CRACO modelling

CLAUDE.md

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+# CLAUDE.md
+
+This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
+
+## Project Overview
+
+The `zdm` package is a Python library for Fast Radio Burst (FRB) redshift-dispersion measure (z-DM) calculations. It implements statistical models for analyzing FRB populations, computing likelihoods, and constraining cosmological and FRB population parameters.
+
+## Build and Installation
+
+```bash
+# Install in development mode
+pip install -e .[dev]
+
+# Install dependencies for external FRB packages
+pip install git+https://github.com/FRBs/ne2001.git#egg=ne2001
+pip install git+https://github.com/FRBs/FRB.git#egg=frb
+```
+
+## Running Tests
+
+```bash
+# Run all tests with pytest
+pytest
+
+# Run tests with tox
+tox -e test-alldeps
+
+# Run a single test file
+pytest zdm/tests/test_energetics.py
+
+# Run a specific test
+pytest zdm/tests/test_energetics.py::test_init_gamma
+```
+
+## Architecture
+
+### Core Classes
+
+- **`parameters.State`** ([parameters.py](zdm/parameters.py)): Central configuration object containing all model parameters organized in dataclasses (`CosmoParams`, `FRBDemoParams`, `EnergyParams`, `HostParams`, `MWParams`, etc.). Use `state.update_param_dict(vparams)` to update parameters.
+
+- **`survey.Survey`** ([survey.py](zdm/survey.py)): Represents an FRB survey with instrument properties, beam patterns, and detected FRB data. Handles efficiency calculations, DM processing, and FRB metadata.
+
+- **`grid.Grid`** ([grid.py](zdm/grid.py)): Core computational class that builds 2D z-DM grids representing probability distributions of FRB detection rates. Takes a Survey and State, computes thresholds, detection efficiencies, and expected rates across the z-DM plane.
+
+- **`repeat_grid.repeat_Grid`** ([repeat_grid.py](zdm/repeat_grid.py)): Extension of Grid for handling repeating FRBs with additional rate parameters.
+
+### Key Modules
+
+- **`cosmology`** ([cosmology.py](zdm/cosmology.py)): Lambda CDM cosmology calculations including distance measures and volume elements.
+
+- **`pcosmic`** ([pcosmic.py](zdm/pcosmic.py)): Computes p(DM|z) - the probability distribution of cosmic DM given redshift, implementing the Macquart relation.
+
+- **`energetics`** ([energetics.py](zdm/energetics.py)): FRB luminosity function implementations using incomplete gamma functions with spline interpolation for efficiency.
+
+- **`iteration`** ([iteration.py](zdm/iteration.py)): Likelihood calculation routines. Key function `get_log_likelihood(grid, survey)` computes total log-likelihood for a grid given survey data.
+
+- **`loading`** ([loading.py](zdm/loading.py)): High-level functions to load surveys and initialize states. `set_state()` creates default parameter configurations, `load_CHIME()` loads CHIME survey data.
+
+- **`MCMC`** ([MCMC.py](zdm/MCMC.py)): MCMC parameter estimation using emcee. `calc_log_posterior()` is the main posterior evaluation function.
+
+### Data Flow
+
+1. Initialize a `State` with desired parameters via `loading.set_state()` or `parameters.State()`
+2. Load survey data via `Survey` class pointing to survey files in `zdm/data/Surveys/`
+3. Build a `Grid` from the survey and state
+4. Compute likelihoods using `iteration.get_log_likelihood(grid, survey)`
+5. For parameter estimation, use MCMC functions to explore parameter space
+
+### Data Files
+
+Survey data and beam patterns are stored in `zdm/data/`:
+- `Surveys/`: Survey definition files (ECSV format) for CHIME, ASKAP, Parkes, etc.
+- `BeamData/`: Beam response histograms for different telescopes
+- `Cube/`: Precomputed parameter grids
+
+## Console Scripts
+
+```bash
+zdm_build_cube   # Build parameter cubes (zdm/scripts/build_cube.py)
+zdm_pzdm         # Compute p(z|DM) distributions (zdm/scripts/pzdm.py)
+```
+
+## Dependencies
+
+Key external dependencies:
+- `frb`: FRB utilities from the FRBs organization
+- `ne2001`: Galactic electron density model
+- `emcee`: MCMC sampling
+- `astropy`: Cosmology and astronomical utilities

