diff --git a/modelling/data/thrupp-lake-birds/resident/black_headed_gull_classification.json b/modelling/data/thrupp-lake-birds/resident/black_headed_gull_classification.json new file mode 100644 index 0000000..c539c75 --- /dev/null +++ b/modelling/data/thrupp-lake-birds/resident/black_headed_gull_classification.json @@ -0,0 +1,105 @@ +{ + "schema_version": "resident-classification/v1", + "species": "Black Headed Gull", + "model_family": "resident_detectability", + "classification": { + "primary_class": "resident_with_summer_detectability_collapse", + "baseline_presence": "weak", + "detectability_peak_timing": "spring", + "detectability_trough_timing": "autumn", + "spring_carryover": "weak", + "summer_suppression": "moderate", + "summer_decay_acceleration": "strong", + "pre_summer_retention": "strong", + "autumn_component": "weak", + "year_end_component": "meaningful", + "response_dynamics": "rapid_decline_biased", + "traits": [ + "resident_detectability_pattern", + "weak_baseline_presence", + "spring_detectability_peak", + "autumn_detectability_trough", + "weak_spring_carryover", + "moderate_summer_suppression", + "strong_summer_decay_acceleration", + "strong_pre_summer_retention", + "weak_autumn_component", + "meaningful_year_end_component", + "rapid_decline_biased_response_dynamics" + ], + "confidence": "medium" + }, + "derived_metrics": { + "target_peak_month": 4, + "target_peak_label": "April", + "target_trough_month": 10, + "target_trough_label": "October", + "target_peak_value": 0.6179902708529666, + "target_trough_value": 0.0, + "target_mean_value": 0.16947003086875745, + "target_amplitude": 0.6179902708529666, + "baseline_to_peak_ratio": 0.06796223497504335, + "autumn_to_winter_weight_ratio": 0.05078125, + "year_end_to_winter_weight_ratio": 0.34375, + "decay_to_growth_ratio": 1.4795042897998094, + "monthly_target": { + "January": 0.10643691104661826, + "February": 0.13051214942192935, + "March": 0.3530032990742757, + "April": 0.6179902708529666, + "May": 0.34146996043444217, + "June": 0.12672089315357968, + "July": 0.09769095477134637, + "August": 0.041985534101238155, + "September": 0.019990096462397678, + "October": 0.0, + "November": 0.0037420369449616383, + "December": 0.19409826416133383 + } + }, + "parameter_evidence": { + "INITIAL_Y": 0.762, + "GROWTH_RATE": 2.098, + "DECAY_RATE": 3.104, + "SUMMER_DECAY_BOOST": 4.326, + "PRE_SUMMER_DECAY_REDUCTION": 0.558, + "PRE_SUMMER_DECAY_END": 6.965, + "PRE_SUMMER_DECAY_SHARPNESS": 11.384, + "SPRING_CARRYOVER_WEIGHT": 0.064, + "SPRING_CARRYOVER_END": 7.115, + "SPRING_CARRYOVER_SHARPNESS": 16.272, + "BASELINE": 0.042, + "WINTER_WEIGHT": 0.512, + "AUTUMN_WEIGHT": 0.026, + "WINTER_PEAK": 3.995, + "AUTUMN_PEAK": 11.015, + "AUTUMN_ONSET": 11.37, + "AUTUMN_GATE_SHARPNESS": 7.514, + "WINTER_WIDTH": 11.343, + "WINTER_RISE_WIDTH": 10.62, + "WINTER_FALL_WIDTH": 11.09, + "AUTUMN_WIDTH": 7.326, + "AUTUMN_RISE_WIDTH": 7.566, + "AUTUMN_FALL_WIDTH": 8.245, + "SUMMER_DIP": 0.102, + "SUMMER_LOW": 9.77, + "SUMMER_ONSET": 7.925, + "SUMMER_GATE_SHARPNESS": 4.756, + "SUMMER_DECAY_ONSET": 7.25, + "SUMMER_DECAY_GATE_SHARPNESS": 18.102, + "SUMMER_WIDTH": 23.421, + "SUMMER_RISE_WIDTH": 37.333, + "SUMMER_FALL_WIDTH": 8.923, + "SCALE": 1.126, + "YEAR_END_WEIGHT": 0.176, + "YEAR_END_PEAK": 12.147, + "YEAR_END_WIDTH": 79.51, + "YEAR_END_RISE_WIDTH": 148.126, + "YEAR_END_FALL_WIDTH": 9.832 + }, + "fit": { + "score": 0.201 + }, + "warnings": [], + "summary": "Black Headed Gull is classified as resident with summer detectability collapse. The fitted resident detectability target peaks around April and reaches its lowest point around October. The model indicates weak baseline presence, weak spring carry-over, strong pre-summer retention, moderate summer suppression, and strong summer decay acceleration." +} diff --git a/modelling/data/thrupp-lake-birds/resident/black_headed_gull_consensus.json b/modelling/data/thrupp-lake-birds/resident/black_headed_gull_consensus.json new file mode 100644 index 0000000..63ed28e --- /dev/null +++ b/modelling/data/thrupp-lake-birds/resident/black_headed_gull_consensus.json @@ -0,0 +1,42 @@ +{ + "SCORE": "0.201", + "INITIAL_Y": "0.762", + "GROWTH_RATE": "2.098", + "DECAY_RATE": "3.104", + "SUMMER_DECAY_BOOST": "4.326", + "PRE_SUMMER_DECAY_REDUCTION": "0.558", + "PRE_SUMMER_DECAY_END": "6.965", + "PRE_SUMMER_DECAY_SHARPNESS": "11.384", + "SPRING_CARRYOVER_WEIGHT": "0.064", + "SPRING_CARRYOVER_END": "7.115", + "SPRING_CARRYOVER_SHARPNESS": "16.272", + "BASELINE": "0.042", + "WINTER_WEIGHT": "0.512", + "AUTUMN_WEIGHT": "0.026", + "WINTER_PEAK": "3.995", + "AUTUMN_PEAK": "11.015", + "AUTUMN_ONSET": "11.37", + "AUTUMN_GATE_SHARPNESS": "7.514", + "WINTER_WIDTH": "11.343", + "WINTER_RISE_WIDTH": "10.62", + "WINTER_FALL_WIDTH": "11.09", + "AUTUMN_WIDTH": "7.326", + "AUTUMN_RISE_WIDTH": "7.566", + "AUTUMN_FALL_WIDTH": "8.245", + "SUMMER_DIP": "0.102", + "SUMMER_LOW": "9.77", + "SUMMER_ONSET": "7.925", + "SUMMER_GATE_SHARPNESS": "4.756", + "SUMMER_DECAY_ONSET": "7.25", + "SUMMER_DECAY_GATE_SHARPNESS": "18.102", + "SUMMER_WIDTH": "23.421", + "SUMMER_RISE_WIDTH": "37.333", + "SUMMER_FALL_WIDTH": "8.923", + "SCALE": "1.126", + "YEAR_END_WEIGHT": "0.176", + "YEAR_END_PEAK": "12.147", + "YEAR_END_WIDTH": "79.51", + "YEAR_END_RISE_WIDTH": "148.126", + "YEAR_END_FALL_WIDTH": "9.832", + "SPECIES": "Black Headed Gull" +} diff --git a/modelling/data/thrupp-lake-birds/resident/black_headed_gull_observed.csv b/modelling/data/thrupp-lake-birds/resident/black_headed_gull_observed.csv new file mode 100644 index 0000000..35b4abf --- /dev/null +++ b/modelling/data/thrupp-lake-birds/resident/black_headed_gull_observed.csv @@ -0,0 +1,13 @@ +month,value +1,14 +2,12 +3,10 +4,20 +5,10 +6,7 +7,5 +8,2 +9,1 +10,0 +11,5 +12,3 diff --git a/modelling/data/thrupp-lake-birds/resident/black_headed_gull_parameters.csv b/modelling/data/thrupp-lake-birds/resident/black_headed_gull_parameters.csv new file mode 100644 index 0000000..9a73b27 --- /dev/null +++ b/modelling/data/thrupp-lake-birds/resident/black_headed_gull_parameters.csv @@ -0,0 +1,201 @@ 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a/modelling/data/thrupp-lake-birds/resident/black_headed_gull_simulated.png b/modelling/data/thrupp-lake-birds/resident/black_headed_gull_simulated.png new file mode 100644 index 0000000..a1d0c2f Binary files /dev/null and b/modelling/data/thrupp-lake-birds/resident/black_headed_gull_simulated.png differ diff --git a/modelling/data/thrupp-lake-birds/resident/black_headed_gull_synthesised.csv b/modelling/data/thrupp-lake-birds/resident/black_headed_gull_synthesised.csv new file mode 100644 index 0000000..88c3b7c --- /dev/null +++ b/modelling/data/thrupp-lake-birds/resident/black_headed_gull_synthesised.csv @@ -0,0 +1,13 @@ +month,observed,simulated_raw,synthesised +1,14,0.4892404,15.676289671034079 +2,12,0.2394368,7.672057815964202 +3,10,0.3797075,12.166625569483164 +4,20,0.545026,17.46377742771247 +5,10,0.3871352,12.404624673378796 +6,7,0.2001351,6.412748826428423 +7,5,0.08612107,2.759499910676638 +8,2,0.04301278,1.3782197848674418 +9,1,0.009917672399999999,0.3177830477712383 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"moderate", + "detectability_peak_timing": "spring", + "detectability_trough_timing": "autumn", + "spring_carryover": "weak", + "summer_suppression": "moderate", + "summer_decay_acceleration": "moderate", + "pre_summer_retention": "strong", + "autumn_component": "weak", + "year_end_component": "meaningful", + "response_dynamics": "decline_biased", + "traits": [ + "resident_detectability_pattern", + "moderate_baseline_presence", + "spring_detectability_peak", + "autumn_detectability_trough", + "weak_spring_carryover", + "moderate_summer_suppression", + "moderate_summer_decay_acceleration", + "strong_pre_summer_retention", + "weak_autumn_component", + "meaningful_year_end_component", + "decline_biased_response_dynamics" + ], + "confidence": "high" + }, + "derived_metrics": { + "target_peak_month": 4, + "target_peak_label": "April", + "target_trough_month": 10, + "target_trough_label": "October", + "target_peak_value": 0.7674704377843766, + "target_trough_value": 0.15430857340849072, + "target_mean_value": 0.3482162216062972, + "target_amplitude": 0.6131618643758859, + "baseline_to_peak_ratio": 0.3101096645325991, + "autumn_to_winter_weight_ratio": 0.04790419161676647, + "year_end_to_winter_weight_ratio": 0.31137724550898205, + "decay_to_growth_ratio": 1.3198680956306679, + "monthly_target": { + "January": 0.28028459806045974, + "February": 0.2974200684896655, + "March": 0.4715316429083119, + "April": 0.7674704377843766, + "May": 0.5847052332515325, + "June": 0.316653381249031, + "July": 0.265904390267645, + "August": 0.23799825007507175, + "September": 0.22450032576363066, + "October": 0.15430857340849072, + "November": 0.2045126911701282, + "December": 0.37330506684722314 + } + }, + "parameter_evidence": { + "INITIAL_Y": 0.308, + "GROWTH_RATE": 2.426, + "DECAY_RATE": 3.202, + "SUMMER_DECAY_BOOST": 3.844, + "PRE_SUMMER_DECAY_REDUCTION": 0.491, + "PRE_SUMMER_DECAY_END": 7.065, + "PRE_SUMMER_DECAY_SHARPNESS": 8.98, + "SPRING_CARRYOVER_WEIGHT": 0.042, + "SPRING_CARRYOVER_END": 7.04, + "SPRING_CARRYOVER_SHARPNESS": 15.506, + "BASELINE": 0.238, + "WINTER_WEIGHT": 0.501, + "AUTUMN_WEIGHT": 0.024, + "WINTER_PEAK": 4.205, + "AUTUMN_PEAK": 11.16, + "AUTUMN_ONSET": 11.36, + "AUTUMN_GATE_SHARPNESS": 7.652, + "WINTER_WIDTH": 9.802, + "WINTER_RISE_WIDTH": 9.5, + "WINTER_FALL_WIDTH": 11.396, + "AUTUMN_WIDTH": 7.8, + "AUTUMN_RISE_WIDTH": 8.472, + "AUTUMN_FALL_WIDTH": 7.488, + "SUMMER_DIP": 0.085, + "SUMMER_LOW": 9.855, + "SUMMER_ONSET": 8.45, + "SUMMER_GATE_SHARPNESS": 4.217, + "SUMMER_DECAY_ONSET": 7.095, + "SUMMER_DECAY_GATE_SHARPNESS": 14.045, + "SUMMER_WIDTH": 23.528, + "SUMMER_RISE_WIDTH": 34.559, + "SUMMER_FALL_WIDTH": 9.756, + "SCALE": 0.971, + "YEAR_END_WEIGHT": 0.156, + "YEAR_END_PEAK": 12.149, + "YEAR_END_WIDTH": 87.122, + "YEAR_END_RISE_WIDTH": 161.228, + "YEAR_END_FALL_WIDTH": 11.088 + }, + "fit": { + "score": 0.195 + }, + "warnings": [], + "summary": "Canada Goose is classified as resident with summer detectability collapse. The fitted resident detectability target peaks around April and reaches its lowest point around October. The model indicates moderate baseline presence, weak spring carry-over, strong pre-summer retention, moderate summer suppression, and moderate summer decay acceleration." +} diff --git a/modelling/data/thrupp-lake-birds/resident/canada_goose_consensus.json b/modelling/data/thrupp-lake-birds/resident/canada_goose_consensus.json new file mode 100644 index 0000000..503498f --- /dev/null +++ b/modelling/data/thrupp-lake-birds/resident/canada_goose_consensus.json @@ -0,0 +1,42 @@ +{ + "SCORE": "0.195", + "INITIAL_Y": "0.308", + "GROWTH_RATE": "2.426", + "DECAY_RATE": "3.202", + "SUMMER_DECAY_BOOST": "3.844", + "PRE_SUMMER_DECAY_REDUCTION": "0.491", + "PRE_SUMMER_DECAY_END": "7.065", + "PRE_SUMMER_DECAY_SHARPNESS": "8.98", + "SPRING_CARRYOVER_WEIGHT": "0.042", + "SPRING_CARRYOVER_END": "7.04", + "SPRING_CARRYOVER_SHARPNESS": "15.506", + "BASELINE": "0.238", + "WINTER_WEIGHT": "0.501", + "AUTUMN_WEIGHT": "0.024", + "WINTER_PEAK": "4.205", + "AUTUMN_PEAK": "11.16", + "AUTUMN_ONSET": "11.36", + 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0000000..5a9c96d Binary files /dev/null and b/modelling/data/thrupp-lake-birds/resident/canada_goose_simulated.png differ diff --git a/modelling/data/thrupp-lake-birds/resident/canada_goose_synthesised.csv b/modelling/data/thrupp-lake-birds/resident/canada_goose_synthesised.csv new file mode 100644 index 0000000..91e9453 --- /dev/null +++ b/modelling/data/thrupp-lake-birds/resident/canada_goose_synthesised.csv @@ -0,0 +1,13 @@ +month,observed,simulated_raw,synthesised +1,4,0.2960295,5.726778059263605 +2,11,0.3182431,6.156506708257229 +3,10,0.5064058,9.796569681480506 +4,19,0.7163166999999999,13.857358003320986 +5,9,0.5880725,11.376436099295159 +6,6,0.3777254,7.3072093596974925 +7,5,0.26958699999999997,5.215240091486481 +8,5,0.2388505,4.62063342620969 +9,2,0.1979504,3.8294089188491496 +10,1,0.1631435,3.1560591640747693 +11,1,0.2131856,4.124138359963947 +12,2,0.3419741,6.615589908155836 diff --git a/modelling/data/thrupp-lake-birds/resident/canada_goose_synthesised.png b/modelling/data/thrupp-lake-birds/resident/canada_goose_synthesised.png new file mode 100644 index 0000000..17f73f9 Binary files /dev/null and b/modelling/data/thrupp-lake-birds/resident/canada_goose_synthesised.png differ diff --git a/modelling/data/thrupp-lake-birds/resident/coot_classification.json b/modelling/data/thrupp-lake-birds/resident/coot_classification.json new file mode 100644 index 0000000..e8734f2 --- /dev/null +++ b/modelling/data/thrupp-lake-birds/resident/coot_classification.json @@ -0,0 +1,105 @@ +{ + "schema_version": "resident-classification/v1", + "species": "Coot", + "model_family": "resident_detectability", + "classification": { + "primary_class": "resident_with_summer_detectability_collapse", + "baseline_presence": "weak", + "detectability_peak_timing": "spring", + "detectability_trough_timing": "autumn", + "spring_carryover": "weak", + "summer_suppression": "moderate", + "summer_decay_acceleration": "moderate", + "pre_summer_retention": "strong", + "autumn_component": "weak", + "year_end_component": "meaningful", + "response_dynamics": "decline_biased", + "traits": [ + "resident_detectability_pattern", + "weak_baseline_presence", + "spring_detectability_peak", + "autumn_detectability_trough", + "weak_spring_carryover", + "moderate_summer_suppression", + "moderate_summer_decay_acceleration", + "strong_pre_summer_retention", + "weak_autumn_component", + "meaningful_year_end_component", + "decline_biased_response_dynamics" + ], + "confidence": "high" + }, + "derived_metrics": { + "target_peak_month": 4, + "target_peak_label": "April", + "target_trough_month": 10, + "target_trough_label": "October", + "target_peak_value": 0.6181439771517633, + "target_trough_value": 0.0, + "target_mean_value": 0.1971152169988278, + "target_amplitude": 0.6181439771517633, + "baseline_to_peak_ratio": 0.08735828867704429, + "autumn_to_winter_weight_ratio": 0.051233396584440226, + "year_end_to_winter_weight_ratio": 0.4250474383301708, + "decay_to_growth_ratio": 1.3846456692913385, + "monthly_target": { + "January": 0.10933531571340487, + "February": 0.1985605599561208, + "March": 0.4873308852375905, + "April": 0.6181439771517633, + "May": 0.36839821892830144, + "June": 0.1526451310211331, + "July": 0.08925391764843972, + "August": 0.05400091381293727, + "September": 0.020811057411157283, + "October": 0.0, + "November": 0.02679111913032249, + "December": 0.24011150797476308 + } + }, + "parameter_evidence": { + "INITIAL_Y": 0.631, + "GROWTH_RATE": 2.54, + "DECAY_RATE": 3.517, + "SUMMER_DECAY_BOOST": 2.876, + "PRE_SUMMER_DECAY_REDUCTION": 0.527, + "PRE_SUMMER_DECAY_END": 7.04, + "PRE_SUMMER_DECAY_SHARPNESS": 9.202, + "SPRING_CARRYOVER_WEIGHT": 0.049, + "SPRING_CARRYOVER_END": 7.045, + "SPRING_CARRYOVER_SHARPNESS": 15.64, + "BASELINE": 0.054, + "WINTER_WEIGHT": 0.527, + "AUTUMN_WEIGHT": 0.027, + "WINTER_PEAK": 3.775, + "AUTUMN_PEAK": 10.73, + "AUTUMN_ONSET": 11.39, + "AUTUMN_GATE_SHARPNESS": 6.044, + "WINTER_WIDTH": 8.864, + "WINTER_RISE_WIDTH": 7.616, + "WINTER_FALL_WIDTH": 6.554, + "AUTUMN_WIDTH": 8.183, + "AUTUMN_RISE_WIDTH": 9.01, + "AUTUMN_FALL_WIDTH": 8.343, + "SUMMER_DIP": 0.106, + "SUMMER_LOW": 9.67, + "SUMMER_ONSET": 8.3, + "SUMMER_GATE_SHARPNESS": 5.142, + "SUMMER_DECAY_ONSET": 7.16, + "SUMMER_DECAY_GATE_SHARPNESS": 14.21, + "SUMMER_WIDTH": 22.841, + "SUMMER_RISE_WIDTH": 36.676, + "SUMMER_FALL_WIDTH": 10.348, + "SCALE": 1.16, + "YEAR_END_WEIGHT": 0.224, + "YEAR_END_PEAK": 12.146, + "YEAR_END_WIDTH": 83.712, + "YEAR_END_RISE_WIDTH": 159.258, + "YEAR_END_FALL_WIDTH": 10.137 + }, + "fit": { + "score": 0.2 + }, + "warnings": [], + "summary": "Coot is classified as resident with summer detectability collapse. The fitted resident detectability target peaks around April and reaches its lowest point around October. The model indicates weak baseline presence, weak spring carry-over, strong pre-summer retention, moderate summer suppression, and moderate summer decay acceleration." +} diff --git a/modelling/data/thrupp-lake-birds/resident/coot_consensus.json b/modelling/data/thrupp-lake-birds/resident/coot_consensus.json new file mode 100644 index 0000000..2d52307 --- /dev/null +++ b/modelling/data/thrupp-lake-birds/resident/coot_consensus.json @@ -0,0 +1,42 @@ +{ + "SCORE": "0.2", + "INITIAL_Y": "0.631", + "GROWTH_RATE": "2.54", + "DECAY_RATE": "3.517", + "SUMMER_DECAY_BOOST": "2.876", + "PRE_SUMMER_DECAY_REDUCTION": "0.527", + "PRE_SUMMER_DECAY_END": "7.04", + "PRE_SUMMER_DECAY_SHARPNESS": "9.202", + "SPRING_CARRYOVER_WEIGHT": "0.049", + "SPRING_CARRYOVER_END": "7.045", + "SPRING_CARRYOVER_SHARPNESS": "15.64", + "BASELINE": "0.054", + "WINTER_WEIGHT": "0.527", + "AUTUMN_WEIGHT": "0.027", + "WINTER_PEAK": "3.775", + "AUTUMN_PEAK": "10.73", + "AUTUMN_ONSET": "11.39", + "AUTUMN_GATE_SHARPNESS": 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"species": "Cormorant", + "model_family": "resident_detectability", + "classification": { + "primary_class": "resident_with_summer_detectability_collapse", + "baseline_presence": "moderate", + "detectability_peak_timing": "spring", + "detectability_trough_timing": "autumn", + "spring_carryover": "weak", + "summer_suppression": "moderate", + "summer_decay_acceleration": "strong", + "pre_summer_retention": "moderate", + "autumn_component": "weak", + "year_end_component": "meaningful", + "response_dynamics": "rapid_decline_biased", + "traits": [ + "resident_detectability_pattern", + "moderate_baseline_presence", + "spring_detectability_peak", + "autumn_detectability_trough", + "weak_spring_carryover", + "moderate_summer_suppression", + "strong_summer_decay_acceleration", + "moderate_pre_summer_retention", + "weak_autumn_component", + "meaningful_year_end_component", + "rapid_decline_biased_response_dynamics" + ], + "confidence": "medium" + }, + "derived_metrics": { + "target_peak_month": 4, + "target_peak_label": "April", + "target_trough_month": 10, + "target_trough_label": "October", + "target_peak_value": 0.7475240340490378, + "target_trough_value": 0.10521762508589634, + "target_mean_value": 0.3287265919768473, + "target_amplitude": 0.6423064089631414, + "baseline_to_peak_ratio": 0.2862784208299603, + "autumn_to_winter_weight_ratio": 0.04583333333333333, + "year_end_to_winter_weight_ratio": 0.3854166666666667, + "decay_to_growth_ratio": 2.5930309007232086, + "monthly_target": { + "January": 0.2701626071368548, + "February": 0.2820642374211755, + "March": 0.4546564472242138, + "April": 0.7475240340490378, + "May": 0.5550622497444283, + "June": 0.3158240693015237, + "July": 0.26342110642559025, + "August": 0.2140039151732369, + "September": 0.2089324792962474, + "October": 0.10521762508589634, + "November": 0.16791916274705757, + "December": 0.359931170116905 + } + }, + "parameter_evidence": { + "INITIAL_Y": 0.653, + "GROWTH_RATE": 1.521, + "DECAY_RATE": 3.944, + "SUMMER_DECAY_BOOST": 4.099, + "PRE_SUMMER_DECAY_REDUCTION": 0.412, + "PRE_SUMMER_DECAY_END": 6.955, + "PRE_SUMMER_DECAY_SHARPNESS": 8.525, + "SPRING_CARRYOVER_WEIGHT": 0.056, + "SPRING_CARRYOVER_END": 7.09, + "SPRING_CARRYOVER_SHARPNESS": 19.858, + "BASELINE": 0.214, + "WINTER_WEIGHT": 0.48, + "AUTUMN_WEIGHT": 0.022, + "WINTER_PEAK": 4.08, + "AUTUMN_PEAK": 10.675, + "AUTUMN_ONSET": 11.365, + "AUTUMN_GATE_SHARPNESS": 5.37, + "WINTER_WIDTH": 9.857, + "WINTER_RISE_WIDTH": 11.789, + "WINTER_FALL_WIDTH": 8.895, + "AUTUMN_WIDTH": 7.357, + "AUTUMN_RISE_WIDTH": 7.532, + "AUTUMN_FALL_WIDTH": 7.582, + "SUMMER_DIP": 0.109, + "SUMMER_LOW": 9.97, + "SUMMER_ONSET": 8.32, + "SUMMER_GATE_SHARPNESS": 3.994, + "SUMMER_DECAY_ONSET": 7.045, + "SUMMER_DECAY_GATE_SHARPNESS": 14.047, + "SUMMER_WIDTH": 27.8, + "SUMMER_RISE_WIDTH": 46.085, + "SUMMER_FALL_WIDTH": 10.958, + "SCALE": 1.21, + "YEAR_END_WEIGHT": 0.185, + "YEAR_END_PEAK": 12.157, + "YEAR_END_WIDTH": 84.406, + "YEAR_END_RISE_WIDTH": 157.562, + "YEAR_END_FALL_WIDTH": 9.868 + }, + "fit": { + "score": 0.206 + }, + "warnings": [], + "summary": "Cormorant is classified as resident with summer detectability collapse. The fitted resident detectability target peaks around April and reaches its lowest point around October. The model indicates moderate baseline presence, weak spring carry-over, moderate pre-summer retention, moderate summer suppression, and strong summer decay acceleration." +} diff --git a/modelling/data/thrupp-lake-birds/resident/cormorant_consensus.json b/modelling/data/thrupp-lake-birds/resident/cormorant_consensus.json new file mode 100644 index 0000000..4d765de --- /dev/null +++ b/modelling/data/thrupp-lake-birds/resident/cormorant_consensus.json @@ -0,0 +1,42 @@ +{ + "SCORE": "0.206", + "INITIAL_Y": "0.653", + "GROWTH_RATE": "1.521", + "DECAY_RATE": "3.944", + "SUMMER_DECAY_BOOST": "4.099", + "PRE_SUMMER_DECAY_REDUCTION": "0.412", + "PRE_SUMMER_DECAY_END": "6.955", + "PRE_SUMMER_DECAY_SHARPNESS": "8.525", + "SPRING_CARRYOVER_WEIGHT": "0.056", + "SPRING_CARRYOVER_END": "7.09", + "SPRING_CARRYOVER_SHARPNESS": "19.858", + "BASELINE": "0.214", + "WINTER_WEIGHT": "0.48", + "AUTUMN_WEIGHT": "0.022", + "WINTER_PEAK": "4.08", + "AUTUMN_PEAK": "10.675", + "AUTUMN_ONSET": "11.365", + "AUTUMN_GATE_SHARPNESS": "5.37", + "WINTER_WIDTH": "9.857", + "WINTER_RISE_WIDTH": "11.789", + "WINTER_FALL_WIDTH": "8.895", + "AUTUMN_WIDTH": "7.357", + "AUTUMN_RISE_WIDTH": "7.532", + "AUTUMN_FALL_WIDTH": "7.582", + "SUMMER_DIP": "0.109", + "SUMMER_LOW": "9.97", + "SUMMER_ONSET": "8.32", + "SUMMER_GATE_SHARPNESS": "3.994", + "SUMMER_DECAY_ONSET": "7.045", + "SUMMER_DECAY_GATE_SHARPNESS": "14.047", + "SUMMER_WIDTH": "27.8", + "SUMMER_RISE_WIDTH": "46.085", + "SUMMER_FALL_WIDTH": "10.958", + "SCALE": "1.21", + "YEAR_END_WEIGHT": "0.185", + "YEAR_END_PEAK": "12.157", + "YEAR_END_WIDTH": "84.406", + "YEAR_END_RISE_WIDTH": "157.562", + "YEAR_END_FALL_WIDTH": "9.868", + "SPECIES": "Cormorant" +} diff --git a/modelling/data/thrupp-lake-birds/resident/cormorant_observed.csv b/modelling/data/thrupp-lake-birds/resident/cormorant_observed.csv new file mode 100644 index 0000000..6f42e77 --- /dev/null +++ b/modelling/data/thrupp-lake-birds/resident/cormorant_observed.csv @@ -0,0 +1,13 @@ +month,value +1,11 +2,12 +3,10 +4,17 +5,6 +6,4 +7,5 +8,6 +9,3 +10,1 +11,5 +12,4 diff --git a/modelling/data/thrupp-lake-birds/resident/cormorant_parameters.csv b/modelling/data/thrupp-lake-birds/resident/cormorant_parameters.csv new file mode 100644 index 0000000..b74b3e8 --- /dev/null +++ b/modelling/data/thrupp-lake-birds/resident/cormorant_parameters.csv @@ -0,0 +1,201 @@ 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0000000..66d26fb Binary files /dev/null and b/modelling/data/thrupp-lake-birds/resident/cormorant_simulated.png differ diff --git a/modelling/data/thrupp-lake-birds/resident/cormorant_synthesised.csv b/modelling/data/thrupp-lake-birds/resident/cormorant_synthesised.csv new file mode 100644 index 0000000..285983b --- /dev/null +++ b/modelling/data/thrupp-lake-birds/resident/cormorant_synthesised.csv @@ -0,0 +1,13 @@ +month,observed,simulated_raw,synthesised +1,11,0.43759040000000005,9.412081850190354 +2,12,0.3126138,6.723974458989587 +3,10,0.45319919999999997,9.747809743634201 +4,17,0.6472945,13.922583345471105 +5,6,0.5285404,11.368314994872716 +6,4,0.33738450000000003,7.256764611347843 +7,5,0.241875,5.202461702804247 +8,6,0.21451030000000001,4.613877501217777 +9,3,0.1782327,3.8335867532295542 +10,1,0.11391930000000001,2.4502771905334075 +11,5,0.16199780000000003,3.4843921465159355 +12,4,0.29530409999999996,6.351662102040621 diff --git a/modelling/data/thrupp-lake-birds/resident/cormorant_synthesised.png b/modelling/data/thrupp-lake-birds/resident/cormorant_synthesised.png new file mode 100644 index 0000000..d078c3d Binary files /dev/null and b/modelling/data/thrupp-lake-birds/resident/cormorant_synthesised.png differ diff --git a/modelling/data/thrupp-lake-birds/resident/egret_classification.json b/modelling/data/thrupp-lake-birds/resident/egret_classification.json new file mode 100644 index 0000000..45f8e01 --- /dev/null +++ b/modelling/data/thrupp-lake-birds/resident/egret_classification.json @@ -0,0 +1,105 @@ +{ + "schema_version": "resident-classification/v1", + "species": "Egret", + "model_family": "resident_detectability", + "classification": { + "primary_class": "resident_with_spring_persistence_and_summer_suppression", + "baseline_presence": "weak", + "detectability_peak_timing": "late_spring_early_summer", + "detectability_trough_timing": "autumn", + "spring_carryover": "moderate", + "summer_suppression": "strong", + "summer_decay_acceleration": "strong", + "pre_summer_retention": "strong", + "autumn_component": "weak", + "year_end_component": "meaningful", + "response_dynamics": "rapid_decline_biased", + "traits": [ + "resident_detectability_pattern", + "weak_baseline_presence", + "late_spring_early_summer_detectability_peak", + "autumn_detectability_trough", + "moderate_spring_carryover", + "strong_summer_suppression", + "strong_summer_decay_acceleration", + "strong_pre_summer_retention", + "weak_autumn_component", + "meaningful_year_end_component", + "rapid_decline_biased_response_dynamics" + ], + "confidence": "low" + }, + "derived_metrics": { + "target_peak_month": 6, + "target_peak_label": "June", + "target_trough_month": 9, + "target_trough_label": "September", + "target_peak_value": 0.6047184866384768, + "target_trough_value": 0.05666092014744522, + "target_mean_value": 0.24327861629341369, + "target_amplitude": 0.5480575664910315, + "baseline_to_peak_ratio": 0.08599042554339427, + "autumn_to_winter_weight_ratio": 0.05429864253393665, + "year_end_to_winter_weight_ratio": 0.4298642533936652, + "decay_to_growth_ratio": 1.6503992901508429, + "monthly_target": { + "January": 0.24316192356875355, + "February": 0.24299892107629592, + "March": 0.24226257073040558, + "April": 0.23362294749928092, + "May": 0.31384333062902603, + "June": 0.6047184866384768, + "July": 0.4937811224842998, + "August": 0.14582884801809173, + "September": 0.05666092014744522, + "October": 0.0638054056088705, + "November": 0.0755869522510641, + "December": 0.2030719668689542 + } + }, + "parameter_evidence": { + "INITIAL_Y": 0.209, + "GROWTH_RATE": 2.254, + "DECAY_RATE": 3.72, + "SUMMER_DECAY_BOOST": 4.482, + "PRE_SUMMER_DECAY_REDUCTION": 0.502, + "PRE_SUMMER_DECAY_END": 7.04, + "PRE_SUMMER_DECAY_SHARPNESS": 8.708, + "SPRING_CARRYOVER_WEIGHT": 0.191, + "SPRING_CARRYOVER_END": 6.965, + "SPRING_CARRYOVER_SHARPNESS": 17.89, + "BASELINE": 0.052, + "WINTER_WEIGHT": 0.442, + "AUTUMN_WEIGHT": 0.024, + "WINTER_PEAK": 6.51, + "AUTUMN_PEAK": 10.815, + "AUTUMN_ONSET": 