pythonCRO 0.1.8__tar.gz

pythoncro-0.1.8/LICENSE

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pythoncro-0.1.8/PKG-INFO

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+Metadata-Version: 2.4
+Name: pythonCRO
+Version: 0.1.8
+Summary: Community Recharge Oscillator
+Author: CRO team led by Soong-Ki Kim and Sen Zhao
+License: CC-BY-4.0
+Project-URL: Homepage, https://github.com/senclimate/CRO
+Project-URL: Documentation, https://senclimate.github.io/CRO/python/
+Project-URL: Repository, https://github.com/senclimate/CRO
+Project-URL: Issues, https://github.com/senclimate/CRO/issues
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.20
+Requires-Dist: scipy>=1.8
+Requires-Dist: pandas>=1.3
+Requires-Dist: xarray>=2023.1.0
+Requires-Dist: matplotlib>=3.5
+Requires-Dist: statsmodels>=0.13
+Dynamic: license-file
+
+# CRO: Community Recharge Oscillator Model
+
+## What is CRO?
+
+The recharge oscillator (RO) model is one of the leading theoretical frameworks for understanding the El Niño–Southern Oscillation (Jin, 1997, Jin et al., 2020, Vialard et al., 2025).
+
+While many RO variants exist in the literature, **CRO** is an open-source Python/Matlab package for:
+
+- solving the recharge oscillator equations  
+- fitting model parameters to observational and climate model data  
+- applying the model in research and teaching applications
+
+Key methodological foundations are described in Kim et al. (2025).
+
+---
+
+## Key Features
+
+- **Solver**: Numerical and analytical solvers for the RO equations.
+
+- **Fitting**: Parameter estimation from observations, reanalysis, or climate model data.
+
+- **Applications**: Simulations, sensitivity experiments, and analysis of ENSO dynamics.
+
+---
+
+## Installation
+
+```bash
+pip install CRO
+```
+
+---
+
+## Quick Start (Python)
+
+```python
+import pyCRO
+
+print(pyCRO.__version__)
+```
+
+---
+
+## Data Included
+
+CRO includes curated datasets for benchmarking and teaching:
+
+- Precomputed ORAS5 ENSO SST and WWV indices
+- Precomputed CESM1 Large Ensemble ENSO time series  
+- Precomputed CMIP6 ENSO time series
+- Precomputed parameter libraries  
+
+---
+
+## Documentation
+
+- Documentation: https://senclimate.github.io/CRO/python/  
+- Source code: https://github.com/senclimate/CRO  
+
+---
+
+## Citation
+
+If you use CRO in your research, please cite:
+
+Kim, S.-K., Zhao, S., & et al. (2025). Community Recharge Oscillator (CRO) v1.0: an open-source Python and MATLAB package for solving, parameter fitting, and practical applications of the ENSO recharge oscillator. In preparation.

pythoncro-0.1.8/README.md

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+# CRO: Community Recharge Oscillator Model
+
+## What is CRO?
+
+The recharge oscillator (RO) model is one of the leading theoretical frameworks for understanding the El Niño–Southern Oscillation (Jin, 1997, Jin et al., 2020, Vialard et al., 2025).
+
+While many RO variants exist in the literature, **CRO** is an open-source Python/Matlab package for:
+
+- solving the recharge oscillator equations  
+- fitting model parameters to observational and climate model data  
+- applying the model in research and teaching applications
+
+Key methodological foundations are described in Kim et al. (2025).
+
+---
+
+## Key Features
+
+- **Solver**: Numerical and analytical solvers for the RO equations.
+
+- **Fitting**: Parameter estimation from observations, reanalysis, or climate model data.
+
+- **Applications**: Simulations, sensitivity experiments, and analysis of ENSO dynamics.
+
+---
+
+## Installation
+
+```bash
+pip install CRO
+```
+
+---
+
+## Quick Start (Python)
+
+```python
+import pyCRO
+
+print(pyCRO.__version__)
+```
+
+---
+
+## Data Included
+
+CRO includes curated datasets for benchmarking and teaching:
+
+- Precomputed ORAS5 ENSO SST and WWV indices
+- Precomputed CESM1 Large Ensemble ENSO time series  
+- Precomputed CMIP6 ENSO time series
+- Precomputed parameter libraries  
+
+---
+
+## Documentation
+
+- Documentation: https://senclimate.github.io/CRO/python/  
+- Source code: https://github.com/senclimate/CRO  
+
+---
+
+## Citation
+
+If you use CRO in your research, please cite:
+
+Kim, S.-K., Zhao, S., & et al. (2025). Community Recharge Oscillator (CRO) v1.0: an open-source Python and MATLAB package for solving, parameter fitting, and practical applications of the ENSO recharge oscillator. In preparation.

