Index

A

add_significance_bracket() (in module digimuh.viz_base) aggregate_per_cow() (in module digimuh.stats_annual_yield)

attach_crossing_flags() (in module digimuh.stats_production) attach_daily_climate_means() (in module digimuh.stats_production) attach_dim() (in module digimuh.stats_lactation_curve)

B

banner() (in module digimuh.console) BASELINE_LOOKBACK_DAYS (in module digimuh.stats_annual_yield)

build_create_table_sql() (in module digimuh.ingest) build_median_surface() (in module digimuh.stats_annual_yield)

C

check_null_rates() (in module digimuh.validate_db) check_referential_integrity() (in module digimuh.validate_db) check_table_counts() (in module digimuh.validate_db) check_temporal_coverage() (in module digimuh.validate_db) check_value_ranges() (in module digimuh.validate_db) classify() (in module digimuh.milk_yield_classification) classify_cow_years_by_wood_residual() (in module digimuh.stats_production) compute_annual_zscores() (in module digimuh.stats_annual_yield) compute_below_above() (in module digimuh.stats_core) compute_breakpoint_icc() (in module digimuh.stats_longitudinal) compute_circadian_null_model() (in module digimuh.stats_temporal) compute_climate_eta() (in module digimuh.stats_temporal) compute_cross_correlation() (in module digimuh.stats_temporal) compute_crossing_times() (in module digimuh.stats_temporal) compute_daily_crossing_flags() (in module digimuh.stats_production) compute_daily_entropy() (in module digimuh.analysis_12_motility_entropy) compute_derivative_ccf() (in module digimuh.stats_temporal)

compute_digestive_efficiency() (in module digimuh.analysis_06_digestive) compute_dilution_partition() (in module digimuh.stats_milk_composition) compute_disruption_index() (in module digimuh.analysis_11_circadian) compute_event_triggered_average() (in module digimuh.stats_temporal) compute_heatstress_duration_deltas() (in module digimuh.stats_annual_yield) compute_lagged_correlations() (in module digimuh.analysis_06_digestive) compute_predisease_trends() (in module digimuh.analysis_12_motility_entropy) compute_production_impact() (in module digimuh.analysis_03_heat_stress) compute_spearman() (in module digimuh.stats_core) compute_stability() (in module digimuh.stats_longitudinal) compute_thermoneutral_fraction() (in module digimuh.stats_production) compute_thi_daily_profile() (in module digimuh.stats_temporal) compute_tnf_yield_analysis() (in module digimuh.stats_production) compute_tnf_yield_by_class() (in module digimuh.stats_production) compute_wood_residuals() (in module digimuh.stats_lactation_curve) connect_db() (in module digimuh.analysis_utils) CowDBIngester (class in digimuh.ingest) crossing_day_comparison() (in module digimuh.stats_production)

D

daily_climate_vs_yield_correlations() (in module digimuh.stats_production) database (digimuh.config.DigiMuhConfig attribute) DELTA_MODERATE (in module digimuh.constants) DELTA_STABLE (in module digimuh.constants) digimuh module digimuh.analysis_01_ketosis module digimuh.analysis_03_heat_stress module digimuh.analysis_06_digestive module digimuh.analysis_11_circadian module digimuh.analysis_12_motility_entropy module digimuh.analysis_utils module digimuh.config module digimuh.console module digimuh.constants module digimuh.extract module digimuh.ingest module digimuh.milk_yield_classification module digimuh.paths module digimuh.run_annual_yield module digimuh.run_frontiers_2026 module digimuh.stats_annual_yield module digimuh.stats_core module

digimuh.stats_lactation_curve module digimuh.stats_longitudinal module digimuh.stats_milk_composition module digimuh.stats_production module digimuh.stats_runner module digimuh.stats_temporal module digimuh.validate_db module digimuh.viz_annual_yield module digimuh.viz_base module digimuh.viz_breakpoints module digimuh.viz_correlation module digimuh.viz_longitudinal module digimuh.viz_milk_composition module digimuh.viz_production module digimuh.viz_runner module digimuh.viz_temporal module DigiMuhConfig (class in digimuh.config) dilution_partition_summary() (in module digimuh.stats_milk_composition) DIM_BIN_DAYS (in module digimuh.stats_annual_yield) DIM_MAX (in module digimuh.stats_lactation_curve) DIM_MIN (in module digimuh.stats_lactation_curve) DIMENSION_TABLES_SQL (in module digimuh.ingest) done() (in module digimuh.console) DOY_BIN_DAYS (in module digimuh.stats_annual_yield)