papers/CRACO/ImprovedSurveys/CRAFT_CRACO_1300.ecsv

@@ -0,0 +1,29 @@
+# %ECSV 1.0
+# ---
+# datatype:
+# - {name: TNS, datatype: string}
+# - {name: BW, datatype: float64}
+# - {name: DM, datatype: float64}
+# - {name: DMG, datatype: float64}
+# - {name: FBAR, datatype: float64}
+# - {name: FRES, datatype: float64}
+# - {name: Gb, datatype: string, subtype: 'float64[null]'}
+# - {name: Gl, datatype: string, subtype: 'float64[null]'}
+# - {name: NREP, datatype: int64}
+# - {name: SNR, datatype: float64}
+# - {name: SNRTHRESH, datatype: float64}
+# - {name: THRESH, datatype: float64}
+# - {name: TRES, datatype: float64}
+# - {name: WIDTH, datatype: float64}
+# - {name: XDec, datatype: string, subtype: 'float64[null]'}
+# - {name: XRA, datatype: string, subtype: 'float64[null]'}
+# - {name: Z, datatype: float64}
+# meta: !!omap
+# - {survey_data: '{"observing": {"NORM_FRB": 1,"TOBS": 1,"MAX_IW": 8, "MAXWMETH": 2},
+#                   "telescope": {"BEAM": "CRACO_1300", "DMMASK": "craco_1300_mask.npy",
+#                                 "DIAM": 12.0, "NBEAMS": 1, "NBINS": 5, "FBAR": 1392,
+#                                 "TRES": 13.8}  }'}
+# schema: astropy-2.0
+TNS   BW    DM    DMG  FBAR   FRES Gb Gl NREP SNR  SNRTHRESH THRESH TRES WIDTH XDec XRA Z
+DUMMY 288.0 401.4 35.0 1300.5 1.0  "" "" 1    27.9 9.5       0.99   13.8  4.0   ""   "" 0.1
+

papers/CRACO/ImprovedSurveys/CRAFT_CRACO_1300_imp2.1_div2.ecsv

@@ -0,0 +1,29 @@
+# %ECSV 1.0
+# ---
+# datatype:
+# - {name: TNS, datatype: string}
+# - {name: BW, datatype: float64}
+# - {name: DM, datatype: float64}
+# - {name: DMG, datatype: float64}
+# - {name: FBAR, datatype: float64}
+# - {name: FRES, datatype: float64}
+# - {name: Gb, datatype: string, subtype: 'float64[null]'}
+# - {name: Gl, datatype: string, subtype: 'float64[null]'}
+# - {name: NREP, datatype: int64}
+# - {name: SNR, datatype: float64}
+# - {name: SNRTHRESH, datatype: float64}
+# - {name: THRESH, datatype: float64}
+# - {name: TRES, datatype: float64}
+# - {name: WIDTH, datatype: float64}
+# - {name: XDec, datatype: string, subtype: 'float64[null]'}
+# - {name: XRA, datatype: string, subtype: 'float64[null]'}
+# - {name: Z, datatype: float64}
+# meta: !!omap
+# - {survey_data: '{"observing": {"NORM_FRB": 1,"TOBS": 1,"MAX_IW": 8, "MAXWMETH": 2},
+#                   "telescope": {"BEAM": "CRACO_1300", "DMMASK": "craco_1300_mask_div2.npy",
+#                                 "DIAM": 12.0, "NBEAMS": 1, "NBINS": 5,
+#                                    "TRES": 6.9, "THRESH": 0.99}  }'}
+# schema: astropy-2.0
+TNS   BW    DM    DMG  FBAR   FRES Gb Gl NREP SNR  SNRTHRESH THRESH TRES WIDTH XDec XRA Z
+DUMMY 288.0 401.4 35.0 1300.5    1.0  "" "" 1    27.9 9.5       0.99   6.9  4.0   ""   "" 0.1
+

