doc: materials for Kalman filter articles by pipipyau · Pull Request #133 · Digiratory/FluctuationAnalysisTools

pipipyau · 2026-06-16T16:38:30Z

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kilo-code-bot · 2026-06-16T16:44:37Z

Code Review Summary

Status: No Issues Found | Recommendation: Merge

Files Reviewed (1 file)

research/kalman_filter/reconstruction_of_long_term_complex_system_dynamics/dendrochronological_series.ipynb

Previous Review Summaries (5 snapshots, latest commit 2cb28c6)

Current summary above is authoritative. Previous snapshots are kept for context only.

Previous review (commit `2cb28c6`)

Status: No Issues Found | Recommendation: Merge

Resolved Issues (from previous review)

All previously identified issues in dendrochronological_series.ipynb have been addressed:

File	Line	Issue	Fix	Status
`dendrochronological_series.ipynb`	321 (new)	dplR 71-series path pointed to wrong directory	Now uses `DPLR_DIR` variable	✅ Fixed
`dendrochronological_series.ipynb`	324 (new)	dplR 15-series path pointed to wrong directory	Now uses `DPLR_DIR` variable	✅ Fixed
`dendrochronological_series.ipynb`	31	Output directory may not exist before savefig	Added `OUTPUT_DATA_DIR.mkdir(parents=True, exist_ok=True)`	✅ Fixed
`.gitignore`	-	Broad `research/data` exclusion hid outputs	Replaced with specific paths	✅ Fixed
`dendrochronological_series.ipynb`	160 (new)	`init_kf()` only assigned `F` for Kasdin method	Removed conditional, F is now always assigned	✅ Fixed

New Changes in This Increment

File	Change	Assessment
`StatTools/analysis/dpcca.py`	Changed `np.linalg.inv(R)` to `np.linalg.pinv(R, rcond=1e-10)`	✅ Good - improves numerical stability for singular/near-singular matrices
`pyproject.toml`	Pinned `setuptools-scm==8.2.0`	✅ Acceptable - intentional version lock
`research/kalman_filter/README.md`	Added documentation	✅ No issues
`research/kalman_filter/__init__.py`	Added module exports	✅ No issues
`examples/svd_dfa_demo.ipynb`	Moved from research/kalman_filter/	✅ No issues
`data/tree_rwi.csv`	Added tree ring width data	✅ No issues

Files Reviewed (8 files)

.gitignore - 0 issues
StatTools/analysis/dpcca.py - 0 issues
pyproject.toml - 0 issues
research/kalman_filter/README.md - 0 issues
research/kalman_filter/__init__.py - 0 issues
research/kalman_filter/reconstruction_of_long_term_complex_system_dynamics/__init__.py - 0 issues
research/kalman_filter/reconstruction_of_long_term_complex_system_dynamics/dendrochronological_series.ipynb - 0 issues (all fixes verified)
research/kalman_filter/reconstruction_of_long_term_complex_system_dynamics/data/tree_rwi.csv - 0 issues (data added)

Previous review (commit `2ccf3dc`)

Status: No Issues Found | Recommendation: Merge

All previously identified issues have been addressed in this incremental commit:

Resolved Issues (from previous review)

File	Line	Issue	Fix	Status
`dendrochronological_series.ipynb`	316 (old) → 321 (new)	dplR 71-series path pointed to wrong directory	Now uses `DPLR_DIR` variable	✅ Fixed
`dendrochronological_series.ipynb`	319 (old) → 324 (new)	dplR 15-series path pointed to wrong directory	Now uses `DPLR_DIR` variable	✅ Fixed
`dendrochronological_series.ipynb`	401 (old) → 406 (new)	Output directory may not exist before savefig	Added `OUTPUT_DATA_DIR.mkdir(parents=True, exist_ok=True)`	✅ Fixed
`.gitignore`	23 (old)	Broad `research/data` exclusion hid outputs	Replaced with specific paths	✅ Fixed
`dendrochronological_series.ipynb`	154 (old) → 160 (new)	`init_kf()` only assigned `F` for Kasdin method	Removed conditional, F is now always assigned	✅ Fixed

Files Reviewed (3 files)

.gitignore - 0 issues (updated correctly)
pyproject.toml - 0 issues (version pin change is intentional)
dendrochronological_series.ipynb - 0 issues (all fixes verified)

