The first call downloads Python packages once; later calls and later R sessions reuse the cache.
  • On Linux, the default PyTorch build from PyPI bundles CUDA libraries (roughly 2.5 GB). If you do not have an NVIDIA GPU and prefer a small CPU-only build (roughly 200 MB), use Option 2 — or, before Python initializes, replace the declared requirement with a CPU-only one.

Option 2: a persistent environment with setup_ustats()

setup_ustats() creates a dedicated environment and installs all dependencies into it. By default it installs the CPU-only PyTorch build:

library(ustats)

setup_ustats()                # virtualenv/conda + CPU-only torch
setup_ustats(gpu = TRUE)      # default PyPI torch (CUDA-enabled on Linux)
setup_ustats(
  method  = "virtualenv",     # or "conda"
  envname = "r-ustats",
  persist = TRUE              # print the RETICULATE_PYTHON line to add
)                             # to your .Rprofile (no files are written)

For GPU builds on Windows, or for a wheel matching a specific CUDA version, see https://pytorch.org/get-started/locally/ and use Option 3.

Option 3: bring your own environment

If you already maintain a conda or virtualenv environment (for example, one with a carefully chosen CUDA-enabled PyTorch), install the one missing piece:

pip install u-stats

and tell reticulate to use that environment before Python initializes (i.e. right after loading the package, before the first ustat() call):

library(ustats)
reticulate::use_condaenv("your_env_name", required = TRUE)
# or: reticulate::use_virtualenv("~/.virtualenvs/your_env")

Alternatively, set RETICULATE_PYTHON to the path of the Python binary in .Renviron or .Rprofile, which takes effect for all sessions.

Verifying the setup 

check_ustats_setup()
#> === ustats Environment Status ===
#>
#> [OK] Python: /path/to/python
#>   Version: 3.12
#> [OK] u_stats available
#> [OK] NumPy available
#> [OK] PyTorch available (version 2.5.1, CUDA available)
#>
#> ---------------------------------
#>  Environment fully ready (Torch backend available)

Computing U-statistics

ustat() takes a list of kernel tensors (R vectors or matrices) and an Einstein summation expression describing how their indices are contracted, with distinct letters ranging over distinct observation indices:

library(ustats)

set.seed(1)
n <- 300

H1 <- rnorm(n)
H2 <- matrix(rnorm(n * n), n, n)
H3 <- rnorm(n)

result <- ustat(
  tensors    = list(H1, H2, H2, H3),
  expression = "a,ab,bc,c->",
  backend    = "torch",  # falls back to numpy if torch is unavailable
  average    = TRUE,     # divide by the number of index tuples
  dtype      = NULL      # auto: float32 on GPU, float64 on CPU
)
print(result)

The index structure can equivalently be given as a list of numeric index vectors, which is convenient when the expression is built programmatically:

ustat(list(H1, H2, H2, H3), list(1, c(1, 2), c(2, 3), 3))

GPU acceleration

With backend = "torch", computations run on the GPU automatically whenever PyTorch reports that CUDA is available:

torch <- reticulate::import("torch")
torch$cuda$is_available()

Troubleshooting

  • check_ustats_setup() reports a missing module. The session is bound to a Python environment that lacks the dependency. Either install it there (pip install u-stats), or restart R and select a different environment (Options 2-3 above).
  • reticulate ignores use_condaenv() / RETICULATE_PYTHON. reticulate binds to a single Python per R session, at the moment Python is first initialized. Restart R and configure the environment before anything touches Python.
  • The first call seems stuck. It is most likely downloading PyTorch; see Options 1-2 for how to choose the much smaller CPU-only build.
  • ustat() warns “Torch backend not available”. The bound environment has no PyTorch; the computation falls back to NumPy, which is slower and can be less numerically stable. Install torch with setup_ustats() or pip install torch --index-url https://download.pytorch.org/whl/cpu.