.flake8
.gitignore
.pre-commit-config.yaml
.readthedocs.yaml
LICENSE
README.md
environment.yaml
pyproject.toml
requirements-dev.txt
requirements.txt
tox.ini
.github/dependabot.yml
.github/workflows/pr.yaml
.github/workflows/pypi.yaml
docs/_config.yml
docs/_toc.yml
docs/algo.md
docs/algo1.ipynb
docs/algo2.ipynb
docs/api.rst
docs/core_data_structure.md
docs/custom_echopop.css
docs/example_notebooks.md
docs/glossary.md
docs/implementation.md
docs/index.md
docs/input_files.md
docs/install.md
docs/quick_start.ipynb
docs/references.bib
docs/requirements.txt
docs/theory.md
docs/zbibliography.md
docs/example_notebooks/diagnostic_plotting.ipynb
docs/example_notebooks/example_echopop_workflow.ipynb
docs/example_notebooks/plotting.ipynb
docs/example_notebooks/report_generation.ipynb
docs/example_notebooks/notebook_images/cropped_kriging_mesh_interactive.png
docs/example_notebooks/notebook_images/inpfc_strata_results.png
docs/images/Echopop_input_schematic.png
docs/images/noaa_fisheries_logo.png
docs/images/symbols.jpeg
docs/implementation/echopro_vs_echopop.md
docs/implementation/preprocessing_data.md
docs/theory/acoustics.md
docs/theory/apportion_abundance.md
docs/theory/apportion_biomass.md
docs/theory/bio_estimates.md
docs/theory/kriging.md
docs/theory/kriging_eq.md
docs/theory/other.md
docs/theory/semivariogram_eq.md
docs/theory/stratification.md
echopop/__init__.py
echopop/_testing.py
echopop/_version.py
echopop/utils.py
echopop.egg-info/PKG-INFO
echopop.egg-info/SOURCES.txt
echopop.egg-info/dependency_links.txt
echopop.egg-info/requires.txt
echopop.egg-info/top_level.txt
echopop/core/__init__.py
echopop/core/echoview.py
echopop/core/validators.py
echopop/geostatistics/__init__.py
echopop/geostatistics/cropping.py
echopop/geostatistics/kriging.py
echopop/geostatistics/projection.py
echopop/geostatistics/variogram.py
echopop/geostatistics/variogram_models.py
echopop/graphics/__init__.py
echopop/graphics/age_length_heatmap.py
echopop/graphics/diagnostics.py
echopop/graphics/kriged_mesh.py
echopop/graphics/transect_map.py
echopop/graphics/utils.py
echopop/graphics/variogram_gui.py
echopop/ingest/__init__.py
echopop/ingest/biological.py
echopop/ingest/mesh.py
echopop/ingest/nasc.py
echopop/ingest/params.py
echopop/ingest/strata.py
echopop/ingest/sv.py
echopop/inversion/__init__.py
echopop/inversion/inversion_base.py
echopop/inversion/inversion_length_TS.py
echopop/inversion/inversion_matrix.py
echopop/inversion/pcdwba.py
echopop/inversion/post_inversion.py
echopop/inversion/utils.py
echopop/survey/__init__.py
echopop/survey/biology.py
echopop/survey/proportions.py
echopop/survey/statistics.py
echopop/survey/stratified.py
echopop/survey/transect.py
echopop/tests/__init__.py
echopop/tests/conftest.py
echopop/tests/fixtures/__init__.py
echopop/tests/fixtures/fixtures_basic_plotting.py
echopop/tests/fixtures/fixtures_binning.py
echopop/tests/fixtures/fixtures_biodata_loader.py
echopop/tests/fixtures/fixtures_biology.py
echopop/tests/fixtures/fixtures_cropping.py
echopop/tests/fixtures/fixtures_data_loader.py
echopop/tests/fixtures/fixtures_echoview_ingestion.py
echopop/tests/fixtures/fixtures_geostatistics_loader.py
echopop/tests/fixtures/fixtures_geostats_class.py
echopop/tests/fixtures/fixtures_inversion.py
echopop/tests/fixtures/fixtures_kriging.py
