Add example for Python/R interoperability using mass univariate t-test by aman-coder03 · Pull Request #13729 · mne-tools/mne-python

aman-coder03 · 2026-03-09T15:17:42Z

Reference issue (if any)

What does this implement/fix?

adds a tutorial example that runs a 2 sample mass univariate t-test on Epochs data,.., first in python using scipy.stats then the same test in R via rpy2 showing that both give identical results. The goal is to show the users how to get data into R, run stats there, and then bring the results back into Python, as starting point for more complex R based workflows

Additional information

follows the approach suggested by @larsoner in the issue ...keeping it simple and focused on one clear use case rather than trying to build general purpose utility

aman-coder03 · 2026-03-09T17:09:43Z

windows 3.13 pip pre failure is unrelated to this PR, it's a missing nightly wheel for statsmodels>=0.15.0.dev697 on the scientific python nightly wheels index, which affects other PRs too

larsoner · 2026-03-09T17:11:24Z

Being fixed in #13728

larsoner · 2026-03-13T15:58:45Z

CircleCI failure is real

I think you need to add rpy2 to the doc dependency group in pyproject.toml

for more information, see https://pre-commit.ci

aman-coder03 · 2026-03-13T16:59:08Z

@larsoner the failure is because rpy2 requires R to be installed at build time, which isn't available in the CI environment. Would wrapping the rpy2 imports in a try/except to skip the R section gracefully when R isn't present be the right approach here?

larsoner · 2026-03-13T17:50:39Z

Can you try updating the CI to have R installed? Would be doable with an apt command

for more information, see https://pre-commit.ci

aman-coder03 · 2026-03-14T09:13:44Z

towncrier fragments errors about "Famous Raj Bhat" are pre existing and unrelated to this PR.. @larsoner

Famous077 · 2026-03-16T14:09:58Z

towncrier fragments errors about "Famous Raj Bhat" are pre existing and unrelated to this PR.. @larsoner

Hi @aman-coder03 , Can you specify where you are getting an error. Would Love to co-ordinate with you to fix the issue.

larsoner · 2026-03-16T19:04:48Z

Hi @aman-coder03 , Can you specify where you are getting an error. Would Love to co-ordinate with you to fix the issue.

No need, I fixed it in main and then merged main into this branch

aman-coder03 · 2026-03-16T19:51:06Z

thanks @larsoner !!

larsoner · 2026-03-16T20:00:57Z

@@ -1,5 +1,7 @@
 #!/bin/bash -ef

+sudo apt-get install -y r-base libtirpc-dev


This isn't the best place, tools/circleci_bash_env.sh would make more sense

larsoner

Example looks good

https://output.circle-artifacts.com/output/job/05c66585-d8d4-43fe-b5d3-bdb6fa583fc1/artifacts/0/html/auto_examples/preprocessing/r_interop.html#sphx-glr-auto-examples-preprocessing-r-interop-py

@drammock feel free to merge if you're happy, I defer to your (far) superior R experience!

drammock

In the long run, I think it would be better / more interesting to showcase an example of something where R/rpy2 actually makes it easier to achieve the desired result (i.e., demonstrate something that is hard to do in Python but easy in R). But for now, however, let's stick with the t-test (subject to the modifications I propose in the below comments)

drammock · 2026-03-17T15:07:26Z

file is in the wrong folder. This should be in stats folder, not preprocessing

drammock · 2026-03-17T15:10:38Z

@@ -0,0 +1 @@
+Add example showing how to run a mass-univariate t-test in both Python and R using ``rpy2``, demonstrating Python–R interoperability with :class:`~mne.Epochs` data by `Aman Srivastava`_. (:gh:`13729`)


Suggested change

Add example showing how to run a mass-univariate t-test in both Python and R using ``rpy2``, demonstrating Python–R interoperability with :class:`~mne.Epochs` data by `Aman Srivastava`_. (:gh:`13729`)

Add example showing how to interoperate with R using ``rpy2``, by `Aman Srivastava`_.