9.91, + "AUTUMN_GATE_SHARPNESS": 6.924, + "WINTER_WIDTH": 10.496, + "WINTER_RISE_WIDTH": 11.209, + "WINTER_FALL_WIDTH": 9.923, + "AUTUMN_WIDTH": 6.403, + "AUTUMN_RISE_WIDTH": 6.153, + "AUTUMN_FALL_WIDTH": 7.175, + "SUMMER_DIP": 0.164, + "SUMMER_LOW": 2.87, + "SUMMER_ONSET": 4.3, + "SUMMER_GATE_SHARPNESS": 4.136, + "SUMMER_DECAY_ONSET": 7.17, + "SUMMER_DECAY_GATE_SHARPNESS": 15.554, + "SUMMER_WIDTH": 28.248, + "SUMMER_RISE_WIDTH": 46.217, + "SUMMER_FALL_WIDTH": 12.865, + "SCALE": 1.004, + "YEAR_END_WEIGHT": 0.19, + "YEAR_END_PEAK": 12.174, + "YEAR_END_WIDTH": 80.432, + "YEAR_END_RISE_WIDTH": 149.956, + "YEAR_END_FALL_WIDTH": 9.652 + }, + "fit": { + "score": 0.628 + }, + "warnings": [], + "summary": "Egret is classified as resident with spring persistence and summer suppression. The fitted resident detectability target peaks around June and reaches its lowest point around September. The model indicates weak baseline presence, moderate spring carry-over, strong pre-summer retention, strong summer suppression, and strong summer decay acceleration." +} diff --git a/modelling/data/thrupp-lake-birds/resident/egret_consensus.json b/modelling/data/thrupp-lake-birds/resident/egret_consensus.json new file mode 100644 index 0000000..48adf6b --- /dev/null +++ b/modelling/data/thrupp-lake-birds/resident/egret_consensus.json @@ -0,0 +1,42 @@ +{ + "SCORE": "0.628", + "INITIAL_Y": "0.209", + "GROWTH_RATE": "2.254", + "DECAY_RATE": "3.72", + "SUMMER_DECAY_BOOST": "4.482", + "PRE_SUMMER_DECAY_REDUCTION": "0.502", + "PRE_SUMMER_DECAY_END": "7.04", + "PRE_SUMMER_DECAY_SHARPNESS": "8.708", + "SPRING_CARRYOVER_WEIGHT": "0.191", + "SPRING_CARRYOVER_END": "6.965", + "SPRING_CARRYOVER_SHARPNESS": "17.89", + "BASELINE": "0.052", + "WINTER_WEIGHT": "0.442", + "AUTUMN_WEIGHT": "0.024", + "WINTER_PEAK": "6.51", + "AUTUMN_PEAK": "10.815", + "AUTUMN_ONSET": "9.91", + "AUTUMN_GATE_SHARPNESS": 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+7,4,0.4192247,1.976897083605564 +8,2,0.13342421,0.6291755510383246 +9,1,0.05936039,0.2799200091804917 +10,0,0.06529,0.30788169348945155 +11,3,0.07580592,0.35747059314023405 +12,0,0.1781914,0.8402798284156264 diff --git a/modelling/data/thrupp-lake-birds/resident/egret_synthesised.png b/modelling/data/thrupp-lake-birds/resident/egret_synthesised.png new file mode 100644 index 0000000..d560e15 Binary files /dev/null and b/modelling/data/thrupp-lake-birds/resident/egret_synthesised.png differ diff --git a/modelling/data/thrupp-lake-birds/resident/gadwall_classification.json b/modelling/data/thrupp-lake-birds/resident/gadwall_classification.json new file mode 100644 index 0000000..0e291d8 --- /dev/null +++ b/modelling/data/thrupp-lake-birds/resident/gadwall_classification.json @@ -0,0 +1,105 @@ +{ + "schema_version": "resident-classification/v1", + "species": "Gadwall", + "model_family": "resident_detectability", + "classification": { + "primary_class": "resident_with_summer_detectability_collapse", + "baseline_presence": "weak", + "detectability_peak_timing": "winter", + "detectability_trough_timing": "late_spring_early_summer", + "spring_carryover": "weak", + "summer_suppression": "moderate", + "summer_decay_acceleration": "strong", + "pre_summer_retention": "strong", + "autumn_component": "weak", + "year_end_component": "meaningful", + "response_dynamics": "rapid_decline_biased", + "traits": [ + "resident_detectability_pattern", + "weak_baseline_presence", + "winter_detectability_peak", + "late_spring_early_summer_detectability_trough", + "weak_spring_carryover", + "moderate_summer_suppression", + "strong_summer_decay_acceleration", + "strong_pre_summer_retention", + "weak_autumn_component", + "meaningful_year_end_component", + "rapid_decline_biased_response_dynamics" + ], + "confidence": "medium" + }, + "derived_metrics": { + "target_peak_month": 2, + "target_peak_label": "February", + "target_trough_month": 5, + "target_trough_label": "May", + "target_peak_value": 0.46794273225834354, + "target_trough_value": 0.0, + "target_mean_value": 0.14814267954656787, + "target_amplitude": 0.46794273225834354, + "baseline_to_peak_ratio": 0.08548054546537258, + "autumn_to_winter_weight_ratio": 0.06912442396313365, + "year_end_to_winter_weight_ratio": 0.3824884792626728, + "decay_to_growth_ratio": 1.5404651162790697, + "monthly_target": { + "January": 0.44860933628428834, + "February": 0.46794273225834354, + "March": 0.17102321998712774, + "April": 0.09471274353659044, + "May": 0.0, + "June": 0.04275228104360464, + "July": 0.07257074484305977, + "August": 0.03995793639944281, + "September": 0.040000556677168696, + "October": 0.04569648793672306, + "November": 0.07314229104970443, + "December": 0.281303824542761 + } + }, + "parameter_evidence": { + "INITIAL_Y": 1.03, + "GROWTH_RATE": 2.15, + "DECAY_RATE": 3.312, + "SUMMER_DECAY_BOOST": 4.227, + "PRE_SUMMER_DECAY_REDUCTION": 0.59, + "PRE_SUMMER_DECAY_END": 6.9, + "PRE_SUMMER_DECAY_SHARPNESS": 8.256, + "SPRING_CARRYOVER_WEIGHT": 0.055, + "SPRING_CARRYOVER_END": 7.04, + "SPRING_CARRYOVER_SHARPNESS": 17.646, + "BASELINE": 0.04, + "WINTER_WEIGHT": 0.434, + "AUTUMN_WEIGHT": 0.03, + "WINTER_PEAK": 1.575, + "AUTUMN_PEAK": 10.635, + "AUTUMN_ONSET": 10.145, + "AUTUMN_GATE_SHARPNESS": 8.3, + "WINTER_WIDTH": 9.952, + "WINTER_RISE_WIDTH": 9.015, + "WINTER_FALL_WIDTH": 12.222, + "AUTUMN_WIDTH": 7.34, + "AUTUMN_RISE_WIDTH": 7.26, + "AUTUMN_FALL_WIDTH": 7.149, + "SUMMER_DIP": 0.122, + "SUMMER_LOW": 4.95, + "SUMMER_ONSET": 4.185, + "SUMMER_GATE_SHARPNESS": 4.798, + "SUMMER_DECAY_ONSET": 7.115, + "SUMMER_DECAY_GATE_SHARPNESS": 15.699, + "SUMMER_WIDTH": 25.455, + "SUMMER_RISE_WIDTH": 42.748, + "SUMMER_FALL_WIDTH": 11.078, + "SCALE": 1.384, + "YEAR_END_WEIGHT": 0.166, + "YEAR_END_PEAK": 12.13, + "YEAR_END_WIDTH": 78.229, + "YEAR_END_RISE_WIDTH": 147.33, + "YEAR_END_FALL_WIDTH": 9.407 + }, + "fit": { + "score": 0.234 + }, + "warnings": [], + "summary": "Gadwall is classified as resident with summer detectability collapse. The fitted resident detectability target peaks around February and reaches its lowest point around May. The model indicates weak baseline presence, weak spring carry-over, strong pre-summer retention, moderate summer suppression, and strong summer decay acceleration." +} diff --git a/modelling/data/thrupp-lake-birds/resident/gadwall_consensus.json b/modelling/data/thrupp-lake-birds/resident/gadwall_consensus.json new file mode 100644 index 0000000..9c102ab --- /dev/null +++ b/modelling/data/thrupp-lake-birds/resident/gadwall_consensus.json @@ -0,0 +1,42 @@ +{ + "SCORE": "0.234", + "INITIAL_Y": "1.03", + "GROWTH_RATE": "2.15", + "DECAY_RATE": "3.312", + "SUMMER_DECAY_BOOST": "4.227", + "PRE_SUMMER_DECAY_REDUCTION": "0.59", + "PRE_SUMMER_DECAY_END": "6.9", + "PRE_SUMMER_DECAY_SHARPNESS": "8.256", + "SPRING_CARRYOVER_WEIGHT": "0.055", + "SPRING_CARRYOVER_END": "7.04", + "SPRING_CARRYOVER_SHARPNESS": "17.646", + "BASELINE": "0.04", + "WINTER_WEIGHT": "0.434", + "AUTUMN_WEIGHT": "0.03", + "WINTER_PEAK": "1.575", + "AUTUMN_PEAK": "10.635", + "AUTUMN_ONSET": "10.145", + "AUTUMN_GATE_SHARPNESS": 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"resident-classification/v1", + "species": "Great Crested Grebe", + "model_family": "resident_detectability", + "classification": { + "primary_class": "resident_with_summer_detectability_collapse", + "baseline_presence": "moderate", + "detectability_peak_timing": "spring", + "detectability_trough_timing": "autumn", + "spring_carryover": "weak", + "summer_suppression": "moderate", + "summer_decay_acceleration": "moderate", + "pre_summer_retention": "moderate", + "autumn_component": "weak", + "year_end_component": "weak", + "response_dynamics": "rapid_decline_biased", + "traits": [ + "resident_detectability_pattern", + "moderate_baseline_presence", + "spring_detectability_peak", + "autumn_detectability_trough", + "weak_spring_carryover", + "moderate_summer_suppression", + "moderate_summer_decay_acceleration", + "moderate_pre_summer_retention", + "weak_autumn_component", + "weak_year_end_component", + "rapid_decline_biased_response_dynamics" + ], + "confidence": "medium" + }, + "derived_metrics": { + "target_peak_month": 4, + "target_peak_label": "April", + "target_trough_month": 9, + "target_trough_label": "September", + "target_peak_value": 0.7636370221397343, + "target_trough_value": 0.1772430303824128, + "target_mean_value": 0.36423483227881115, + "target_amplitude": 0.5863939917573214, + "baseline_to_peak_ratio": 0.33654732883416016, + "autumn_to_winter_weight_ratio": 0.0425531914893617, + "year_end_to_winter_weight_ratio": 0.2936170212765957, + "decay_to_growth_ratio": 1.654708520179372, + "monthly_target": { + "January": 0.30513018111586715, + "February": 0.3583644433043783, + "March": 0.6082542137713084, + "April": 0.7636370221397343, + "May": 0.4635648412063155, + "June": 0.31270506688691957, + "July": 0.29297206304179296, + "August": 0.2561554740726417, + "September": 0.1772430303824128, + "October": 0.19777895992116343, + "November": 0.2645781300937982, + "December": 0.3704345614094017 + } + }, + "parameter_evidence": { + "INITIAL_Y": 0.814, + "GROWTH_RATE": 1.784, + "DECAY_RATE": 2.952, + "SUMMER_DECAY_BOOST": 3.936, + "PRE_SUMMER_DECAY_REDUCTION": 0.379, + "PRE_SUMMER_DECAY_END": 6.935, + "PRE_SUMMER_DECAY_SHARPNESS": 9.453, + "SPRING_CARRYOVER_WEIGHT": 0.046, + "SPRING_CARRYOVER_END": 7.08, + "SPRING_CARRYOVER_SHARPNESS": 15.87, + "BASELINE": 0.257, + "WINTER_WEIGHT": 0.47, + "AUTUMN_WEIGHT": 0.02, + "WINTER_PEAK": 3.84, + "AUTUMN_PEAK": 10.78, + "AUTUMN_ONSET": 10.73, + "AUTUMN_GATE_SHARPNESS": 7.243, + "WINTER_WIDTH": 11.054, + "WINTER_RISE_WIDTH": 8.852, + "WINTER_FALL_WIDTH": 11.465, + "AUTUMN_WIDTH": 6.512, + "AUTUMN_RISE_WIDTH": 6.198, + "AUTUMN_FALL_WIDTH": 6.458, + "SUMMER_DIP": 0.091, + "SUMMER_LOW": 9.205, + "SUMMER_ONSET": 7.525, + "SUMMER_GATE_SHARPNESS": 4.062, + "SUMMER_DECAY_ONSET": 7.18, + "SUMMER_DECAY_GATE_SHARPNESS": 16.41, + "SUMMER_WIDTH": 27.096, + "SUMMER_RISE_WIDTH": 44.896, + "SUMMER_FALL_WIDTH": 9.814, + "SCALE": 1.184, + "YEAR_END_WEIGHT": 0.138, + "YEAR_END_PEAK": 12.162, + "YEAR_END_WIDTH": 86.406, + "YEAR_END_RISE_WIDTH": 160.04, + "YEAR_END_FALL_WIDTH": 11.359 + }, + "fit": { + "score": 0.224 + }, + "warnings": [], + "summary": "Great Crested Grebe is classified as resident with summer detectability collapse. The fitted resident detectability target peaks around April and reaches its lowest point around September. The model indicates moderate baseline presence, weak spring carry-over, moderate pre-summer retention, moderate summer suppression, and moderate summer decay acceleration." +} diff --git a/modelling/data/thrupp-lake-birds/resident/great_crested_grebe_consensus.json b/modelling/data/thrupp-lake-birds/resident/great_crested_grebe_consensus.json new file mode 100644 index 0000000..9a98cee --- /dev/null +++ b/modelling/data/thrupp-lake-birds/resident/great_crested_grebe_consensus.json @@ -0,0 +1,42 @@ +{ + "SCORE": "0.224", + "INITIAL_Y": "0.814", + "GROWTH_RATE": "1.784", + "DECAY_RATE": "2.952", + "SUMMER_DECAY_BOOST": "3.936", + "PRE_SUMMER_DECAY_REDUCTION": "0.379", + "PRE_SUMMER_DECAY_END": "6.935", + "PRE_SUMMER_DECAY_SHARPNESS": "9.453", + "SPRING_CARRYOVER_WEIGHT": "0.046", + "SPRING_CARRYOVER_END": "7.08", + "SPRING_CARRYOVER_SHARPNESS": "15.87", + "BASELINE": "0.257", + "WINTER_WEIGHT": "0.47", + "AUTUMN_WEIGHT": "0.02", + "WINTER_PEAK": "3.84", + "AUTUMN_PEAK": "10.78", + "AUTUMN_ONSET": "10.73", + "AUTUMN_GATE_SHARPNESS": "7.243", + "WINTER_WIDTH": "11.054", + "WINTER_RISE_WIDTH": "8.852", + "WINTER_FALL_WIDTH": "11.465", + "AUTUMN_WIDTH": "6.512", + "AUTUMN_RISE_WIDTH": "6.198", + "AUTUMN_FALL_WIDTH": "6.458", + "SUMMER_DIP": "0.091", + "SUMMER_LOW": "9.205", + "SUMMER_ONSET": "7.525", + "SUMMER_GATE_SHARPNESS": "4.062", + "SUMMER_DECAY_ONSET": "7.18", + "SUMMER_DECAY_GATE_SHARPNESS": "16.41", + "SUMMER_WIDTH": "27.096", + "SUMMER_RISE_WIDTH": "44.896", + "SUMMER_FALL_WIDTH": "9.814", + "SCALE": "1.184", + "YEAR_END_WEIGHT": "0.138", + "YEAR_END_PEAK": "12.162", + "YEAR_END_WIDTH": "86.406", + "YEAR_END_RISE_WIDTH": "160.04", + "YEAR_END_FALL_WIDTH": "11.359", + "SPECIES": "Great Crested Grebe" +} diff --git a/modelling/data/thrupp-lake-birds/resident/great_crested_grebe_observed.csv b/modelling/data/thrupp-lake-birds/resident/great_crested_grebe_observed.csv new file mode 100644 index 0000000..c2884c7 --- /dev/null +++ b/modelling/data/thrupp-lake-birds/resident/great_crested_grebe_observed.csv @@ -0,0 +1,13 @@ +month,value +1,12 +2,10 +3,10 +4,17 +5,7 +6,5 +7,5 +8,5 +9,1 +10,1 +11,4 +12,2 diff --git a/modelling/data/thrupp-lake-birds/resident/great_crested_grebe_parameters.csv b/modelling/data/thrupp-lake-birds/resident/great_crested_grebe_parameters.csv new file mode 100644 index 0000000..3fe33e9 --- /dev/null +++ b/modelling/data/thrupp-lake-birds/resident/great_crested_grebe_parameters.csv @@ -0,0 +1,201 @@ 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b/modelling/data/thrupp-lake-birds/resident/great_crested_grebe_simulated.png new file mode 100644 index 0000000..473f700 Binary files /dev/null and b/modelling/data/thrupp-lake-birds/resident/great_crested_grebe_simulated.png differ diff --git a/modelling/data/thrupp-lake-birds/resident/great_crested_grebe_synthesised.csv b/modelling/data/thrupp-lake-birds/resident/great_crested_grebe_synthesised.csv new file mode 100644 index 0000000..66b6352 --- /dev/null +++ b/modelling/data/thrupp-lake-birds/resident/great_crested_grebe_synthesised.csv @@ -0,0 +1,13 @@ +month,observed,simulated_raw,synthesised +1,12,0.5647242,10.498676313435636 +2,10,0.4175588,7.762753363547389 +3,10,0.5918542,11.003044796995415 +4,17,0.6878878,12.788386529497675 +5,7,0.4931329,9.167736563451369 +6,5,0.3459498,6.431484556351216 +7,5,0.28257089999999996,5.253219916370131 +8,5,0.24567239999999999,4.567247174363849 +9,1,0.1761257,3.2743181800554515 +10,1,0.19991050000000002,3.716496709645301 +11,4,0.251853,4.682149490968698 +12,2,0.3373107,6.27087675073672 diff --git a/modelling/data/thrupp-lake-birds/resident/great_crested_grebe_synthesised.png b/modelling/data/thrupp-lake-birds/resident/great_crested_grebe_synthesised.png new file mode 100644 index 0000000..3c5384e Binary files /dev/null and b/modelling/data/thrupp-lake-birds/resident/great_crested_grebe_synthesised.png differ diff --git a/modelling/data/thrupp-lake-birds/resident/grey_heron_classification.json b/modelling/data/thrupp-lake-birds/resident/grey_heron_classification.json new file mode 100644 index 0000000..64f6d71 --- /dev/null +++ b/modelling/data/thrupp-lake-birds/resident/grey_heron_classification.json @@ -0,0 +1,105 @@ +{ + "schema_version": "resident-classification/v1", + "species": "Grey Heron", + "model_family": "resident_detectability", + "classification": { + "primary_class": "resident_with_summer_detectability_collapse", + "baseline_presence": "weak", + "detectability_peak_timing": "winter", + "detectability_trough_timing": "autumn", + "spring_carryover": "weak", + "summer_suppression": "moderate", + "summer_decay_acceleration": "moderate", + "pre_summer_retention": "strong", + "autumn_component": "weak", + "year_end_component": "meaningful", + "response_dynamics": "rapid_decline_biased", + "traits": [ + "resident_detectability_pattern", + "weak_baseline_presence", + "winter_detectability_peak", + "autumn_detectability_trough", + "weak_spring_carryover", + "moderate_summer_suppression", + "moderate_summer_decay_acceleration", + "strong_pre_summer_retention", + "weak_autumn_component", + "meaningful_year_end_component", + "rapid_decline_biased_response_dynamics" + ], + "confidence": "medium" + }, + "derived_metrics": { + "target_peak_month": 2, + "target_peak_label": "February", + "target_trough_month": 10, + "target_trough_label": "October", + "target_peak_value": 0.4679473054720798, + "target_trough_value": 0.0, + "target_mean_value": 0.14318723330885133, + "target_amplitude": 0.4679473054720798, + "baseline_to_peak_ratio": 0.08120572456692408, + "autumn_to_winter_weight_ratio": 0.06684491978609626, + "year_end_to_winter_weight_ratio": 0.42513368983957217, + "decay_to_growth_ratio": 1.7088607594936709, + "monthly_target": { + "January": 0.2890144505696381, + "February": 0.4679473054720798, + "March": 0.28867838178034944, + "April": 0.11989590459548385, + "May": 0.09461811894631447, + "June": 0.0940010414072419, + "July": 0.09366459472871956, + "August": 0.03799862216405955, + "September": 0.025136006703430934, + "October": 0.0, + "November": 0.0, + "December": 0.20729237333889847 + } + }, + "parameter_evidence": { + "INITIAL_Y": 1.05, + "GROWTH_RATE": 1.58, + "DECAY_RATE": 2.7, + "SUMMER_DECAY_BOOST": 3.618, + "PRE_SUMMER_DECAY_REDUCTION": 0.546, + "PRE_SUMMER_DECAY_END": 7.1, + "PRE_SUMMER_DECAY_SHARPNESS": 9.838, + "SPRING_CARRYOVER_WEIGHT": 0.056, + "SPRING_CARRYOVER_END": 7.285, + "SPRING_CARRYOVER_SHARPNESS": 17.936, + "BASELINE": 0.038, + "WINTER_WEIGHT": 0.374, + "AUTUMN_WEIGHT": 0.025, + "WINTER_PEAK": 1.985, + "AUTUMN_PEAK": 10.83, + "AUTUMN_ONSET": 11.39, + "AUTUMN_GATE_SHARPNESS": 6.146, + "WINTER_WIDTH": 8.812, + "WINTER_RISE_WIDTH": 9.684, + "WINTER_FALL_WIDTH": 9.137, + "AUTUMN_WIDTH": 7.73, + "AUTUMN_RISE_WIDTH": 6.829, + "AUTUMN_FALL_WIDTH": 8.9, + "SUMMER_DIP": 0.122, + "SUMMER_LOW": 10.0, + "SUMMER_ONSET": 8.45, + "SUMMER_GATE_SHARPNESS": 4.747, + "SUMMER_DECAY_ONSET": 7.115, + "SUMMER_DECAY_GATE_SHARPNESS": 15.403, + "SUMMER_WIDTH": 21.796, + "SUMMER_RISE_WIDTH": 31.422, + "SUMMER_FALL_WIDTH": 12.004, + "SCALE": 1.462, + "YEAR_END_WEIGHT": 0.159, + "YEAR_END_PEAK": 12.107, + "YEAR_END_WIDTH": 92.091, + "YEAR_END_RISE_WIDTH": 174.963, + "YEAR_END_FALL_WIDTH": 9.564 + }, + "fit": { + "score": 0.212 + }, + "warnings": [], + "summary": "Grey Heron is classified as resident with summer detectability collapse. The fitted resident detectability target peaks around February and reaches its lowest point around October. The model indicates weak baseline presence, weak spring carry-over, strong pre-summer retention, moderate summer suppression, and moderate summer decay acceleration." +} diff --git a/modelling/data/thrupp-lake-birds/resident/grey_heron_consensus.json b/modelling/data/thrupp-lake-birds/resident/grey_heron_consensus.json new file mode 100644 index 0000000..92ee222 --- /dev/null +++ b/modelling/data/thrupp-lake-birds/resident/grey_heron_consensus.json @@ -0,0 +1,42 @@ +{ + "SCORE": "0.212", + "INITIAL_Y": "1.05", + "GROWTH_RATE": "1.58", + "DECAY_RATE": "2.7", + "SUMMER_DECAY_BOOST": "3.618", + "PRE_SUMMER_DECAY_REDUCTION": "0.546", + "PRE_SUMMER_DECAY_END": "7.1", + "PRE_SUMMER_DECAY_SHARPNESS": "9.838", + "SPRING_CARRYOVER_WEIGHT": "0.056", + "SPRING_CARRYOVER_END": "7.285", + "SPRING_CARRYOVER_SHARPNESS": "17.936", + "BASELINE": "0.038", + "WINTER_WEIGHT": "0.374", + "AUTUMN_WEIGHT": "0.025", + "WINTER_PEAK": "1.985", + "AUTUMN_PEAK": "10.83", + "AUTUMN_ONSET": "11.39", + 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+month,value +1,8 +2,2 +3,1 +4,3 +5,1 +6,1 +7,3 +8,1 +9,1 +10,0 +11,2 +12,2 diff --git a/modelling/data/thrupp-lake-birds/resident/grey_heron_parameters.csv b/modelling/data/thrupp-lake-birds/resident/grey_heron_parameters.csv new file mode 100644 index 0000000..a2370c8 --- /dev/null +++ b/modelling/data/thrupp-lake-birds/resident/grey_heron_parameters.csv @@ -0,0 +1,201 @@ 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a/modelling/data/thrupp-lake-birds/resident/grey_heron_simulated.png b/modelling/data/thrupp-lake-birds/resident/grey_heron_simulated.png new file mode 100644 index 0000000..763fbc0 Binary files /dev/null and b/modelling/data/thrupp-lake-birds/resident/grey_heron_simulated.png differ diff --git a/modelling/data/thrupp-lake-birds/resident/grey_heron_synthesised.csv b/modelling/data/thrupp-lake-birds/resident/grey_heron_synthesised.csv new file mode 100644 index 0000000..fdc9167 --- /dev/null +++ b/modelling/data/thrupp-lake-birds/resident/grey_heron_synthesised.csv @@ -0,0 +1,13 @@ +month,observed,simulated_raw,synthesised +1,8,0.7876971,6.378685029452737 +2,2,0.5370976,4.349357666132063 +3,1,0.3560746,2.8834531958901097 +4,3,0.19513609999999998,1.5801908116404033 +5,1,0.1249293,1.0116638180463147 +6,1,0.10307294,0.834673403418243 +7,3,0.07620465000000001,0.6170969273972007 +8,1,0.04106683,0.33255470120187125 +9,1,0.0138408057,0.1120813319157251 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+ "detectability_peak_timing": "spring", + "detectability_trough_timing": "autumn", + "spring_carryover": "weak", + "summer_suppression": "moderate", + "summer_decay_acceleration": "moderate", + "pre_summer_retention": "strong", + "autumn_component": "weak", + "year_end_component": "meaningful", + "response_dynamics": "rapid_decline_biased", + "traits": [ + "resident_detectability_pattern", + "weak_baseline_presence", + "spring_detectability_peak", + "autumn_detectability_trough", + "weak_spring_carryover", + "moderate_summer_suppression", + "moderate_summer_decay_acceleration", + "strong_pre_summer_retention", + "weak_autumn_component", + "meaningful_year_end_component", + "rapid_decline_biased_response_dynamics" + ], + "confidence": "medium" + }, + "derived_metrics": { + "target_peak_month": 4, + "target_peak_label": "April", + "target_trough_month": 9, + "target_trough_label": "September", + "target_peak_value": 0.5167853771102201, + "target_trough_value": 0.0, + "target_mean_value": 0.14597129978518344, + "target_amplitude": 0.5167853771102201, + "baseline_to_peak_ratio": 0.09094684579276674, + "autumn_to_winter_weight_ratio": 0.0630841121495327, + "year_end_to_winter_weight_ratio": 0.32710280373831774, + "decay_to_growth_ratio": 1.3330258302583027, + "monthly_target": { + "January": 0.0932505554354724, + "February": 0.11365206059310286, + "March": 0.31729119221773405, + "April": 0.5167853771102201, + "May": 0.25957753281157536, + "June": 0.10550272781831123, + "July": 0.09264581711521012, + "August": 0.02589397155434702, + "September": 0.0, + "October": 0.0, + "November": 0.059817607450868684, + "December": 0.16723875531535945 + } + }, + "parameter_evidence": { + "INITIAL_Y": 0.744, + "GROWTH_RATE": 2.168, + "DECAY_RATE": 2.89, + "SUMMER_DECAY_BOOST": 3.956, + "PRE_SUMMER_DECAY_REDUCTION": 0.514, + "PRE_SUMMER_DECAY_END": 6.89, + "PRE_SUMMER_DECAY_SHARPNESS": 10.164, + "SPRING_CARRYOVER_WEIGHT": 0.046, + "SPRING_CARRYOVER_END": 7.26, + "SPRING_CARRYOVER_SHARPNESS": 17.704, + "BASELINE": 0.047, + "WINTER_WEIGHT": 0.428, + "AUTUMN_WEIGHT": 0.027, + "WINTER_PEAK": 3.885, + "AUTUMN_PEAK": 10.7, + "AUTUMN_ONSET": 10.835, + "AUTUMN_GATE_SHARPNESS": 7.236, + "WINTER_WIDTH": 11.038, + "WINTER_RISE_WIDTH": 11.929, + "WINTER_FALL_WIDTH": 10.916, + "AUTUMN_WIDTH": 6.199, + "AUTUMN_RISE_WIDTH": 7.204, + "AUTUMN_FALL_WIDTH": 5.882, + "SUMMER_DIP": 0.108, + "SUMMER_LOW": 8.845, + "SUMMER_ONSET": 7.205, + "SUMMER_GATE_SHARPNESS": 4.912, + "SUMMER_DECAY_ONSET": 7.095, + "SUMMER_DECAY_GATE_SHARPNESS": 15.194, + "SUMMER_WIDTH": 21.827, + "SUMMER_RISE_WIDTH": 32.682, + "SUMMER_FALL_WIDTH": 8.056, + "SCALE": 1.086, + "YEAR_END_WEIGHT": 0.14, + "YEAR_END_PEAK": 12.152, + "YEAR_END_WIDTH": 89.1, + "YEAR_END_RISE_WIDTH": 169.886, + "YEAR_END_FALL_WIDTH": 9.838 + }, + "fit": { + "score": 0.217 + }, + "warnings": [], + "summary": "Herring Gull is classified as resident with summer detectability collapse. The fitted resident detectability target peaks around April and reaches its lowest point around September. The model indicates weak baseline presence, weak spring carry-over, strong pre-summer retention, moderate summer suppression, and moderate summer decay acceleration." +} diff --git a/modelling/data/thrupp-lake-birds/resident/herring_gull_consensus.json b/modelling/data/thrupp-lake-birds/resident/herring_gull_consensus.json new file mode 100644 index 0000000..fb891bd --- /dev/null +++ b/modelling/data/thrupp-lake-birds/resident/herring_gull_consensus.json @@ -0,0 +1,42 @@ +{ + "SCORE": "0.217", + "INITIAL_Y": "0.744", + "GROWTH_RATE": "2.168", + "DECAY_RATE": "2.89", + "SUMMER_DECAY_BOOST": "3.956", + "PRE_SUMMER_DECAY_REDUCTION": "0.514", + "PRE_SUMMER_DECAY_END": "6.89", + "PRE_SUMMER_DECAY_SHARPNESS": "10.164", + "SPRING_CARRYOVER_WEIGHT": "0.046", + "SPRING_CARRYOVER_END": "7.26", + "SPRING_CARRYOVER_SHARPNESS": "17.704", + "BASELINE": "0.047", + "WINTER_WEIGHT": "0.428", + "AUTUMN_WEIGHT": "0.027", + "WINTER_PEAK": "3.885", + "AUTUMN_PEAK": "10.7", + "AUTUMN_ONSET": "10.835", + 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a/modelling/data/thrupp-lake-birds/resident/herring_gull_simulated.png b/modelling/data/thrupp-lake-birds/resident/herring_gull_simulated.png new file mode 100644 index 0000000..86a45fc Binary files /dev/null and b/modelling/data/thrupp-lake-birds/resident/herring_gull_simulated.png differ diff --git a/modelling/data/thrupp-lake-birds/resident/herring_gull_synthesised.csv b/modelling/data/thrupp-lake-birds/resident/herring_gull_synthesised.csv new file mode 100644 index 0000000..5df0710 --- /dev/null +++ b/modelling/data/thrupp-lake-birds/resident/herring_gull_synthesised.csv @@ -0,0 +1,13 @@ +month,observed,simulated_raw,synthesised +1,9,0.46888820000000003,11.302740030633867 +2,11,0.2176952,5.247630995015114 +3,8,0.3401917,8.20045875686227 +4,13,0.4568808,11.013296788846521 +5,5,0.3061984,7.38103648800725 +6,2,0.1596712,3.8489389666435336 +7,1,0.08289463999999999,1.99820888188908 +8,1,0.014883828600000001,0.3587807185728138 +9,0,4.5623007999999995e-05,0.0010997610919607896 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"detectability_peak_timing": "spring", + "detectability_trough_timing": "autumn", + "spring_carryover": "weak", + "summer_suppression": "moderate", + "summer_decay_acceleration": "moderate", + "pre_summer_retention": "strong", + "autumn_component": "weak", + "year_end_component": "meaningful", + "response_dynamics": "rapid_decline_biased", + "traits": [ + "resident_detectability_pattern", + "weak_baseline_presence", + "spring_detectability_peak", + "autumn_detectability_trough", + "weak_spring_carryover", + "moderate_summer_suppression", + "moderate_summer_decay_acceleration", + "strong_pre_summer_retention", + "weak_autumn_component", + "meaningful_year_end_component", + "rapid_decline_biased_response_dynamics" + ], + "confidence": "medium" + }, + "derived_metrics": { + "target_peak_month": 4, + "target_peak_label": "April", + "target_trough_month": 10, + "target_trough_label": "October", + "target_peak_value": 0.5370318557806412, + "target_trough_value": 0.0, + "target_mean_value": 0.17342487130885215, + "target_amplitude": 0.5370318557806412, + "baseline_to_peak_ratio": 0.10055269425591974, + "autumn_to_winter_weight_ratio": 0.055299539170506916, + "year_end_to_winter_weight_ratio": 0.3548387096774194, + "decay_to_growth_ratio": 1.5104299702000852, + "monthly_target": { + "January": 