Previous review (commit `e2b2e55`)

Status: 5 Issues Found | Recommendation: Address before merge

Overview

Severity	Count
CRITICAL	0
WARNING	3
SUGGESTION	2

Issue Details (click to expand)

CRITICAL

File	Line	Issue

WARNING

File	Line	Issue
`research/kalman_filter/reconstruction_of_long-term_complex_system_dynamics/dendrochronological_series.ipynb`	316	dplR 71-series output path points to `.../data` instead of the bundled file under `.../dplR/results/dplr/`.
`research/kalman_filter/reconstruction_of_long-term_complex_system_dynamics/dendrochronological_series.ipynb`	319	dplR 15-series augmented output path points to `.../data` instead of the bundled file under `.../dplR/results/dplr/`.
`research/kalman_filter/reconstruction_of_long-term_complex_system_dynamics/dendrochronological_series.ipynb`	401	`plt.savefig()` writes to `research/data/output/...`, but that directory is not created in the notebook or present in the repo.

SUGGESTION

File	Line	Issue
`research/kalman_filter/reconstruction_of_long-term_complex_system_dynamics/dendrochronological_series.ipynb`	154	`init_kf()` only assigns `F` for `method == "Kasdin"` but passes `F` unconditionally to `KalmanFilter`.

Other Observations (not in diff)

Issues found in unchanged code that cannot receive inline comments:

File	Line	Issue
`.gitignore`	23	`research/data` remains ignored, so generated outputs/model signals under that path are untracked and other contributors may not be able to reproduce analyses that depend on them.

Files Reviewed (18 files)

research/kalman_filter/README.md - 0 issues
research/kalman_filter/reconstruction_of_long-term_complex_system_dynamics/data/tree_rwi.csv - 0 issues
research/kalman_filter/reconstruction_of_long-term_complex_system_dynamics/dendrochronological_series.ipynb - 4 issues
research/kalman_filter/reconstruction_of_long-term_complex_system_dynamics/dendrochronological_series_h_acf_noise.ipynb - 0 issues (deleted)
research/kalman_filter/reconstruction_of_long-term_complex_system_dynamics/dplR/README.md - 0 issues
research/kalman_filter/reconstruction_of_long-term_complex_system_dynamics/dplR/data/norw010-rwl-noaa.txt - 0 issues
research/kalman_filter/reconstruction_of_long-term_complex_system_dynamics/dplR/data/norw010.rwl - 0 issues
research/kalman_filter/reconstruction_of_long-term_complex_system_dynamics/dplR/data/norw010.txt - 0 issues
research/kalman_filter/reconstruction_of_long-term_complex_system_dynamics/dplR/examples/preprocessingtrw.ipynb - 0 issues
research/kalman_filter/reconstruction_of_long-term_complex_system_dynamics/dplR/results/dplr/tree_rwi_dplr_15.csv - 0 issues
research/kalman_filter/reconstruction_of_long-term_complex_system_dynamics/dplR/results/dplr/tree_rwi_dplr_71.csv - 0 issues
research/kalman_filter/reconstruction_of_long-term_complex_system_dynamics/dplR/results/python/tree_rwi_python_15.csv - 0 issues
research/kalman_filter/reconstruction_of_long-term_complex_system_dynamics/dplR/results/python/tree_rwi_python_71.csv - 0 issues
research/kalman_filter/reconstruction_of_long-term_complex_system_dynamics/dplR/scripts/Download_rwl.R - 0 issues
research/kalman_filter/reconstruction_of_long-term_complex_system_dynamics/dplR/scripts/Preprocess_rwl.R - 0 issues
research/kalman_filter/reconstruction_of_long-term_complex_system_dynamics/dplR/scripts/preprocessingtrw.py - 0 issues
research/kalman_filter/reconstruction_of_long-term_complex_system_dynamics/gen_filter_save.py - 0 issues
research/kalman_filter/reconstruction_of_long-term_complex_system_dynamics/synthetic_benchmarks.ipynb - 0 issues

Previous review (commit `9d03f1d`)

Status: 5 Issues Found | Recommendation: Address before merge

Overview

Severity	Count
CRITICAL	0
WARNING	3
SUGGESTION	2

Issue Details (click to expand)