PR number will get added automatically, and the details (epochs, t-test) are not really the point.

drammock · 2026-03-17T15:22:20Z

+# We average over channels and time to get one value per epoch, then run
+# a 2-sample t-test comparing the two conditions.


this is... not something anyone would ever do in practice. What we show can be much simpler than what most real neuroscience studies do, but it should at least be plausible. Probably the shortest path to something plausible would be:

pick a few sensors as an "ROI" (ones that should differ between auditory L vs R conditions)

pick a typical ERP time window

average over just those channels and those times

do the t-test (1 observation per epoch)

Probably worthwhile to do a plot_compare_evokeds or similar, as a way to motivate what the stats are testing.

drammock · 2026-03-17T15:30:09Z

+with localconverter(default_converter + numpy2ri.converter):
+    r_left = ro.FloatVector(epochs_left)
+    r_right = ro.FloatVector(epochs_right)
+
+r_ttest = ro.r["t.test"]
+result = r_ttest(r_left, r_right, **{"var.equal": True})
+
+t_r = float(result.rx2("statistic")[0])
+p_r = float(result.rx2("p.value")[0])


these steps are the important "new learning" from this, so there should be more explanation/comments here. E.g., things like

rpy2.robjects (imported here as ro) has an attribute r that provides access to the R namespace, through a dictionary-like interface

Unlike Python, R functions can have parameter names that contain a ., so you may need to pass function arguments as a dict and unpack them with **

what is FloatVector and why do we need it

what is the rx2 attribute of the result, and why do we need the [0] after it

aman-coder03 · 2026-03-18T06:55:37Z

moved example to stats, added ROI + evoked plot, and explained the rpy2 API in more detail.

drammock · 2026-03-20T20:20:44Z

+# ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+#
+# We first plot the evoked responses to motivate the statistical test.
+# Auditory left vs right stimuli should differ over lateral temporal sensors.


EEG059 is not really lateral/temporal. Use MEG 1323

drammock · 2026-03-20T20:24:57Z

+# and a typical N1 time window (80–120 ms). This gives one value per epoch,
+# which is a plausible neuroscience analysis.
+
+roi_channels = ["EEG 059", "EEG 058", "EEG 057"]


Suggested change

roi_channels = ["EEG 059", "EEG 058", "EEG 057"]

roi_channels = ["MEG 1323"]

drammock · 2026-03-20T20:25:01Z

+    .crop(tmin_roi, tmax_roi)
+    .get_data(picks=roi_channels)
+    .mean(axis=(1, 2))
+)


unnecessary copying. something this should be fine:

epochs.crop(tmin, tmax).pick(roi_chs) epo_left = epochs["auditory/left"].get_data().mean(axis=(1, 2)) epo_right = epochs["auditory/right"].get_data().mean(axis=(1, 2))

drammock · 2026-03-20T20:29:42Z

+
+mne.viz.plot_compare_evokeds(
+    {"auditory/left": evoked_left, "auditory/right": evoked_right},
+    picks="EEG 059",


Suggested change

picks="EEG 059",

picks="MEG 1323",

drammock · 2026-03-20T20:30:33Z

+.. _r-interop:
+
+==============================================
+Mass-univariate t-test: Python and R compared


Let's make the point of the tutorial clearer in the title

Suggested change

Mass-univariate t-test: Python and R compared

Integrating with R via rpy2

aman-coder03 · 2026-03-21T08:02:36Z

thanks @drammock
addressed all your comments!!

drammock · 2026-03-23T15:37:37Z

thanks @aman-coder03

aman-coder03 · 2026-03-23T15:47:36Z

looking forward to contribute more @drammock
thanks for your guidance!!

