From 5d30f73bc400e38c6f76af33a39e7c212ca11ce2 Mon Sep 17 00:00:00 2001 From: Arshed Nabeel Date: Wed, 18 Sep 2024 10:43:17 +0530 Subject: [PATCH 1/2] Add new datasets, notebooks, and citations in the docs --- docs/source/citation.rst | 4 ++-- docs/source/datasets.rst | 12 ++++++------ docs/source/index.rst | 2 +- docs/source/tutorials.rst | 13 +++++++++++++ 4 files changed, 22 insertions(+), 9 deletions(-) diff --git a/docs/source/citation.rst b/docs/source/citation.rst index 24bfdd7..4354431 100644 --- a/docs/source/citation.rst +++ b/docs/source/citation.rst @@ -1,6 +1,6 @@ Citing PyDaddy ============== -If you are using this package or any of the included code in your research, please cite the associated manuscript as follows: +If you are using this package in your research, please cite the associated paper as follows: -Nabeel, A., Karichannavar, A., Palathingal, S., Jhawar, J., Brückner, D., Danny Raj, M., & Guttal, V. (2022). PyDaddy: A Python package for discovering stochastic dynamical equations from timeseries data. arXiv preprint arXiv:2205.02645. +Nabeel, A., Karichannavar, A., Palathingal, S., Jhawar, J., Brückner, D. B., Danny Raj, M., & Guttal, V., "Discovering stochastic dynamical equations from ecological time series data", arXiv preprint `arXiv:2205.02645 `_, to appear in *The American Naturalist*. \ No newline at end of file diff --git a/docs/source/datasets.rst b/docs/source/datasets.rst index 7b37f2e..c87eed2 100644 --- a/docs/source/datasets.rst +++ b/docs/source/datasets.rst @@ -10,15 +10,15 @@ PyDaddy comes pre-packaged with several sample datasets. These can be loaded eas The following sample datasets are available: - :code:`fish-data-etroplus`: Group polarization data from a fish schooling experiment [1]_. - - :code:`model-data-scalar-pairwise` and :code:`model-data-scalar-ternary`: Scalar (1-D) simulated datasets generated from a stochastic Gillespie simulation, with pairwise and ternary interaction models respectively [1]_ [2]_. - - :code:`model-data-vector-pairwise` and :code:`model-data-vector-ternary`: Vector (2-D) simulated datasets generated from a stochastic Gillespie simulation, with pairwise and ternary interaction models respectively [1]_ [2]_. + - :code:`cell-data-cellhopping`: Dataset from a confined cell migration experiment [2]_ + - :code:`model-data-scalar-pairwise` and :code:`model-data-scalar-ternary`: Scalar (1-D) simulated datasets generated from a stochastic Gillespie simulation, with pairwise and ternary interaction models respectively [1]_ [3]_. + - :code:`model-data-vector-pairwise` and :code:`model-data-vector-ternary`: Vector (2-D) simulated datasets generated from a stochastic Gillespie simulation, with pairwise and ternary interaction models respectively [1]_ [3]_. The fish schooling dataset contains the time series of the group polarization vector $\mathbf m$ (2-dimensional), for a group of 15 fish (\emph{Etroplus suratensis}). The polarization time series is available at a uniform interval of 0.12 second. The dataset contains many missing data points [1]_. The simulated datasets were generated using a continuous-time stochastic simulation algorithm, with pairwise and ternary interaction models respectively. Each simulated time series was resampled to a suitable uniform sampling interval [1]_ [2]_. Simulated datasets are provided for both 1-D and 2-D. -.. [1] Jhawar, J., Morris, R. G., Amith-Kumar, U. R., Danny Raj, M., Rogers, T., Rajendran, H., & Guttal, V. (2020). Noise-induced schooling of fish. Nature Physics, 16(4), 488-493. -.. [2] Jhawar, J., & Guttal, V. (2020). Noise-induced effects in collective dynamics and inferring local interactions from data. Philosophical Transactions of the Royal Society B, 375(1807), 20190381. - - +.. [1] Jhawar, J., Morris, R. G., Amith-Kumar, U. R., Danny Raj, M., Rogers, T., Rajendran, H., & Guttal, V. (2020). Noise-induced schooling of fish. Nature Physics, 16(4), 488-493 (`doi `_). +.. [2] Brückner, D. B., Fink, A., Schreiber, C. et al. Stochastic nonlinear dynamics of confined cell migration in two-state systems. Nat. Phys. 15, 