pythoncro-0.1.8/pyCRO/__init__.py

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+# __init__.py
+
+__version__ = "0.1.8"
+
+from .fitting import RO_fitting
+from .solver import RO_solver
+
+from .analytic import RO_analytic_std, RO_analytic_solver
+
+from .utils import RO_BWJ, func_mon_std
+from .par_load import par_load
+
+from .fit_LR import fit_LR
+from .fit_MLE import fit_MLE
+
+from .visual import plot_RO_par, plot_ens_RO_par

pythoncro-0.1.8/pyCRO/analytic.py

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+import sys
+import numpy as np
+
+def RO_analytic_std(par):
+    """
+    Compute analytical standard deviation of T and h for the Recharge Oscillator (RO) model.
+    ONLY for linear RO model with white noise (annual mean parameters only)
+
+    Parameters
+    ----------
+    par : dict
+        Dictionary containing parameter arrays:
+        'R', 'F1', 'epsilon', 'F2', 'sigma_T', 'sigma_h'.
+
+    Returns
+    -------
+    T_std : float
+        Standard deviation of T.
+    h_std : float
+        Standard deviation of h.
+    """
+    
+    R_value = par['R'][0]
+    F1_value = par['F1'][0]
+    epsilon_value = par['epsilon'][0]
+    F2_value = par['F2'][0]
+    sigma_T_value = par['sigma_T'][0]
+    sigma_h_value = par['sigma_h'][0]
+
+    # Precompute useful terms
+    numerator_T = ((F1_value * F2_value - epsilon_value * R_value + epsilon_value**2) * sigma_T_value**2 +
+                   (F1_value**2) * sigma_h_value**2)
+    denominator = 2 * (-R_value + epsilon_value) * (F1_value * F2_value - R_value * epsilon_value)
+    T_std = np.sqrt(numerator_T / denominator)
+
+    numerator_h = ((F2_value**2) * sigma_T_value**2 +
+                   (F1_value * F2_value - epsilon_value * R_value + R_value**2) * sigma_h_value**2)
+    h_std = np.sqrt(numerator_h / denominator)
+
+    return T_std, h_std
+
+
+def RO_analytic_solver(par, IC, N, NE, dt=0.1, saveat=1.0, savemethod="sampling", noise_custom=None):
+    """
+    Analytical solution of the Recharge Oscillator (RO) model with deterministic and stochastic forcing.
+    ONLY for linear RO model with white noise (annual mean parameters only)
+
+    Parameters
+    ----------
+    par : dict
+        Dictionary of model parameters, each as at least a one-element array:
+        
+        - ``'R'`` : float
+            Damping parameter.
+        - ``'F1'`` : float
+            Feedback parameter relating thermocline depth to SST.
+        - ``'epsilon'`` : float
+            Thermocline damping parameter.
+        - ``'F2'`` : float
+            Feedback parameter relating SST to thermocline.
+        - ``'sigma_T'`` : float
+            Noise amplitude for SST.
+        - ``'sigma_h'`` : float
+            Noise amplitude for thermocline depth.
+    IC : tuple of float
+        Initial condition ``(To, ho)``:
+        
+        - ``To`` : initial SST anomaly.
+        - ``ho`` : initial thermocline depth anomaly.
+    N : float
+        Total simulation length (time units).
+    NE : int
+        Number of ensemble members.
+    dt : float, optional
+        Numerical integration time step. Default is ``0.1``.
+    saveat : float, optional
+        Output saving interval. Must be divisible by ``dt``. Default is ``1.0``.
+    savemethod : {'sampling', 'mean'}, optional
+        Method for saving results:
+        
+        - ``'sampling'`` : take samples every ``saveat``.
+        - ``'mean'`` : average values over each ``saveat`` interval.
+    noise_custom : {None, int, ndarray}, optional