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(mne-tools#13827) * [pre-commit.ci] pre-commit autoupdate (mne-tools#13839) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> Co-authored-by: Eric Larson <[email protected]> * FIX: Ref [skip azp] [skip actions] * BUG: Fix bug with logging level (mne-tools#13843) * fix env var in actions (mne-tools#13844) Co-authored-by: Scott Huberty <[email protected]> * TST: Add regression coverage for OPM topomap grouping via `plot_joint()` and `ICA` (mne-tools#13842) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Customize annotation colors (mne-tools#13838) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * DOC: Remove invalid ndarray option from colormap docstrings (mne-tools#13797) * Fix versionadded for annotation_colors (mne-tools#13853) * [dependabot]: Bump the actions group with 2 updates (mne-tools#13852) Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> * [pre-commit.ci] pre-commit autoupdate (mne-tools#13854) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> * MAINT: Links [circle deploy] [skip azp] [skip actions] * MAINT: add OPM overlap grouping helper (mne-tools#13847) * FIX: Correct fNIRS interpolation with reordered picks (mne-tools#13856) * MAINT: Modernize numpydoc checks (mne-tools#13865) * Allow concatenating `BaseRaw` objects (mne-tools#13263) Co-authored-by: Copilot <[email protected]> Co-authored-by: Eric Larson <[email protected]> * Add dark theme to Matplotlib-based raw.plot (mne-tools#13861) Co-authored-by: Copilot <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * FIX: Check [ci skip] * FIX: Sets [ci skip] * Update towncrier change type descriptions (mne-tools#13829) * fix numpydoc (missed YD01 ignore) (mne-tools#13868) * FIX: correct label orientation for 0-90 deg nodes in plot_connectivity_circle (mne-tools#13855) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Daniel McCloy <[email protected]> * [dependabot]: Bump the actions group with 3 updates (mne-tools#13871) Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> * [pre-commit.ci] pre-commit autoupdate (mne-tools#13873) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> * Add preload keyward argument to Inst.load_data() method call (mne-tools#13858) * MAINT: Make test dir read-only (mne-tools#13872) * BUG: improve FreeSurfer error message when executable not found (mne-tools#13874) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Eric Larson <[email protected]> * add CI description to contributing guide (mne-tools#13837) Co-authored-by: Daniel McCloy <[email protected]> * Fix grammar [ci skip] (mne-tools#13881) * FIX: handle missing __version__ in check_version (mne-tools#13870) Co-authored-by: Claude Sonnet 4.6 <[email protected]> * apply diataxis to tutorials/inverse/80_brainstorm_phantom_elekta.py (mne-tools#13584) Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * add AI policy (mne-tools#13883) * MAINT: Switch to pip for macOS and minimal jobs (mne-tools#13882) * MAINT: Update code credit (mne-tools#13878) * ENH: Allow passing source detector distances to beer lambert law (mne-tools#13875) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * MAINT: Update for vtk deprecation (mne-tools#13886) * ENH: Add overrides= parameter to read_raw_brainvision for BIDS header repair (mne-tools#13884) * Fix bug with ica.plot_properties (mne-tools#13885) * Fix `picks` being ignored in `Epochs.apply_function()` (mne-tools#13894) * Update describing changes in contributing guide (mne-tools#13895) * Add Zuna to related software list (mne-tools#13849) Co-authored-by: Daniel McCloy <[email protected]> * [dependabot]: Bump github/codeql-action from 4.35.2 to 4.35.3 in the actions group (mne-tools#13897) Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> Co-authored-by: Eric Larson <[email protected]> * DOC: Fix apply_function shape description for Epochs (mne-tools#13891) Co-authored-by: Eric Larson <[email protected]> * Raise warning and errors when np.nan provided to mne.stats.permutation_t_test(). (mne-tools#13813) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Erica R Peterson <[email protected]> * MAINT: Update dependency specifiers (mne-tools#13899) Co-authored-by: autofix-ci[bot] <114827586+autofix-ci[bot]@users.noreply.github.com> Co-authored-by: Eric Larson <[email protected]> * [dependabot]: Bump github/codeql-action from 4.35.3 to 4.35.4 in the actions group (mne-tools#13901) Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> * [pre-commit.ci] pre-commit autoupdate (mne-tools#13902) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> * MAINT: Remove workaround for old PySide6 (mne-tools#13900) * Add spherical montages (mne-tools#13903) * [dependabot]: Bump the actions group with 2 updates (mne-tools#13918) Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> * [pre-commit.ci] pre-commit autoupdate (mne-tools#13919) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> * MAINT: Update dependency specifiers (mne-tools#13916) Co-authored-by: autofix-ci[bot] <114827586+autofix-ci[bot]@users.noreply.github.com> Co-authored-by: Eric Larson <[email protected]> * BUG: set_eeg_reference list ch_type now applies per-type CAR by default (mne-tools#13920) * FIX: Avoid iteration errors caused by None when reading Nihon Kohden .LOG files (mne-tools#13915) * Fix drop_log dtype (mne-tools#13923) * Doc: add guidance on taking over a stale pull request (mne-tools#13877) Co-authored-by: Thomas S. Binns <[email protected]> Co-authored-by: Daniel McCloy <[email protected]> * FIX: Make set_eeg_reference working with a string for a channel name (mne-tools#13917) --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> Co-authored-by: Clemens Brunner <[email protected]> Co-authored-by: Aman Srivastava <[email protected]> Co-authored-by: Daniel McCloy <[email protected]> Co-authored-by: Himanshu Mahor <[email protected]> Co-authored-by: Scott Huberty <[email protected]> Co-authored-by: Victor Férat <[email protected]> Co-authored-by: Marijn van Vliet <[email protected]> Co-authored-by: Eric Larson <[email protected]> Co-authored-by: Aniket <[email protected]> Co-authored-by: Carina Forster <[email protected]> Co-authored-by: Thomas S. 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aman-coder03 requested review from agramfort, drammock and larsoner as code owners March 9, 2026 15:17