0.11765077500797781, + "February": 0.18080630545500914, + "March": 0.4203087921006915, + "April": 0.5370318557806412, + "May": 0.3089154969615748, + "June": 0.1412932738194972, + "July": 0.110305191490553, + "August": 0.053908074231316314, + "September": 0.00019819539866673325, + "October": 0.0, + "November": 0.032680302975887046, + "December": 0.17800019248441112 + } + }, + "parameter_evidence": { + "INITIAL_Y": 0.615, + "GROWTH_RATE": 2.349, + "DECAY_RATE": 3.548, + "SUMMER_DECAY_BOOST": 3.988, + "PRE_SUMMER_DECAY_REDUCTION": 0.484, + "PRE_SUMMER_DECAY_END": 6.995, + "PRE_SUMMER_DECAY_SHARPNESS": 9.679, + "SPRING_CARRYOVER_WEIGHT": 0.06, + "SPRING_CARRYOVER_END": 7.135, + "SPRING_CARRYOVER_SHARPNESS": 18.606, + "BASELINE": 0.054, + "WINTER_WEIGHT": 0.434, + "AUTUMN_WEIGHT": 0.024, + "WINTER_PEAK": 3.78, + "AUTUMN_PEAK": 10.825, + "AUTUMN_ONSET": 11.37, + "AUTUMN_GATE_SHARPNESS": 6.716, + "WINTER_WIDTH": 9.481, + "WINTER_RISE_WIDTH": 8.298, + "WINTER_FALL_WIDTH": 7.712, + "AUTUMN_WIDTH": 7.604, + "AUTUMN_RISE_WIDTH": 7.648, + "AUTUMN_FALL_WIDTH": 5.912, + "SUMMER_DIP": 0.118, + "SUMMER_LOW": 9.605, + "SUMMER_ONSET": 8.31, + "SUMMER_GATE_SHARPNESS": 4.87, + "SUMMER_DECAY_ONSET": 7.15, + "SUMMER_DECAY_GATE_SHARPNESS": 14.566, + "SUMMER_WIDTH": 19.619, + "SUMMER_RISE_WIDTH": 29.82, + "SUMMER_FALL_WIDTH": 11.938, + "SCALE": 1.034, + "YEAR_END_WEIGHT": 0.154, + "YEAR_END_PEAK": 12.184, + "YEAR_END_WIDTH": 74.41, + "YEAR_END_RISE_WIDTH": 139.704, + "YEAR_END_FALL_WIDTH": 10.06 + }, + "fit": { + "score": 0.24 + }, + "warnings": [], + "summary": "Mallard is classified as resident with summer detectability collapse. The fitted resident detectability target peaks around April and reaches its lowest point around October. The model indicates weak baseline presence, weak spring carry-over, strong pre-summer retention, moderate summer suppression, and moderate summer decay acceleration." +} diff --git a/modelling/data/thrupp-lake-birds/resident/mallard_consensus.json b/modelling/data/thrupp-lake-birds/resident/mallard_consensus.json new file mode 100644 index 0000000..66ec020 --- /dev/null +++ b/modelling/data/thrupp-lake-birds/resident/mallard_consensus.json @@ -0,0 +1,42 @@ +{ + "SCORE": "0.24", + "INITIAL_Y": "0.615", + "GROWTH_RATE": "2.349", + "DECAY_RATE": "3.548", + "SUMMER_DECAY_BOOST": "3.988", + "PRE_SUMMER_DECAY_REDUCTION": "0.484", + "PRE_SUMMER_DECAY_END": "6.995", + "PRE_SUMMER_DECAY_SHARPNESS": "9.679", + "SPRING_CARRYOVER_WEIGHT": "0.06", + "SPRING_CARRYOVER_END": "7.135", + "SPRING_CARRYOVER_SHARPNESS": "18.606", + "BASELINE": "0.054", + "WINTER_WEIGHT": "0.434", + "AUTUMN_WEIGHT": "0.024", + "WINTER_PEAK": "3.78", + "AUTUMN_PEAK": "10.825", + "AUTUMN_ONSET": "11.37", + "AUTUMN_GATE_SHARPNESS": "6.716", + "WINTER_WIDTH": "9.481", + "WINTER_RISE_WIDTH": "8.298", + "WINTER_FALL_WIDTH": "7.712", + "AUTUMN_WIDTH": "7.604", + "AUTUMN_RISE_WIDTH": "7.648", + "AUTUMN_FALL_WIDTH": "5.912", + "SUMMER_DIP": "0.118", + "SUMMER_LOW": "9.605", + "SUMMER_ONSET": "8.31", + "SUMMER_GATE_SHARPNESS": "4.87", + "SUMMER_DECAY_ONSET": "7.15", + "SUMMER_DECAY_GATE_SHARPNESS": "14.566", + "SUMMER_WIDTH": "19.619", + "SUMMER_RISE_WIDTH": "29.82", + "SUMMER_FALL_WIDTH": "11.938", + "SCALE": "1.034", + "YEAR_END_WEIGHT": "0.154", + "YEAR_END_PEAK": "12.184", + "YEAR_END_WIDTH": "74.41", + "YEAR_END_RISE_WIDTH": "139.704", + "YEAR_END_FALL_WIDTH": "10.06", + "SPECIES": "Mallard" +} diff --git a/modelling/data/thrupp-lake-birds/resident/mallard_observed.csv b/modelling/data/thrupp-lake-birds/resident/mallard_observed.csv new file mode 100644 index 0000000..b1813a6 --- /dev/null +++ b/modelling/data/thrupp-lake-birds/resident/mallard_observed.csv @@ -0,0 +1,13 @@ +month,value +1,11 +2,13 +3,10 +4,18 +5,10 +6,6 +7,5 +8,5 +9,3 +10,0 +11,4 +12,5 diff --git a/modelling/data/thrupp-lake-birds/resident/mallard_parameters.csv b/modelling/data/thrupp-lake-birds/resident/mallard_parameters.csv new file mode 100644 index 0000000..43b0f0e --- /dev/null +++ b/modelling/data/thrupp-lake-birds/resident/mallard_parameters.csv @@ -0,0 +1,201 @@ 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a/modelling/data/thrupp-lake-birds/resident/mallard_simulated.png b/modelling/data/thrupp-lake-birds/resident/mallard_simulated.png new file mode 100644 index 0000000..4855ed8 Binary files /dev/null and b/modelling/data/thrupp-lake-birds/resident/mallard_simulated.png differ diff --git a/modelling/data/thrupp-lake-birds/resident/mallard_synthesised.csv b/modelling/data/thrupp-lake-birds/resident/mallard_synthesised.csv new file mode 100644 index 0000000..0f19b9d --- /dev/null +++ b/modelling/data/thrupp-lake-birds/resident/mallard_synthesised.csv @@ -0,0 +1,13 @@ +month,observed,simulated_raw,synthesised +1,11,0.3729154,12.394793552696088 +2,13,0.24162559999999997,8.031042507352401 +3,10,0.4221813,14.032271274688181 +4,18,0.49176169999999997,16.344953167991633 +5,10,0.32578019999999996,10.828135074486175 +6,6,0.1741161,5.787192252453472 +7,5,0.08853661,2.9427398353770533 +8,5,0.0499761,1.6610830286678828 +9,3,0.00483678726,0.16076294930702936 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"winter", + "detectability_trough_timing": "autumn", + "spring_carryover": "weak", + "summer_suppression": "moderate", + "summer_decay_acceleration": "moderate", + "pre_summer_retention": "strong", + "autumn_component": "weak", + "year_end_component": "meaningful", + "response_dynamics": "rapid_decline_biased", + "traits": [ + "resident_detectability_pattern", + "weak_baseline_presence", + "winter_detectability_peak", + "autumn_detectability_trough", + "weak_spring_carryover", + "moderate_summer_suppression", + "moderate_summer_decay_acceleration", + "strong_pre_summer_retention", + "weak_autumn_component", + "meaningful_year_end_component", + "rapid_decline_biased_response_dynamics" + ], + "confidence": "medium" + }, + "derived_metrics": { + "target_peak_month": 2, + "target_peak_label": "February", + "target_trough_month": 10, + "target_trough_label": "October", + "target_peak_value": 0.5625065901827299, + "target_trough_value": 0.0, + "target_mean_value": 0.16693178065509032, + "target_amplitude": 0.5625065901827299, + "baseline_to_peak_ratio": 0.08355457664012805, + "autumn_to_winter_weight_ratio": 0.06331877729257641, + "year_end_to_winter_weight_ratio": 0.38209606986899564, + "decay_to_growth_ratio": 1.358095238095238, + "monthly_target": { + "January": 0.3006807495431222, + "February": 0.5625065901827299, + "March": 0.39630124067748956, + "April": 0.15971900037468972, + "May": 0.11086124095769907, + "June": 0.109006534859371, + "July": 0.08079448369147071, + "August": 0.046998775989472656, + "September": 0.04129365503598058, + "October": 0.0, + "November": 0.0, + "December": 0.19501909654905838 + } + }, + "parameter_evidence": { + "INITIAL_Y": 0.784, + "GROWTH_RATE": 2.1, + "DECAY_RATE": 2.852, + "SUMMER_DECAY_BOOST": 3.72, + "PRE_SUMMER_DECAY_REDUCTION": 0.693, + "PRE_SUMMER_DECAY_END": 7.045, + "PRE_SUMMER_DECAY_SHARPNESS": 9.184, + "SPRING_CARRYOVER_WEIGHT": 0.062, + "SPRING_CARRYOVER_END": 7.01, + "SPRING_CARRYOVER_SHARPNESS": 18.078, + "BASELINE": 0.047, + "WINTER_WEIGHT": 0.458, + "AUTUMN_WEIGHT": 0.029, + "WINTER_PEAK": 2.12, + "AUTUMN_PEAK": 10.605, + "AUTUMN_ONSET": 11.365, + "AUTUMN_GATE_SHARPNESS": 5.916, + "WINTER_WIDTH": 9.284, + "WINTER_RISE_WIDTH": 9.988, + "WINTER_FALL_WIDTH": 8.708, + "AUTUMN_WIDTH": 7.388, + "AUTUMN_RISE_WIDTH": 7.96, + "AUTUMN_FALL_WIDTH": 7.776, + "SUMMER_DIP": 0.118, + "SUMMER_LOW": 10.22, + "SUMMER_ONSET": 8.18, + "SUMMER_GATE_SHARPNESS": 4.082, + "SUMMER_DECAY_ONSET": 7.205, + "SUMMER_DECAY_GATE_SHARPNESS": 13.724, + "SUMMER_WIDTH": 21.02, + "SUMMER_RISE_WIDTH": 28.85, + "SUMMER_FALL_WIDTH": 9.938, + "SCALE": 1.098, + "YEAR_END_WEIGHT": 0.175, + "YEAR_END_PEAK": 12.156, + "YEAR_END_WIDTH": 85.542, + "YEAR_END_RISE_WIDTH": 164.561, + "YEAR_END_FALL_WIDTH": 10.261 + }, + "fit": { + "score": 0.251 + }, + "warnings": [], + "summary": "Moorhen is classified as resident with summer detectability collapse. The fitted resident detectability target peaks around February and reaches its lowest point around October. The model indicates weak baseline presence, weak spring carry-over, strong pre-summer retention, moderate summer suppression, and moderate summer decay acceleration." +} diff --git a/modelling/data/thrupp-lake-birds/resident/moorhen_consensus.json b/modelling/data/thrupp-lake-birds/resident/moorhen_consensus.json new file mode 100644 index 0000000..a5d4698 --- /dev/null +++ b/modelling/data/thrupp-lake-birds/resident/moorhen_consensus.json @@ -0,0 +1,42 @@ +{ + "SCORE": "0.251", + "INITIAL_Y": "0.784", + "GROWTH_RATE": "2.1", + "DECAY_RATE": "2.852", + "SUMMER_DECAY_BOOST": "3.72", + "PRE_SUMMER_DECAY_REDUCTION": "0.693", + "PRE_SUMMER_DECAY_END": "7.045", + "PRE_SUMMER_DECAY_SHARPNESS": "9.184", + "SPRING_CARRYOVER_WEIGHT": "0.062", + "SPRING_CARRYOVER_END": "7.01", + "SPRING_CARRYOVER_SHARPNESS": "18.078", + "BASELINE": "0.047", + "WINTER_WEIGHT": "0.458", + "AUTUMN_WEIGHT": "0.029", + "WINTER_PEAK": "2.12", + "AUTUMN_PEAK": "10.605", + "AUTUMN_ONSET": "11.365", + 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a/modelling/data/thrupp-lake-birds/resident/moorhen_simulated.png b/modelling/data/thrupp-lake-birds/resident/moorhen_simulated.png new file mode 100644 index 0000000..8dfae96 Binary files /dev/null and b/modelling/data/thrupp-lake-birds/resident/moorhen_simulated.png differ diff --git a/modelling/data/thrupp-lake-birds/resident/moorhen_synthesised.csv b/modelling/data/thrupp-lake-birds/resident/moorhen_synthesised.csv new file mode 100644 index 0000000..42064cd --- /dev/null +++ b/modelling/data/thrupp-lake-birds/resident/moorhen_synthesised.csv @@ -0,0 +1,13 @@ +month,observed,simulated_raw,synthesised +1,9,0.6691594000000001,11.416044262588507 +2,11,0.5831147999999999,9.94809961119943 +3,7,0.46809880000000004,7.985894870586239 +4,8,0.2965552,5.059313654565395 +5,4,0.1898493,3.2388815161551108 +6,2,0.1424679,2.430541739977101 +7,3,0.08188976,1.3970619329456477 +8,3,0.049021560000000006,0.8363213589783515 +9,2,0.026251234000000002,0.4478533056422257 +10,0,0.000395213687,0.006742454703577055 +11,5,0.01088017414,0.18561877718061023 +12,4,0.17417403,2.9714570786473575 diff --git a/modelling/data/thrupp-lake-birds/resident/moorhen_synthesised.png b/modelling/data/thrupp-lake-birds/resident/moorhen_synthesised.png new file mode 100644 index 0000000..b8223ca Binary files /dev/null and b/modelling/data/thrupp-lake-birds/resident/moorhen_synthesised.png differ diff --git a/modelling/data/thrupp-lake-birds/resident/mute_swan_classification.json b/modelling/data/thrupp-lake-birds/resident/mute_swan_classification.json new file mode 100644 index 0000000..7bcf9fd --- /dev/null +++ b/modelling/data/thrupp-lake-birds/resident/mute_swan_classification.json @@ -0,0 +1,105 @@ +{ + "schema_version": "resident-classification/v1", + "species": "Mute Swan", + "model_family": "resident_detectability", + "classification": { + "primary_class": "resident_with_summer_detectability_collapse", + "baseline_presence": "moderate", + "detectability_peak_timing": "spring", + "detectability_trough_timing": "autumn", + "spring_carryover": "weak", + "summer_suppression": "moderate", + "summer_decay_acceleration": "strong", + "pre_summer_retention": "strong", + "autumn_component": "weak", + "year_end_component": "meaningful", + "response_dynamics": "rapid_decline_biased", + "traits": [ + "resident_detectability_pattern", + "moderate_baseline_presence", + "spring_detectability_peak", + "autumn_detectability_trough", + "weak_spring_carryover", + "moderate_summer_suppression", + "strong_summer_decay_acceleration", + "strong_pre_summer_retention", + "weak_autumn_component", + "meaningful_year_end_component", + "rapid_decline_biased_response_dynamics" + ], + "confidence": "high" + }, + "derived_metrics": { + "target_peak_month": 4, + "target_peak_label": "April", + "target_trough_month": 10, + "target_trough_label": "October", + "target_peak_value": 0.6669139392911505, + "target_trough_value": 0.09033154694543219, + "target_mean_value": 0.3036181953356336, + "target_amplitude": 0.5765823923457183, + "baseline_to_peak_ratio": 0.2923915493613188, + "autumn_to_winter_weight_ratio": 0.060085836909871244, + "year_end_to_winter_weight_ratio": 0.40987124463519314, + "decay_to_growth_ratio": 1.6731898238747553, + "monthly_target": { + "January": 0.2526156856541697, + "February": 0.29469008634939997, + "March": 0.5878683407060562, + "April": 0.6669139392911505, + "May": 0.3610067390728229, + "June": 0.25728195388949515, + "July": 0.25007810850661705, + "August": 0.19499782003588292, + "September": 0.17839711871715924, + "October": 0.09033154694543219, + "November": 0.1652097000489483, + "December": 0.34402730481046945 + } + }, + "parameter_evidence": { + "INITIAL_Y": 0.861, + "GROWTH_RATE": 2.044, + "DECAY_RATE": 3.42, + "SUMMER_DECAY_BOOST": 4.369, + "PRE_SUMMER_DECAY_REDUCTION": 0.628, + "PRE_SUMMER_DECAY_END": 7.06, + "PRE_SUMMER_DECAY_SHARPNESS": 9.54, + "SPRING_CARRYOVER_WEIGHT": 0.057, + "SPRING_CARRYOVER_END": 7.185, + "SPRING_CARRYOVER_SHARPNESS": 18.062, + "BASELINE": 0.195, + "WINTER_WEIGHT": 0.466, + "AUTUMN_WEIGHT": 0.028, + "WINTER_PEAK": 3.6, + "AUTUMN_PEAK": 10.91, + "AUTUMN_ONSET": 11.38, + "AUTUMN_GATE_SHARPNESS": 6.993, + "WINTER_WIDTH": 11.24, + "WINTER_RISE_WIDTH": 