E

extract_calvings() (in module digimuh.extract) extract_circadian_features() (in module digimuh.analysis_11_circadian) extract_climate() (in module digimuh.extract) extract_daily_milk_yield() (in module digimuh.extract) extract_daily_milk_yield_full() (in module digimuh.extract)

extract_entity_id_from_filename() (in module digimuh.ingest) extract_mlp_test_days() (in module digimuh.extract) extract_production() (in module digimuh.extract) extract_respiration_barn() (in module digimuh.extract) extract_rumen_barn() (in module digimuh.extract)

F

fit_circadian_harmonic() (in module digimuh.analysis_11_circadian) fit_dose_response() (in module digimuh.analysis_03_heat_stress)

fit_wood() (in module digimuh.stats_lactation_curve) fit_wood_per_lactation() (in module digimuh.stats_lactation_curve) FOLDER_CONFIG (in module digimuh.ingest)

G

GRID_STEPS (in module digimuh.constants)

guess_column_type() (in module digimuh.ingest)

K

kv() (in module digimuh.console)

kv_pair() (in module digimuh.console)

L

LACTATION_CAP (in module digimuh.stats_annual_yield) load_calvings() (in module digimuh.stats_lactation_curve) load_circadian_data() (in module digimuh.analysis_11_circadian) load_config() (in module digimuh.config) load_daily_yields() (in module digimuh.milk_yield_classification)

load_daily_yields_for_fitting() (in module digimuh.stats_lactation_curve) load_digestive_data() (in module digimuh.analysis_06_digestive) load_heat_data() (in module digimuh.analysis_03_heat_stress) load_ketosis_data() (in module digimuh.analysis_01_ketosis) load_mlp_test_days() (in module digimuh.stats_milk_composition) load_tierauswahl() (in module digimuh.extract)

M

main() (in module digimuh.analysis_01_ketosis) (in module digimuh.analysis_03_heat_stress) (in module digimuh.analysis_06_digestive) (in module digimuh.analysis_11_circadian) (in module digimuh.analysis_12_motility_entropy) (in module digimuh.config) (in module digimuh.extract) (in module digimuh.ingest) (in module digimuh.milk_yield_classification) (in module digimuh.run_annual_yield) (in module digimuh.run_frontiers_2026) (in module digimuh.stats_runner) (in module digimuh.validate_db) (in module digimuh.viz_runner) make_summary_table() (in module digimuh.stats_longitudinal) merge_mlp_with_cowday() (in module digimuh.stats_milk_composition) MIN_COHORT_SIZE (in module digimuh.constants) MIN_COWS_PER_CELL (in module digimuh.stats_annual_yield) MIN_DAYS_PER_COW_YEAR (in module digimuh.stats_annual_yield) MIN_POINTS_PER_LACTATION (in module digimuh.stats_lactation_curve) MIN_READINGS (in module digimuh.constants) mlp_climate_correlations() (in module digimuh.stats_milk_composition) module digimuh digimuh.analysis_01_ketosis digimuh.analysis_03_heat_stress digimuh.analysis_06_digestive digimuh.analysis_11_circadian digimuh.analysis_12_motility_entropy digimuh.analysis_utils digimuh.config digimuh.console digimuh.constants digimuh.extract digimuh.ingest digimuh.milk_yield_classification digimuh.paths digimuh.run_annual_yield digimuh.run_frontiers_2026 digimuh.stats_annual_yield digimuh.stats_core digimuh.stats_lactation_curve digimuh.stats_longitudinal digimuh.stats_milk_composition digimuh.stats_production digimuh.stats_runner digimuh.stats_temporal digimuh.validate_db digimuh.viz_annual_yield digimuh.viz_base digimuh.viz_breakpoints digimuh.viz_correlation digimuh.viz_longitudinal digimuh.viz_milk_composition digimuh.viz_production digimuh.viz_runner digimuh.viz_temporal

MUESCHNER_SIEMENS (in module digimuh.milk_yield_classification)

N

n_jobs (digimuh.config.DigiMuhConfig attribute)

O

output (digimuh.config.DigiMuhConfig attribute)