CRITICAL

File	Line	Issue

WARNING

File	Line	Issue
`research/kalman_filter/reconstruction_of_long-term_complex_system_dynamics/dendrochronological_series.ipynb`	316	dplR 71-series output path points to `.../data` instead of the bundled file under `.../dplR/results/dplr/`.
`research/kalman_filter/reconstruction_of_long-term_complex_system_dynamics/dendrochronological_series.ipynb`	319	dplR 15-series augmented output path points to `.../data` instead of the bundled file under `.../dplR/results/dplr/`.
`research/kalman_filter/reconstruction_of_long-term_complex_system_dynamics/dendrochronological_series.ipynb`	401	`plt.savefig()` writes to `research/data/output/...`, but that directory is not created in the notebook or present in the repo.

SUGGESTION

File	Line	Issue
`research/kalman_filter/reconstruction_of_long-term_complex_system_dynamics/dendrochronological_series.ipynb`	154	`init_kf()` only assigns `F` for `method == "Kasdin"` but passes `F` unconditionally to `KalmanFilter`.

Other Observations (not in diff)

Issues found in unchanged code that cannot receive inline comments:

File	Line	Issue
`.gitignore`	23	`research/data` remains ignored, so generated outputs/model signals under that path are untracked and other contributors may not be able to reproduce analyses that depend on them.

Files Reviewed (18 files)

research/kalman_filter/README.md - 0 issues
research/kalman_filter/reconstruction_of_long-term_complex_system_dynamics/data/tree_rwi.csv - 0 issues
research/kalman_filter/reconstruction_of_long-term_complex_system_dynamics/dendrochronological_series.ipynb - 4 issues
research/kalman_filter/reconstruction_of_long-term_complex_system_dynamics/dendrochronological_series_h_acf_noise.ipynb - 0 issues (deleted)
research/kalman_filter/reconstruction_of_long-term_complex_system_dynamics/dplR/README.md - 0 issues
research/kalman_filter/reconstruction_of_long-term_complex_system_dynamics/dplR/data/norw010-rwl-noaa.txt - 0 issues
research/kalman_filter/reconstruction_of_long-term_complex_system_dynamics/dplR/data/norw010.rwl - 0 issues
research/kalman_filter/reconstruction_of_long-term_complex_system_dynamics/dplR/data/norw010.txt - 0 issues
research/kalman_filter/reconstruction_of_long-term_complex_system_dynamics/dplR/examples/preprocessingtrw.ipynb - 0 issues
research/kalman_filter/reconstruction_of_long-term_complex_system_dynamics/dplR/results/dplr/tree_rwi_dplr_15.csv - 0 issues
research/kalman_filter/reconstruction_of_long-term_complex_system_dynamics/dplR/results/dplr/tree_rwi_dplr_71.csv - 0 issues
research/kalman_filter/reconstruction_of_long-term_complex_system_dynamics/dplR/results/python/tree_rwi_python_15.csv - 0 issues
research/kalman_filter/reconstruction_of_long-term_complex_system_dynamics/dplR/results/python/tree_rwi_python_71.csv - 0 issues
research/kalman_filter/reconstruction_of_long-term_complex_system_dynamics/dplR/scripts/Download_rwl.R - 0 issues
research/kalman_filter/reconstruction_of_long-term_complex_system_dynamics/dplR/scripts/Preprocess_rwl.R - 0 issues
research/kalman_filter/reconstruction_of_long-term_complex_system_dynamics/dplR/scripts/preprocessingtrw.py - 0 issues
research/kalman_filter/reconstruction_of_long-term_complex_system_dynamics/gen_filter_save.py - 0 issues
research/kalman_filter/reconstruction_of_long-term_complex_system_dynamics/synthetic_benchmarks.ipynb - 0 issues

Previous review (commit `d782c27`)

Status: No Issues Found | Recommendation: Merge

Files Reviewed (6 files)

.gitignore - 1 line changed
StatTools/analysis/dpcca.py - 1 line changed
examples/svd_dfa_demo.ipynb - file renamed
research/kalman_filter/README.md - new file
research/kalman_filter/reconstruction_of_long-term_complex_system_dynamics/dendrochronological_series_h_acf_noise.ipynb - new file
research/kalman_filter/reconstruction_of_long-term_complex_system_dynamics/gen_filter_save.py - new file
research/kalman_filter/reconstruction_of_long-term_complex_system_dynamics/synthetic_benchmarks.ipynb - new file