add mass univariate t-test python/R interoperability example

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aman-coder03 force-pushed the doc-r-interop branch from 55cfb78 to fd55fd3 Compare March 9, 2026 20:44

sharifhsn mentioned this pull request Mar 10, 2026

PERF: Speed up permutation cluster tests via Numba union-find + compact graph #13731

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aman-coder03 and others added 3 commits March 13, 2026 22:11

adding rpy2 to doc dependencies

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aman-coder03 and others added 6 commits March 13, 2026 23:29

install R

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add libtirpc-dev for rpy2 build

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fix rpy2 cross reference warnings

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Merge branch 'main' into doc-r-interop

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Merge branch 'main' into doc-r-interop

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move r_interop to stats and expand rpy2

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drammock approved these changes Mar 23, 2026

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drammock merged commit 6c94c0a into mne-tools:main Mar 23, 2026
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1himan mentioned this pull request Mar 29, 2026

rpy2 in API mode cannot be built without R. #13796

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		@@ -1,5 +1,7 @@
		#!/bin/bash -ef

		sudo apt-get install -y r-base libtirpc-dev

		@@ -0,0 +1 @@
		Add example showing how to run a mass-univariate t-test in both Python and R using ``rpy2``, demonstrating Python–R interoperability with :class:`~mne.Epochs` data by `Aman Srivastava`_. (:gh:`13729`) No newline at end of file

	Add example showing how to run a mass-univariate t-test in both Python and R using ``rpy2``, demonstrating Python–R interoperability with :class:`~mne.Epochs` data by `Aman Srivastava`_. (:gh:`13729`)
	Add example showing how to interoperate with R using ``rpy2``, by `Aman Srivastava`_.

		# We average over channels and time to get one value per epoch, then run
		# a 2-sample t-test comparing the two conditions.

	roi_channels = ["EEG 059", "EEG 058", "EEG 057"]
	roi_channels = ["MEG 1323"]

	Mass-univariate t-test: Python and R compared
	Integrating with R via rpy2

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