papers/CRACO/ImprovedSurveys/CRAFT_CRACO_1300_imp2.1_div4.ecsv

@@ -0,0 +1,29 @@
+# %ECSV 1.0
+# ---
+# datatype:
+# - {name: TNS, datatype: string}
+# - {name: BW, datatype: float64}
+# - {name: DM, datatype: float64}
+# - {name: DMG, datatype: float64}
+# - {name: FBAR, datatype: float64}
+# - {name: FRES, datatype: float64}
+# - {name: Gb, datatype: string, subtype: 'float64[null]'}
+# - {name: Gl, datatype: string, subtype: 'float64[null]'}
+# - {name: NREP, datatype: int64}
+# - {name: SNR, datatype: float64}
+# - {name: SNRTHRESH, datatype: float64}
+# - {name: THRESH, datatype: float64}
+# - {name: TRES, datatype: float64}
+# - {name: WIDTH, datatype: float64}
+# - {name: XDec, datatype: string, subtype: 'float64[null]'}
+# - {name: XRA, datatype: string, subtype: 'float64[null]'}
+# - {name: Z, datatype: float64}
+# meta: !!omap
+# - {survey_data: '{"observing": {"NORM_FRB": 1,"TOBS": 1,"MAX_IW": 8, "MAXWMETH": 2},
+#                   "telescope": {"BEAM": "CRACO_1300", "DMMASK": "craco_1300_mask_div4.npy",
+#                                 "DIAM": 12.0, "NBEAMS": 1, "NBINS": 5,
+#                                    "TRES": 3.4, "THRESH": 0.99}  }'}
+# schema: astropy-2.0
+TNS   BW    DM    DMG  FBAR   FRES Gb Gl NREP SNR  SNRTHRESH THRESH TRES WIDTH XDec XRA Z
+DUMMY 288.0 401.4 35.0 1300.5    1.0  "" "" 1    27.9 9.5       0.99   3.4  4.0   ""   "" 0.1
+

papers/CRACO/ImprovedSurveys/CRAFT_CRACO_1300_imp2.1_div8.ecsv

@@ -0,0 +1,29 @@
+# %ECSV 1.0
+# ---
+# datatype:
+# - {name: TNS, datatype: string}
+# - {name: BW, datatype: float64}
+# - {name: DM, datatype: float64}
+# - {name: DMG, datatype: float64}
+# - {name: FBAR, datatype: float64}
+# - {name: FRES, datatype: float64}
+# - {name: Gb, datatype: string, subtype: 'float64[null]'}
+# - {name: Gl, datatype: string, subtype: 'float64[null]'}
+# - {name: NREP, datatype: int64}
+# - {name: SNR, datatype: float64}
+# - {name: SNRTHRESH, datatype: float64}
+# - {name: THRESH, datatype: float64}
+# - {name: TRES, datatype: float64}
+# - {name: WIDTH, datatype: float64}
+# - {name: XDec, datatype: string, subtype: 'float64[null]'}
+# - {name: XRA, datatype: string, subtype: 'float64[null]'}
+# - {name: Z, datatype: float64}
+# meta: !!omap
+# - {survey_data: '{"observing": {"NORM_FRB": 1,"TOBS": 1,"MAX_IW": 8, "MAXWMETH": 2},
+#                   "telescope": {"BEAM": "CRACO_1300", "DMMASK": "craco_1300_mask_div8.npy",
+#                                 "DIAM": 12.0, "NBEAMS": 1, "NBINS": 5,
+#                                    "TRES": 1.7, "THRESH": 0.99}  }'}
+# schema: astropy-2.0
+TNS   BW    DM    DMG  FBAR   FRES Gb Gl NREP SNR  SNRTHRESH THRESH TRES WIDTH XDec XRA Z
+DUMMY 288.0 401.4 35.0 1300.5    1.0  "" "" 1    27.9 9.5       0.99   1.7  4.0   ""   "" 0.1
+

