diff --git a/modelling/data/thrupp-lake-birds/analysis/activity_heatmap.png b/modelling/data/thrupp-lake-birds/analysis/activity_heatmap.png new file mode 100644 index 0000000..f8ee62c Binary files /dev/null and b/modelling/data/thrupp-lake-birds/analysis/activity_heatmap.png differ diff --git a/modelling/data/thrupp-lake-birds/analysis/calendar_activity.json b/modelling/data/thrupp-lake-birds/analysis/calendar_activity.json new file mode 100644 index 0000000..a99ff84 --- /dev/null +++ b/modelling/data/thrupp-lake-birds/analysis/calendar_activity.json @@ -0,0 +1,441 @@ +{ + "schema_version": "seasonal-ecological-calendar-activity/v1", + "source_cluster_schema_version": "seasonal-ecological-calendar-clusters/v1", + "n_clusters": 5, + "normalisation": { + "method": "species_max", + "description": "Each species is normalised to its own maximum synthesised value before cluster-level monthly aggregation.", + "value_column": "synthesised" + }, + "clusters": [ + { + "cluster_id": 1, + "calendar_label": "Egret neighbourhood", + "description": "Single-species cluster containing Egret, mainly representing resident with spring persistence and summer suppression. Detectability peaks around June and and is lowest around September. The shared pattern includes weak baseline presence, strong summer suppression, weak autumn component, and rapid decline biased response dynamics. Its defining traits include resident detectability pattern, weak baseline presence, and late spring early summer detectability peak. Compared with the full species set, fit score is higher than the whole-set average and peak month is higher than the whole-set average.", + "n_species": 1, + "species": [ + "Egret" + ], + "monthly_activity": [ + { + "month": 1, + "month_name": "January", + "mean_activity": 0.393717, + "n_species_contributing": 1 + }, + { + "month": 2, + "month_name": "February", + "mean_activity": 0.416956, + "n_species_contributing": 1 + }, + { + "month": 3, + "month_name": "March", + "mean_activity": 0.416598, + "n_species_contributing": 1 + }, + { + "month": 4, + "month_name": "April", + "mean_activity": 0.419177, + "n_species_contributing": 1 + }, + { + "month": 5, + "month_name": "May", + "mean_activity": 0.59773, + "n_species_contributing": 1 + }, + { + "month": 6, + "month_name": "June", + "mean_activity": 1.0, + "n_species_contributing": 1 + }, + { + "month": 7, + "month_name": "July", + "mean_activity": 0.724159, + "n_species_contributing": 1 + }, + { + "month": 8, + "month_name": "August", + "mean_activity": 0.230474, + "n_species_contributing": 1 + }, + { + "month": 9, + "month_name": "September", + "mean_activity": 0.102538, + "n_species_contributing": 1 + }, + { + "month": 10, + "month_name": "October", + "mean_activity": 0.11278, + "n_species_contributing": 1 + }, + { + "month": 11, + "month_name": "November", + "mean_activity": 0.130945, + "n_species_contributing": 1 + }, + { + "month": 12, + "month_name": "December", + "mean_activity": 0.307803, + "n_species_contributing": 1 + } + ] + }, + { + "cluster_id": 2, + "calendar_label": "Egyptian Goose neighbourhood", + "description": "Single-species cluster containing Egyptian Goose, mainly representing moderate spring seasonal presence. The fitted active window runs roughly from January to May, with a mean peak around April, and and an average width of 3.3 months. It is characterised by moderate season and sharp active window. Its defining traits include spring peak, moderate season, and sharp seasonal window. Compared with the full species set, season start month is lower than the whole-set average and season end month is higher than the whole-set average.", + "n_species": 1, + "species": [ + "Egyptian Goose" + ], + "monthly_activity": [ + { + "month": 1, + "month_name": "January", + "mean_activity": 0.116621, + "n_species_contributing": 1 + }, + { + "month": 2, + "month_name": "February", + "mean_activity": 0.6738, + "n_species_contributing": 1 + }, + { + "month": 3, + "month_name": "March", + "mean_activity": 1.0, + "n_species_contributing": 1 + }, + { + "month": 4, + "month_name": "April", + "mean_activity": 0.84981, + "n_species_contributing": 1 + }, + { + "month": 5, + "month_name": "May", + "mean_activity": 0.027143, + "n_species_contributing": 1 + }, + { + "month": 6, + "month_name": "June", + "mean_activity": 5e-06, + "n_species_contributing": 1 + }, + { + "month": 7, + "month_name": "July", + "mean_activity": 0.0, + "n_species_contributing": 1 + }, + { + "month": 8, + "month_name": "August", + "mean_activity": 0.0, + "n_species_contributing": 1 + }, + { + "month": 9, + "month_name": "September", + "mean_activity": 0.0, + "n_species_contributing": 1 + }, + { + "month": 10, + "month_name": "October", + "mean_activity": 0.0, + "n_species_contributing": 1 + }, + { + "month": 11, + "month_name": "November", + "mean_activity": 0.0, + "n_species_contributing": 1 + }, + { + "month": 12, + "month_name": "December", + "mean_activity": 0.0, + "n_species_contributing": 1 + } + ] + }, + { + "cluster_id": 3, + "calendar_label": "Resident With Summer Detectability Collapse", + "description": "Cluster of 14 species, mainly representing resident with summer detectability collapse. Detectability peaks around April and and is lowest around October. The shared pattern includes weak baseline presence, moderate summer suppression, weak autumn component, and rapid decline biased response dynamics. Common high-support traits include resident detectability pattern, weak spring carryover, and moderate summer suppression.", + "n_species": 14, + "species": [ + "Gadwall", + "Grey Heron", + "Moorhen", + "Great Crested Grebe", + "Canada Goose", + "Cormorant", + "Mute Swan", + "Robin", + "Greylag Goose", + "Tufted Duck", + "Coot", + "Black Headed Gull", + "Herring Gull", + "Mallard" + ], + "monthly_activity": [ + { + "month": 1, + "month_name": "January", + "mean_activity": 0.81491, + "n_species_contributing": 14 + }, + { + "month": 2, + "month_name": "February", + "mean_activity": 0.540296, + "n_species_contributing": 14 + }, + { + "month": 3, + "month_name": "March", + "mean_activity": 0.715115, + "n_species_contributing": 14 + }, + { + "month": 4, + "month_name": "April", + "mean_activity": 0.836126, + "n_species_contributing": 14 + }, + { + "month": 5, + "month_name": "May", + "mean_activity": 0.582005, + "n_species_contributing": 14 + }, + { + "month": 6, + "month_name": "June", + "mean_activity": 0.340775, + "n_species_contributing": 14 + }, + { + "month": 7, + "month_name": "July", + "mean_activity": 0.201882, + "n_species_contributing": 14 + }, + { + "month": 8, + "month_name": "August", + "mean_activity": 0.139093, + "n_species_contributing": 14 + }, + { + "month": 9, + "month_name": "September", + "mean_activity": 0.089702, + "n_species_contributing": 14 + }, + { + "month": 10, + "month_name": "October", + "mean_activity": 0.076192, + "n_species_contributing": 14 + }, + { + "month": 11, + "month_name": "November", + "mean_activity": 0.134063, + "n_species_contributing": 14 + }, + { + "month": 12, + "month_name": "December", + "mean_activity": 0.346784, + "n_species_contributing": 14 + } + ] + }, + { + "cluster_id": 4, + "calendar_label": "Oystercatcher neighbourhood", + "description": "Single-species cluster containing Oystercatcher, mainly representing narrow early spring seasonal presence. The fitted active window runs roughly from February to April, with a mean peak around March, and and an average width of 1.8 months. It is characterised by narrow season and sharp active window. Its defining traits include early spring peak, narrow season, and sharp seasonal window. Compared with the full species set, season start month is higher than the whole-set average and season end month is lower than the whole-set average.", + "n_species": 1, + "species": [ + "Oystercatcher" + ], + "monthly_activity": [ + { + "month": 1, + "month_name": "January", + "mean_activity": 0.000203, + "n_species_contributing": 1 + }, + { + "month": 2, + "month_name": "February", + "mean_activity": 0.212025, + "n_species_contributing": 1 + }, + { + "month": 3, + "month_name": "March", + "mean_activity": 1.0, + "n_species_contributing": 1 + }, + { + "month": 4, + "month_name": "April", + "mean_activity": 0.363604, + "n_species_contributing": 1 + }, + { + "month": 5, + "month_name": "May", + "mean_activity": 0.000335, + "n_species_contributing": 1 + }, + { + "month": 6, + "month_name": "June", + "mean_activity": 0.0, + "n_species_contributing": 1 + }, + { + "month": 7, + "month_name": "July", + "mean_activity": 0.0, + "n_species_contributing": 1 + }, + { + "month": 8, + "month_name": "August", + "mean_activity": 0.0, + "n_species_contributing": 1 + }, + { + "month": 9, + "month_name": "September", + "mean_activity": 0.0, + "n_species_contributing": 1 + }, + { + "month": 10, + "month_name": "October", + "mean_activity": 0.0, + "n_species_contributing": 1 + }, + { + "month": 11, + "month_name": "November", + "mean_activity": 0.0, + "n_species_contributing": 1 + }, + { + "month": 12, + "month_name": "December", + "mean_activity": 0.0, + "n_species_contributing": 1 + } + ] + }, + { + "cluster_id": 5, + "calendar_label": "Winter Visitor With Autumn Arrival Component", + "description": "Cluster of 2 species, mainly representing winter visitor with autumn arrival component. The defining pattern is a winter peak around February, a moderate autumn component, moderate summer suppression, and slow arrival fast departure response dynamics. Common high-support traits include year wrapping winter presence, core winter winter peak, and moderate summer suppression. Compared with the full species set, trough month is lower than the whole-set average and autumn to winter weight ratio is higher than the whole-set average.", + "n_species": 2, + "species": [ + "Pochard", + "Shoveler" + ], + "monthly_activity": [ + { + "month": 1, + "month_name": "January", + "mean_activity": 1.0, + "n_species_contributing": 2 + }, + { + "month": 2, + "month_name": "February", + "mean_activity": 0.950373, + "n_species_contributing": 2 + }, + { + "month": 3, + "month_name": "March", + "mean_activity": 0.712531, + "n_species_contributing": 2 + }, + { + "month": 4, + "month_name": "April", + "mean_activity": 0.334949, + "n_species_contributing": 2 + }, + { + "month": 5, + "month_name": "May", + "mean_activity": 0.068042, + "n_species_contributing": 2 + }, + { + "month": 6, + "month_name": "June", + "mean_activity": 0.009605, + "n_species_contributing": 2 + }, + { + "month": 7, + "month_name": "July", + "mean_activity": 0.001426, + "n_species_contributing": 2 + }, + { + "month": 8, + "month_name": "August", + "mean_activity": 0.000223, + "n_species_contributing": 2 + }, + { + "month": 9, + "month_name": "September", + "mean_activity": 0.015553, + "n_species_contributing": 2 + }, + { + "month": 10, + "month_name": "October", + "mean_activity": 0.092916, + "n_species_contributing": 2 + }, + { + "month": 11, + "month_name": "November", + "mean_activity": 0.225291, + "n_species_contributing": 2 + }, + { + "month": 12, + "month_name": "December", + "mean_activity": 0.4234, + "n_species_contributing": 2 + } + ] + } + ] +} diff --git a/modelling/data/thrupp-lake-birds/analysis/cluster_analysis.json b/modelling/data/thrupp-lake-birds/analysis/cluster_analysis.json new file mode 100644 index 0000000..5d77a82 --- /dev/null +++ b/modelling/data/thrupp-lake-birds/analysis/cluster_analysis.json @@ -0,0 +1,2084 @@ +{ + "schema_version": "species-similarity-clusters/v2", + "created_utc": "2026-05-24T06:54:35.630835+00:00", + "source_similarity_schema_version": "species-similarity/v1", + "source_feature_schema_version": "species-feature-table/v1", + "n_species": 19, + "n_clusters": 5, + "method": { + "description": "Hierarchical clustering over pairwise species similarity, followed by cluster-level summaries from the species feature matrix.", + "linkage_method": "average", + "cluster_cut": { + "criterion": "maxclust", + "n_clusters_requested": 5 + }, + "distance_definition": "distance = 1 - similarity", + "cluster_caveat": "Clusters should be interpreted as exploratory seasonal assemblages rather than fixed ecological categories." + }, + "species_order": [ + "Egret", + "Egyptian Goose", + "Gadwall", + "Grey Heron", + "Moorhen", + "Great Crested Grebe", + "Canada Goose", + "Cormorant", + "Mute Swan", + "Robin", + "Greylag Goose", + "Tufted Duck", + "Coot", + "Black Headed Gull", + "Herring Gull", + "Mallard", + "Oystercatcher", + "Pochard", + "Shoveler" + ], + "linkage": { + "format": "scipy.cluster.hierarchy.linkage", + "columns": [ + "left_child", + "right_child", + "distance", + "n_leaves" + ], + "node_id_convention": "Leaf nodes are 0..n_species-1 in species_input_order; internal nodes are n_species..2*n_species-2 in linkage row order.", + "species_input_order": [ + "Black Headed Gull", + "Canada Goose", + "Coot", + "Cormorant", + "Egret", + "Gadwall", + "Great Crested Grebe", + "Grey Heron", + "Greylag Goose", + "Herring Gull", + "Mallard", + "Moorhen", + "Mute Swan", + "Robin", + "Tufted Duck", + "Egyptian Goose", + "Oystercatcher", + "Pochard", + "Shoveler" + ], + "leaf_order_indices": [ + 4, + 15, + 5, + 7, + 11, + 6, + 1, + 3, + 12, + 13, + 8, + 14, + 2, + 0, + 9, + 10, + 16, + 17, + 18 + ], + "leaf_order_species": [ + "Egret", + "Egyptian Goose", + "Gadwall", + "Grey Heron", + "Moorhen", + "Great Crested