13.217, + "WINTER_FALL_WIDTH": 10.569, + "AUTUMN_WIDTH": 8.236, + "AUTUMN_RISE_WIDTH": 7.339, + "AUTUMN_FALL_WIDTH": 8.107, + "SUMMER_DIP": 0.11, + "SUMMER_LOW": 9.785, + "SUMMER_ONSET": 8.59, + "SUMMER_GATE_SHARPNESS": 3.176, + "SUMMER_DECAY_ONSET": 7.16, + "SUMMER_DECAY_GATE_SHARPNESS": 14.883, + "SUMMER_WIDTH": 25.033, + "SUMMER_RISE_WIDTH": 38.799, + "SUMMER_FALL_WIDTH": 12.108, + "SCALE": 1.174, + "YEAR_END_WEIGHT": 0.191, + "YEAR_END_PEAK": 12.162, + "YEAR_END_WIDTH": 96.704, + "YEAR_END_RISE_WIDTH": 187.39, + "YEAR_END_FALL_WIDTH": 9.767 + }, + "fit": { + "score": 0.194 + }, + "warnings": [], + "summary": "Mute Swan is classified as resident with summer detectability collapse. The fitted resident detectability target peaks around April and reaches its lowest point around October. The model indicates moderate baseline presence, weak spring carry-over, strong pre-summer retention, moderate summer suppression, and strong summer decay acceleration." +} diff --git a/modelling/data/thrupp-lake-birds/resident/mute_swan_consensus.json b/modelling/data/thrupp-lake-birds/resident/mute_swan_consensus.json new file mode 100644 index 0000000..ed73db4 --- /dev/null +++ b/modelling/data/thrupp-lake-birds/resident/mute_swan_consensus.json @@ -0,0 +1,42 @@ +{ + "SCORE": "0.194", + "INITIAL_Y": "0.861", + "GROWTH_RATE": "2.044", + "DECAY_RATE": "3.42", + "SUMMER_DECAY_BOOST": "4.369", + "PRE_SUMMER_DECAY_REDUCTION": "0.628", + "PRE_SUMMER_DECAY_END": "7.06", + "PRE_SUMMER_DECAY_SHARPNESS": "9.54", + "SPRING_CARRYOVER_WEIGHT": "0.057", + "SPRING_CARRYOVER_END": "7.185", + "SPRING_CARRYOVER_SHARPNESS": "18.062", + "BASELINE": "0.195", + "WINTER_WEIGHT": "0.466", + "AUTUMN_WEIGHT": "0.028", + "WINTER_PEAK": "3.6", + "AUTUMN_PEAK": "10.91", + "AUTUMN_ONSET": "11.38", + "AUTUMN_GATE_SHARPNESS": "6.993", + "WINTER_WIDTH": "11.24", + "WINTER_RISE_WIDTH": "13.217", + "WINTER_FALL_WIDTH": "10.569", + "AUTUMN_WIDTH": "8.236", + "AUTUMN_RISE_WIDTH": "7.339", + "AUTUMN_FALL_WIDTH": "8.107", + "SUMMER_DIP": "0.11", + "SUMMER_LOW": "9.785", + "SUMMER_ONSET": "8.59", + "SUMMER_GATE_SHARPNESS": "3.176", + "SUMMER_DECAY_ONSET": "7.16", + "SUMMER_DECAY_GATE_SHARPNESS": "14.883", + "SUMMER_WIDTH": "25.033", + "SUMMER_RISE_WIDTH": "38.799", + "SUMMER_FALL_WIDTH": "12.108", + "SCALE": "1.174", + "YEAR_END_WEIGHT": "0.191", + "YEAR_END_PEAK": "12.162", + "YEAR_END_WIDTH": "96.704", + "YEAR_END_RISE_WIDTH": "187.39", + "YEAR_END_FALL_WIDTH": "9.767", + "SPECIES": "Mute Swan" +} diff --git a/modelling/data/thrupp-lake-birds/resident/mute_swan_observed.csv b/modelling/data/thrupp-lake-birds/resident/mute_swan_observed.csv new file mode 100644 index 0000000..6ab9516 --- /dev/null +++ b/modelling/data/thrupp-lake-birds/resident/mute_swan_observed.csv @@ -0,0 +1,13 @@ 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b/modelling/data/thrupp-lake-birds/resident/mute_swan_synthesised.png new file mode 100644 index 0000000..d9712d9 Binary files /dev/null and b/modelling/data/thrupp-lake-birds/resident/mute_swan_synthesised.png differ diff --git a/modelling/data/thrupp-lake-birds/resident/robin_classification.json b/modelling/data/thrupp-lake-birds/resident/robin_classification.json new file mode 100644 index 0000000..247190f --- /dev/null +++ b/modelling/data/thrupp-lake-birds/resident/robin_classification.json @@ -0,0 +1,105 @@ +{ + "schema_version": "resident-classification/v1", + "species": "Robin", + "model_family": "resident_detectability", + "classification": { + "primary_class": "resident_with_summer_detectability_collapse", + "baseline_presence": "weak", + "detectability_peak_timing": "spring", + "detectability_trough_timing": "summer", + "spring_carryover": "weak", + "summer_suppression": "moderate", + "summer_decay_acceleration": "strong", + "pre_summer_retention": "moderate", + "autumn_component": "weak", + "year_end_component": "meaningful", + "response_dynamics": "decline_biased", + "traits": [ + "resident_detectability_pattern", + "weak_baseline_presence", + "spring_detectability_peak", + "summer_detectability_trough", + "weak_spring_carryover", + "moderate_summer_suppression", + "strong_summer_decay_acceleration", + "moderate_pre_summer_retention", + "weak_autumn_component", + "meaningful_year_end_component", + "decline_biased_response_dynamics" + ], + "confidence": "medium" + }, + "derived_metrics": { + "target_peak_month": 3, + "target_peak_label": "March", + "target_trough_month": 8, + "target_trough_label": "August", + "target_peak_value": 0.5084182030498415, + "target_trough_value": 0.0, + "target_mean_value": 0.16707274043568313, + "target_amplitude": 0.5084182030498415, + "baseline_to_peak_ratio": 0.10621177541651915, + "autumn_to_winter_weight_ratio": 0.052742616033755275, + "year_end_to_winter_weight_ratio": 0.3333333333333333, + "decay_to_growth_ratio": 1.11448395490026, + "monthly_target": { + "January": 0.11351224195211758, + "February": 0.22261669367383619, + "March": 0.5084182030498415, + "April": 0.5044189562411799, + "May": 0.19253640341675138, + "June": 0.10780338385479186, + "July": 0.013263904687650825, + "August": 0.0, + "September": 0.02824101888217328, + "October": 0.054405693348501864, + "November": 0.0780586667347739, + "December": 0.1815977193865791 + } + }, + "parameter_evidence": { + "INITIAL_Y": 0.85, + "GROWTH_RATE": 2.306, + "DECAY_RATE": 2.57, + "SUMMER_DECAY_BOOST": 4.016, + "PRE_SUMMER_DECAY_REDUCTION": 0.42, + "PRE_SUMMER_DECAY_END": 7.015, + "PRE_SUMMER_DECAY_SHARPNESS": 10.362, + "SPRING_CARRYOVER_WEIGHT": 0.051, + "SPRING_CARRYOVER_END": 7.08, + "SPRING_CARRYOVER_SHARPNESS": 17.716, + "BASELINE": 0.054, + "WINTER_WEIGHT": 0.474, + "AUTUMN_WEIGHT": 0.025, + "WINTER_PEAK": 3.525, + "AUTUMN_PEAK": 10.765, + "AUTUMN_ONSET": 10.335, + "AUTUMN_GATE_SHARPNESS": 7.218, + "WINTER_WIDTH": 11.26, + "WINTER_RISE_WIDTH": 8.508, + "WINTER_FALL_WIDTH": 11.042, + "AUTUMN_WIDTH": 7.075, + "AUTUMN_RISE_WIDTH": 6.936, + "AUTUMN_FALL_WIDTH": 7.914, + "SUMMER_DIP": 0.136, + "SUMMER_LOW": 7.465, + "SUMMER_ONSET": 6.1, + "SUMMER_GATE_SHARPNESS": 4.243, + "SUMMER_DECAY_ONSET": 7.025, + "SUMMER_DECAY_GATE_SHARPNESS": 14.831, + "SUMMER_WIDTH": 21.855, + "SUMMER_RISE_WIDTH": 32.76, + "SUMMER_FALL_WIDTH": 10.021, + "SCALE": 1.414, + "YEAR_END_WEIGHT": 0.158, + "YEAR_END_PEAK": 12.162, + "YEAR_END_WIDTH": 89.078, + "YEAR_END_RISE_WIDTH": 168.204, + "YEAR_END_FALL_WIDTH": 9.178 + }, + "fit": { + "score": 0.23 + }, + "warnings": [], + "summary": "Robin is classified as resident with summer detectability collapse. The fitted resident detectability target peaks around March and reaches its lowest point around August. The model indicates weak baseline presence, weak spring carry-over, moderate pre-summer retention, moderate summer suppression, and strong summer decay acceleration." +} diff --git a/modelling/data/thrupp-lake-birds/resident/robin_consensus.json b/modelling/data/thrupp-lake-birds/resident/robin_consensus.json new file mode 100644 index 0000000..9e2bf73 --- /dev/null +++ b/modelling/data/thrupp-lake-birds/resident/robin_consensus.json @@ -0,0 +1,42 @@ +{ + "SCORE": "0.23", + "INITIAL_Y": "0.85", + "GROWTH_RATE": "2.306", + "DECAY_RATE": "2.57", + "SUMMER_DECAY_BOOST": "4.016", + "PRE_SUMMER_DECAY_REDUCTION": "0.42", + "PRE_SUMMER_DECAY_END": "7.015", + "PRE_SUMMER_DECAY_SHARPNESS": "10.362", + "SPRING_CARRYOVER_WEIGHT": "0.051", + "SPRING_CARRYOVER_END": "7.08", + "SPRING_CARRYOVER_SHARPNESS": "17.716", + "BASELINE": "0.054", + "WINTER_WEIGHT": "0.474", + "AUTUMN_WEIGHT": "0.025", + "WINTER_PEAK": "3.525", + "AUTUMN_PEAK": "10.765", + "AUTUMN_ONSET": "10.335", + "AUTUMN_GATE_SHARPNESS": "7.218", + "WINTER_WIDTH": "11.26", + "WINTER_RISE_WIDTH": "8.508", + "WINTER_FALL_WIDTH": "11.042", + "AUTUMN_WIDTH": "7.075", + "AUTUMN_RISE_WIDTH": "6.936", + "AUTUMN_FALL_WIDTH": "7.914", + "SUMMER_DIP": "0.136", + "SUMMER_LOW": "7.465", + "SUMMER_ONSET": "6.1", + "SUMMER_GATE_SHARPNESS": "4.243", + "SUMMER_DECAY_ONSET": "7.025", + "SUMMER_DECAY_GATE_SHARPNESS": "14.831", + "SUMMER_WIDTH": "21.855", + "SUMMER_RISE_WIDTH": "32.76", + "SUMMER_FALL_WIDTH": "10.021", + "SCALE": "1.414", + "YEAR_END_WEIGHT": "0.158", + "YEAR_END_PEAK": "12.162", + "YEAR_END_WIDTH": "89.078", + "YEAR_END_RISE_WIDTH": "168.204", + "YEAR_END_FALL_WIDTH": "9.178", + "SPECIES": "Robin" +} diff --git a/modelling/data/thrupp-lake-birds/resident/robin_observed.csv b/modelling/data/thrupp-lake-birds/resident/robin_observed.csv new file mode 100644 index 0000000..ae64a7d --- /dev/null +++ b/modelling/data/thrupp-lake-birds/resident/robin_observed.csv @@ -0,0 +1,13 @@ +month,value +1,11 +2,8 +3,9 +4,13 +5,10 +6,2 +7,1 +8,0 +9,1 +10,1 +11,3 +12,1 diff --git a/modelling/data/thrupp-lake-birds/resident/robin_parameters.csv b/modelling/data/thrupp-lake-birds/resident/robin_parameters.csv new file mode 100644 index 0000000..86e4871 --- /dev/null +++ b/modelling/data/thrupp-lake-birds/resident/robin_parameters.csv @@ -0,0 +1,201 @@ +TIMESTAMP,OBSERVED,SCORE,INITIAL_Y,GROWTH_RATE,DECAY_RATE,SUMMER_DECAY_BOOST,PRE_SUMMER_DECAY_REDUCTION,PRE_SUMMER_DECAY_END,PRE_SUMMER_DECAY_SHARPNESS,SPRING_CARRYOVER_WEIGHT,SPRING_CARRYOVER_END,SPRING_CARRYOVER_SHARPNESS,BASELINE,WINTER_WEIGHT,AUTUMN_WEIGHT,WINTER_PEAK,AUTUMN_PEAK,AUTUMN_ONSET,AUTUMN_GATE_SHARPNESS,WINTER_WIDTH,WINTER_RISE_WIDTH,WINTER_FALL_WIDTH,AUTUMN_WIDTH,AUTUMN_RISE_WIDTH,AUTUMN_FALL_WIDTH,SUMMER_DIP,SUMMER_LOW,SUMMER_ONSET,SUMMER_GATE_SHARPNESS,SUMMER_DECAY_ONSET,SUMMER_DECAY_GATE_SHARPNESS,SUMMER_WIDTH,SUMMER_RISE_WIDTH,SUMMER_FALL_WIDTH,SCALE,YEAR_END_WEIGHT,YEAR_END_PEAK,YEAR_END_WIDTH,YEAR_END_RISE_WIDTH,YEAR_END_FALL_WIDTH +2026-05-23 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+4,13,0.4715242,10.790742525159066 +5,10,0.2622464,6.001459480870493 +6,2,0.1404414,3.213974992742418 +7,1,0.0224582628,0.5139531151045014 +8,0,0.0010274096,0.02351207522641821 +9,1,0.028142269999999997,0.6440305495317276 +10,1,0.05695472,1.303398042163112 +11,3,0.07542988,1.726198599740258 +12,1,0.16121539999999998,3.6893840708292993 diff --git a/modelling/data/thrupp-lake-birds/resident/robin_synthesised.png b/modelling/data/thrupp-lake-birds/resident/robin_synthesised.png new file mode 100644 index 0000000..9194df2 Binary files /dev/null and b/modelling/data/thrupp-lake-birds/resident/robin_synthesised.png differ diff --git a/modelling/data/thrupp-lake-birds/resident/tufted_duck_classification.json b/modelling/data/thrupp-lake-birds/resident/tufted_duck_classification.json new file mode 100644 index 0000000..18ab99c --- /dev/null +++ b/modelling/data/thrupp-lake-birds/resident/tufted_duck_classification.json @@ -0,0 +1,105 @@ +{ + "schema_version": "resident-classification/v1", + "species": "Tufted Duck", + "model_family": "resident_detectability", + "classification": { + "primary_class": "resident_with_summer_detectability_collapse", + "baseline_presence": "weak", + "detectability_peak_timing": "spring", + "detectability_trough_timing": "autumn", + "spring_carryover": "weak", + "summer_suppression": "moderate", + "summer_decay_acceleration": "strong", + "pre_summer_retention": "strong", + "autumn_component": "weak", + "year_end_component": "meaningful", + "response_dynamics": "decline_biased", + "traits": [ + "resident_detectability_pattern", + "weak_baseline_presence", + "spring_detectability_peak", + "autumn_detectability_trough", + "weak_spring_carryover", + "moderate_summer_suppression", + "strong_summer_decay_acceleration", + "strong_pre_summer_retention", + "weak_autumn_component", + "meaningful_year_end_component", + "decline_biased_response_dynamics" + ], + "confidence": "medium" + }, + "derived_metrics": { + "target_peak_month": 4, + "target_peak_label": "April", + "target_trough_month": 9, + "target_trough_label": "September", + "target_peak_value": 0.4901607409405049, + "target_trough_value": 0.0, + "target_mean_value": 0.1435558094373643, + "target_amplitude": 0.4901607409405049, + "baseline_to_peak_ratio": 0.08568617698637335, + "autumn_to_winter_weight_ratio": 0.06896551724137931, + "year_end_to_winter_weight_ratio": 0.4827586206896552, + "decay_to_growth_ratio": 0.9955787781350482, + "monthly_target": { + "January": 0.08746883406668136, + "February": 0.11240531368056499, + "March": 0.3095683329929725, + "April": 0.4901607409405049, + "May": 0.2586216664352318, + "June": 0.10251980570899384, + "July": 0.08656727401468682, + "August": 0.04032030442701822, + "September": 0.0, + "October": 0.0, + "November": 0.04728553694761649, + "December": 0.18775190403410041 + } + }, + "parameter_evidence": { + "INITIAL_Y": 0.65, + "GROWTH_RATE": 2.488, + "DECAY_RATE": 2.477, + "SUMMER_DECAY_BOOST": 4.278, + "PRE_SUMMER_DECAY_REDUCTION": 0.518, + "PRE_SUMMER_DECAY_END": 6.93, + "PRE_SUMMER_DECAY_SHARPNESS": 9.588, + "SPRING_CARRYOVER_WEIGHT": 0.045, + "SPRING_CARRYOVER_END": 7.23, + "SPRING_CARRYOVER_SHARPNESS": 18.522, + "BASELINE": 0.042, + "WINTER_WEIGHT": 0.406, + "AUTUMN_WEIGHT": 0.028, + "WINTER_PEAK": 3.9, + "AUTUMN_PEAK": 10.49, + "AUTUMN_ONSET": 10.925, + "AUTUMN_GATE_SHARPNESS": 6.306, + "WINTER_WIDTH": 11.125, + "WINTER_RISE_WIDTH": 10.727, + "WINTER_FALL_WIDTH": 10.238, + "AUTUMN_WIDTH": 6.52, + "AUTUMN_RISE_WIDTH": 6.302, + "AUTUMN_FALL_WIDTH": 6.905, + "SUMMER_DIP": 0.138, + "SUMMER_LOW": 9.16, + "SUMMER_ONSET": 7.305, + "SUMMER_GATE_SHARPNESS": 3.768, + "SUMMER_DECAY_ONSET": 7.085, + "SUMMER_DECAY_GATE_SHARPNESS": 15.701, + "SUMMER_WIDTH": 