echopop/tests/fixtures/fixtures_partition_transect.py
echopop/tests/fixtures/fixtures_proportions.py
echopop/tests/fixtures/fixtures_spatial.py
echopop/tests/fixtures/fixtures_statistics.py
echopop/tests/fixtures/fixtures_stratification_loader.py
echopop/tests/fixtures/fixtures_stratified.py
echopop/tests/fixtures/fixtures_transect.py
echopop/tests/fixtures/fixtures_variogram.py
echopop/tests/fixtures/fixtures_variogram_fitting.py
echopop/tests/fixtures/fixtures_variogram_modeling.py
echopop/tests/graphics/__init__.py
echopop/tests/graphics/test_basic_plotting.py
echopop/tests/graphics/test_helpers.py
echopop/tests/graphics/test_utils.py
echopop/tests/helpers/__init__.py
echopop/tests/helpers/helpers_echoview_ingestion.py
echopop/tests/ingest/__init__.py
echopop/tests/ingest/test_biodata_loader.py
echopop/tests/ingest/test_echoview_ingestion.py
echopop/tests/ingest/test_geostatistics_loader.py
echopop/tests/ingest/test_inversion_sv_ingestion.py
echopop/tests/ingest/test_stratification_loader.py
echopop/tests/inversion/__init__.py
echopop/tests/inversion/test_inversion_base.py
echopop/tests/inversion/test_inversion_length_TS.py
echopop/tests/inversion/test_inversion_matrix.py
echopop/tests/inversion/test_inversion_utils.py
echopop/tests/processing/__init__.py
echopop/tests/processing/test_binning.py
echopop/tests/processing/test_biology.py
echopop/tests/processing/test_proportions.py
echopop/tests/processing/test_statistics.py
echopop/tests/processing/test_stratified.py
echopop/tests/processing/test_transect.py
echopop/tests/spatial/__init__.py
echopop/tests/spatial/test_cropping.py
echopop/tests/spatial/test_kriging.py
echopop/tests/spatial/test_spatial.py
echopop/tests/spatial/test_validators.py
echopop/tests/spatial/test_variogram.py
echopop/tests/spatial/test_variogram_fitting.py
echopop/tests/spatial/test_variogram_modeling.py
echopop/tests/utils/__init__.py
echopop/tests/utils/test_utils.py
echopop/tests/validators/__init__.py
echopop/tests/validators/test_base.py
echopop/tests/validators/test_inversion.py
echopop/tests/validators/test_kriging.py
echopop/tests/validators/test_spatial.py
echopop/tests/validators/test_variogram.py
echopop/validators/__init__.py
echopop/validators/inversion.py
echopop/validators/kriging.py
echopop/validators/scattering.py
echopop/validators/scattering_models.py
echopop/validators/spatial.py
echopop/validators/variogram.py
echopop/workflows/__init__.py
echopop/workflows/nwfsc_feat/__init__.py
echopop/workflows/nwfsc_feat/apportionment.py
echopop/workflows/nwfsc_feat/biology.py
echopop/workflows/nwfsc_feat/functions.py
echopop/workflows/nwfsc_feat/parameters.py
echopop/workflows/nwfsc_feat/reporter.py
echopop/workflows/nwfsc_feat/tests/__init__.py
echopop/workflows/nwfsc_feat/tests/conftest.py
echopop/workflows/nwfsc_feat/tests/fixtures/__init__.py
echopop/workflows/nwfsc_feat/tests/fixtures/fixtures_FEAT.py
echopop/workflows/nwfsc_feat/tests/fixtures/fixtures_apportion.py
echopop/workflows/nwfsc_feat/tests/fixtures/fixtures_spatial.py
echopop/workflows/nwfsc_feat/tests/processing/test_apportion.py
echopop/workflows/nwfsc_feat/tests/processing/test_asfc_nasc_format.py
echopop/workflows/nwfsc_feat/tests/processing/test_biology.py
echopop/workflows/nwfsc_feat/tests/processing/test_transect_population_estimates.py