Grebe", + "Canada Goose", + "Cormorant", + "Mute Swan", + "Robin", + "Greylag Goose", + "Tufted Duck", + "Coot", + "Black Headed Gull", + "Herring Gull", + "Mallard", + "Oystercatcher", + "Pochard", + "Shoveler" + ], + "matrix": [ + [ + 7, + 11, + 0.041916, + 2 + ], + [ + 9, + 10, + 0.046194, + 2 + ], + [ + 0, + 20, + 0.074055, + 3 + ], + [ + 3, + 12, + 0.074737, + 2 + ], + [ + 2, + 21, + 0.111643, + 4 + ], + [ + 1, + 22, + 0.125962, + 3 + ], + [ + 14, + 23, + 0.129125, + 5 + ], + [ + 6, + 24, + 0.13772, + 4 + ], + [ + 8, + 25, + 0.145748, + 6 + ], + [ + 5, + 19, + 0.196069, + 3 + ], + [ + 13, + 27, + 0.206009, + 7 + ], + [ + 26, + 29, + 0.230218, + 11 + ], + [ + 17, + 18, + 0.231272, + 2 + ], + [ + 28, + 30, + 0.311201, + 14 + ], + [ + 15, + 32, + 0.36527, + 15 + ], + [ + 4, + 33, + 0.409987, + 16 + ], + [ + 16, + 31, + 0.485781, + 3 + ], + [ + 34, + 35, + 0.576063, + 19 + ] + ], + "merges": [ + { + "node_id": 19, + "left_child": 7, + "right_child": 11, + "distance": 0.041916, + "n_leaves": 2, + "species": [ + "Grey Heron", + "Moorhen" + ], + "left_species": [ + "Grey Heron" + ], + "right_species": [ + "Moorhen" + ] + }, + { + "node_id": 20, + "left_child": 9, + "right_child": 10, + "distance": 0.046194, + "n_leaves": 2, + "species": [ + "Herring Gull", + "Mallard" + ], + "left_species": [ + "Herring Gull" + ], + "right_species": [ + "Mallard" + ] + }, + { + "node_id": 21, + "left_child": 0, + "right_child": 20, + "distance": 0.074055, + "n_leaves": 3, + "species": [ + "Black Headed Gull", + "Herring Gull", + "Mallard" + ], + "left_species": [ + "Black Headed Gull" + ], + "right_species": [ + "Herring Gull", + "Mallard" + ] + }, + { + "node_id": 22, + "left_child": 3, + "right_child": 12, + "distance": 0.074737, + "n_leaves": 2, + "species": [ + "Cormorant", + "Mute Swan" + ], + "left_species": [ + "Cormorant" + ], + "right_species": [ + "Mute Swan" + ] + }, + { + "node_id": 23, + "left_child": 2, + "right_child": 21, + "distance": 0.111643, + "n_leaves": 4, + "species": [ + "Coot", + "Black Headed Gull", + "Herring Gull", + "Mallard" + ], + "left_species": [ + "Coot" + ], + "right_species": [ + "Black Headed Gull", + "Herring Gull", + "Mallard" + ] + }, + { + "node_id": 24, + "left_child": 1, + "right_child": 22, + "distance": 0.125962, + "n_leaves": 3, + "species": [ + "Canada Goose", + "Cormorant", + "Mute Swan" + ], + "left_species": [ + "Canada Goose" + ], + "right_species": [ + "Cormorant", + "Mute Swan" + ] + }, + { + "node_id": 25, + "left_child": 14, + "right_child": 23, + "distance": 0.129125, + "n_leaves": 5, + "species": [ + "Tufted Duck", + "Coot", + "Black Headed Gull", + "Herring Gull", + "Mallard" + ], + "left_species": [ + "Tufted Duck" + ], + "right_species": [ + "Coot", + "Black Headed Gull", + "Herring Gull", + "Mallard" + ] + }, + { + "node_id": 26, + "left_child": 6, + "right_child": 24, + "distance": 0.13772, + "n_leaves": 4, + "species": [ + "Great Crested Grebe", + "Canada Goose", + "Cormorant", + "Mute Swan" + ], + "left_species": [ + "Great Crested Grebe" + ], + "right_species": [ + "Canada Goose", + "Cormorant", + "Mute Swan" + ] + }, + { + "node_id": 27, + "left_child": 8, + "right_child": 25, + "distance": 0.145748, + "n_leaves": 6, + "species": [ + "Greylag Goose", + "Tufted Duck", + "Coot", + "Black Headed Gull", + "Herring Gull", + "Mallard" + ], + "left_species": [ + "Greylag Goose" + ], + "right_species": [ + "Tufted Duck", + "Coot", + "Black Headed Gull", + "Herring Gull", + "Mallard" + ] + }, + { + "node_id": 28, + "left_child": 5, + "right_child": 19, + "distance": 0.196069, + "n_leaves": 3, + "species": [ + "Gadwall", + "Grey Heron", + "Moorhen" + ], + "left_species": [ + "Gadwall" + ], + "right_species": [ + "Grey Heron", + "Moorhen" + ] + }, + { + "node_id": 29, + "left_child": 13, + "right_child": 27, + "distance": 0.206009, + "n_leaves": 7, + "species": [ + "Robin", + "Greylag Goose", + "Tufted Duck", + "Coot", + "Black Headed Gull", + "Herring Gull", + "Mallard" + ], + "left_species": [ + "Robin" + ], + "right_species": [ + "Greylag Goose", + "Tufted Duck", + "Coot", + "Black Headed Gull", + "Herring Gull", + "Mallard" + ] + }, + { + "node_id": 30, + "left_child": 26, + "right_child": 29, + "distance": 0.230218, + "n_leaves": 11, + "species": [ + "Great Crested Grebe", + "Canada Goose", + "Cormorant", + "Mute Swan", + "Robin", + "Greylag Goose", + "Tufted Duck", + "Coot", + "Black Headed Gull", + "Herring Gull", + "Mallard" + ], + "left_species": [ + "Great Crested Grebe", + "Canada Goose", + "Cormorant", + "Mute Swan" + ], + "right_species": [ + "Robin", + "Greylag Goose", + "Tufted Duck", + "Coot", + "Black Headed Gull", + "Herring Gull", + "Mallard" + ] + }, + { + "node_id": 31, + "left_child": 17, + "right_child": 18, + "distance": 0.231272, + "n_leaves": 2, + "species": [ + "Pochard", + "Shoveler" + ], + "left_species": [ + "Pochard" + ], + "right_species": [ + "Shoveler" + ] + }, + { + "node_id": 32, + "left_child": 28, + "right_child": 30, + "distance": 0.311201, + "n_leaves": 14, + "species": [ + "Gadwall", + "Grey Heron", + "Moorhen", + "Great Crested Grebe", + "Canada Goose", + "Cormorant", + "Mute Swan", + "Robin", + "Greylag Goose", + "Tufted Duck", + "Coot", + "Black Headed Gull", + "Herring Gull", + "Mallard" + ], + "left_species": [ + "Gadwall", + "Grey Heron", + "Moorhen" + ], + "right_species": [ + "Great Crested Grebe", + "Canada Goose", + "Cormorant", + "Mute Swan", + "Robin", + "Greylag Goose", + "Tufted Duck", + "Coot", + "Black Headed Gull", + "Herring Gull", + "Mallard" + ] + }, + { + "node_id": 33, + "left_child": 15, + "right_child": 32, + "distance": 0.36527, + "n_leaves": 15, + "species": [ + "Egyptian Goose", + "Gadwall", + "Grey Heron", + "Moorhen", + "Great Crested Grebe", + "Canada Goose", + "Cormorant", + "Mute Swan", + "Robin", + "Greylag Goose", + "Tufted Duck", + "Coot", + "Black Headed Gull", + "Herring Gull", + "Mallard" + ], + "left_species": [ + "Egyptian Goose" + ], + "right_species": [ + "Gadwall", + "Grey Heron", + "Moorhen", + "Great Crested Grebe", + "Canada Goose", + "Cormorant", + "Mute Swan", + "Robin", + "Greylag Goose", + "Tufted Duck", + "Coot", + "Black Headed Gull", + "Herring Gull", + "Mallard" + ] + }, + { + "node_id": 34, + "left_child": 4, + "right_child": 33, + "distance": 0.409987, + "n_leaves": 16, + "species": [ + "Egret", + "Egyptian Goose", + "Gadwall", + "Grey Heron", + "Moorhen", + "Great Crested Grebe", + "Canada Goose", + "Cormorant", + "Mute Swan", + "Robin", + "Greylag Goose", + "Tufted Duck", + "Coot", + "Black Headed Gull", + "Herring Gull", + "Mallard" + ], + "left_species": [ + "Egret" + ], + "right_species": [ + "Egyptian Goose", + "Gadwall", + "Grey Heron", + "Moorhen", + "Great Crested Grebe", + "Canada Goose", + "Cormorant", + "Mute Swan", + "Robin", + "Greylag Goose", + "Tufted Duck", + "Coot", + "Black Headed Gull", + "Herring Gull", + "Mallard" + ] + }, + { + "node_id": 35, + "left_child": 16, + "right_child": 31, + "distance": 0.485781, + "n_leaves": 3, + "species": [ + "Oystercatcher", + "Pochard", + "Shoveler" + ], + "left_species": [ + "Oystercatcher" + ], + "right_species": [ + "Pochard", + "Shoveler" + ] + }, + { + "node_id": 36, + "left_child": 34, + "right_child": 35, + "distance": 0.576063, + "n_leaves": 19, + "species": [ + "Egret", + "Egyptian Goose", + "Gadwall", + "Grey Heron", + "Moorhen", + "Great Crested Grebe", + "Canada Goose", + "Cormorant", + "Mute Swan", + "Robin", + "Greylag Goose", + "Tufted Duck", + "Coot", + "Black Headed Gull", + "Herring Gull", + "Mallard", + "Oystercatcher", + "Pochard", + "Shoveler" + ], + "left_species": [ + "Egret", + "Egyptian Goose", + "Gadwall", + "Grey Heron", + "Moorhen", + "Great Crested Grebe", + "Canada Goose", + "Cormorant", + "Mute Swan", + "Robin", + "Greylag Goose", + "Tufted Duck", + "Coot", + "Black Headed Gull", + "Herring Gull", + "Mallard" + ], + "right_species": [ + "Oystercatcher", + "Pochard", + "Shoveler" + ] + } + ] + }, + "species_cluster_ids": { + "Black Headed Gull": 3, + "Canada Goose": 3, + "Coot": 3, + "Cormorant": 3, + "Egret": 1, + "Gadwall": 3, + "Great Crested Grebe": 3, + "Grey Heron": 3, + "Greylag Goose": 3, + "Herring Gull": 3, + "Mallard": 3, + "Moorhen": 3, + "Mute Swan": 3, + "Robin": 3, + "Tufted Duck": 3, + "Egyptian Goose": 2, + "Oystercatcher": 4, + "Pochard": 5, + "Shoveler": 5 + }, + "clusters": [ + { + "cluster_id": 1, + "n_species": 1, + "species": [ + "Egret" + ], + "description": "Single-species cluster containing Egret, mainly representing resident with spring persistence and summer suppression. Detectability peaks around June and and is lowest around September. The shared pattern includes weak baseline presence, strong summer suppression, weak autumn component, and rapid decline biased response dynamics. Its defining traits include resident detectability pattern, weak baseline presence, and late spring early summer detectability peak. Compared with the full species set, fit score is higher than the whole-set average and peak month is higher than the whole-set average.", + "dominant_model_family": "resident_detectability", + "dominant_primary_class": "resident_with_spring_persistence_and_summer_suppression", + "numeric_summary": { + "peak_month": { + "n": 1, + "mean": 6.0, + "min": 6.0, + "max": 6.0 + }, + "trough_month": { + "n": 1, + "mean": 9.0, + "min": 9.0, + "max": 9.0 + }, + "target_mean_value": { + "n": 1, + "mean": 0.243279, + "min": 0.243279, + "max": 0.243279 + }, + "target_amplitude": { + "n": 1, + "mean": 0.548058, + "min": 0.548058, + "max": 0.548058 + }, + "baseline_to_peak_ratio": { + "n": 1, + "mean": 0.08599, + "min": 0.08599, + "max": 0.08599 + }, + "autumn_to_winter_weight_ratio": { + "n": 1, + "mean": 0.054299, + "min": 0.054299, + "max": 0.054299 + }, + "year_end_to_winter_weight_ratio": { + "n": 1, + "mean": 0.429864, + "min": 0.429864, + "max": 0.429864 + }, + "decay_to_growth_ratio": { + "n": 1, + "mean": 1.650399, + "min": 1.650399, + "max": 1.650399 + }, + "fit_score": { + "n": 1, + "mean": 0.628, + "min": 0.628, + "max": 0.628 + } + }, + "categorical_summary": { + "model_family": { + "dominant": "resident_detectability", + "dominant_count": 1, + "dominant_fraction": 1.0, + "values": [ + { + "value": "resident_detectability", + "count": 1, + "fraction": 1.0 + } + ] + }, + "primary_class": { + "dominant": "resident_with_spring_persistence_and_summer_suppression", + "dominant_count": 1, + "dominant_fraction": 1.0, + "values": [ + { + "value": "resident_with_spring_persistence_and_summer_suppression", + "count": 1, + "fraction": 1.0 + } + ] + }, + "confidence": { + "dominant": "low", + "dominant_count": 1, + "dominant_fraction": 1.0, + "values": [ + { + "value": "low", + "count": 1, + "fraction": 1.0 + } + ] + }, + "baseline_presence": { + "dominant": "weak", + "dominant_count": 1, + "dominant_fraction": 1.0, + "values": [ + { + "value": "weak", + "count": 1, + "fraction": 1.0 + } + ] + }, + "timing": { + "dominant": "late_spring_early_summer", + "dominant_count": 1, + "dominant_fraction": 1.0, + "values": [ + { + "value": "late_spring_early_summer", + "count": 1, + "fraction": 1.0 + } + ] + }, + "summer_suppression": { + "dominant": "strong", + "dominant_count": 1, + "dominant_fraction": 1.0, + "values": [ + { + "value": "strong", + "count": 1, + "fraction": 1.0 + } + ] + }, + "autumn_component": { + "dominant": "weak", + "dominant_count": 1, + "dominant_fraction": 1.0, + "values": [ + { + "value": "weak", + "count": 1, + "fraction": 1.0 + } + ] + }, + "response_dynamics": { + "dominant": "rapid_decline_biased", + "dominant_count": 1, + "dominant_fraction": 1.0, + "values": [ + { + "value": "rapid_decline_biased", + "count": 1, + "fraction": 1.0 + } + ] + } + }, + "common_traits": [ + { + "trait": "resident_detectability_pattern", + "count": 1, + "fraction": 1.0 + }, + { + "trait": "weak_baseline_presence", + "count": 1, + "fraction": 1.0 + }, + { + "trait": "late_spring_early_summer_detectability_peak", + "count": 1, + "fraction": 1.0 + }, + { + "trait": "autumn_detectability_trough", + "count": 1, + "fraction": 1.0 + }, + { + "trait": "moderate_spring_carryover", + "count": 1, + "fraction": 1.0 + }, + { + "trait": "strong_summer_suppression", + "count": 1, + "fraction": 1.0 + }, + { + "trait": "strong_summer_decay_acceleration", + "count": 1, + "fraction": 1.0 + }, + { + "trait": "strong_pre_summer_retention", + "count": 1, + "fraction": 1.0 + }, + { + "trait": "weak_autumn_component", + "count": 1, + "fraction": 1.0 + }, + { + "trait": "meaningful_year_end_component", + "count": 1, + "fraction": 1.0 + } + ], + "distinguishing_numeric_features": [ + { + "feature": "fit_score", + "cluster_mean": 0.628, + "global_mean": 0.221526, + "difference": 0.406474, + "scaled_difference": 0.654548, + "direction": "higher" + }, + { + "feature": "peak_month", + "cluster_mean": 6.0, + "global_mean": 3.484948, + "difference": 2.515052, + "scaled_difference": 0.628763, + "direction": "higher" + }, + { + "feature": "year_end_to_winter_weight_ratio", + "cluster_mean": 0.429864, + "global_mean": 0.368498, + "difference": 0.061366, + "scaled_difference": 0.253597, + "direction": "higher" + }, + { + "feature": "baseline_to_peak_ratio", + "cluster_mean": 0.08599, + "global_mean": 0.143562, + "difference": -0.057572, + "scaled_difference": -0.20315, + "direction": "lower" + }, + { + "feature": "target_mean_value", + "cluster_mean": 