papers/CRACO/ImprovedSurveys/CRAFT_CRACO_900.ecsv

@@ -0,0 +1,28 @@
+# %ECSV 1.0
+# ---
+# datatype:
+# - {name: TNS, datatype: string}
+# - {name: BW, datatype: float64}
+# - {name: DM, datatype: float64}
+# - {name: DMG, datatype: float64}
+# - {name: FBAR, datatype: float64}
+# - {name: FRES, datatype: float64}
+# - {name: Gb, datatype: string, subtype: 'float64[null]'}
+# - {name: Gl, datatype: string, subtype: 'float64[null]'}
+# - {name: NREP, datatype: int64}
+# - {name: SNR, datatype: float64}
+# - {name: SNRTHRESH, datatype: float64}
+# - {name: THRESH, datatype: float64}
+# - {name: TRES, datatype: float64}
+# - {name: WIDTH, datatype: float64}
+# - {name: XDec, datatype: string, subtype: 'float64[null]'}
+# - {name: XRA, datatype: string, subtype: 'float64[null]'}
+# - {name: Z, datatype: float64}
+# meta: !!omap
+# - {survey_data: '{"observing": {"NORM_FRB": 1,"TOBS": 1,"MAX_IW": 8, "MAXWMETH": 2},
+#                   "telescope": {"BEAM": "CRACO_900", "DMMASK": "craco_900_mask.npy",
+#                                 "DIAM": 12.0, "NBEAMS": 1, "NBINS": 5, "FBAR": 906, "TRES": 13.8}  }'}
+# schema: astropy-2.0
+TNS   BW    DM    DMG  FBAR   FRES Gb Gl NREP SNR  SNRTHRESH THRESH TRES WIDTH XDec XRA Z
+DUMMY 288.0 401.4 35.0 906    1.0  "" "" 1    27.9 9.5       0.99   13.8  4.0   ""   "" 0.1
+

papers/CRACO/ImprovedSurveys/CRAFT_CRACO_900_imp1.ecsv

@@ -0,0 +1,29 @@
+# %ECSV 1.0
+# ---
+# datatype:
+# - {name: TNS, datatype: string}
+# - {name: BW, datatype: float64}
+# - {name: DM, datatype: float64}
+# - {name: DMG, datatype: float64}
+# - {name: FBAR, datatype: float64}
+# - {name: FRES, datatype: float64}
+# - {name: Gb, datatype: string, subtype: 'float64[null]'}
+# - {name: Gl, datatype: string, subtype: 'float64[null]'}
+# - {name: NREP, datatype: int64}
+# - {name: SNR, datatype: float64}
+# - {name: SNRTHRESH, datatype: float64}
+# - {name: THRESH, datatype: float64}
+# - {name: TRES, datatype: float64}
+# - {name: WIDTH, datatype: float64}
+# - {name: XDec, datatype: string, subtype: 'float64[null]'}
+# - {name: XRA, datatype: string, subtype: 'float64[null]'}
+# - {name: Z, datatype: float64}
+# meta: !!omap
+# - {survey_data: '{"observing": {"NORM_FRB": 1,"TOBS": 1,"MAX_IW": 8, "MAXWMETH": 2},
+#                   "telescope": {"BEAM": "CRACO_900", "DMMASK": "craco_900_mask.npy",
+#                                 "DIAM": 12.0, "NBEAMS": 1, "NBINS": 5, "FBAR": 906,
+#                                    "TRES": 13.8, "THRESH": 0.309}  }'}
+# schema: astropy-2.0
+TNS   BW    DM    DMG  FBAR   FRES Gb Gl NREP SNR  SNRTHRESH THRESH TRES WIDTH XDec XRA Z
+DUMMY 288.0 401.4 35.0 906    1.0  "" "" 1    27.9 9.5       0.309   13.8  4.0   ""   "" 0.1
+