+        Specification of stochastic noise:
+        
+        - ``None`` (default): new Gaussian noise is generated for each ensemble.
+        - ``int`` : seed for reproducible noise (same across ensembles).
+        - ``ndarray`` of shape ``(NT-1, 4)`` : user-provided noise, repeated across ensembles.
+        - ``ndarray`` of shape ``(NT-1, 4, NE)`` : user-provided noise for each ensemble.
+
+    Returns
+    -------
+    T_anal_out : ndarray of shape (N_out, NE)
+        SST anomalies including deterministic and stochastic forcing, 
+        after applying the saving scheme. The final row is NaN-padded 
+        for dimensional consistency.
+    h_anal_out : ndarray of shape (N_out, NE)
+        Thermocline anomalies including deterministic and stochastic forcing, 
+        after applying the saving scheme. The final row is NaN-padded.
+    noise_array : ndarray of shape (NT-1, 4, NE)
+        Realizations of Gaussian noise used in the simulation.
+
+    Notes
+    -----
+    The analytical solution consists of:
+    
+    - Deterministic part: exponential-sinusoidal functions of time.
+    - Stochastic part: weighted sums (discrete convolutions) of noise 
+      with exponential and sinusoidal kernels.
+    
+    Ensemble members are evaluated simultaneously using vectorized 
+    NumPy broadcasting, avoiding explicit Python loops.
+
+    Examples
+    --------
+    >>> par = {'R':[0.5], 'F1':[1.2], 'epsilon':[0.3], 'F2':[0.8],
+    ...        'sigma_T':[0.2], 'sigma_h':[0.1]}
+    >>> IC = (0.1, -0.2)
+    >>> T, h, noise = RO_solver_analytic(par, IC, N=50, NE=10, dt=0.1, saveat=1.0)
+    >>> T.shape, h.shape
+    ((51, 10), (51, 10))
+    """
+    
+    NT = int(round(N / dt))
+    step = int(round(saveat / dt))
+    ratio = saveat / dt
+
+    ### Checking simulation setups ###
+    ##################################
+    print("---------------------------------------------------------------------------------")
+    print("Welcome to the CRO Analytical Solver!")
+    print("Ensure that the same arguments are provided as for RO_solver,\n except that 'NM' and 'EF' are not required.")
+    print("---------------------------------------------------------------------------------")
+
+    ### Check timestep settings ###
+    if dt > saveat:
+        raise ValueError(f"dt={dt} and saveat={saveat}: The numerical time step (dt) must be smaller than or equal to the data saving interval (saveat).")
+    if not ratio.is_integer():
+        raise ValueError(f"dt = {dt}, saveat = {saveat}: saveat must be divisible by dt so that saveat/dt results in an integer.")
+    ###############################
+
+    ### extracting linear and noise amplitude parameters ###
+    ########################################################
+    R_value = par['R'][0]
+    F1_value = par['F1'][0]
+    epsilon_value = par['epsilon'][0]
+    F2_value = par['F2'][0]
+    sigma_T_value = par['sigma_T'][0]
+    sigma_h_value = par['sigma_h'][0]
+    ########################################################
+    ########################################################
+
+
+    ### initial setups ###
+    ######################
+    To, ho = IC
+    t = np.arange(NT) * dt
+    gr = (R_value - epsilon_value) / 2
+    w = np.sqrt(4 * F1_value * F2_value - (R_value + epsilon_value)**2) / 2
+
+    T_anal_out = np.zeros((NT, NE))
+    h_anal_out = np.zeros((NT, NE))
+
+    T_det = np.exp(gr * t) * (To * np.cos(w * t) +
+        To * (R_value + epsilon_value) / (2 * w) * np.sin(w * t) +
