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Update citations format and fix typos in paper and references
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dadelforge committed Dec 21, 2024
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2 changes: 2 additions & 0 deletions paper.bib
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Expand Up @@ -142,6 +142,7 @@ @inproceedings{seabold_statsmodels_2010
booktitle = {9th {Python} in {Science} {Conference}},
author = {Seabold, Skipper and Perktold, Josef},
year = {2010},
doi = {10.25080/Majora-92bf1922-011}
}

@inproceedings{mckinney_data_2010,
Expand Down Expand Up @@ -185,6 +186,7 @@ @article{pedregosa_scikit-learn_2011
author = {Pedregosa, F. and Varoquaux, G. and Gramfort, A. and Michel, V. and Thirion, B. and Grisel, O. and Blondel, M. and Prettenhofer, P. and Weiss, R. and Dubourg, V. and Vanderplas, J. and Passos, A. and Cournapeau, D. and Brucher, M. and Perrot, M. and Duchesnay, E.},
year = {2011},
pages = {2825--2830},
url = {http://jmlr.org/papers/v12/pedregosa11a.html}
}

@book{durbin_time_2012,
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18 changes: 9 additions & 9 deletions paper.md
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Expand Up @@ -34,10 +34,10 @@ bibliography: paper.bib

Singular Spectrum Analysis (SSA) is a method developed in the 1980s for
analyzing and decomposing time-series data
[@broomhead_extracting_1986, @vautard_singular_1989]. Using time-delayed
[@broomhead_extracting_1986; @vautard_singular_1989]. Using time-delayed
trajectories or covariance matrices, SSA takes advantage of temporal
dependencies to identify structured components such as trends and cycles
[@elsner_singular_1996, golyandina_singular_2020]. Time-series decomposition
[@elsner_singular_1996; @golyandina_singular_2020]. Time-series decomposition
has various applications, including denoising, filtering, signal modeling,
interpolation (or gap filling), and extrapolation (or forecasting).

Expand All @@ -47,13 +47,13 @@ advantage of SSA is the ability to extract nonlinear trends and phase- or
amplitude-modulated cycles. The Singular Spectrum Analysis Library (`ssalib`)
is a Python package that simplifies SSA implementation and visualization
through an easy-to-use API, operating time series as `numpy.Array`
[@harris_array_2020] or `pandas.Series` [mckinney_data_2010] objects, and
[@harris_array_2020] or `pandas.Series` [@mckinney_data_2010] objects, and
requiring minimal knowledge of linear algebra. It uses decomposition algorithms
from robust Python scientific packages like `numpy` [@harris_array_2020],
`scipy` [@virtanen_scipy_2020], and `sklearn` [@pedregosa_scikit-learn_2011].
SSALib also incorporates the Monte Carlo SSA approach [@allen_monte_1996] for
identifying significant components by comparison to randomly generated data
(i.e., surogate data), relying on `statsmodels` [@seabold_statsmodels_2010] for
(i.e., surrogate data), relying on `statsmodels` [@seabold_statsmodels_2010] for
fitting autoregressive processes and generate the surrogate data.

The basic Singular Spectrum Analysis (SSA) algorithm for univariate time series,
Expand All @@ -67,9 +67,9 @@ evolved beyond being a single method and has transformed into a modular
analytical framework, consisting of interchangeable steps that can be combined
into multiple variants. Consequently, both experts and newcomers would benefit
from SSA software that allows for configurable analyses, saving time in the
process. Moreover, SSA empirical nature relies heavily on data visualization.
This makes the implementation of software essential for providing users with
established visualization features.
process. Moreover, SSA empirical nature relies heavily on data and SSA outcomes
visualization. This makes the implementation of software essential for
providing users with established visualization features.

@golyandina_singular_2020 mention some existing software dedicated to
SSA, such as the GUI-based SSA-MTM toolkit, Caterpillar-SSA software, and the
Expand Down Expand Up @@ -98,11 +98,11 @@ Toeplitz structure, meaning that its diagonal values are identical.
Regarding Step 2, `ssalib` relies on Singular Value Decomposition (SVD) with
methods implemented in the NumPy, SciPy, and Scikit-learn libraries. In
particular, scikit-learn features a randomized SVD algorithm for efficient
decomposition [halko_finding_2010]. Step 3 involves visualizations created with
decomposition [@halko_finding_2010]. Step 3 involves visualizations created with
Matplotlib, drawing inspiration from the R rSSA package
[@golyandina_singular_2018].

Significance testing is based on the work of Allen and Smith (1996). In
Significance testing is based on the work of @allen_monte_1996. In
`ssalib`, an autoregressive (AR) process of a specified maximum order is fitted
relying on a state space modeling framework [@durbin_time_2012] and utilizing
the `statsmodels` library [@seabold_statsmodels_2010]. The AR random surrogates
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