papers/CRACO/ImprovedSurveys/CRAFT_CRACO_900_imp2.1_div2.ecsv

@@ -0,0 +1,29 @@
+# %ECSV 1.0
+# ---
+# datatype:
+# - {name: TNS, datatype: string}
+# - {name: BW, datatype: float64}
+# - {name: DM, datatype: float64}
+# - {name: DMG, datatype: float64}
+# - {name: FBAR, datatype: float64}
+# - {name: FRES, datatype: float64}
+# - {name: Gb, datatype: string, subtype: 'float64[null]'}
+# - {name: Gl, datatype: string, subtype: 'float64[null]'}
+# - {name: NREP, datatype: int64}
+# - {name: SNR, datatype: float64}
+# - {name: SNRTHRESH, datatype: float64}
+# - {name: THRESH, datatype: float64}
+# - {name: TRES, datatype: float64}
+# - {name: WIDTH, datatype: float64}
+# - {name: XDec, datatype: string, subtype: 'float64[null]'}
+# - {name: XRA, datatype: string, subtype: 'float64[null]'}
+# - {name: Z, datatype: float64}
+# meta: !!omap
+# - {survey_data: '{"observing": {"NORM_FRB": 1,"TOBS": 1,"MAX_IW": 8, "MAXWMETH": 2},
+#                   "telescope": {"BEAM": "CRACO_900", "DMMASK": "craco_900_mask_div2.npy",
+#                                 "DIAM": 12.0, "NBEAMS": 1, "NBINS": 5,
+#                                    "TRES": 6.9, "THRESH": 0.99}  }'}
+# schema: astropy-2.0
+TNS   BW    DM    DMG  FBAR   FRES Gb Gl NREP SNR  SNRTHRESH THRESH TRES WIDTH XDec XRA Z
+DUMMY 288.0 401.4 35.0 906    1.0  "" "" 1    27.9 9.5       0.99   6.9  4.0   ""   "" 0.1
+

papers/CRACO/ImprovedSurveys/CRAFT_CRACO_900_imp2.1_div4.ecsv

@@ -0,0 +1,29 @@
+# %ECSV 1.0
+# ---
+# datatype:
+# - {name: TNS, datatype: string}
+# - {name: BW, datatype: float64}
+# - {name: DM, datatype: float64}
+# - {name: DMG, datatype: float64}
+# - {name: FBAR, datatype: float64}
+# - {name: FRES, datatype: float64}
+# - {name: Gb, datatype: string, subtype: 'float64[null]'}
+# - {name: Gl, datatype: string, subtype: 'float64[null]'}
+# - {name: NREP, datatype: int64}
+# - {name: SNR, datatype: float64}
+# - {name: SNRTHRESH, datatype: float64}
+# - {name: THRESH, datatype: float64}
+# - {name: TRES, datatype: float64}
+# - {name: WIDTH, datatype: float64}
+# - {name: XDec, datatype: string, subtype: 'float64[null]'}
+# - {name: XRA, datatype: string, subtype: 'float64[null]'}
+# - {name: Z, datatype: float64}
+# meta: !!omap
+# - {survey_data: '{"observing": {"NORM_FRB": 1,"TOBS": 1,"MAX_IW": 8, "MAXWMETH": 2},
+#                   "telescope": {"BEAM": "CRACO_900", "DMMASK": "craco_900_mask_div4.npy",
+#                                 "DIAM": 12.0, "NBEAMS": 1, "NBINS": 5,
+#                                    "TRES": 3.4, "THRESH": 0.99}  }'}
+# schema: astropy-2.0
+TNS   BW    DM    DMG  FBAR   FRES Gb Gl NREP SNR  SNRTHRESH THRESH TRES WIDTH XDec XRA Z
+DUMMY 288.0 401.4 35.0 906    1.0  "" "" 1    27.9 9.5       0.99   3.4  4.0   ""   "" 0.1
+