echopop/workflows/nwfsc_feat/tests/report_generation/__init__.py
echopop/workflows/nwfsc_feat/tests/report_generation/test_Reporter.py
echopop/workflows/nwfsc_feat/tests/report_generation/test_helpers.py
echopop/workflows/nwfsc_feat/tests/spatial/test_feat_cropping.py
echopop/workflows/nwfsc_feat/tests/spatial/test_transect_filtering.py
echopop/workflows/nwfsc_feat/workflows/feat_hake.py
echopop/workflows/nwfsc_feat/workflows/feat_hake_age1_excluded.py
echopop/workflows/nwfsc_feat/workflows/feat_hake_kriging_without_extrapolation.py
echopop/workflows/nwfsc_feat/workflows/feat_krill.py
echopop/workflows/nwfsc_feat/workflows/feat_plotting.py
echopop/workflows/nwfsc_feat/workflows/feat_report_generation.py
echopop/workflows/nwfsc_feat/workflows/transect_processing_expressions.md
echopop/workflows/nwfsc_feat/workflows/demo_files/figures/kriged_abundance_age_length_heatmap.png
echopop/workflows/nwfsc_feat/workflows/demo_files/figures/kriged_biomass_age_length_heatmap_female_noage1.png
echopop/workflows/nwfsc_feat/workflows/demo_files/figures/kriged_biomass_age_length_heatmap_male_noage1.png
echopop/workflows/nwfsc_feat/workflows/demo_files/figures/kriged_biomass_age_length_heatmap_noage1.png
echopop/workflows/nwfsc_feat/workflows/demo_files/figures/kriged_biomass_age_length_heatmap_plus.png
echopop/workflows/nwfsc_feat/workflows/demo_files/figures/kriged_mesh_hexbin_base.png
echopop/workflows/nwfsc_feat/workflows/demo_files/figures/kriged_mesh_hexbin_plus.png
echopop/workflows/nwfsc_feat/workflows/demo_files/figures/kriged_mesh_pcolormesh.png
echopop/workflows/nwfsc_feat/workflows/demo_files/figures/kriged_mesh_scatter.png
echopop/workflows/nwfsc_feat/workflows/demo_files/figures/transect_map_base.png
echopop/workflows/nwfsc_feat/workflows/demo_files/figures/transect_map_plus.png
echopop/workflows/nwfsc_feat/workflows/notebooks/diagnostic_plotting_demo.ipynb
echopop/workflows/nwfsc_feat/workflows/year_specific/__init__.py
echopop/workflows/nwfsc_feat/workflows/year_specific/cli_utils.py
echopop/workflows/nwfsc_feat/workflows/year_specific/hake_1995.py
echopop/workflows/nwfsc_feat/workflows/year_specific/hake_1998.py
echopop/workflows/nwfsc_feat/workflows/year_specific/hake_2001.py
echopop/workflows/nwfsc_feat/workflows/year_specific/hake_2003.py
echopop/workflows/nwfsc_feat/workflows/year_specific/hake_2005.py
echopop/workflows/nwfsc_feat/workflows/year_specific/hake_2007.py
echopop/workflows/nwfsc_feat/workflows/year_specific/hake_2009.py
echopop/workflows/nwfsc_feat/workflows/year_specific/hake_2011.py
echopop/workflows/nwfsc_feat/workflows/year_specific/hake_2012.py
echopop/workflows/nwfsc_feat/workflows/year_specific/hake_2013.py
echopop/workflows/nwfsc_feat/workflows/year_specific/hake_2015.py
echopop/workflows/nwfsc_feat/workflows/year_specific/hake_2017.py
echopop/workflows/nwfsc_feat/workflows/year_specific/hake_2019.py
echopop/workflows/nwfsc_feat/workflows/year_specific/hake_2021.py
echopop/workflows/nwfsc_feat/workflows/year_specific/hake_2023.py
echopop/workflows/nwfsc_feat/workflows/year_specific/run_year_specific.bat
echopop/workflows/nwfsc_feat/workflows/year_specific/year_specific_workflow.py
echopop/workflows/nwfsc_feat/workflows/year_specific/year_specific_workflows.ipynb