0.243279, + "global_mean": 0.212189, + "difference": 0.03109, + "scaled_difference": 0.138579, + "direction": "higher" + }, + { + "feature": "autumn_to_winter_weight_ratio", + "cluster_mean": 0.054299, + "global_mean": 0.07231, + "difference": -0.018011, + "scaled_difference": -0.102299, + "direction": "lower" + }, + { + "feature": "trough_month", + "cluster_mean": 9.0, + "global_mean": 9.206867, + "difference": -0.206867, + "scaled_difference": -0.041373, + "direction": "lower" + }, + { + "feature": "target_amplitude", + "cluster_mean": 0.548058, + "global_mean": 0.554524, + "difference": -0.006466, + "scaled_difference": -0.037084, + "direction": "lower" + } + ], + "suggested_label_terms": [ + "resident_detectability", + "late_spring_early_summer", + "resident_with_spring_persistence_and_summer_suppression", + "mean_peak_month_6.0", + "resident_detectability_pattern", + "weak_baseline_presence", + "late_spring_early_summer_detectability_peak" + ] + }, + { + "cluster_id": 2, + "n_species": 1, + "species": [ + "Egyptian Goose" + ], + "description": "Single-species cluster containing Egyptian Goose, mainly representing moderate spring seasonal presence. The fitted active window runs roughly from January to May, with a mean peak around April, and and an average width of 3.3 months. It is characterised by moderate season and sharp active window. Its defining traits include spring peak, moderate season, and sharp seasonal window. Compared with the full species set, season start month is lower than the whole-set average and season end month is higher than the whole-set average.", + "dominant_model_family": "seasonal_presence", + "dominant_primary_class": "moderate_spring_seasonal_presence", + "numeric_summary": { + "peak_month": { + "n": 1, + "mean": 3.915, + "min": 3.915, + "max": 3.915 + }, + "season_start_month": { + "n": 1, + "mean": 1.43, + "min": 1.43, + "max": 1.43 + }, + "season_end_month": { + "n": 1, + "mean": 4.725, + "min": 4.725, + "max": 4.725 + }, + "season_width_months": { + "n": 1, + "mean": 3.295, + "min": 3.295, + "max": 3.295 + }, + "season_midpoint_month": { + "n": 1, + "mean": 3.0775, + "min": 3.0775, + "max": 3.0775 + }, + "fit_score": { + "n": 1, + "mean": 0.131, + "min": 0.131, + "max": 0.131 + } + }, + "categorical_summary": { + "model_family": { + "dominant": "seasonal_presence", + "dominant_count": 1, + "dominant_fraction": 1.0, + "values": [ + { + "value": "seasonal_presence", + "count": 1, + "fraction": 1.0 + } + ] + }, + "primary_class": { + "dominant": "moderate_spring_seasonal_presence", + "dominant_count": 1, + "dominant_fraction": 1.0, + "values": [ + { + "value": "moderate_spring_seasonal_presence", + "count": 1, + "fraction": 1.0 + } + ] + }, + "confidence": { + "dominant": "medium", + "dominant_count": 1, + "dominant_fraction": 1.0, + "values": [ + { + "value": "medium", + "count": 1, + "fraction": 1.0 + } + ] + }, + "timing": { + "dominant": "spring", + "dominant_count": 1, + "dominant_fraction": 1.0, + "values": [ + { + "value": "spring", + "count": 1, + "fraction": 1.0 + } + ] + }, + "season_width_class": { + "dominant": "moderate", + "dominant_count": 1, + "dominant_fraction": 1.0, + "values": [ + { + "value": "moderate", + "count": 1, + "fraction": 1.0 + } + ] + }, + "window_shape": { + "dominant": "sharp", + "dominant_count": 1, + "dominant_fraction": 1.0, + "values": [ + { + "value": "sharp", + "count": 1, + "fraction": 1.0 + } + ] + }, + "post_peak_decline": { + "dominant": "strong", + "dominant_count": 1, + "dominant_fraction": 1.0, + "values": [ + { + "value": "strong", + "count": 1, + "fraction": 1.0 + } + ] + }, + "offseason_suppression": { + "dominant": "moderate", + "dominant_count": 1, + "dominant_fraction": 1.0, + "values": [ + { + "value": "moderate", + "count": 1, + "fraction": 1.0 + } + ] + } + }, + "common_traits": [ + { + "trait": "spring_peak", + "count": 1, + "fraction": 1.0 + }, + { + "trait": "moderate_season", + "count": 1, + "fraction": 1.0 + }, + { + "trait": "sharp_seasonal_window", + "count": 1, + "fraction": 1.0 + }, + { + "trait": "strong_post_peak_decline", + "count": 1, + "fraction": 1.0 + }, + { + "trait": "moderate_offseason_suppression", + "count": 1, + "fraction": 1.0 + }, + { + "trait": "late_peak_alignment", + "count": 1, + "fraction": 1.0 + } + ], + "distinguishing_numeric_features": [ + { + "feature": "season_start_month", + "cluster_mean": 1.43, + "global_mean": 1.93, + "difference": -0.5, + "scaled_difference": -0.5, + "direction": "lower" + }, + { + "feature": "season_end_month", + "cluster_mean": 4.725, + "global_mean": 4.4975, + "difference": 0.2275, + "scaled_difference": 0.5, + "direction": "higher" + }, + { + "feature": "season_width_months", + "cluster_mean": 3.295, + "global_mean": 2.5675, + "difference": 0.7275, + "scaled_difference": 0.5, + "direction": "higher" + }, + { + "feature": "season_midpoint_month", + "cluster_mean": 3.0775, + "global_mean": 3.21375, + "difference": -0.13625, + "scaled_difference": -0.5, + "direction": "lower" + }, + { + "feature": "fit_score", + "cluster_mean": 0.131, + "global_mean": 0.221526, + "difference": -0.090526, + "scaled_difference": -0.145775, + "direction": "lower" + }, + { + "feature": "peak_month", + "cluster_mean": 3.915, + "global_mean": 3.484948, + "difference": 0.430052, + "scaled_difference": 0.107513, + "direction": "higher" + } + ], + "suggested_label_terms": [ + "seasonal_presence", + "spring", + "moderate", + "moderate_spring_seasonal_presence", + "mean_peak_month_3.915", + "spring_peak", + "moderate_season", + "sharp_seasonal_window" + ] + }, + { + "cluster_id": 3, + "n_species": 14, + "species": [ + "Gadwall", + "Grey Heron", + "Moorhen", + "Great Crested Grebe", + "Canada Goose", + "Cormorant", + "Mute Swan", + "Robin", + "Greylag Goose", + "Tufted Duck", + "Coot", + "Black Headed Gull", + "Herring Gull", + "Mallard" + ], + "description": "Cluster of 14 species, mainly representing resident with summer detectability collapse. Detectability peaks around April and and is lowest around October. The shared pattern includes weak baseline presence, moderate summer suppression, weak autumn component, and rapid decline biased response dynamics. Common high-support traits include resident detectability pattern, weak spring carryover, and moderate summer suppression.", + "dominant_model_family": "resident_detectability", + "dominant_primary_class": "resident_with_summer_detectability_collapse", + "numeric_summary": { + "peak_month": { + "n": 14, + "mean": 3.53117, + "min": 2.0, + "max": 4.0 + }, + "trough_month": { + "n": 14, + "mean": 9.522853, + "min": 5.0, + "max": 10.0 + }, + "target_mean_value": { + "n": 14, + "mean": 0.209968, + "min": 0.139886, + "max": 0.364235 + }, + "target_amplitude": { + "n": 14, + "mean": 0.554986, + "min": 0.467943, + "max": 0.642306 + }, + "baseline_to_peak_ratio": { + "n": 14, + "mean": 0.147674, + "min": 0.053151, + "max": 0.336547 + }, + "autumn_to_winter_weight_ratio": { + "n": 14, + "mean": 0.056304, + "min": 0.042553, + "max": 0.069124 + }, + "year_end_to_winter_weight_ratio": { + "n": 14, + "mean": 0.364115, + "min": 0.240777, + "max": 0.482759 + }, + "decay_to_growth_ratio": { + "n": 14, + "mean": 1.530581, + "min": 0.995579, + "max": 2.593031 + }, + "fit_score": { + "n": 14, + "mean": 0.2275, + "min": 0.194, + "max": 0.356 + } + }, + "categorical_summary": { + "model_family": { + "dominant": "resident_detectability", + "dominant_count": 14, + "dominant_fraction": 1.0, + "values": [ + { + "value": "resident_detectability", + "count": 14, + "fraction": 1.0 + } + ] + }, + "primary_class": { + "dominant": "resident_with_summer_detectability_collapse", + "dominant_count": 14, + "dominant_fraction": 1.0, + "values": [ + { + "value": "resident_with_summer_detectability_collapse", + "count": 14, + "fraction": 1.0 + } + ] + }, + "confidence": { + "dominant": "medium", + "dominant_count": 10, + "dominant_fraction": 0.714286, + "values": [ + { + "value": "medium", + "count": 10, + "fraction": 0.714286 + }, + { + "value": "high", + "count": 3, + "fraction": 0.214286 + }, + { + "value": "low", + "count": 1, + "fraction": 0.071429 + } + ] + }, + "baseline_presence": { + "dominant": "weak", + "dominant_count": 10, + "dominant_fraction": 0.714286, + "values": [ + { + "value": "weak", + "count": 10, + "fraction": 0.714286 + }, + { + "value": "moderate", + "count": 4, + "fraction": 0.285714 + } + ] + }, + "timing": { + "dominant": "spring", + "dominant_count": 11, + "dominant_fraction": 0.785714, + "values": [ + { + "value": "spring", + "count": 11, + "fraction": 0.785714 + }, + { + "value": "winter", + "count": 3, + "fraction": 0.214286 + } + ] + }, + "summer_suppression": { + "dominant": "moderate", + "dominant_count": 14, + "dominant_fraction": 1.0, + "values": [ + { + "value": "moderate", + "count": 14, + "fraction": 1.0 + } + ] + }, + "autumn_component": { + "dominant": "weak", + "dominant_count": 14, + "dominant_fraction": 1.0, + "values": [ + { + "value": "weak", + "count": 14, + "fraction": 1.0 + } + ] + }, + "response_dynamics": { + "dominant": "rapid_decline_biased", + "dominant_count": 10, + "dominant_fraction": 0.714286, + "values": [ + { + "value": "rapid_decline_biased", + "count": 10, + "fraction": 0.714286 + }, + { + "value": "decline_biased", + "count": 4, + "fraction": 0.285714 + } + ] + } + }, + "common_traits": [ + { + "trait": "resident_detectability_pattern", + "count": 14, + "fraction": 1.0 + }, + { + "trait": "weak_spring_carryover", + "count": 14, + "fraction": 1.0 + }, + { + "trait": "moderate_summer_suppression", + "count": 14, + "fraction": 1.0 + }, + { + "trait": "weak_autumn_component", + "count": 14, + "fraction": 1.0 + }, + { + "trait": "meaningful_year_end_component", + "count": 12, + "fraction": 0.857143 + }, + { + "trait": "autumn_detectability_trough", + "count": 12, + "fraction": 0.857143 + }, + { + "trait": "spring_detectability_peak", + "count": 11, + "fraction": 0.785714 + }, + { + "trait": "weak_baseline_presence", + "count": 10, + "fraction": 0.714286 + }, + { + "trait": "strong_pre_summer_retention", + "count": 10, + "fraction": 0.714286 + }, + { + "trait": "rapid_decline_biased_response_dynamics", + "count": 10, + "fraction": 0.714286 + } + ], + "distinguishing_numeric_features": [ + { + "feature": "autumn_to_winter_weight_ratio", + "cluster_mean": 0.056304, + "global_mean": 0.07231, + "difference": -0.016006, + "scaled_difference": -0.090911, + "direction": "lower" + }, + { + "feature": "decay_to_growth_ratio", + "cluster_mean": 1.530581, + "global_mean": 1.71438, + "difference": -0.183799, + "scaled_difference": -0.070988, + "direction": "lower" + }, + { + "feature": "trough_month", + "cluster_mean": 9.522853, + "global_mean": 9.206867, + "difference": 0.315986, + "scaled_difference": 0.063197, + "direction": "higher" + }, + { + "feature": "year_end_to_winter_weight_ratio", + "cluster_mean": 0.364115, + "global_mean": 0.368498, + "difference": -0.004383, + "scaled_difference": -0.018113, + "direction": "lower" + }, + { + "feature": "baseline_to_peak_ratio", + "cluster_mean": 0.147674, + "global_mean": 0.143562, + "difference": 0.004112, + "scaled_difference": 0.01451, + "direction": "higher" + }, + { + "feature": "peak_month", + "cluster_mean": 3.53117, + "global_mean": 3.484948, + "difference": 0.046222, + "scaled_difference": 0.011556, + "direction": "higher" + }, + { + "feature": "target_mean_value", + "cluster_mean": 0.209968, + "global_mean": 0.212189, + "difference": -0.002221, + "scaled_difference": -0.0099, + "direction": "lower" + }, + { + "feature": "fit_score", + "cluster_mean": 0.2275, + "global_mean": 0.221526, + "difference": 0.005974, + "scaled_difference": 0.00962, + "direction": "higher" + } + ], + "suggested_label_terms": [ + "resident_detectability", + "spring", + "resident_with_summer_detectability_collapse", + "mean_peak_month_3.53117", + "resident_detectability_pattern", + "weak_spring_carryover", + "moderate_summer_suppression" + ] + }, + { + "cluster_id": 4, + "n_species": 1, + "species": [ + "Oystercatcher" + ], + "description": "Single-species cluster containing Oystercatcher, mainly representing narrow early spring seasonal presence. The fitted active window runs roughly from February to April, with a mean peak around March, and and an average width of 1.8 months. It is characterised by narrow season and sharp active window. Its defining traits include early spring peak, narrow season, and sharp seasonal window. Compared with the full species set, season start month is higher than the whole-set average and season end month is lower than the whole-set average.", + "dominant_model_family": "seasonal_presence", + "dominant_primary_class": "narrow_early_spring_seasonal_presence", + "numeric_summary": { + "peak_month": { + "n": 1, + "mean": 3.3, + "min": 3.3, + "max": 3.3 + }, + "season_start_month": { + "n": 1, + "mean": 2.43, + "min": 2.43, + "max": 2.43 + }, + "season_end_month": { + "n": 1, + "mean": 4.27, + "min": 4.27, + "max": 4.27 + }, + "season_width_months": { + "n": 1, + "mean": 1.84, + "min": 1.84, + "max": 1.84 + }, + "season_midpoint_month": { + "n": 1, + "mean": 3.35, + "min": 3.35, + "max": 3.35 + }, + "fit_score": { + "n": 1, + "mean": 0.007, + "min": 0.007, + "max": 0.007 + } + }, + "categorical_summary": { + "model_family": { + "dominant": "seasonal_presence", + "dominant_count": 1, + "dominant_fraction": 1.0, + "values": [ + { + "value": "seasonal_presence", + "count": 1, + "fraction": 1.0 + } + ] + }, + "primary_class": { + "dominant": "narrow_early_spring_seasonal_presence", + "dominant_count": 1, + "dominant_fraction": 1.0, + "values": [ + { + "value": "narrow_early_spring_seasonal_presence", + "count": 1, + "fraction": 1.0 + } + ] + }, + "confidence": { + "dominant": "high", + "dominant_count": 1, + "dominant_fraction": 1.0, + "values": [ + { + "value": "high", + "count": 1, + "fraction": 1.0 + } + ] + }, + "timing": { + "dominant": "early_spring", + "dominant_count": 1, + "dominant_fraction": 1.0, + "values": [ + { + "value": "early_spring", + "count": 1, + "fraction": 1.0 + } + ] + }, + "season_width_class": { + "dominant": "narrow", + "dominant_count": 1, + "dominant_fraction": 1.0, + "values": [ + { + "value": "narrow", + "count": 1, + "fraction": 1.0 + } + ] + }, + "window_shape": { + "dominant": "sharp", + "dominant_count": 1, + "dominant_fraction": 1.0, + "values": [ + { + "value": "sharp", + "count": 1, + "fraction": 1.0 + } + ] + }, + "post_peak_decline": { + "dominant": "strong", + "dominant_count": 1, + "dominant_fraction": 1.0, + "values": [ + { + "value": "strong", + "count": 1, + "fraction": 1.0 + } + ] + }, + "offseason_suppression": { + "dominant": "strong", + "dominant_count": 1, + "dominant_fraction": 1.0, + "values": [ + { + "value": "strong", + "count": 1, + "fraction": 1.0 + } + ] + } + }, + "common_traits": [ + { + "trait": "early_spring_peak", + "count": 1, + "fraction": 1.0 + }, + { + "trait": "narrow_season", + "count": 1, + "fraction": 1.0 + }, + { + "trait": "sharp_seasonal_window", + "count": 1, + "fraction": 1.0 + }, + { + "trait": "strong_post_peak_decline", + "count": 1, + "fraction": 1.0 + }, + { + "trait": "strong_offseason_suppression", + "count": 1, + "fraction": 1.0 + }, + { + "trait": "central_peak_alignment", + "count": 1, + "fraction": 1.0 + } + ], + "distinguishing_numeric_features": [ + { + "feature": "season_start_month", + "cluster_mean": 2.43, + "global_mean": 1.93, + "difference": 0.5, + "scaled_difference": 0.5, + "direction": "higher" + }, + { + "feature": "season_end_month", + "cluster_mean": 4.27, + "global_mean": 4.4975, + "difference": -0.2275, + "scaled_difference": -0.5, + "direction": "lower" + }, + { + "feature": "season_width_months", + "cluster_mean": 1.84, + "global_mean": 2.5675, + "difference": -0.7275, + "scaled_difference": -0.5, + "direction": "lower" + }, + { + "feature": "season_midpoint_month", + "cluster_mean": 3.35, + "global_mean": 3.21375, + "difference": 0.13625, + "scaled_difference": 0.5, + "direction": "higher" + }, + { + "feature": "fit_score", + "cluster_mean": 0.007, + "global_mean": 0.221526, + "difference": -0.214526, + "scaled_difference": -0.345452, + "direction": "lower" + }, + { + "feature": "peak_month", + "cluster_mean": 3.3, + "global_mean": 3.484948, + "difference": -0.184948, + "scaled_difference": -0.046237, + "direction": "lower" + } + ], + "suggested_label_terms": [ + "seasonal_presence", + "early_spring", + "narrow", + "narrow_early_spring_seasonal_presence", + "mean_peak_month_3.3", + "early_spring_peak", + "narrow_season", + "sharp_seasonal_window" + ] + }, + { + "cluster_id": 5, + "n_species": 2, + "species": [ + "Pochard", + "Shoveler" + ], + "description": "Cluster of 2 species, mainly representing winter visitor with autumn arrival component. The defining pattern is a winter peak around February, a moderate autumn component, moderate summer suppression, and slow arrival fast departure response dynamics. Common high-support traits include year wrapping winter presence, core winter winter peak, and moderate summer suppression. Compared with the full species set, trough month is lower than the whole-set average and autumn to winter weight ratio is higher than the whole-set average.", + "dominant_model_family": "winter_presence", + "dominant_primary_class": "winter_visitor_with_autumn_arrival_component", + "numeric_summary": { + "peak_month": { + "n": 2, + "mean": 2.0, + "min": 2.0, + "max": 2.0 + }, + "trough_month": { + "n": 2, + "mean": 5.5, + "min": 5.0, + "max": 6.0 + }, + "autumn_to_winter_weight_ratio": { + "n": 2, + "mean": 0.193359, + "min": 0.168103, + "max": 0.218615 + }, + "decay_to_growth_ratio": { + "n": 2, + "mean": 3.032964, + "min": 2.481183, + "max": 3.584746 + }, + "active_month_count_ge_0_10": { + "n": 2, + "mean": 7.0, + "min": 7.0, + "max": 7.0 + }, + "fit_score": { + "n": 2, + "mean": 0.129, + "min": 0.097, + "max": 0.161 + } + }, + "categorical_summary": { + "model_family": { + "dominant": "winter_presence", + "dominant_count": 2, + "dominant_fraction": 1.0, + "values": [ + { + "value": "winter_presence", + "count": 2, + "fraction": 1.0 + } + ] + }, + "primary_class": { + "dominant": "winter_visitor_with_autumn_arrival_component", + "dominant_count": 1, + "dominant_fraction": 0.5, + "values": [ + { + "value": "winter_visitor_with_autumn_arrival_component", + "count": 1, + "fraction": 0.5 + }, + { + "value": "winter_visitor_with_weak_autumn_arrival_component", + "count": 1, + "fraction": 0.5 + } + ] + }, + "confidence": { + "dominant": "low", + "dominant_count": 1, + "dominant_fraction": 0.5, + "values": [ + { + "value": "low", + "count": 1, + "fraction": 0.5 + }, + { + "value": "medium", + "count": 1, + "fraction": 0.5 + } + ] + }, + "baseline_presence": { + "dominant": "low", + "dominant_count": 2, + "dominant_fraction": 1.0, + "values": [ + { + "value": "low", + "count": 2, + "fraction": 1.0 + } + ] + }, + "timing": { + "dominant": "core_winter", + "dominant_count": 2, + "dominant_fraction": 1.0, + "values": [ + { + "value": "core_winter", + "count": 2, + "fraction": 1.0 + } + ] + }, + "summer_suppression": { + "dominant": "moderate", + "dominant_count": 2, + "dominant_fraction": 1.0, + "values": [ + { + "value": "moderate", + "count": 2, + "fraction": 1.0 + } + ] + }, + "autumn_component": { + "dominant": "moderate", + "dominant_count": 1, + "dominant_fraction": 0.5, + "values": [ + { + "value": "moderate", + "count": 1, + "fraction": 0.5 + }, + { + "value": "weak", + "count": 1, + "fraction": 0.5 + } + ] + }, + "response_dynamics": { + "dominant": "slow_arrival_fast_departure", + "dominant_count": 1, + "dominant_fraction": 0.5, + "values": [ + { + "value": "slow_arrival_fast_departure", + "count": 1, + "fraction": 0.5 + }, + { + "value": "faster_departure_than_arrival", + "count": 1, + "fraction": 0.5 + } + ] + } + }, + "common_traits": [ + { + "trait": "year_wrapping_winter_presence", + "count": 2, + "fraction": 1.0 + }, + { + "trait": "core_winter_winter_peak", + "count": 2, + "fraction": 1.0 + }, + { + "trait": "moderate_summer_suppression", + "count": 2, + "fraction": 1.0 + }, + { + "trait": "low_baseline_presence", + "count": 2, + "fraction": 1.0 + }, + { + "trait": "moderate_winter_bump", + "count": 2, + "fraction": 1.0 + }, + { + "trait": "moderate_autumn_component", + "count": 1, + "fraction": 0.5 + }, + { + "trait": "slow_arrival_fast_departure_response_dynamics", + "count": 1, + "fraction": 0.5 + }, + { + "trait": "weak_autumn_component", + "count": 1, + "fraction": 0.5 + }, + { + "trait": "faster_departure_than_arrival_response_dynamics", + "count": 1, + "fraction": 0.5 + } + ], + "distinguishing_numeric_features": [ + { + "feature": "trough_month", + "cluster_mean": 5.5, + "global_mean": 9.206867, + "difference": -3.706867, + "scaled_difference": -0.741373, + "direction": "lower" + }, + { + "feature": "autumn_to_winter_weight_ratio", + "cluster_mean": 0.193359, + "global_mean": 0.07231, + "difference": 0.121049, + "scaled_difference": 0.687536, + "direction": "higher" + }, + { + "feature": "decay_to_growth_ratio", + "cluster_mean": 3.032964, + "global_mean": 1.71438, + "difference": 1.318584, + "scaled_difference": 0.50927, + "direction": "higher" + }, + { + "feature": "peak_month", + "cluster_mean": 2.0, + "global_mean": 3.484948, + "difference": -1.484948, + "scaled_difference": -0.371237, + "direction": "lower" + }, + { + "feature": "fit_score", + "cluster_mean": 0.129, + "global_mean": 0.221526, + "difference": -0.092526, + "scaled_difference": -0.148995, + "direction": "lower" + } + ], + "suggested_label_terms": [ + "winter_presence", + "core_winter", + "winter_visitor_with_autumn_arrival_component", + "mean_peak_month_2.0", + "year_wrapping_winter_presence", + "core_winter_winter_peak", + "moderate_summer_suppression" + ] + } + ] +} \ No newline at end of file diff --git a/modelling/data/thrupp-lake-birds/analysis/cluster_dendrogram.png b/modelling/data/thrupp-lake-birds/analysis/cluster_dendrogram.png new file mode 100644 index 0000000..c9ec244 Binary files /dev/null and b/modelling/data/thrupp-lake-birds/analysis/cluster_dendrogram.png differ diff --git a/modelling/data/thrupp-lake-birds/analysis/cluster_summary.txt b/modelling/data/thrupp-lake-birds/analysis/cluster_summary.txt new file mode 100644 index 0000000..7f09714 --- /dev/null +++ b/modelling/data/thrupp-lake-birds/analysis/cluster_summary.txt @@ -0,0 +1,119 @@ + +Species clusters +================ + +Cluster 1 +--------- +Single-species cluster containing Egret, mainly representing resident with spring persistence and summer suppression. Detectability peaks around June and and is lowest around September. The shared pattern includes weak baseline presence, strong summer suppression, weak autumn component, and rapid decline biased response dynamics. Its defining traits include resident detectability pattern, weak baseline presence, and late spring early summer detectability peak. Compared with the full species set, fit score is higher than the whole-set average and peak month is higher than the whole-set average. + +Species (1): + Egret + +Dominant model family : resident_detectability +Dominant class : resident_with_spring_persistence_and_summer_suppression +Common traits : resident_detectability_pattern (1, 100%), weak_baseline_presence (1, 100%), late_spring_early_summer_detectability_peak (1, 100%), autumn_detectability_trough (1, 100%), moderate_spring_carryover (1, 100%) + +Peak month mean/range : 6.00 (6.00 - 6.00) + +Distinguishing numeric features: + - fit_score (higher, scaled_difference=0.65) + - peak_month (higher, scaled_difference=0.63) + - year_end_to_winter_weight_ratio (higher, scaled_difference=0.25) + - baseline_to_peak_ratio (lower, scaled_difference=-0.20) + - target_mean_value (higher, scaled_difference=0.14) + +Cluster 2 +--------- +Single-species cluster containing Egyptian Goose, mainly representing moderate spring seasonal presence. The fitted active window runs roughly from January to May, with a mean peak around April, and and an average width of 3.3 months. It is characterised by moderate season and sharp active window. Its defining traits include spring peak, moderate season, and sharp seasonal window. Compared with the full species set, season start month is lower than the whole-set average and season end month is higher than the whole-set average. + +Species (1): + Egyptian Goose + +Dominant model family : seasonal_presence +Dominant class : moderate_spring_seasonal_presence +Common traits : spring_peak (1, 100%), moderate_season (1, 100%), sharp_seasonal_window (1, 100%), strong_post_peak_decline (1, 100%), moderate_offseason_suppression (1, 100%) + +Peak month mean/range : 3.92 (3.92 - 3.92) +Season width mean : 3.29 months + +Distinguishing numeric features: + - season_start_month (lower, scaled_difference=-0.50) + - season_end_month (higher, scaled_difference=0.50) + - season_width_months (higher, scaled_difference=0.50) + - season_midpoint_month (lower, scaled_difference=-0.50) + - fit_score (lower, scaled_difference=-0.15) + +Cluster 3 +--------- +Cluster of 14 species, mainly representing resident with summer detectability collapse. Detectability peaks around April and and is lowest around October. The shared pattern includes weak baseline presence, moderate summer suppression, weak autumn component, and rapid decline biased response dynamics. Common high-support traits include resident detectability pattern, weak spring carryover, and moderate summer suppression. + +Species (14): + Gadwall + Grey Heron + Moorhen + Great Crested Grebe + Canada Goose + Cormorant + Mute Swan + Robin + Greylag Goose + Tufted Duck + Coot + Black Headed Gull + Herring Gull + Mallard + +Dominant model family : resident_detectability +Dominant class : resident_with_summer_detectability_collapse +Common traits : resident_detectability_pattern (14, 100%), weak_spring_carryover (14, 100%), moderate_summer_suppression (14, 100%), weak_autumn_component (14, 100%), meaningful_year_end_component (12, 86%) + +Peak month mean/range : 3.53 (2.00 - 4.00) + +Distinguishing numeric features: + - autumn_to_winter_weight_ratio (lower, scaled_difference=-0.09) + - decay_to_growth_ratio (lower, scaled_difference=-0.07) + - trough_month (higher, scaled_difference=0.06) + - year_end_to_winter_weight_ratio (lower, scaled_difference=-0.02) + - baseline_to_peak_ratio (higher, scaled_difference=0.01) + +Cluster 4 +--------- +Single-species cluster containing Oystercatcher, mainly representing narrow early spring seasonal presence. The fitted active window runs roughly from February to April, with a mean peak around March, and and an average width of 1.8 months. It is characterised by narrow season and sharp active window. Its defining traits include early spring