Other Observations (not in diff)

File	Line	Issue
`.gitignore`	23	Adding `research/data` means all data files referenced by the new notebooks (`research/data/tree/`, `research/data/model_signals/`) are untracked. Other contributors will not be able to reproduce the analysis from this repo alone without separately obtaining the data.
`research/kalman_filter/README.md`	2	Typo: "numererical" should be "numerical"
`research/kalman_filter/README.md`	2	Typo: "genertion" should be "generation"
`research/kalman_filter/reconstruction_of_long-term_complex_system_dynamics/synthetic_benchmarks.ipynb`	15	Hardcoded absolute path `Path("/Users/a1/Downloads/model_signals")` will break for any user other than the original author.
`research/kalman_filter/reconstruction_of_long-term_complex_system_dynamics/dendrochronological_series_h_acf_noise.ipynb`	(in init_kf cell)	`init_kf()` only sets `F` for method=="Kasdin" but uses `F` unconditionally when creating `KalmanFilter`. Currently safe because `method` is always "Kasdin", but a latent bug if the method parameter is ever changed.

_{Reviewed by step-3.7-flash · Input: 91.4K · Output: 12.1K · Cached: 514.2K}

Co-authored-by: Copilot Autofix powered by AI <223894421+github-code-quality[bot]@users.noreply.github.com>

…' of https://github.com/Digiratory/FluctuationAnalysisTools into 132-reconstruction-of-long-term-complex-system-dynamics

+x = x.set_index("year").apply(pd.to_numeric, errors="coerce")
+
+if keep_series is not None:
+    missing = sorted(set(keep_series) - set(x.columns))


doc: materials for Kalman filter articles

d782c27

pipipyau requested a review from Sinitca-Aleksandr June 16, 2026 16:38

pipipyau self-assigned this Jun 16, 2026

pipipyau added documentation Improvements or additions to documentation enhancement New feature or request labels Jun 16, 2026

pipipyau linked an issue Jun 16, 2026 that may be closed by this pull request

Reconstruction of long-term complex system dynamics #132

Open

pipipyau added 2 commits June 16, 2026 20:01

doc: dplr data

c22244d

format: dplr

9d03f1d

github-code-quality Bot found potential problems Jun 16, 2026

View reviewed changes

Comment thread ..._filter/reconstruction_of_long_term_complex_system_dynamics/dplR/scripts/preprocessingtrw.py Fixed

kilo-code-bot Bot reviewed Jun 16, 2026

View reviewed changes

pipipyau and others added 5 commits June 17, 2026 12:33

Potential fix for pull request finding 'Unreachable code'

e2b2e55

Co-authored-by: Copilot Autofix powered by AI <223894421+github-code-quality[bot]@users.noreply.github.com>

refactor: update paths

cc6993b

Merge branch '132-reconstruction-of-long-term-complex-system-dynamics…

05b1506

…' of https://github.com/Digiratory/FluctuationAnalysisTools into 132-reconstruction-of-long-term-complex-system-dynamics

build: setuptools-scm version

2ccf3dc

refactor: rename folder

2cb28c6

github-code-quality Bot found potential problems Jun 23, 2026

View reviewed changes

Comment thread ..._filter/reconstruction_of_long_term_complex_system_dynamics/dplR/scripts/preprocessingtrw.py

x = x.set_index("year").apply(pd.to_numeric, errors="coerce")

if keep_series is not None:

missing = sorted(set(keep_series) - set(x.columns))

doc: update distribution figure

5534d63

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doc: materials for Kalman filter articles - #133

doc: materials for Kalman filter articles#133
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Code Review Summary

Previous review (commit 2cb28c6)

Resolved Issues (from previous review)

New Changes in This Increment

Previous review (commit 2ccf3dc)

Resolved Issues (from previous review)

Previous review (commit e2b2e55)

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CRITICAL

WARNING

SUGGESTION

Previous review (commit 9d03f1d)

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Previous review (commit d782c27)

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kilo-code-bot Bot commented Jun 16, 2026 •

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