PyMC implementation of M0 model

posterior_database/models/info/M0_model.info.json

@@ -11,6 +11,10 @@
     "stan": {
       "model_code": "models/stan/M0_model.stan",
       "stan_version": ">=2.26.0"
+    },
+    "pymc": {
+      "model_code": "models/pymc/M0_model.py",
+      "pymc_version": ">=5.16.0"
     }
   }
 }

posterior_database/models/pymc/M0_model.py

@@ -0,0 +1,25 @@
+import numpy as np
+import pymc as pm
+
+def model(data):
+    y = np.array(data["y"])  # capture history matrix
+    T = np.array(data["T"])  # time periods
+    coords = {"individual": np.arange(data["M"]),
+              "capture_period": np.arange(data["T"])}
+    with pm.Model(coords=coords) as pymc_model:
+
+        # Inclusion probability
+        omega = pm.Uniform("omega", 0, 1)
+        # Capture probability
+        p = pm.Uniform("p", 0, 1) 
+
+        # Inclusion indicator
+        z = pm.Bernoulli("z", p=omega, dims="individual")
+
+        y_obs = pm.Bernoulli("y_obs", p=z[:, None]*p, observed=y, dims=("individual", "capture_period"))
+
+        N = pm.Deterministic("N", pm.math.sum(z))
+
+        omega_nd = pm.Deterministic("omega_nd", (omega * (1 -p)**T)  / (omega * (1 - p)**T  + (1 - omega)))
+
+    return pymc_model