+        ho * (F1_value / w) * np.sin(w * t))
+
+    h_det = np.exp(gr * t) * (ho * np.cos(w * t) -
+        ho * (R_value + epsilon_value) / (2 * w) * np.sin(w * t) -
+        To * (F2_value / w) * np.sin(w * t))
+    ######################
+    ######################
+
+    ########################################################
+    # Noise generation (vectorized for all NE)
+    if noise_custom is None:
+        noise_array = np.random.randn(NT - 1, 4, NE)
+    elif np.isscalar(noise_custom):
+        np.random.seed(int(noise_custom))
+        noise_array = np.random.randn(NT - 1, 4, NE)
+    elif noise_custom.shape == (NT - 1, 4):
+        noise_array = np.repeat(noise_custom[..., None], NE, axis=2)
+    elif noise_custom.shape == (NT - 1, 4, NE):
+        noise_array = noise_custom
+    else:
+        raise ValueError(f"Invalid 'noise_custom' input: expected None, scalar, shape ({NT-1},4) or ({NT-1},4,{NE}).")
+
+    w_T = sigma_T_value * noise_array[:, 0, :] / np.sqrt(dt)  # (NT-1, NE)
+    w_h = sigma_h_value * noise_array[:, 1, :] / np.sqrt(dt)  # (NT-1, NE)
+
+    # Vectorized convolution-like integral for stochastic terms
+    T_sto = np.zeros((NT - 1, NE))
+    h_sto = np.zeros((NT - 1, NE))
+
+    ### analytical calculations
+    ########################################################
+    for i in range(1, NT - 1):
+        tau = t[:i+1]                     # (i+1,)
+        delta = t[i] - tau                 # (i+1,)
+        sin = np.sin(w * delta)            # (i+1,)
+        cos = np.cos(w * delta)            # (i+1,)
+        expgr = np.exp(gr * delta)         # (i+1,)
+
+        # (i+1, NE) via broadcasting
+        T_kernel = (
+            w_T[:i+1, :] * cos[:, None] +
+            w_T[:i+1, :] * (R_value + epsilon_value) / (2 * w) * sin[:, None] +
+            w_h[:i+1, :] * (F1_value / w) * sin[:, None]
+        )
+        h_kernel = (
+            w_h[:i+1, :] * cos[:, None] -
+            w_h[:i+1, :] * (R_value + epsilon_value) / (2 * w) * sin[:, None] -
+            w_T[:i+1, :] * (F2_value / w) * sin[:, None]
+        )
+
+        T_sto[i, :] = np.sum(dt * expgr[:, None] * T_kernel, axis=0)
+        h_sto[i, :] = np.sum(dt * expgr[:, None] * h_kernel, axis=0)
+
+    # Add deterministic and stochastic contributions
+    T_anal_out = np.vstack([T_det[:-1, None] + T_sto, np.full((1, NE), np.nan)])
+    h_anal_out = np.vstack([h_det[:-1, None] + h_sto, np.full((1, NE), np.nan)])
+
+    ### save data ###
+    #################
+    if savemethod == "sampling":
+        T_anal_out = T_anal_out[::step, :]
+        h_anal_out = h_anal_out[::step, :]
+    elif savemethod == "mean":
+        T_anal_out = T_anal_out[int(np.ceil(step/2)):NT-int(step/2),:]
+        h_anal_out = h_anal_out[int(np.ceil(step/2)):NT-int(step/2),:]
+        T_anal_out = T_anal_out.reshape(-1, step, NE).mean(axis=1)
+        h_anal_out = h_anal_out.reshape(-1, step, NE).mean(axis=1)
+        if NE > 1:
+            T_anal_out = np.vstack([T_anal_out[0:1, :], T_anal_out])
+            h_anal_out = np.vstack([h_anal_out[0:1, :], h_anal_out])
+        elif NE == 1:
+            T_anal_out = np.concatenate([[T_anal_out[0]], T_anal_out])
+            h_anal_out = np.concatenate([[h_anal_out[0]], h_anal_out])
+    
+    print("All steps are successfully completed!")
+    print("---------------------------------------------------------------------------------")
+    #################
+    #################
+    return T_anal_out, h_anal_out, noise_array