P

p_to_stars() (in module digimuh.stats_core) permutation_entropy() (in module digimuh.analysis_12_motility_entropy) plot_bodytemp_vs_resp_scatter() (in module digimuh.viz_breakpoints) plot_breakpoint_icc() (in module digimuh.viz_longitudinal) plot_breakpoint_raincloud() (in module digimuh.viz_longitudinal) plot_breakpoint_retest() (in module digimuh.viz_longitudinal) plot_breakpoint_value_raincloud() (in module digimuh.viz_longitudinal) plot_circadian_null_model() (in module digimuh.viz_temporal) plot_circadian_results() (in module digimuh.analysis_11_circadian) plot_climate() (in module digimuh.viz_breakpoints) plot_climate_eta() (in module digimuh.viz_correlation) plot_composition_heatmap() (in module digimuh.viz_milk_composition) plot_cross_correlation() (in module digimuh.viz_correlation) plot_crossing_day_raincloud() (in module digimuh.viz_production) plot_crossing_raster() (in module digimuh.viz_temporal) plot_daily_climate_vs_yield() (in module digimuh.viz_production) plot_derivative_ccf() (in module digimuh.viz_correlation) plot_digestive_results() (in module digimuh.analysis_06_digestive) plot_dilution_partition() (in module digimuh.viz_milk_composition) plot_entropy_results() (in module digimuh.analysis_12_motility_entropy) plot_event_triggered_average() (in module digimuh.viz_correlation) plot_examples() (in module digimuh.viz_breakpoints) plot_grouped_boxplots() (in module digimuh.viz_breakpoints) plot_heat_overview() (in module digimuh.analysis_03_heat_stress)

plot_heatstress_duration() (in module digimuh.viz_annual_yield) plot_ketosis_overview() (in module digimuh.analysis_01_ketosis) plot_longitudinal_breakpoints() (in module digimuh.viz_longitudinal) plot_longitudinal_sankey() (in module digimuh.viz_longitudinal) plot_paired_below_above() (in module digimuh.viz_breakpoints) plot_paired_rumen_vs_resp() (in module digimuh.viz_breakpoints) plot_per_year_histogram() (in module digimuh.milk_yield_classification) plot_pooled_histogram() (in module digimuh.milk_yield_classification) plot_predictors() (in module digimuh.viz_breakpoints) plot_residual_histogram() (in module digimuh.milk_yield_classification) plot_spearman() (in module digimuh.viz_breakpoints) plot_stability() (in module digimuh.viz_breakpoints) plot_thi_daily_profile() (in module digimuh.viz_temporal) plot_thi_vs_temp_scatter() (in module digimuh.viz_breakpoints) plot_thin_milk_hypothesis() (in module digimuh.viz_milk_composition) plot_threshold_sankey() (in module digimuh.viz_longitudinal) plot_tnf_yield() (in module digimuh.viz_production) plot_tnf_yield_by_class() (in module digimuh.viz_production) plot_wood_example_fits() (in module digimuh.milk_yield_classification) plot_yield_lines() (in module digimuh.viz_annual_yield) predict_wood() (in module digimuh.stats_lactation_curve) print_config() (in module digimuh.config) print_summary() (in module digimuh.milk_yield_classification) print_wood_summary() (in module digimuh.milk_yield_classification) progress() (in module digimuh.console)

Q

query_df() (in module digimuh.analysis_utils)

R

read_csv_sample() (in module digimuh.ingest) reset_steps() (in module digimuh.console) residual_terciles() (in module digimuh.stats_lactation_curve) resolve_input() (in module digimuh.paths)

resolve_output() (in module digimuh.paths) result_table() (in module digimuh.console) run() (digimuh.ingest.CowDBIngester method) run_broken_stick_fits() (in module digimuh.stats_core) run_statistical_tests() (in module digimuh.stats_core)

S

sample_entropy() (in module digimuh.analysis_12_motility_entropy) sanitise_column_name() (in module digimuh.ingest) save_fig() (in module digimuh.analysis_utils) save_figure() (in module digimuh.viz_base) section() (in module digimuh.console) setup_figure() (in module digimuh.viz_base) setup_interactive() (in module digimuh.config)

setup_logging() (in module digimuh.console) setup_plotting() (in module digimuh.analysis_utils) sigmoid() (in module digimuh.analysis_03_heat_stress) smaxtec_drink_correction (digimuh.config.DigiMuhConfig attribute) STANDALONE_FILES (in module digimuh.ingest) stars_styled() (in module digimuh.console) summarise_duration_deltas() (in module digimuh.stats_annual_yield)

T

TEMP_RANGE (in module digimuh.constants) test_duration_medians() (in module digimuh.stats_annual_yield) THI_RANGE (in module digimuh.constants) THI_REFERENCE (in module digimuh.constants)

thin_milk_verdict() (in module digimuh.stats_milk_composition) tierauswahl (digimuh.config.DigiMuhConfig attribute) tnf_yield_correlations_by_class() (in module digimuh.stats_production) train_ketosis_classifier() (in module digimuh.analysis_01_ketosis)

Y

YAN (in module digimuh.milk_yield_classification)