peak, narrow season, and sharp seasonal window. Compared with the full species set, season start month is higher than the whole-set average and season end month is lower than the whole-set average. + +Species (1): + Oystercatcher + +Dominant model family : seasonal_presence +Dominant class : narrow_early_spring_seasonal_presence +Common traits : early_spring_peak (1, 100%), narrow_season (1, 100%), sharp_seasonal_window (1, 100%), strong_post_peak_decline (1, 100%), strong_offseason_suppression (1, 100%) + +Peak month mean/range : 3.30 (3.30 - 3.30) +Season width mean : 1.84 months + +Distinguishing numeric features: + - season_start_month (higher, scaled_difference=0.50) + - season_end_month (lower, scaled_difference=-0.50) + - season_width_months (lower, scaled_difference=-0.50) + - season_midpoint_month (higher, scaled_difference=0.50) + - fit_score (lower, scaled_difference=-0.35) + +Cluster 5 +--------- +Cluster of 2 species, mainly representing winter visitor with autumn arrival component. The defining pattern is a winter peak around February, a moderate autumn component, moderate summer suppression, and slow arrival fast departure response dynamics. Common high-support traits include year wrapping winter presence, core winter winter peak, and moderate summer suppression. Compared with the full species set, trough month is lower than the whole-set average and autumn to winter weight ratio is higher than the whole-set average. + +Species (2): + Pochard + Shoveler + +Dominant model family : winter_presence +Dominant class : winter_visitor_with_autumn_arrival_component +Common traits : year_wrapping_winter_presence (2, 100%), core_winter_winter_peak (2, 100%), moderate_summer_suppression (2, 100%), low_baseline_presence (2, 100%), moderate_winter_bump (2, 100%) + +Peak month mean/range : 2.00 (2.00 - 2.00) + +Distinguishing numeric features: + - trough_month (lower, scaled_difference=-0.74) + - autumn_to_winter_weight_ratio (higher, scaled_difference=0.69) + - decay_to_growth_ratio (higher, scaled_difference=0.51) + - peak_month (lower, scaled_difference=-0.37) + - fit_score (lower, scaled_difference=-0.15) diff --git a/modelling/data/thrupp-lake-birds/analysis/extracted_clusters.json b/modelling/data/thrupp-lake-birds/analysis/extracted_clusters.json new file mode 100644 index 0000000..cd5cee1 --- /dev/null +++ b/modelling/data/thrupp-lake-birds/analysis/extracted_clusters.json @@ -0,0 +1,69 @@ +{ + "schema_version": "seasonal-ecological-calendar-clusters/v1", + "source_schema_version": "species-similarity-clusters/v2", + "source_created_utc": "2026-05-24T06:54:35.630835+00:00", + "n_species": 19, + "n_clusters": 5, + "cluster_caveat": "Clusters should be interpreted as exploratory seasonal assemblages rather than fixed ecological categories.", + "clusters": [ + { + "cluster_id": 1, + "calendar_label": "Egret neighbourhood", + "description": "Single-species cluster containing Egret, mainly representing resident with spring persistence and summer suppression. Detectability peaks around June and and is lowest around September. The shared pattern includes weak baseline presence, strong summer suppression, weak autumn component, and rapid decline biased response dynamics. Its defining traits include resident detectability pattern, weak baseline presence, and late spring early summer detectability peak. Compared with the full species set, fit score is higher than the whole-set average and peak month is higher than the whole-set average.", + "n_species": 1, + "species": [ + "Egret" + ] + }, + { + "cluster_id": 2, + "calendar_label": "Egyptian Goose neighbourhood", + "description": "Single-species cluster containing Egyptian Goose, mainly representing moderate spring seasonal presence. The fitted active window runs roughly from January to May, with a mean peak around April, and and an average width of 3.3 months. It is characterised by moderate season and sharp active window. Its defining traits include spring peak, moderate season, and sharp seasonal window. Compared with the full species set, season start month is lower than the whole-set average and season end month is higher than the whole-set average.", + "n_species": 1, + "species": [ + "Egyptian Goose" + ] + }, + { + "cluster_id": 3, + "calendar_label": "Resident With Summer Detectability Collapse", + "description": "Cluster of 14 species, mainly representing resident with summer detectability collapse. Detectability peaks around April and and is lowest around October. The shared pattern includes weak baseline presence, moderate summer suppression, weak autumn component, and rapid decline biased response dynamics. Common high-support traits include resident detectability pattern, weak spring carryover, and moderate summer suppression.", + "n_species": 14, + "species": [ + "Gadwall", + "Grey Heron", + "Moorhen", + "Great Crested Grebe", + "Canada Goose", + "Cormorant", + "Mute Swan", + "Robin", + "Greylag Goose", + "Tufted Duck", + "Coot", + "Black Headed Gull", + "Herring Gull", + "Mallard" + ] + }, + { + "cluster_id": 4, + "calendar_label": "Oystercatcher neighbourhood", + "description": "Single-species cluster containing Oystercatcher, mainly representing narrow early spring seasonal presence. The fitted active window runs roughly from February to April, with a mean peak around March, and and an average width of 1.8 months. It is characterised by narrow season and sharp active window. Its defining traits include early spring peak, narrow season, and sharp seasonal window. Compared with the full species set, season start month is higher than the whole-set average and season end month is lower than the whole-set average.", + "n_species": 1, + "species": [ + "Oystercatcher" + ] + }, + { + "cluster_id": 5, + "calendar_label": "Winter Visitor With Autumn Arrival Component", + "description": "Cluster of 2 species, mainly representing winter visitor with autumn arrival component. The defining pattern is a winter peak around February, a moderate autumn component, moderate summer suppression, and slow arrival fast departure response dynamics. Common high-support traits include year wrapping winter presence, core winter winter peak, and moderate summer suppression. Compared with the full species set, trough month is lower than the whole-set average and autumn to winter weight ratio is higher than the whole-set average.", + "n_species": 2, + "species": [ + "Pochard", + "Shoveler" + ] + } + ] +} \ No newline at end of file diff --git a/modelling/data/thrupp-lake-birds/analysis/feature_matrix.json b/modelling/data/thrupp-lake-birds/analysis/feature_matrix.json new file mode 100644 index 0000000..ba7f2c6 --- /dev/null +++ b/modelling/data/thrupp-lake-birds/analysis/feature_matrix.json @@ -0,0 +1,980 @@ +{ + "schema_version": "species-feature-table/v1", + "created_utc": "2026-05-24T06:54:35.302377+00:00", + "description": "Whole-set seasonal ecology feature table compiled from per-species classification JSON files.", + "n_species": 19, + "source_files": [ + "/Users/dave/Dropbox/Development/Projects/OdeSolver/modelling/data/thrupp-lake-birds/resident/black_headed_gull_classification.json", + "/Users/dave/Dropbox/Development/Projects/OdeSolver/modelling/data/thrupp-lake-birds/resident/canada_goose_classification.json", + "/Users/dave/Dropbox/Development/Projects/OdeSolver/modelling/data/thrupp-lake-birds/resident/coot_classification.json", + "/Users/dave/Dropbox/Development/Projects/OdeSolver/modelling/data/thrupp-lake-birds/resident/cormorant_classification.json", + "/Users/dave/Dropbox/Development/Projects/OdeSolver/modelling/data/thrupp-lake-birds/resident/egret_classification.json", + "/Users/dave/Dropbox/Development/Projects/OdeSolver/modelling/data/thrupp-lake-birds/resident/gadwall_classification.json", + "/Users/dave/Dropbox/Development/Projects/OdeSolver/modelling/data/thrupp-lake-birds/resident/great_crested_grebe_classification.json", + "/Users/dave/Dropbox/Development/Projects/OdeSolver/modelling/data/thrupp-lake-birds/resident/grey_heron_classification.json", + "/Users/dave/Dropbox/Development/Projects/OdeSolver/modelling/data/thrupp-lake-birds/resident/greylag_goose_classification.json", + "/Users/dave/Dropbox/Development/Projects/OdeSolver/modelling/data/thrupp-lake-birds/resident/herring_gull_classification.json", + "/Users/dave/Dropbox/Development/Projects/OdeSolver/modelling/data/thrupp-lake-birds/resident/mallard_classification.json", + "/Users/dave/Dropbox/Development/Projects/OdeSolver/modelling/data/thrupp-lake-birds/resident/moorhen_classification.json", + "/Users/dave/Dropbox/Development/Projects/OdeSolver/modelling/data/thrupp-lake-birds/resident/mute_swan_classification.json", + "/Users/dave/Dropbox/Development/Projects/OdeSolver/modelling/data/thrupp-lake-birds/resident/robin_classification.json", + "/Users/dave/Dropbox/Development/Projects/OdeSolver/modelling/data/thrupp-lake-birds/resident/tufted_duck_classification.json", + "/Users/dave/Dropbox/Development/Projects/OdeSolver/modelling/data/thrupp-lake-birds/seasonal/egyptian_goose_classification.json", + "/Users/dave/Dropbox/Development/Projects/OdeSolver/modelling/data/thrupp-lake-birds/seasonal/oystercatcher_classification.json", + "/Users/dave/Dropbox/Development/Projects/OdeSolver/modelling/data/thrupp-lake-birds/winter/pochard_classification.json", + "/Users/dave/Dropbox/Development/Projects/OdeSolver/modelling/data/thrupp-lake-birds/winter/shoveler_classification.json" + ], + "features": [ + { + "species": "Black Headed Gull", + "model_family": "resident_detectability", + "schema_version": "resident-classification/v1", + "primary_class": "resident_with_summer_detectability_collapse", + "confidence": "medium", + "fit_score": 0.201, + "n_warnings": 0, + "peak_month": 4, + "peak_label": "April", + "trough_month": 10, + "trough_label": "October", + "season_start_month": null, + "season_start_label": null, + "season_end_month": null, + "season_end_label": null, + "season_width_months": null, + "season_midpoint_month": null, + "baseline_presence": "weak", + "timing": "spring", + "season_width_class": null, + "window_shape": null, + "post_peak_decline": null, + "offseason_suppression": null, + "summer_suppression": "moderate", + "autumn_component": "weak", + "response_dynamics": "rapid_decline_biased", + "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, + "active_month_count_ge_0_10": null, + "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" + ], + "trait_count": 11, + "source_file": "/Users/dave/Dropbox/Development/Projects/OdeSolver/modelling/data/thrupp-lake-birds/resident/black_headed_gull_classification.json", + "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." + }, + { + "species": "Canada Goose", + "model_family": "resident_detectability", + "schema_version": "resident-classification/v1", + "primary_class": "resident_with_summer_detectability_collapse", + "confidence": "high", + "fit_score": 0.195, + "n_warnings": 0, + "peak_month": 4, + "peak_label": "April", + "trough_month": 10, + "trough_label": "October", + "season_start_month": null, + "season_start_label": null, + "season_end_month": null, + "season_end_label": null, + "season_width_months": null, + "season_midpoint_month": null, + "baseline_presence": "moderate", + "timing": "spring", + "season_width_class": null, + "window_shape": null, + "post_peak_decline": null, + "offseason_suppression": null, + "summer_suppression": "moderate", + "autumn_component": "weak", + "response_dynamics": "decline_biased", + "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, + "active_month_count_ge_0_10": null, + "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" + ], + "trait_count": 11, + "source_file": "/Users/dave/Dropbox/Development/Projects/OdeSolver/modelling/data/thrupp-lake-birds/resident/canada_goose_classification.json", + "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." + }, + { + "species": "Coot", + "model_family": "resident_detectability", + "schema_version": "resident-classification/v1", + "primary_class": "resident_with_summer_detectability_collapse", + "confidence": "high", + "fit_score": 0.2, + "n_warnings": 0, + "peak_month": 4, + "peak_label": "April", + "trough_month": 10, + "trough_label": "October", + "season_start_month": null, + "season_start_label": null, + "season_end_month": null, + "season_end_label": null, + "season_width_months": null, + "season_midpoint_month": null, + "baseline_presence": "weak", + "timing": "spring", + "season_width_class": null, + "window_shape": null, + "post_peak_decline": null, + "offseason_suppression": null, + "summer_suppression": "moderate", + "autumn_component": "weak", + "response_dynamics": "decline_biased", + "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, + "active_month_count_ge_0_10": null, + "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" + ], + "trait_count": 11, + "source_file": "/Users/dave/Dropbox/Development/Projects/OdeSolver/modelling/data/thrupp-lake-birds/resident/coot_classification.json", + "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." + }, + { + "species": "Cormorant", + "model_family": "resident_detectability", + "schema_version": "resident-classification/v1", + "primary_class": "resident_with_summer_detectability_collapse", + "confidence": "medium", + "fit_score": 0.206, + "n_warnings": 0, + "peak_month": 4, + "peak_label": "April", + "trough_month": 