595–601 (2019) (`doi `_. +.. [3] Jhawar, J., & Guttal, V. (2020). Noise-induced effects in collective dynamics and inferring local interactions from data. Philosophical Transactions of the Royal Society B, 375(1807), 20190381. (`doi `_) diff --git a/docs/source/index.rst b/docs/source/index.rst index 1deac72..6d3847a 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -33,7 +33,7 @@ Citation If you are using this package in your research, please cite the associated paper as follows: -Nabeel, A., Karichannavar, A., Palathingal, S., Jhawar, J., Brückner, D. B., Danny Raj, M., & Guttal, V., "Discovering stochastic dynamical equations from ecological time series data", arXiv preprint [arXiv:2205.02645](https://arxiv.org/abs/2205.02645), to appear in *The American Naturalist*. +Nabeel, A., Karichannavar, A., Palathingal, S., Jhawar, J., Brückner, D. B., Danny Raj, M., & Guttal, V., "Discovering stochastic dynamical equations from ecological time series data", arXiv preprint `arXiv:2205.02645 `_, to appear in *The American Naturalist*. Contents -------- diff --git a/docs/source/tutorials.rst b/docs/source/tutorials.rst index 0b3aba3..418bde1 100644 --- a/docs/source/tutorials.rst +++ b/docs/source/tutorials.rst @@ -49,6 +49,12 @@ Tutorials (no installation required) .. |github-cell| image:: https://img.shields.io/badge/Open_in_GitHub-grey?logo=github :target: https://www.github.com/tee-lab/PyDaddy/blob/master/notebooks/8_example_cell_migration.ipynb +.. |colab-3d| image:: https://colab.research.google.com/assets/colab-badge.svg + :target: https://colab.research.google.com/github/tee-lab/PyDaddy/blob/colab/notebooks/9_higher_dimensions.ipynb + +.. |github-3d| image:: https://img.shields.io/badge/Open_in_GitHub-grey?logo=github + :target: https://www.github.com/tee-lab/PyDaddy/blob/master/notebooks/9_higher_dimensions.ipynb + .. |colab| image:: https://colab.research.google.com/assets/colab-badge.svg .. |github| image:: https://img.shields.io/badge/Open_in_GitHub-grey?logo=github @@ -116,4 +122,11 @@ Example analysis: Cell hopping An example analysis of a confined cell migration dataset (Brückner et. al., Nature Physics, 2019) using PyDaddy. +Higher dimensions +^^^^^^^^^^^^^^^^^ +|colab-3d| |github-3d| + +This notebooks demonstrates how to use the principles of SDE estimations and tools in PyDaddy to estimate SDEs for higher-dimensional systems. The notebook uses the example of a (3-dimensional) stochastic Lorenz system. + + From dc67a3aa8a0492b063231209e2df819623617a0e Mon Sep 17 00:00:00 2001 From: Arshed Nabeel Date: Wed, 18 Sep 2024 11:01:19 +0530 Subject: [PATCH 2/2] Add new datasets, notebooks, and citations in the docs --- docs/source/datasets.rst | 2 +- docs/source/tutorials.rst | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/source/datasets.rst b/docs/source/datasets.rst index c87eed2..fd410fa 100644 --- a/docs/source/datasets.rst +++ b/docs/source/datasets.rst @@ -20,5 +20,5 @@ The simulated datasets were generated using a continuous-time stochastic simulat .. [1] Jhawar, J., Morris, R. G., Amith-Kumar, U. R., Danny Raj, M., Rogers, T., Rajendran, H., & Guttal, V. (2020). Noise-induced schooling of fish. Nature Physics, 16(4), 488-493 (`doi `_). -.. [2] Brückner, D. B., Fink, A., Schreiber, C. et al. Stochastic nonlinear dynamics of confined cell migration in two-state systems. Nat. Phys. 15, 595–601 (2019) (`doi `_. +.. [2] Brückner, D. B., Fink, A., Schreiber, C. et al. Stochastic nonlinear dynamics of confined cell migration in two-state systems. Nat. Phys. 15, 595–601 (2019) (`doi `_). .. [3] Jhawar, J., & Guttal, V. (2020). Noise-induced effects in collective dynamics and inferring local interactions from data. Philosophical Transactions of the Royal Society B, 375(1807), 20190381. (`doi `_) diff --git a/docs/source/tutorials.rst b/docs/source/tutorials.rst index 418bde1..85c0c6c 100644 --- a/docs/source/tutorials.rst +++ b/docs/source/tutorials.rst @@ -1,4 +1,4 @@ -Tutorials (no installation required) +Tutorials ========= .. |colab-getting-started| image:: https://colab.research.google.com/assets/colab-badge.svg