posterior_database/reference_posteriors/draws/info/M0.pymc.info.json

@@ -0,0 +1 @@
+{"name": "M0", "inference": {"method": "pymc_sampling", "method_arguments": {"chains": 10, "iter": 3000, "warmup": 1000, "thin": 1, "seed": 4711, "control": {"adapt_delta": 0.95}}}, "diagnostics": {"diagnostic_information": {"names": ["N", "omega", "omega_nd", "p"]}, "ndraws": 20000, "nchains": 10, "effective_sample_size_bulk": [4150.0, 5378.0, 4048.0, 4964.0], "effective_sample_size_tail": [7490.0, 7239.0, 6248.0, 7974.0], "r_hat": [1.0, 1.0, 1.0, 1.0], "divergent_transitions": [0, 0, 0, 0], "expected_fraction_of_missing_information": [0, 0, 0, 0]}, "checks_made": {"ndraws_is_10k": true, "nchains_is_gte_4": true, "ess_within_bounds": true, "r_hat_below_1_01": true, "efmi_above_0_2": false}, "comments": "", "added_by": "Chris Fonnesbeck", "added_date": "2024-08-12", "versions": {"pymc_version": "5.16.2+11.gb407c01ac.dirty", "python_version": "3.11.9 | packaged by conda-forge | (main, Apr 19 2024, 18:36:13) [GCC 12.3.0]", "python_environment": "['Babel==2.14.0', 'Brotli==1.1.0', 'MarkupSafe==2.1.5', 'PySocks==1.7.1', 'PyYAML==6.0.1', 'SQLAlchemy==2.0.31', 'absl-py==2.1.0', 'accessible-pygments==0.0.5', 'alabaster==0.7.16', 'arviz==0.18.0', 'asttokens==2.4.1', 'attrs==23.2.0', 'beautifulsoup4==4.12.3', 'betterproto==2.0.0b6', 'blackjax==0.0.0', 'bleach==6.1.0', 'cached-property==1.5.2', 'cachetools==5.3.3', 'certifi==2024.7.4', 'cffi==1.16.0', 'cfgv==3.3.1', 'charset-normalizer==3.3.2', 'chex==0.1.86', 'click==8.1.7', 'cloudpickle==3.0.0', 'colorama==0.4.6', 'comm==0.2.2', 'cons==0.4.6', 'contourpy==1.2.1', 'coverage==7.5.4', 'cycler==0.12.1', 'debugpy==1.8.2', 'decorator==5.1.1', 'defusedxml==0.7.1', 'distlib==0.3.8', 'dm-tree==0.1.8', 'docutils==0.21.2', 'entrypoints==0.4', 'etils==1.9.2', 'etuples==0.3.9', 'exceptiongroup==1.2.0', 'executing==2.0.1', 'fastjsonschema==2.20.0', 'fastprogress==1.0.3', 'filelock==3.15.4', 'fonttools==4.53.0', 'graphviz==0.20.3', 'greenlet==3.0.3', 'grpclib==0.4.7', 'h2==4.1.0', 'h5netcdf==1.3.0', 'h5py==3.11.0', 'hagelkorn==1.2.3', 'hpack==4.0.0', 'hyperframe==6.0.1', 'identify==2.5.36', 'idna==3.7', 'imagesize==1.4.1', 'importlib-metadata==8.0.0', 'importlib-resources==6.4.0', 'iniconfig==2.0.0', 'ipykernel==6.29.4', 'ipython==8.25.0', 'ipywidgets==8.1.3', 'jax==0.4.28', 'jaxlib==0.4.28.dev20240710', 'jaxopt==0.8.3', 'jedi==0.19.1', 'jinja2==3.1.4', 'joblib==1.4.2', 'jsonschema==4.22.0', 'jsonschema-specifications==2023.12.1', 'jupyter-cache==1.0.0', 'jupyter-client==8.6.2', 'jupyter-core==5.7.2', 'jupyter-sphinx==0.5.3', 'jupyterlab-pygments==0.3.0', 'jupyterlab-widgets==3.0.11', 'kiwisolver==1.4.5', 'logical-unification==0.4.6', 'markdown-it-py==3.0.0', 'matplotlib==3.8.4', 'matplotlib-inline==0.1.7', 'mcbackend==0.5.2', 'mdit-py-plugins==0.4.1', 'mdurl==0.1.2', 'miniKanren==1.0.3', 'mistune==3.0.2', 'mkl-service==2.4.1', 'ml-dtypes==0.4.0', 'multidict==6.0.5', 'multipledispatch==0.6.0', 'munkres==1.1.4', 'mypy==1.5.1', 'mypy-extensions==1.0.0', 'myst-nb==1.1.0', 'myst-parser==3.0.1', 'nbclient==0.10.0', 'nbconvert==7.16.4', 'nbformat==5.10.4', 'nest-asyncio==1.6.0', 'networkx==3.3', 'nodeenv==1.9.1', 'numdifftools==0.9.41', 'numpy==1.26.4', 'numpydoc==1.7.0', 'numpyro==0.15.1', 'opt-einsum==3.3.0', 'optax==0.2.2', 'packaging==24.1', 'pandas==2.2.2', 'pandocfilters==1.5.0', 'parso==0.8.4', 'pexpect==4.9.0', 'pickleshare==0.7.5', 'pillow==10.3.0', 'pip==24.0', 'pkgutil-resolve-name==1.3.10', 'platformdirs==4.2.2', 'pluggy==1.5.0', 'polyagamma==1.3.6', 'pre-commit==3.7.1', 'prompt-toolkit==3.0.47', 'psutil==6.0.0', 'ptyprocess==0.7.0', 'pure-eval==0.2.2', 'pycparser==2.22', 'pydata-sphinx-theme==0.14.4', 'pygments==2.18.0', 'pymc==5.16.2+11.gb407c01ac.dirty', 'pymc-experimental==0.1.1', 'pymc-sphinx-theme==0.14.0', 'pyparsing==3.1.2', 'pytensor==2.25.2', 'pytest==8.2.2', 'pytest-cov==5.0.0', 'python-dateutil==2.9.0', 'pytz==2024.1', 'pyzmq==26.0.3', 'referencing==0.35.1', 'requests==2.32.3', 'rich==13.7.1', 'rpds-py==0.18.1', 'scikit-learn==1.5.1', 'scipy==1.13.1', 'setuptools==70.1.1', 'six==1.16.0', 'snowballstemmer==2.2.0', 'soupsieve==2.5', 'sphinx==7.3.7', 'sphinx-copybutton==0.5.2', 'sphinx-design==0.6.0', 'sphinx-notfound-page==1.0.2', 'sphinx-remove-toctrees==1.0.0.post1', 'sphinxcontrib-applehelp==1.0.8', 'sphinxcontrib-devhelp==1.0.6', 'sphinxcontrib-htmlhelp==2.0.5', 'sphinxcontrib-jsmath==1.0.1', 'sphinxcontrib-qthelp==1.0.7', 'sphinxcontrib-serializinghtml==1.1.10', 'sphinxext-rediraffe==0.2.7', 'stack-data==0.6.2', 'tabulate==0.9.0', 'threadpoolctl==3.5.0', 'tinycss2==1.3.0', 'toml==0.10.2', 'tomli==2.0.1', 'toolz==0.12.1', 'tornado==6.4.1', 'tqdm==4.66.4', 'traitlets==5.14.3', 'types-cachetools==5.3.0.7', 'typing-extensions==4.12.2', 'tzdata==2024.1', 'ukkonen==1.0.1', 'urllib3==2.2.2', 'virtualenv==20.26.3', 'watermark==2.4.3', 'wcwidth==0.2.13', 'webencodings==0.5.1', 'wheel==0.43.0', 'widgetsnbextension==4.0.11', 'xarray==2024.6.0', 'xarray-einstats==0.7.0', 'zipp==3.19.2', 'zstandard==0.22.0']"}}

posterior_database/reference_posteriors/summary_statistics/mean/mean/mean_summary.json

@@ -0,0 +1 @@
+{"names": ["N", "omega", "omega_nd", "p"], "mean": [100.349, 0.424, 0.089, 0.496], "sd": [5.263, 0.039, 0.026, 0.038], "mcse_mean": [0.082, 0.001, 0.0, 0.001]}