10, + "trough_label": "October", + "season_start_month": null, + "season_start_label": null, + "season_end_month": null, + "season_end_label": null, + "season_width_months": null, + "season_midpoint_month": null, + "baseline_presence": "moderate", + "timing": "spring", + "season_width_class": null, + "window_shape": null, + "post_peak_decline": null, + "offseason_suppression": null, + "summer_suppression": "moderate", + "autumn_component": "weak", + "response_dynamics": "rapid_decline_biased", + "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, + "active_month_count_ge_0_10": null, + "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" + ], + "trait_count": 11, + "source_file": "/Users/dave/Dropbox/Development/Projects/OdeSolver/modelling/data/thrupp-lake-birds/resident/cormorant_classification.json", + "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." + }, + { + "species": "Egret", + "model_family": "resident_detectability", + "schema_version": "resident-classification/v1", + "primary_class": "resident_with_spring_persistence_and_summer_suppression", + "confidence": "low", + "fit_score": 0.628, + "n_warnings": 0, + "peak_month": 6, + "peak_label": "June", + "trough_month": 9, + "trough_label": "September", + "season_start_month": null, + "season_start_label": null, + "season_end_month": null, + "season_end_label": null, + "season_width_months": null, + "season_midpoint_month": null, + "baseline_presence": "weak", + "timing": "late_spring_early_summer", + "season_width_class": null, + "window_shape": null, + "post_peak_decline": null, + "offseason_suppression": null, + "summer_suppression": "strong", + "autumn_component": "weak", + "response_dynamics": "rapid_decline_biased", + "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, + "active_month_count_ge_0_10": null, + "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" + ], + "trait_count": 11, + "source_file": "/Users/dave/Dropbox/Development/Projects/OdeSolver/modelling/data/thrupp-lake-birds/resident/egret_classification.json", + "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." + }, + { + "species": "Gadwall", + "model_family": "resident_detectability", + "schema_version": "resident-classification/v1", + "primary_class": "resident_with_summer_detectability_collapse", + "confidence": "medium", + "fit_score": 0.234, + "n_warnings": 0, + "peak_month": 2, + "peak_label": "February", + "trough_month": 5, + "trough_label": "May", + "season_start_month": null, + "season_start_label": null, + "season_end_month": null, + "season_end_label": null, + "season_width_months": null, + "season_midpoint_month": null, + "baseline_presence": "weak", + "timing": "winter", + "season_width_class": null, + "window_shape": null, + "post_peak_decline": null, + "offseason_suppression": null, + "summer_suppression": "moderate", + "autumn_component": "weak", + "response_dynamics": "rapid_decline_biased", + "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, + "active_month_count_ge_0_10": null, + "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" + ], + "trait_count": 11, + "source_file": "/Users/dave/Dropbox/Development/Projects/OdeSolver/modelling/data/thrupp-lake-birds/resident/gadwall_classification.json", + "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." + }, + { + "species": "Great Crested Grebe", + "model_family": "resident_detectability", + "schema_version": "resident-classification/v1", + "primary_class": "resident_with_summer_detectability_collapse", + "confidence": "medium", + "fit_score": 0.224, + "n_warnings": 0, + "peak_month": 4, + "peak_label": "April", + "trough_month": 9, + "trough_label": "September", + "season_start_month": null, + "season_start_label": null, + "season_end_month": null, + "season_end_label": null, + "season_width_months": null, + "season_midpoint_month": null, + "baseline_presence": "moderate", + "timing": "spring", + "season_width_class": null, + "window_shape": null, + "post_peak_decline": null, + "offseason_suppression": null, + "summer_suppression": "moderate", + "autumn_component": "weak", + "response_dynamics": "rapid_decline_biased", + "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, + "active_month_count_ge_0_10": null, + "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" + ], + "trait_count": 11, + "source_file": "/Users/dave/Dropbox/Development/Projects/OdeSolver/modelling/data/thrupp-lake-birds/resident/great_crested_grebe_classification.json", + "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." + }, + { + "species": "Grey Heron", + "model_family": "resident_detectability", + "schema_version": "resident-classification/v1", + "primary_class": "resident_with_summer_detectability_collapse", + "confidence": "medium", + "fit_score": 0.212, + "n_warnings": 0, + "peak_month": 2, + "peak_label": "February", + "trough_month": 10, + "trough_label": "October", + "season_start_month": null, + "season_start_label": null, + "season_end_month": null, + "season_end_label": null, + "season_width_months": null, + "season_midpoint_month": null, + "baseline_presence": "weak", + "timing": "winter", + "season_width_class": null, + "window_shape": null, + "post_peak_decline": null, + "offseason_suppression": null, + "summer_suppression": "moderate", + "autumn_component": "weak", + "response_dynamics": "rapid_decline_biased", + "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, + "active_month_count_ge_0_10": null, + "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" + ], + "trait_count": 11, + "source_file": "/Users/dave/Dropbox/Development/Projects/OdeSolver/modelling/data/thrupp-lake-birds/resident/grey_heron_classification.json", + "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." + }, + { + "species": "Greylag Goose", + "model_family": "resident_detectability", + "schema_version": "resident-classification/v1", + "primary_class": "resident_with_summer_detectability_collapse", + "confidence": "low", + "fit_score": 0.356, + "n_warnings": 0, + "peak_month": 4, + "peak_label": "April", + "trough_month": 10, + "trough_label": "October", + "season_start_month": null, + "season_start_label": null, + "season_end_month": null, + "season_end_label": null, + "season_width_months": null, + "season_midpoint_month": null, + "baseline_presence": "weak", + "timing": "spring", + "season_width_class": null, + "window_shape": null, + "post_peak_decline": null, + "offseason_suppression": null, + "summer_suppression": "moderate", + "autumn_component": "weak", + "response_dynamics": "rapid_decline_biased", + "target_mean_value": 0.139885619245235, + "target_amplitude": 0.5644268966925725, + "baseline_to_peak_ratio": 0.05315125869407346, + "autumn_to_winter_weight_ratio": 0.05048543689320388, + "year_end_to_winter_weight_ratio": 0.2407766990291262, + "decay_to_growth_ratio": 1.7622466216216217, + "active_month_count_ge_0_10": null, + "traits": [ + "resident_detectability_pattern", + "weak_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", + "weak_year_end_component", + "rapid_decline_biased_response_dynamics" + ], + "trait_count": 11, + "source_file": "/Users/dave/Dropbox/Development/Projects/OdeSolver/modelling/data/thrupp-lake-birds/resident/greylag_goose_classification.json", + "summary": "Greylag 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 weak baseline presence, weak spring carry-over, moderate pre-summer retention, moderate summer suppression, and strong summer decay acceleration." + }, + { + "species": "Herring Gull", + "model_family": "resident_detectability", + "schema_version": "resident-classification/v1", + "primary_class": "resident_with_summer_detectability_collapse", + "confidence": "medium", + "fit_score": 0.217, + "n_warnings": 0, + "peak_month": 4, + "peak_label": "April", + "trough_month": 9, + "trough_label": "September", + "season_start_month": null, + "season_start_label": null, + "season_end_month": null, + "season_end_label": null, + "season_width_months": null, + "season_midpoint_month": null, + "baseline_presence": "weak", + "timing": "spring", + "season_width_class": null, + "window_shape": null, + "post_peak_decline": null, + "offseason_suppression": null, + "summer_suppression": "moderate", + "autumn_component": "weak", + "response_dynamics": "rapid_decline_biased", + "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, + "active_month_count_ge_0_10": null, + "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" + ], + "trait_count": 11, + "source_file": "/Users/dave/Dropbox/Development/Projects/OdeSolver/modelling/data/thrupp-lake-birds/resident/herring_gull_classification.json", + "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." + }, + { + "species": "Mallard", + "model_family": "resident_detectability", + "schema_version": "resident-classification/v1", + "primary_class": "resident_with_summer_detectability_collapse", + "confidence": "medium", + "fit_score": 0.24, + "n_warnings": 0, + "peak_month": 4, + "peak_label": "April", + "trough_month": 10, + "trough_label": "October", + "season_start_month": null, + "season_start_label": null, + "season_end_month": null, + "season_end_label": null, + "season_width_months": null, + "season_midpoint_month": null, + "baseline_presence": "weak", + "timing": "spring", + "season_width_class": null, + "window_shape": null, + "post_peak_decline": null, + "offseason_suppression": null, + "summer_suppression": "moderate", + "autumn_component": "weak", + "response_dynamics": "rapid_decline_biased", + "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, + "active_month_count_ge_0_10": null, + "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" + ], + "trait_count": 11, + "source_file": "/Users/dave/Dropbox/Development/Projects/OdeSolver/modelling/data/thrupp-lake-birds/resident/mallard_classification.json", + "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." + }, + { + "species": "Moorhen", + "model_family": "resident_detectability", + "schema_version": "resident-classification/v1", + "primary_class": "resident_with_summer_detectability_collapse", + "confidence": "medium", + "fit_score": 0.251, + "n_warnings": 0, + "peak_month": 2, + "peak_label": "February", + "trough_month": 10, + "trough_label": "October", + "season_start_month": null, + "season_start_label": null, + "season_end_month": null, + "season_end_label": null, + "season_width_months": null, + "season_midpoint_month": null, + "baseline_presence": "weak", + "timing": "winter", + "season_width_class": null, + "window_shape": null, + "post_peak_decline": null, + "offseason_suppression": null, + "summer_suppression": "moderate", + "autumn_component": "weak", + "response_dynamics": "rapid_decline_biased", + "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, + "active_month_count_ge_0_10": null, + "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" + ], + "trait_count": 11, + "source_file": "/Users/dave/Dropbox/Development/Projects/OdeSolver/modelling/data/thrupp-lake-birds/resident/moorhen_classification.json", + "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." + }, + { + "species": "Mute Swan", + "model_family": "resident_detectability", + "schema_version": "resident-classification/v1", + "primary_class": "resident_with_summer_detectability_collapse", + "confidence": "high", + "fit_score": 0.194, + "n_warnings": 0, + "peak_month": 4, + "peak_label": "April", + "trough_month": 10, + "trough_label": "October", + "season_start_month": null, + "season_start_label": null, + "season_end_month": null, + "season_end_label": null, + "season_width_months": null, + "season_midpoint_month": null, + "baseline_presence": "moderate", + "timing": "spring", + "season_width_class": null, + "window_shape": null, + "post_peak_decline": null, + "offseason_suppression": null, + "summer_suppression": "moderate", + "autumn_component": "weak", + "response_dynamics": "rapid_decline_biased", + "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, + "active_month_count_ge_0_10": null, + "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" + ], + "trait_count": 11, + "source_file": "/Users/dave/Dropbox/Development/Projects/OdeSolver/modelling/data/thrupp-lake-birds/resident/mute_swan_classification.json", + "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." + }, + { + "species": "Robin", + "model_family": "resident_detectability", + "schema_version": "resident-classification/v1", + "primary_class": "resident_with_summer_detectability_collapse", + "confidence": "medium", + "fit_score": 0.23, + "n_warnings": 0, + "peak_month": 3, + "peak_label": "March", + "trough_month": 8, + "trough_label": "August", + "season_start_month": null, + "season_start_label": null, + "season_end_month": null, + "season_end_label": null, + "season_width_months": null, + "season_midpoint_month": null, + "baseline_presence": "weak", + "timing": "spring", + "season_width_class": null, + "window_shape": null, + "post_peak_decline": null, + "offseason_suppression": null, + "summer_suppression": "moderate", + "autumn_component": "weak", + "response_dynamics": "decline_biased", + "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, + "active_month_count_ge_0_10": null, + "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" + ], + "trait_count": 11, + "source_file": "/Users/dave/Dropbox/Development/Projects/OdeSolver/modelling/data/thrupp-lake-birds/resident/robin_classification.json", + "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." + }, + { + "species": "Tufted