28.144, + "SUMMER_RISE_WIDTH": 46.309, + "SUMMER_FALL_WIDTH": 10.879, + "SCALE": 1.114, + "YEAR_END_WEIGHT": 0.196, + "YEAR_END_PEAK": 12.174, + "YEAR_END_WIDTH": 90.787, + "YEAR_END_RISE_WIDTH": 173.6, + "YEAR_END_FALL_WIDTH": 9.409 + }, + "fit": { + "score": 0.225 + }, + "warnings": [], + "summary": "Tufted Duck is classified as resident with summer detectability collapse. The fitted resident detectability target peaks around April and reaches its lowest point around September. The model indicates weak baseline presence, weak spring carry-over, strong pre-summer retention, moderate summer suppression, and strong summer decay acceleration." +} diff --git a/modelling/data/thrupp-lake-birds/resident/tufted_duck_consensus.json b/modelling/data/thrupp-lake-birds/resident/tufted_duck_consensus.json new file mode 100644 index 0000000..6026058 --- /dev/null +++ b/modelling/data/thrupp-lake-birds/resident/tufted_duck_consensus.json @@ -0,0 +1,42 @@ +{ + "SCORE": "0.225", + "INITIAL_Y": "0.65", + "GROWTH_RATE": "2.488", + "DECAY_RATE": "2.477", + "SUMMER_DECAY_BOOST": "4.278", + "PRE_SUMMER_DECAY_REDUCTION": "0.518", + "PRE_SUMMER_DECAY_END": "6.93", + "PRE_SUMMER_DECAY_SHARPNESS": "9.588", + "SPRING_CARRYOVER_WEIGHT": "0.045", + "SPRING_CARRYOVER_END": "7.23", + "SPRING_CARRYOVER_SHARPNESS": "18.522", + "BASELINE": "0.042", + "WINTER_WEIGHT": "0.406", + "AUTUMN_WEIGHT": "0.028", + "WINTER_PEAK": "3.9", + "AUTUMN_PEAK": "10.49", + "AUTUMN_ONSET": "10.925", + 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@@ +month,value +1,14 +2,12 +3,10 +4,20 +5,9 +6,6 +7,4 +8,5 +9,1 +10,1 +11,5 +12,4 diff --git a/modelling/data/thrupp-lake-birds/resident/tufted_duck_parameters.csv b/modelling/data/thrupp-lake-birds/resident/tufted_duck_parameters.csv new file mode 100644 index 0000000..59ede29 --- /dev/null +++ b/modelling/data/thrupp-lake-birds/resident/tufted_duck_parameters.csv @@ -0,0 +1,201 @@ 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a/modelling/data/thrupp-lake-birds/resident/tufted_duck_simulated.png b/modelling/data/thrupp-lake-birds/resident/tufted_duck_simulated.png new file mode 100644 index 0000000..63a5b9c Binary files /dev/null and b/modelling/data/thrupp-lake-birds/resident/tufted_duck_simulated.png differ diff --git a/modelling/data/thrupp-lake-birds/resident/tufted_duck_synthesised.csv b/modelling/data/thrupp-lake-birds/resident/tufted_duck_synthesised.csv new file mode 100644 index 0000000..ddfc47a --- /dev/null +++ b/modelling/data/thrupp-lake-birds/resident/tufted_duck_synthesised.csv @@ -0,0 +1,13 @@ +month,observed,simulated_raw,synthesised +1,14,0.4369782,15.961359431624643 +2,12,0.2254677,8.235584749815244 +3,10,0.3390501,12.384371832343762 +4,20,0.44448809999999994,16.23567108652083 +5,9,0.3144188,11.484672413543977 +6,6,0.1719425,6.280487319669769 +7,4,0.08578906,3.133588865442744 +8,5,0.03090288,1.128779365085866 +9,1,0.000548832917,0.02004704000369816 +10,1,0.004207596971,0.15368951494043898 +11,5,0.04469595,1.632594310397918 +12,4,0.16999442,6.209330440261233 diff --git a/modelling/data/thrupp-lake-birds/resident/tufted_duck_synthesised.png b/modelling/data/thrupp-lake-birds/resident/tufted_duck_synthesised.png new file mode 100644 index 0000000..9822639 Binary files /dev/null and b/modelling/data/thrupp-lake-birds/resident/tufted_duck_synthesised.png differ diff --git a/modelling/data/thrupp-lake-birds/seasonal/egyptian_goose_classification.json b/modelling/data/thrupp-lake-birds/seasonal/egyptian_goose_classification.json new file mode 100644 index 0000000..5846bfa --- /dev/null +++ b/modelling/data/thrupp-lake-birds/seasonal/egyptian_goose_classification.json @@ -0,0 +1,49 @@ +{ + "schema_version": "seasonal-classification/v1", + "species": "Egyptian Goose", + "model_family": "seasonal_presence", + "classification": { + "primary_class": "moderate_spring_seasonal_presence", + "timing": "spring", + "season_width": "moderate", + "window_shape": "sharp", + "post_peak_decline": "strong", + "offseason_suppression": "moderate", + "peak_alignment": "late", + "traits": [ + "spring_peak", + "moderate_season", + "sharp_seasonal_window", + "strong_post_peak_decline", + "moderate_offseason_suppression", + "late_peak_alignment" + ], + "confidence": "medium" + }, + "derived_metrics": { + "season_start_month": 1.43, + "season_end_month": 4.725, + "forcing_peak_month": 3.915, + "season_width_months": 3.295, + "season_midpoint_month": 3.0775, + "season_start_label": "January", + "season_end_label": "May", + "forcing_peak_label": "April" + }, + "parameter_evidence": { + "GROWTH": 2.721, + "DECAY": 1.514, + "OOS_DECAY": 3.862, + "POST_PEAK_DECAY": 4.35, + "POST_PEAK_SHARPNESS": 4.498, + "SEASON_START": 1.43, + "SEASON_END": 4.725, + "SHARPNESS": 9.134, + "FORCING_PEAK": 3.915 + }, + "fit": { + "score": 0.131 + }, + "warnings": [], + "summary": "Egyptian Goose is classified as moderate spring seasonal presence. The fitted seasonal window runs from about January to May, with a spring peak around April. The season is moderate, with a sharp active window, strong post-peak decline, and moderate off-season suppression." +} diff --git a/modelling/data/thrupp-lake-birds/seasonal/egyptian_goose_consensus.json b/modelling/data/thrupp-lake-birds/seasonal/egyptian_goose_consensus.json new file mode 100644 index 0000000..f22cc75 --- /dev/null +++ b/modelling/data/thrupp-lake-birds/seasonal/egyptian_goose_consensus.json @@ -0,0 +1,13 @@ +{ + "GROWTH": "2.721", + "DECAY": "1.514", + "OOS_DECAY": "3.862", + "POST_PEAK_DECAY": "4.35", + "POST_PEAK_SHARPNESS": "4.498", + "SEASON_START": "1.43", + "SEASON_END": "4.725", + "SHARPNESS": "9.134", + "FORCING_PEAK": "3.915", + "SCORE": "0.131", + "SPECIES": "Egyptian Goose" +} diff --git a/modelling/data/thrupp-lake-birds/seasonal/egyptian_goose_observed.csv b/modelling/data/thrupp-lake-birds/seasonal/egyptian_goose_observed.csv new file mode 100644 index 0000000..8f6eebe --- /dev/null +++ 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b/modelling/data/thrupp-lake-birds/seasonal/greylag_goose_classification.json @@ -0,0 +1,52 @@ +{ + "schema_version": "seasonal-classification/v1", + "species": "Greylag Goose", + "model_family": "seasonal_presence", + "classification": { + "primary_class": "narrow_spring_seasonal_presence", + "timing": "spring", + "season_width": "narrow", + "window_shape": "sharp", + "post_peak_decline": "strong", + "offseason_suppression": "strong", + "peak_alignment": "early", + "traits": [ + "spring_peak", + "narrow_season", + "sharp_seasonal_window", + "strong_post_peak_decline", + "strong_offseason_suppression", + "early_peak_alignment" + ], + "confidence": "review" + }, + "derived_metrics": { + "season_start_month": 11.27, + "season_end_month": 9.34, + "forcing_peak_month": 4.33, + "season_width_months": -1.93, + "season_midpoint_month": 10.305, + "season_start_label": "November", + "season_end_label": "September", + "forcing_peak_label": "April" + }, + "parameter_evidence": { + "GROWTH": 2.608, + "DECAY": 1.958, + "OOS_DECAY": 4.745, + "POST_PEAK_DECAY": 4.713, + "POST_PEAK_SHARPNESS": 6.812, + "SEASON_START": 11.27, + "SEASON_END": 9.34, + "SHARPNESS": 11.835, + "FORCING_PEAK": 4.33 + }, + "fit": { + "score": 0.348 + }, + "warnings": [ + "Season end is not later than season start; this classifier expects a non-wrapping seasonal model.", + "Forcing peak lies outside the fitted seasonal window." + ], + "summary": "Greylag Goose is classified as narrow spring seasonal presence. The fitted seasonal window runs from about November to September, with a spring peak around April. The season is narrow, with a sharp active window, strong post-peak decline, and strong off-season suppression." +} diff --git a/modelling/data/thrupp-lake-birds/seasonal/greylag_goose_consensus.json b/modelling/data/thrupp-lake-birds/seasonal/greylag_goose_consensus.json new file mode 100644 index 0000000..3a696ab --- /dev/null +++ b/modelling/data/thrupp-lake-birds/seasonal/greylag_goose_consensus.json @@ -0,0 +1,13 @@ +{ + "GROWTH": "2.608", + "DECAY": "1.958", + "OOS_DECAY": "4.745", + "POST_PEAK_DECAY": "4.713", + "POST_PEAK_SHARPNESS": "6.812", + "SEASON_START": "11.27", + "SEASON_END": "9.34", + "SHARPNESS": "11.835", + "FORCING_PEAK": "4.33", + "SCORE": "0.348", + "SPECIES": "Greylag Goose" +} diff --git a/modelling/data/thrupp-lake-birds/seasonal/greylag_goose_observed.csv b/modelling/data/thrupp-lake-birds/seasonal/greylag_goose_observed.csv new file mode 100644 index 0000000..969002b --- /dev/null +++ b/modelling/data/thrupp-lake-birds/seasonal/greylag_goose_observed.csv @@ 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+RungeKutta4,118,11.8,1.99060E-18,0.1,0,0.01,0.00000195806 +RungeKutta4,119,11.9,7.0981E-19,0.1,0,0.01,6.98206E-7 +RungeKutta4,120,12.0,2.48927E-19,0.1,0,0.01,2.44857E-7 +RungeKutta4,121,12.1,8.2850E-20,0.1,0,0.01,8.14955E-8 diff --git a/modelling/data/thrupp-lake-birds/seasonal/greylag_goose_simulated.png b/modelling/data/thrupp-lake-birds/seasonal/greylag_goose_simulated.png new file mode 100644 index 0000000..fbcb70e Binary files /dev/null and b/modelling/data/thrupp-lake-birds/seasonal/greylag_goose_simulated.png differ diff --git a/modelling/data/thrupp-lake-birds/seasonal/greylag_goose_synthesised.csv b/modelling/data/thrupp-lake-birds/seasonal/greylag_goose_synthesised.csv new file mode 100644 index 0000000..b05fb7c --- /dev/null +++ b/modelling/data/thrupp-lake-birds/seasonal/greylag_goose_synthesised.csv @@ -0,0 +1,13 @@ +month,observed,simulated_raw,synthesised +1,1,8.762674012000001e-51,8.998988930195045e-39 +2,2,1.647899072e-45,1.692340201940481e-33 +3,8,2.6289102339000002e-40,2.6998076227581756e-28 +4,19,3.6138156961000004e-35,3.7112743667553654e-23 +5,5,3.5509246510999996e-30,3.646687253622051e-18 +6,4,3.5924674105e-25,3.689350352974874e-13 +7,2,2.9330824015e-20,3.01218281386506e-08 +8,2,1.6128407526e-15,0.0016563364172784251 +9,1,5.7030432e-13,0.5856844903158782 +10,0,1.7087801e-13,0.17548630912184138 +11,0,4.5362156e-13,0.46585498802620606 +12,2,9.00228088e-16,0.0009245057601673393 diff --git a/modelling/data/thrupp-lake-birds/seasonal/greylag_goose_synthesised.png b/modelling/data/thrupp-lake-birds/seasonal/greylag_goose_synthesised.png new file mode 100644 index 0000000..3adb692 Binary files /dev/null and b/modelling/data/thrupp-lake-birds/seasonal/greylag_goose_synthesised.png differ diff --git a/modelling/data/thrupp-lake-birds/seasonal/oystercatcher_classification.json b/modelling/data/thrupp-lake-birds/seasonal/oystercatcher_classification.json new file mode 100644 index 0000000..9dae34f --- /dev/null +++ b/modelling/data/thrupp-lake-birds/seasonal/oystercatcher_classification.json @@ -0,0 +1,49 @@ +{ + "schema_version": "seasonal-classification/v1", + "species": "Oystercatcher", + "model_family": "seasonal_presence", + "classification": { + "primary_class": "narrow_early_spring_seasonal_presence", + "timing": "early_spring", + "season_width": "narrow", + "window_shape": "sharp", + "post_peak_decline": "strong", + "offseason_suppression": "strong", + "peak_alignment": "central", + "traits": [ + "early_spring_peak", + "narrow_season", + "sharp_seasonal_window", + "strong_post_peak_decline", + "strong_offseason_suppression", + "central_peak_alignment" + ], + "confidence": "high" + }, + "derived_metrics": { + "season_start_month": 2.43, + "season_end_month": 4.27, + "forcing_peak_month": 3.3, + "season_width_months": 1.84, + "season_midpoint_month": 3.35, + "season_start_label": "February", + "season_end_label": "April", + "forcing_peak_label": "March" + }, + "parameter_evidence": { + "GROWTH": 3.236, + "DECAY": 1.81, + "OOS_DECAY": 4.999, + "POST_PEAK_DECAY": 4.084, + "POST_PEAK_SHARPNESS": 4.896, + "SEASON_START": 2.43, + "SEASON_END": 4.27, + "SHARPNESS": 8.847, + "FORCING_PEAK": 3.3 + }, + "fit": { + "score": 0.007 + }, + "warnings": [], + "summary": "Oystercatcher is classified as narrow early spring seasonal presence. The fitted seasonal window runs from about February to April, with a early spring peak around March. The season is narrow, with a sharp active window, strong post-peak decline, and strong off-season suppression." +} diff --git a/modelling/data/thrupp-lake-birds/seasonal/oystercatcher_consensus.json b/modelling/data/thrupp-lake-birds/seasonal/oystercatcher_consensus.json new file mode 100644 index 0000000..d526e8f --- /dev/null +++ b/modelling/data/thrupp-lake-birds/seasonal/oystercatcher_consensus.json @@ -0,0 +1,13 @@ +{ + "GROWTH": "3.236", + "DECAY": "1.81", + "OOS_DECAY": "4.999", + "POST_PEAK_DECAY": "4.084", + "POST_PEAK_SHARPNESS": "4.896", + "SEASON_START": "2.43", + "SEASON_END": "4.27", + "SHARPNESS": "8.847", + "FORCING_PEAK": "3.3", + "SCORE": "0.007", + "SPECIES": "Oystercatcher" +} diff --git a/modelling/data/thrupp-lake-birds/seasonal/oystercatcher_observed.csv b/modelling/data/thrupp-lake-birds/seasonal/oystercatcher_observed.csv new file mode 100644 index 0000000..ae4e6bb --- /dev/null +++ b/modelling/data/thrupp-lake-birds/seasonal/oystercatcher_observed.csv @@ -0,0 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"schema_version": "winter-classification/v1", + "species": "Pochard", + "model_family": "winter_presence", + "classification": { + "primary_class": "winter_visitor_with_autumn_arrival_component", + "winter_timing": "core_winter", + "autumn_component": "moderate", + "summer_suppression": "moderate", + "baseline_presence": "low", + "winter_bump_shape": "moderate", + "autumn_bump_shape": "moderate", + "response_dynamics": "slow_arrival_fast_departure", + "traits": [ + "year_wrapping_winter_presence", + "core_winter_winter_peak", + "moderate_autumn_component", + "moderate_summer_suppression", + "low_baseline_presence", + "moderate_winter_bump", + "slow_arrival_fast_departure_response_dynamics" + ], + "confidence": "low" + }, + "derived_metrics": { + "winter_peak_month": 1.755, + "winter_peak_label": "February", + "autumn_peak_month": 11.005, + "autumn_peak_label": "November", + "summer_low_month": 6.565, + "summer_low_label": "July", + "autumn_to_winter_weight_ratio": 0.21861471861471862, + "decay_to_growth_ratio": 3.5847457627118646, + "target_peak_month": 2, + "target_peak_label": "February", + "target_trough_month": 5, + "target_trough_label": "May", + "active_months_ge_0_10": [ + 1, + 2, + 3, + 4, + 10, + 11, + 12 + ], + "monthly_target": { + "January": 0.8862876405166922, + "February": 0.928328532043617, + "March": 0.6471403020542379, + "April": 0.24170135028673018, + "May": 0.0, + "June": 0.0, + "July": 0.0, + "August": 0.0, + "September": 0.0219051630152101, + "October": 0.1685474509097827, + "November": 0.34813098665344727, + "December": 0.6148309231038903 + } + }, + "parameter_evidence": { + "INITIAL_Y": 0.982, + "GROWTH_RATE": 0.708, + "DECAY_RATE": 2.538, + "BASELINE": 0.0, + "WINTER_WEIGHT": 0.924, + "AUTUMN_WEIGHT": 0.202, + "WINTER_PEAK": 1.755, + "AUTUMN_PEAK": 11.005, + "WINTER_WIDTH": 3.214, + "AUTUMN_WIDTH": 3.605, + "SUMMER_DIP": 0.211, + "SUMMER_LOW": 6.565, + "SUMMER_WIDTH": 3.296 + }, + "fit": { + "score": 0.161 + }, + "warnings": [], + "summary": "Pochard is classified as winter visitor with autumn arrival component. The fitted winter component peaks around February, with a moderate autumn component centred around November. The model has low baseline presence and moderate summer suppression centred around July. The fitted response dynamics suggest slow arrival fast departure." +} diff --git a/modelling/data/thrupp-lake-birds/winter/pochard_consensus.json b/modelling/data/thrupp-lake-birds/winter/pochard_consensus.json new file mode 100644 index 0000000..8b17956 --- /dev/null +++ b/modelling/data/thrupp-lake-birds/winter/pochard_consensus.json @@ -0,0 +1,17 @@ +{ + "SCORE": "0.161", + "INITIAL_Y": "0.982", + "GROWTH_RATE": "0.708", + "DECAY_RATE": "2.538", + "BASELINE": "0", + "WINTER_WEIGHT": "0.924", + "AUTUMN_WEIGHT": "0.202", + "WINTER_PEAK": "1.755", + "AUTUMN_PEAK": "11.005", + "WINTER_WIDTH": "3.214", + "AUTUMN_WIDTH": "3.605", + "SUMMER_DIP": "0.211", + "SUMMER_LOW": "6.565", + "SUMMER_WIDTH": "3.296", + "SPECIES": "Pochard" +} diff --git a/modelling/data/thrupp-lake-birds/winter/pochard_observed.csv b/modelling/data/thrupp-lake-birds/winter/pochard_observed.csv new file mode 100644 index 0000000..824365b --- /dev/null +++ b/modelling/data/thrupp-lake-birds/winter/pochard_observed.csv @@ -0,0 +1,13 @@ +month,value +1,6 +2,2 +3,3 +4,0 +5,0 +6,0 +7,0 +8,0 +9,1 +10,0 +11,1 +12,0 diff --git a/modelling/data/thrupp-lake-birds/winter/pochard_parameters.csv b/modelling/data/thrupp-lake-birds/winter/pochard_parameters.csv new file mode 100644 index 0000000..5078d54 --- /dev/null +++ b/modelling/data/thrupp-lake-birds/winter/pochard_parameters.csv @@ -0,0 +1,201 @@ +TIMESTAMP,OBSERVED,SCORE,INITIAL_Y,GROWTH_RATE,DECAY_RATE,BASELINE,WINTER_WEIGHT,AUTUMN_WEIGHT,WINTER_PEAK,AUTUMN_PEAK,WINTER_WIDTH,AUTUMN_WIDTH,SUMMER_DIP,SUMMER_LOW,SUMMER_WIDTH +2026-05-23 20:03:30,pochard_observed.csv,0.2581140557145640398665037036,0.903,1.834,1.754,0.0,1.479,0.6,1.03,11.56,1.167,5.588,0.325,7.61,1.353 +2026-05-23 20:03:30,pochard_observed.csv,0.2763949351914280171293245926,0.797,1.443,2.45,0.0,1.383,0.79,1.57,10.95,1.813,5.235,0.385,7.21,1.167 +2026-05-23 20:03:30,pochard_observed.csv,0.2880336611579429458223148148,0.765,1.738,0.883,0.0,0.934,0.601,2.19,10.04,3.367,1.874,0.035,7.87,2.407 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b/modelling/data/thrupp-lake-birds/winter/pochard_synthesised.csv @@ -0,0 +1,13 @@ +month,observed,simulated_raw,synthesised +1,6,0.9512736,3.8499539608453794 +2,2,0.8871169999999999,3.590302104340192 +3,3,0.6078112,2.4599075774689667 +4,0,0.23241307,0.9406122690661597 +5,0,0.027585212999999997,0.11164169808781978 +6,0,0.0021801246,0.008823307341764187 +7,0,0.00017230179,0.0006973324592117858 +8,0,2.3645173e-05,9.569573616488907e-05 +9,1,0.01895945,0.07673187779304494 +10,0,0.09675435,0.39158008065347355 +11,1,0.22919420000000001,0.9275849956235388 +12,0,0.4268157,1.7273903057606068 diff --git a/modelling/data/thrupp-lake-birds/winter/pochard_synthesised.png b/modelling/data/thrupp-lake-birds/winter/pochard_synthesised.png new file mode 100644 index 0000000..fd2a47b Binary files /dev/null and b/modelling/data/thrupp-lake-birds/winter/pochard_synthesised.png differ diff --git a/modelling/data/thrupp-lake-birds/winter/shoveler_classification.json b/modelling/data/thrupp-lake-birds/winter/shoveler_classification.json new file mode 100644 index 0000000..8c116c8 --- /dev/null +++ b/modelling/data/thrupp-lake-birds/winter/shoveler_classification.json @@ -0,0 +1,82 @@ +{ + "schema_version": "winter-classification/v1", + "species": "Shoveler", + "model_family": "winter_presence", + "classification": { + "primary_class": "winter_visitor_with_weak_autumn_arrival_component", + "winter_timing": "core_winter", + "autumn_component": "weak", + "summer_suppression": "moderate", + "baseline_presence": "low", + "winter_bump_shape": "moderate", + "autumn_bump_shape": "narrow", + "response_dynamics": "faster_departure_than_arrival", + "traits": [ + "year_wrapping_winter_presence", + "core_winter_winter_peak", + "weak_autumn_component", + "moderate_summer_suppression", + "low_baseline_presence", + "moderate_winter_bump", + "faster_departure_than_arrival_response_dynamics" + ], + "confidence": "medium" + }, + "derived_metrics": { + "winter_peak_month": 1.955, + "winter_peak_label": "February", + "autumn_peak_month": 10.595, + "autumn_peak_label": "November", + "summer_low_month": 6.87, + "summer_low_label": "July", + "autumn_to_winter_weight_ratio": 0.16810344827586207, + "decay_to_growth_ratio": 2.4811827956989245, + "target_peak_month": 2, + "target_peak_label": "February", + "target_trough_month": 6, + "target_trough_label": "June", + "active_months_ge_0_10": [ + 1, + 2, + 3, + 4, + 10, + 11, + 12 + ], + "monthly_target": { + "January": 0.8052280536273017, + "February": 0.9303823110598406, + "March": 0.7483728928716504, + "April": 0.36890491218294774, + "May": 0.016129158457228003, + "June": 0.0, + "July": 0.0, + "August": 0.0, + "September": 0.0, + "October": 0.13925586033883958, + "November": 0.2934142915249995, + "December": 0.5229182214954712 + } + }, + "parameter_evidence": { + "INITIAL_Y": 0.996, + "GROWTH_RATE": 0.744, + "DECAY_RATE": 1.846, + "BASELINE": 0.0, + "WINTER_WEIGHT": 0.928, + "AUTUMN_WEIGHT": 0.156, + "WINTER_PEAK": 1.955, + "AUTUMN_PEAK": 10.595, + "WINTER_WIDTH": 2.747, + "AUTUMN_WIDTH": 4.294, + "SUMMER_DIP": 0.24, + "SUMMER_LOW": 6.87, + "SUMMER_WIDTH": 3.002 + }, + "fit": { + "score": 0.097 + }, + "warnings": [], + "summary": "Shoveler is classified as winter visitor with weak autumn arrival component. The fitted winter component peaks around February, with a weak autumn component centred around November. The model has low baseline presence and moderate summer suppression centred around July. The fitted response dynamics suggest faster departure than arrival." +} diff --git a/modelling/data/thrupp-lake-birds/winter/shoveler_consensus.json b/modelling/data/thrupp-lake-birds/winter/shoveler_consensus.json new file mode 100644 index 0000000..c17652a --- /dev/null +++ b/modelling/data/thrupp-lake-birds/winter/shoveler_consensus.json @@ -0,0 +1,17 @@ +{ + "SCORE": "0.097", + "INITIAL_Y": "0.996", + "GROWTH_RATE": "0.744", + "DECAY_RATE": "1.846", + "BASELINE": "0", + "WINTER_WEIGHT": "0.928", + "AUTUMN_WEIGHT": "0.156", + "WINTER_PEAK": "1.955", + "AUTUMN_PEAK": "10.595", + "WINTER_WIDTH": "2.747", + "AUTUMN_WIDTH": "4.294", + "SUMMER_DIP": "0.24", + "SUMMER_LOW": "6.87", + "SUMMER_WIDTH": "3.002", + "SPECIES": "Shoveler" +} diff --git a/modelling/data/thrupp-lake-birds/winter/shoveler_observed.csv b/modelling/data/thrupp-lake-birds/winter/shoveler_observed.csv new file mode 100644 index 0000000..cba4e25 --- /dev/null +++ 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20:05:26,shoveler_observed.csv,0.06675714104892480765381708240,0.985,0.35,2.053,0.0,0.857,0.264,2.16,10.52,1.469,3.12,0.231,5.61,1.308 +2026-05-23 20:05:26,shoveler_observed.csv,0.09475832515976433770897210412,1.23,0.705,2.783,0.0,0.969,0.075,2.28,10.86,3.79,3.998,0.313,7.65,3.712 +2026-05-23 20:05:27,shoveler_observed.csv,0.07910588403679371508475286016,0.797,1.191,2.213,0.0,1.107,0.026,1.97,10.07,3.503,1.589,0.194,7.07,3.961 +2026-05-23 20:05:27,shoveler_observed.csv,0.1491117170969214240055329713,0.957,1.045,2.259,0.0,0.798,0.418,1.85,10.82,2.099,4.7,0.389,5.56,2.458 +2026-05-23 20:05:27,shoveler_observed.csv,0.2361087499734300821855631141,0.839,1.982,2.265,0.0,0.986,0.187,1.4,10.92,0.949,3.44,0.017,7.42,3.234 +2026-05-23 20:05:28,shoveler_observed.csv,0.1171081667234098870052361300,0.998,1.747,1.519,0.0,1.166,0.239,1.16,11.42,3.219,5.037,0.066,7.03,4.149 diff --git a/modelling/data/thrupp-lake-birds/winter/shoveler_simulated.csv 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a/modelling/data/thrupp-lake-birds/winter/shoveler_synthesised.csv b/modelling/data/thrupp-lake-birds/winter/shoveler_synthesised.csv new file mode 100644 index 0000000..e0e0eb1 --- /dev/null +++ b/modelling/data/thrupp-lake-birds/winter/shoveler_synthesised.csv @@ -0,0 +1,13 @@ +month,observed,simulated_raw,synthesised +1,7,0.9343764,5.952134153459516 +2,6,0.9046526,5.762788569441556 +3,3,0.7345292000000001,4.679074019884595 +4,4,0.3976518,2.5331085630637213 +5,1,0.10005834,0.6373883831531537 +6,0,0.015808515000000002,0.1007028880941097 +7,0,0.0024957182,0.01589814290646736 +8,0,0.0003940018,0.002509857451776956 +9,0,0.010441226000000001,0.06651235827295028 +10,0,0.07860219,0.5007091142667067 +11,3,0.1958896,1.2478495587725924 +12,0,0.3719948,2.36966917613645 diff --git a/modelling/data/thrupp-lake-birds/winter/shoveler_synthesised.png b/modelling/data/thrupp-lake-birds/winter/shoveler_synthesised.png new file mode 100644 index 0000000..844e2c4 Binary files /dev/null and b/modelling/data/thrupp-lake-birds/winter/shoveler_synthesised.png differ diff --git a/modelling/src/feature-matrix.py b/modelling/src/feature-matrix.py index 9957fad..81a0a24 100644 --- a/modelling/src/feature-matrix.py +++ b/modelling/src/feature-matrix.py @@ -76,6 +76,8 @@ def main() -> None: parser.add_argument("-ssu", "--similarity-summary", type=Path, help="Species similarity summary output file path") parser.add_argument("-hm", "--heatmap", type=Path, required=True, help="Species similarity summary heatmap image file path") + parser.add_argument("-nc", "--number-of-clusters", type=int, default=8, + help="Number of clusters to generate in the cluster analysis") parser.add_argument("-cl", "--clusters", type=Path, required=True, help="Cluster analysis output file path") parser.add_argument("-csu", "--cluster-summary", type=Path, required=True, help="Cluster analysis summary output file path") @@ -115,7 +117,8 @@ def main() -> None: print_message(f"Species similarity heatmap written to {Path(args.heatmap).name}") # Extract the species similarity clusters - clusters = extract_species_similarity_clusters(similarity, feature_matrix, args.clusters, n_clusters=8) + clusters = extract_species_similarity_clusters(similarity, feature_matrix, args.clusters, + n_clusters=args.number_of_clusters) print_message(f"Species similarity cluster analysis written to {Path(args.clusters).name}") if args.cluster_summary: save_cluster_summary(clusters, args.cluster_summary) diff --git a/modelling/src/process-yil-files.py b/modelling/src/process-yil-files.py index cb0be57..4ac3660 100644 --- a/modelling/src/process-yil-files.py +++ b/modelling/src/process-yil-files.py @@ -7,8 +7,9 @@ FALSE_VALUES = ["false", "no", "n", "0"] SUFFIXES = [ - "_abingdon.xlsx", - "_abingdon_butterfly_flight_period.xlsx" + "_abingdon", + "_abingdon_butterfly_flight_period", + "_thrupp_lake" ] @@ -23,9 +24,11 @@ def rename_year_in_life_files(folder_path: str, pattern: str, new_suffix: str) - directory = Path(folder_path) for filepath in directory.glob(pattern): # Extract species (equivalent to bash parameter expansion) - filename = filepath.name + filename = filepath.stem species = filename.removeprefix("year_in_the_life_") + print(species) for suffix in SUFFIXES: + print(f"Removing {suffix}") species = species.removesuffix(suffix) # Create the new file name and path @@ -89,7 +92,7 @@ def main(): parser = argparse.ArgumentParser() parser.add_argument("-i", "--input", required=True, help="Path to the folder containing the 'Year In The Life' XLSX files") - parser.add_argument("-xp", "--xlsx-pattern", default="year_in_the_life_*.xlsx", help="XLSX file pattern") + parser.add_argument("-xp", "--xlsx-pattern", default="*.xlsx", help="XLSX file pattern") parser.add_argument("-s", "--suffix", default="_observed", help="CSV file name suffix") parser.add_argument("-d", "--delete", type=str.lower, choices=TRUE_VALUES + FALSE_VALUES, help="Delete XLSX files after processing")