papers/CRACO/ImprovedSurveys/CRAFT_CRACO_900_imp2.1_div8.ecsv

@@ -0,0 +1,29 @@
+# %ECSV 1.0
+# ---
+# datatype:
+# - {name: TNS, datatype: string}
+# - {name: BW, datatype: float64}
+# - {name: DM, datatype: float64}
+# - {name: DMG, datatype: float64}
+# - {name: FBAR, datatype: float64}
+# - {name: FRES, datatype: float64}
+# - {name: Gb, datatype: string, subtype: 'float64[null]'}
+# - {name: Gl, datatype: string, subtype: 'float64[null]'}
+# - {name: NREP, datatype: int64}
+# - {name: SNR, datatype: float64}
+# - {name: SNRTHRESH, datatype: float64}
+# - {name: THRESH, datatype: float64}
+# - {name: TRES, datatype: float64}
+# - {name: WIDTH, datatype: float64}
+# - {name: XDec, datatype: string, subtype: 'float64[null]'}
+# - {name: XRA, datatype: string, subtype: 'float64[null]'}
+# - {name: Z, datatype: float64}
+# meta: !!omap
+# - {survey_data: '{"observing": {"NORM_FRB": 1,"TOBS": 1,"MAX_IW": 8, "MAXWMETH": 2},
+#                   "telescope": {"BEAM": "CRACO_900", "DMMASK": "craco_900_mask_div8.npy",
+#                                 "DIAM": 12.0, "NBEAMS": 1, "NBINS": 5,
+#                                    "TRES": 1.7, "THRESH": 0.99}  }'}
+# schema: astropy-2.0
+TNS   BW    DM    DMG  FBAR   FRES Gb Gl NREP SNR  SNRTHRESH THRESH TRES WIDTH XDec XRA Z
+DUMMY 288.0 401.4 35.0 906    1.0  "" "" 1    27.9 9.5       0.99   1.7  4.0   ""   "" 0.1
+

papers/CRACO/ImprovedSurveys/CRAFT_CRACO_900_imp2.2_div2.ecsv

@@ -0,0 +1,29 @@
+# %ECSV 1.0
+# ---
+# datatype:
+# - {name: TNS, datatype: string}
+# - {name: BW, datatype: float64}
+# - {name: DM, datatype: float64}
+# - {name: DMG, datatype: float64}
+# - {name: FBAR, datatype: float64}
+# - {name: FRES, datatype: float64}
+# - {name: Gb, datatype: string, subtype: 'float64[null]'}
+# - {name: Gl, datatype: string, subtype: 'float64[null]'}
+# - {name: NREP, datatype: int64}
+# - {name: SNR, datatype: float64}
+# - {name: SNRTHRESH, datatype: float64}
+# - {name: THRESH, datatype: float64}
+# - {name: TRES, datatype: float64}
+# - {name: WIDTH, datatype: float64}
+# - {name: XDec, datatype: string, subtype: 'float64[null]'}
+# - {name: XRA, datatype: string, subtype: 'float64[null]'}
+# - {name: Z, datatype: float64}
+# meta: !!omap
+# - {survey_data: '{"observing": {"NORM_FRB": 1,"TOBS": 1},
+#                   "telescope": {"BEAM": "CRACO_900", "DMMASK": "craco_900_mask_div2.npy",
+#                                 "DIAM": 12.0, "NBEAMS": 1, "NBINS": 5, "FBAR": 906,
+#                                "TRES": 6.9, "THRESH": 0.99}  }'}
+# schema: astropy-2.0
+TNS   BW    DM    DMG  FBAR   FRES Gb Gl NREP SNR  SNRTHRESH THRESH TRES WIDTH XDec XRA Z
+DUMMY 288.0 401.4 35.0 906    1.0  "" "" 1    27.9 9.5       0.99   6.9  4.0   ""   "" 0.1
+