Duck", + "model_family": "resident_detectability", + "schema_version": "resident-classification/v1", + "primary_class": "resident_with_summer_detectability_collapse", + "confidence": "medium", + "fit_score": 0.225, + "n_warnings": 0, + "peak_month": 4, + "peak_label": "April", + "trough_month": 9, + "trough_label": "September", + "season_start_month": null, + "season_start_label": null, + "season_end_month": null, + "season_end_label": null, + "season_width_months": null, + "season_midpoint_month": null, + "baseline_presence": "weak", + "timing": "spring", + "season_width_class": null, + "window_shape": null, + "post_peak_decline": null, + "offseason_suppression": null, + "summer_suppression": "moderate", + "autumn_component": "weak", + "response_dynamics": "decline_biased", + "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, + "active_month_count_ge_0_10": null, + "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" + ], + "trait_count": 11, + "source_file": "/Users/dave/Dropbox/Development/Projects/OdeSolver/modelling/data/thrupp-lake-birds/resident/tufted_duck_classification.json", + "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." + }, + { + "species": "Egyptian Goose", + "model_family": "seasonal_presence", + "schema_version": "seasonal-classification/v1", + "primary_class": "moderate_spring_seasonal_presence", + "confidence": "medium", + "fit_score": 0.131, + "n_warnings": 0, + "peak_month": 3.915, + "peak_label": "April", + "trough_month": null, + "trough_label": null, + "season_start_month": 1.43, + "season_start_label": "January", + "season_end_month": 4.725, + "season_end_label": "May", + "season_width_months": 3.295, + "season_midpoint_month": 3.0775, + "baseline_presence": null, + "timing": "spring", + "season_width_class": "moderate", + "window_shape": "sharp", + "post_peak_decline": "strong", + "offseason_suppression": "moderate", + "summer_suppression": null, + "autumn_component": null, + "response_dynamics": null, + "target_mean_value": null, + "target_amplitude": null, + "baseline_to_peak_ratio": null, + "autumn_to_winter_weight_ratio": null, + "year_end_to_winter_weight_ratio": null, + "decay_to_growth_ratio": null, + "active_month_count_ge_0_10": null, + "traits": [ + "spring_peak", + "moderate_season", + "sharp_seasonal_window", + "strong_post_peak_decline", + "moderate_offseason_suppression", + "late_peak_alignment" + ], + "trait_count": 6, + "source_file": "/Users/dave/Dropbox/Development/Projects/OdeSolver/modelling/data/thrupp-lake-birds/seasonal/egyptian_goose_classification.json", + "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." + }, + { + "species": "Oystercatcher", + "model_family": "seasonal_presence", + "schema_version": "seasonal-classification/v1", + "primary_class": "narrow_early_spring_seasonal_presence", + "confidence": "high", + "fit_score": 0.007, + "n_warnings": 0, + "peak_month": 3.3, + "peak_label": "March", + "trough_month": null, + "trough_label": null, + "season_start_month": 2.43, + "season_start_label": "February", + "season_end_month": 4.27, + "season_end_label": "April", + "season_width_months": 1.84, + "season_midpoint_month": 3.35, + "baseline_presence": null, + "timing": "early_spring", + "season_width_class": "narrow", + "window_shape": "sharp", + "post_peak_decline": "strong", + "offseason_suppression": "strong", + "summer_suppression": null, + "autumn_component": null, + "response_dynamics": null, + "target_mean_value": null, + "target_amplitude": null, + "baseline_to_peak_ratio": null, + "autumn_to_winter_weight_ratio": null, + "year_end_to_winter_weight_ratio": null, + "decay_to_growth_ratio": null, + "active_month_count_ge_0_10": null, + "traits": [ + "early_spring_peak", + "narrow_season", + "sharp_seasonal_window", + "strong_post_peak_decline", + "strong_offseason_suppression", + "central_peak_alignment" + ], + "trait_count": 6, + "source_file": "/Users/dave/Dropbox/Development/Projects/OdeSolver/modelling/data/thrupp-lake-birds/seasonal/oystercatcher_classification.json", + "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." + }, + { + "species": "Pochard", + "model_family": "winter_presence", + "schema_version": "winter-classification/v1", + "primary_class": "winter_visitor_with_autumn_arrival_component", + "confidence": "low", + "fit_score": 0.161, + "n_warnings": 0, + "peak_month": 2, + "peak_label": "February", + "trough_month": 5, + "trough_label": "May", + "season_start_month": null, + "season_start_label": null, + "season_end_month": null, + "season_end_label": null, + "season_width_months": null, + "season_midpoint_month": null, + "baseline_presence": "low", + "timing": "core_winter", + "season_width_class": null, + "window_shape": null, + "post_peak_decline": null, + "offseason_suppression": null, + "summer_suppression": "moderate", + "autumn_component": "moderate", + "response_dynamics": "slow_arrival_fast_departure", + "target_mean_value": null, + "target_amplitude": null, + "baseline_to_peak_ratio": null, + "autumn_to_winter_weight_ratio": 0.21861471861471862, + "year_end_to_winter_weight_ratio": null, + "decay_to_growth_ratio": 3.5847457627118646, + "active_month_count_ge_0_10": 7, + "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" + ], + "trait_count": 7, + "source_file": "/Users/dave/Dropbox/Development/Projects/OdeSolver/modelling/data/thrupp-lake-birds/winter/pochard_classification.json", + "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." + }, + { + "species": "Shoveler", + "model_family": "winter_presence", + "schema_version": "winter-classification/v1", + "primary_class": "winter_visitor_with_weak_autumn_arrival_component", + "confidence": "medium", + "fit_score": 0.097, + "n_warnings": 0, + "peak_month": 2, + "peak_label": "February", + "trough_month": 6, + "trough_label": "June", + "season_start_month": null, + "season_start_label": null, + "season_end_month": null, + "season_end_label": null, + "season_width_months": null, + "season_midpoint_month": null, + "baseline_presence": "low", + "timing": "core_winter", + "season_width_class": null, + "window_shape": null, + "post_peak_decline": null, + "offseason_suppression": null, + "summer_suppression": "moderate", + "autumn_component": "weak", + "response_dynamics": "faster_departure_than_arrival", + "target_mean_value": null, + "target_amplitude": null, + "baseline_to_peak_ratio": null, + "autumn_to_winter_weight_ratio": 0.16810344827586207, + "year_end_to_winter_weight_ratio": null, + "decay_to_growth_ratio": 2.4811827956989245, + "active_month_count_ge_0_10": 7, + "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" + ], + "trait_count": 7, + "source_file": "/Users/dave/Dropbox/Development/Projects/OdeSolver/modelling/data/thrupp-lake-birds/winter/shoveler_classification.json", + "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/analysis/species_similarity.json b/modelling/data/thrupp-lake-birds/analysis/species_similarity.json new file mode 100644 index 0000000..884b7fa --- /dev/null +++ b/modelling/data/thrupp-lake-birds/analysis/species_similarity.json @@ -0,0 +1,5188 @@ +{ + "schema_version": "species-similarity/v1", + "created_utc": "2026-05-24T06:54:35.305214+00:00", + "source_feature_schema_version": "species-feature-table/v1", + "source_feature_created_utc": "2026-05-24T06:54:35.302377+00:00", + "n_species": 19, + "top_n": 5, + "method": { + "description": "Weighted mixed-feature similarity using circular month distance, min-max scaled numeric distance, categorical exact-match distance, and Jaccard trait distance.", + "distance_range": "0 means identical on compared features; 1 means maximally different", + "similarity_range": "1 means most similar; 0 means least similar", + "component_weights": { + "circular_month": 0.4, + "numeric": 0.25, + "categorical": 0.2, + "traits": 0.15 + }, + "circular_month_features": { + "peak_month": 2.0, + "trough_month": 1.25, + "season_start_month": 1.25, + "season_end_month": 1.25, + "season_midpoint_month": 1.5 + }, + "numeric_features": { + "season_width_months": 1.5, + "target_mean_value": 1.0, + "target_amplitude": 1.0, + "baseline_to_peak_ratio": 1.0, + "autumn_to_winter_weight_ratio": 0.75, + "year_end_to_winter_weight_ratio": 0.75, + "decay_to_growth_ratio": 0.75, + "active_month_count_ge_0_10": 1.0, + "fit_score": 0.25 + }, + "categorical_features": { + "model_family": 1.0, + "primary_class": 1.0, + "confidence": 0.25, + "baseline_presence": 0.75, + "timing": 1.0, + "season_width_class": 0.75, + "window_shape": 0.75, + "post_peak_decline": 0.75, + "offseason_suppression": 0.75, + "summer_suppression": 0.75, + "autumn_component": 0.75, + "response_dynamics": 0.75 + }, + "missing_value_policy": "Missing feature values are skipped for that pair/component. Component weights are renormalised over available components." + }, + "species": [ + { + "species": "Black Headed Gull", + "model_family": "resident_detectability", + "primary_class": "resident_with_summer_detectability_collapse" + }, + { + "species": "Canada Goose", + "model_family": "resident_detectability", + "primary_class": "resident_with_summer_detectability_collapse" + }, + { + "species": "Coot", + "model_family": "resident_detectability", + "primary_class": "resident_with_summer_detectability_collapse" + }, + { + "species": "Cormorant", + "model_family": "resident_detectability", + "primary_class": "resident_with_summer_detectability_collapse" + }, + { + "species": "Egret", + "model_family": "resident_detectability", + "primary_class": "resident_with_spring_persistence_and_summer_suppression" + }, + { + "species": "Gadwall", + "model_family": "resident_detectability", + "primary_class": "resident_with_summer_detectability_collapse" + }, + { + "species": "Great Crested Grebe", + "model_family": "resident_detectability", + "primary_class": "resident_with_summer_detectability_collapse" + }, + { + "species": "Grey Heron", + "model_family": "resident_detectability", + "primary_class": "resident_with_summer_detectability_collapse" + }, + { + "species": "Greylag Goose", + "model_family": "resident_detectability", + "primary_class": "resident_with_summer_detectability_collapse" + }, + { + "species": "Herring Gull", + "model_family": "resident_detectability", + "primary_class": "resident_with_summer_detectability_collapse" + }, + { + "species": "Mallard", + "model_family": "resident_detectability", + "primary_class": "resident_with_summer_detectability_collapse" + }, + { + "species": "Moorhen", + "model_family": "resident_detectability", + "primary_class": "resident_with_summer_detectability_collapse" + }, + { + "species": "Mute Swan", + "model_family": "resident_detectability", + "primary_class": "resident_with_summer_detectability_collapse" + }, + { + "species": "Robin", + "model_family": "resident_detectability", + "primary_class": "resident_with_summer_detectability_collapse" + }, + { + "species": "Tufted Duck", + "model_family": "resident_detectability", + "primary_class": "resident_with_summer_detectability_collapse" + }, + { + "species": "Egyptian Goose", + "model_family": "seasonal_presence", + "primary_class": "moderate_spring_seasonal_presence" + }, + { + "species": "Oystercatcher", + "model_family": "seasonal_presence", + "primary_class": "narrow_early_spring_seasonal_presence" + }, + { + "species": "Pochard", + "model_family": "winter_presence", + "primary_class": "winter_visitor_with_autumn_arrival_component" + }, + { + "species": "Shoveler", + "model_family": "winter_presence", + "primary_class": "winter_visitor_with_weak_autumn_arrival_component" + } + ], + "nearest_neighbours": { + "Black Headed Gull": [ + { + "species": "Mallard", + "model_family": "resident_detectability", + "primary_class": "resident_with_summer_detectability_collapse", + "similarity": 0.944309, + "distance": 0.055691, + "component_distances": { + "circular_month": 0.0, + "numeric": 0.122765, + "categorical": 0.0, + "traits": 0.166667 + } + }, + { + "species": "Herring Gull", + "model_family": "resident_detectability", + "primary_class": "resident_with_summer_detectability_collapse", + "similarity": 0.90758, + "distance": 0.09242, + "component_distances": { + "circular_month": 0.064103, + "numeric": 0.167118, + "categorical": 0.0, + "traits": 0.166667 + } + }, + { + "species": "Greylag Goose", + "model_family": "resident_detectability", + "primary_class": "resident_with_summer_detectability_collapse", + "similarity": 0.90239, + "distance": 0.09761, + "component_distances": { + "circular_month": 0.0, + "numeric": 0.173826, + "categorical": 0.04, + "traits": 0.307692 + } + }, + { + "species": "Coot", + "model_family": "resident_detectability", + "primary_class": "resident_with_summer_detectability_collapse", + "similarity": 0.900286, + "distance": 0.099714, + "component_distances": { + "circular_month": 0.0, + "numeric": 0.086241, + "categorical": 0.16, + "traits": 0.307692 + } + }, + { + "species": "Mute Swan", + "model_family": "resident_detectability", + "primary_class": "resident_with_summer_detectability_collapse", + "similarity": 0.855234, + "distance": 0.144766, + "component_distances": { + "circular_month": 0.0, + "numeric": 0.351063, + "categorical": 0.16, + "traits": 0.166667 + } + } + ], + "Canada Goose": [ + { + "species": "Mute Swan", + "model_family": "resident_detectability", + "primary_class": "resident_with_summer_detectability_collapse", + "similarity": 0.887527, + "distance": 0.112473, + "component_distances": { + "circular_month": 0.0, + "numeric": 0.169275, + "categorical": 0.12, + "traits": 0.307692 + } + }, + { + "species": "Coot", + "model_family": "resident_detectability", + "primary_class": 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{ + "species_a": "Tufted Duck", + "species_b": "Egyptian Goose", + "model_family_a": "resident_detectability", + "model_family_b": "seasonal_presence", + "primary_class_a": "resident_with_summer_detectability_collapse", + "primary_class_b": "moderate_spring_seasonal_presence", + "similarity": 0.683414, + "distance": 0.316586, + "component_distances": { + "circular_month": 0.014167, + "numeric": 0.151369, + "categorical": 0.615385, + "traits": 1.0 + }, + "compared_feature_counts": { + "circular_month": 1, + "numeric": 1, + "categorical": 4, + "traits": 0 + } + }, + { + "species_a": "Tufted Duck", + "species_b": "Oystercatcher", + "model_family_a": "resident_detectability", + "model_family_b": "seasonal_presence", + "primary_class_a": "resident_with_summer_detectability_collapse", + "primary_class_b": "narrow_early_spring_seasonal_presence", + "similarity": 0.515572, + "distance": 0.484428, + "component_distances": { + "circular_month": 0.116667, + "numeric": 0.351047, + "categorical": 1.0, + "traits": 1.0 + }, + "compared_feature_counts": { + "circular_month": 1, + "numeric": 1, + "categorical": 4, + "traits": 0 + } + }, + { + "species_a": "Tufted Duck", + "species_b": "Pochard", + "model_family_a": "resident_detectability", + "model_family_b": "winter_presence", + "primary_class_a": "resident_with_summer_detectability_collapse", + "primary_class_b": "winter_visitor_with_autumn_arrival_component", + "similarity": 0.296315, + "distance": 0.703685, + "component_distances": { + "circular_month": 0.461538, + "numeric": 0.807572, + "categorical": 0.88, + "traits": 0.941176 + }, + "compared_feature_counts": { + "circular_month": 2, + "numeric": 3, + "categorical": 8, + "traits": 1 + } + }, + { + "species_a": "Tufted Duck", + "species_b": "Shoveler", + "model_family_a": "resident_detectability", + "model_family_b": "winter_presence", + "primary_class_a": "resident_with_summer_detectability_collapse", + "primary_class_b": "winter_visitor_with_weak_autumn_arrival_component", + "similarity": 0.436607, + "distance": 0.563393, + "component_distances": { + "circular_month": 0.397436, + "numeric": 0.516673, + "categorical": 0.72, + "traits": 0.875 + }, + "compared_feature_counts": { + "circular_month": 2, + "numeric": 3, + "categorical": 8, + "traits": 2 + } + }, + { + "species_a": "Egyptian Goose", + "species_b": "Oystercatcher", + "model_family_a": "seasonal_presence", + "model_family_b": "seasonal_presence", + "primary_class_a": "moderate_spring_seasonal_presence", + "primary_class_b": "narrow_early_spring_seasonal_presence", + "similarity": 0.500166, + "distance": 0.499834, + "component_distances": { + "circular_month": 0.096042, + "numeric": 0.885668, + "categorical": 0.6, + "traits": 0.8 + }, + "compared_feature_counts": { + "circular_month": 4, + "numeric": 2, + "categorical": 8, + "traits": 2 + } + }, + { + "species_a": "Egyptian Goose", + "species_b": "Pochard", + "model_family_a": "seasonal_presence", + "model_family_b": "winter_presence", + "primary_class_a": "moderate_spring_seasonal_presence", + "primary_class_b": "winter_visitor_with_autumn_arrival_component", + "similarity": 0.510256, + "distance": 0.489744, + "component_distances": { + "circular_month": 0.319167, + "numeric": 0.048309, + "categorical": 1.0, + "traits": 1.0 + }, + "compared_feature_counts": { + "circular_month": 1, + "numeric": 1, + "categorical": 4, + "traits": 0 + } + }, + { + "species_a": "Egyptian Goose", + "species_b": "Shoveler", + "model_family_a": "seasonal_presence", + "model_family_b": "winter_presence", + "primary_class_a": "moderate_spring_seasonal_presence", + "primary_class_b": "winter_visitor_with_weak_autumn_arrival_component", + "similarity": 0.52403, + "distance": 0.47597, + "component_distances": { + "circular_month": 0.319167, + "numeric": 0.05475, + "categorical": 0.923077, + "traits": 1.0 + }, + "compared_feature_counts": { + "circular_month": 1, + "numeric": 1, + "categorical": 4, + "traits": 0 + } + }, + { + "species_a": "Oystercatcher", + "species_b": "Pochard", + "model_family_a": "seasonal_presence", + "model_family_b": "winter_presence", + "primary_class_a": "narrow_early_spring_seasonal_presence", + "primary_class_b": "winter_visitor_with_autumn_arrival_component", + "similarity": 0.501337, + "distance": 0.498663, + "component_distances": { + "circular_month": 0.216667, + "numeric": 0.247987, + "categorical": 1.0, + "traits": 1.0 + }, + "compared_feature_counts": { + "circular_month": 1, + "numeric": 1, + "categorical": 4, + "traits": 0 + } + }, + { + "species_a": "Oystercatcher", + "species_b": "Shoveler", + "model_family_a": "seasonal_presence", + "model_family_b": "winter_presence", + "primary_class_a": "narrow_early_spring_seasonal_presence", + "primary_class_b": "winter_visitor_with_weak_autumn_arrival_component", + "similarity": 0.527101, + "distance": 0.472899, + "component_distances": { + "circular_month": 0.216667, + "numeric": 0.144928, + "categorical": 1.0, + "traits": 1.0 + }, + "compared_feature_counts": { + "circular_month": 1, + "numeric": 1, + "categorical": 4, + "traits": 0 + } + }, + { + "species_a": "Pochard", + "species_b": "Shoveler", + "model_family_a": "winter_presence", + "model_family_b": "winter_presence", + "primary_class_a": "winter_visitor_with_autumn_arrival_component", + "primary_class_b": "winter_visitor_with_weak_autumn_arrival_component", + "similarity": 0.768728, + "distance": 0.231272, + "component_distances": { + "circular_month": 0.064103, + "numeric": 0.203856, + "categorical": 0.44, + "traits": 0.444444 + }, + "compared_feature_counts": { + "circular_month": 2, + "numeric": 4, + "categorical": 8, + "traits": 5 + } + } + ] +} \ No newline at end of file diff --git a/modelling/data/thrupp-lake-birds/analysis/species_similarity.txt b/modelling/data/thrupp-lake-birds/analysis/species_similarity.txt new file mode 100644 index 0000000..c4bd99f --- /dev/null +++ b/modelling/data/thrupp-lake-birds/analysis/species_similarity.txt @@ -0,0 +1,152 @@ + +Black Headed Gull +----------------- + 1. Mallard similarity=0.944 distance=0.056 + 2. Herring Gull similarity=0.908 distance=0.092 + 3. Greylag Goose similarity=0.902 distance=0.098 + 4. Coot similarity=0.900 distance=0.100 + 5. Mute Swan similarity=0.855 distance=0.145 + +Canada Goose +------------ + 1. Mute Swan similarity=0.888 distance=0.112 + 2. Coot similarity=0.866 distance=0.134 + 3. Cormorant similarity=0.861 distance=0.139 + 4. Great Crested Grebe similarity=0.855 distance=0.145 + 5. Mallard similarity=0.798 distance=0.202 + +Coot +---- + 1. Mallard similarity=0.902 distance=0.098 + 2. Black Headed Gull similarity=0.900 distance=0.100 + 3. Tufted Duck similarity=0.880 distance=0.120 + 4. Canada Goose similarity=0.866 distance=0.134 + 5. Herring Gull similarity=0.863 distance=0.137 + +Cormorant +--------- + 1. Mute Swan similarity=0.925 distance=0.075 + 2. Great Crested Grebe similarity=0.872 distance=0.128 + 3. Canada Goose similarity=0.861 distance=0.139 + 4. Black Headed Gull similarity=0.835 distance=0.165 + 5. Mallard similarity=0.802 distance=0.198 + +Egret +----- + 1. Herring Gull similarity=0.685 distance=0.315 + 2. Mallard similarity=0.677 distance=0.323 + 3. Black Headed Gull similarity=0.673 distance=0.327 + 4. Tufted Duck similarity=0.656 distance=0.344 + 5. Greylag Goose similarity=0.646 distance=0.354 + +Gadwall +------- + 1. Grey Heron similarity=0.815 distance=0.185 + 2. Moorhen similarity=0.793 distance=0.207 + 3. Robin similarity=0.713 distance=0.287 + 4. Herring Gull similarity=0.693 distance=0.307 + 5. Tufted Duck similarity=0.667 distance=0.333 + +Great Crested Grebe +------------------- + 1. Cormorant similarity=0.872 distance=0.128 + 2. Mute Swan similarity=0.860 distance=0.140 + 3. Canada Goose similarity=0.855 distance=0.145 + 4. Herring Gull similarity=0.797 distance=0.203 + 5. Greylag Goose similarity=0.787 distance=0.213 + +Grey Heron +---------- + 1. Moorhen similarity=0.958 distance=0.042 + 2. Mallard similarity=0.818 distance=0.182 + 3. Gadwall similarity=0.815 distance=0.185 + 4. Herring Gull similarity=0.801 distance=0.199 + 5. Black Headed Gull similarity=0.775 distance=0.225 + +Greylag Goose +------------- + 1. Black Headed Gull similarity=0.902 distance=0.098 + 2. Mallard similarity=0.884 distance=0.116 + 3. Herring Gull similarity=0.860 distance=0.140 + 4. Coot similarity=0.823 distance=0.177 + 5. Tufted Duck similarity=0.803 distance=0.197 + +Herring Gull +------------ + 1. Mallard similarity=0.954 distance=0.046 + 2. Black Headed Gull similarity=0.908 distance=0.092 + 3. Tufted Duck similarity=0.894 distance=0.106 + 4. Coot similarity=0.863 distance=0.137 + 5. Greylag Goose similarity=0.860 distance=0.140 + +Mallard +------- + 1. Herring Gull similarity=0.954 distance=0.046 + 2. Black Headed Gull similarity=0.944 distance=0.056 + 3. Coot similarity=0.902 distance=0.098 + 4. Greylag Goose similarity=0.884 distance=0.116 + 5. Tufted Duck similarity=0.856 distance=0.144 + +Moorhen +------- + 1. Grey Heron similarity=0.958 distance=0.042 + 2. Mallard similarity=0.843 distance=0.157 + 3. Black Headed Gull similarity=0.812 distance=0.188 + 4. Herring Gull similarity=0.809 distance=0.191 + 5. Gadwall similarity=0.793 distance=0.207 + +Mute Swan +--------- + 1. Cormorant similarity=0.925 distance=0.075 + 2. Canada Goose similarity=0.888 distance=0.112 + 3. Great Crested Grebe similarity=0.860 distance=0.140 + 4. Black Headed Gull similarity=0.855 distance=0.145 + 5. Mallard similarity=0.843 distance=0.157 + +Robin +----- + 1. Tufted Duck similarity=0.849 distance=0.151 + 2. Herring Gull similarity=0.814 distance=0.186 + 3. Mallard similarity=0.785 distance=0.215 + 4. Coot similarity=0.780 distance=0.220 + 5. Black Headed Gull similarity=0.777 distance=0.223 + +Tufted Duck +----------- + 1. Herring Gull similarity=0.894 distance=0.106 + 2. Coot similarity=0.880 distance=0.120 + 3. Mallard similarity=0.856 distance=0.144 + 4. Black Headed Gull similarity=0.854 distance=0.146 + 5. Robin similarity=0.849 distance=0.151 + +Egyptian Goose +-------------- + 1. Black Headed Gull similarity=0.693 distance=0.307 + 2. Cormorant similarity=0.691 distance=0.309 + 3. Herring Gull similarity=0.687 distance=0.313 + 4. Great Crested Grebe similarity=0.684 distance=0.316 + 5. Tufted Duck similarity=0.683 distance=0.317 + +Oystercatcher +------------- + 1. Mute Swan similarity=0.543 distance=0.457 + 2. Canada Goose similarity=0.543 distance=0.457 + 3. Coot similarity=0.541 distance=0.459 + 4. Robin similarity=0.540 distance=0.460 + 5. Shoveler similarity=0.527 distance=0.473 + +Pochard +------- + 1. Shoveler similarity=0.769 distance=0.231 + 2. Egyptian Goose similarity=0.510 distance=0.490 + 3. Gadwall similarity=0.503 distance=0.497 + 4. Oystercatcher similarity=0.501 distance=0.499 + 5. Grey Heron similarity=0.382 distance=0.618 + +Shoveler +-------- + 1. Pochard similarity=0.769 distance=0.231 + 2. Gadwall similarity=0.592 distance=0.408 + 3. Oystercatcher similarity=0.527 distance=0.473 + 4. Egyptian Goose similarity=0.524 distance=0.476 + 5. Grey Heron similarity=0.522 distance=0.478 diff --git a/modelling/data/thrupp-lake-birds/analysis/species_similarity_heatmap.png b/modelling/data/thrupp-lake-birds/analysis/species_similarity_heatmap.png new file mode 100644 index 0000000..a689d7f Binary files /dev/null and b/modelling/data/thrupp-lake-birds/analysis/species_similarity_heatmap.png differ diff --git a/modelling/data/thrupp-lake-birds/resident/gadwall_observed.csv b/modelling/data/thrupp-lake-birds/resident/gadwall_observed.csv deleted file mode 100644 index 5599d19..0000000 --- a/modelling/data/thrupp-lake-birds/resident/gadwall_observed.csv +++ /dev/null @@ -1,13 +0,0 @@ -month,value -1,7 -2,3 -3,1 -4,1 -5,0 -6,0 -7,1 -8,1 -9,0 -10,0 -11,1 -12,0 diff --git a/modelling/data/thrupp-lake-birds/resident/greylag_goose_classification.json b/modelling/data/thrupp-lake-birds/resident/greylag_goose_classification.json new file mode 100644 index 0000000..5786a88 --- /dev/null +++ b/modelling/data/thrupp-lake-birds/resident/greylag_goose_classification.json @@ -0,0 +1,105 @@ +{ + "schema_version": "resident-classification/v1", + "species": "Greylag Goose", + "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": "moderate", + "autumn_component": "weak", + "year_end_component": "weak", + "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", + "moderate_pre_summer_retention", + "weak_autumn_component", + "weak_year_end_component", + "rapid_decline_biased_response_dynamics" + ], + "confidence": "low" + }, + "derived_metrics": { + "target_peak_month": 4, + "target_peak_label": "April", + "target_trough_month": 10, + "target_trough_label": "October", + "target_peak_value": 0.5644268966925725, + "target_trough_value": 0.0, + "target_mean_value": 0.139885619245235, + "target_amplitude": 0.5644268966925725, + "baseline_to_peak_ratio": 0.05315125869407346, + "autumn_to_winter_weight_ratio": 0.05048543689320388, + "year_end_to_winter_weight_ratio": 0.2407766990291262, + "decay_to_growth_ratio": 1.7622466216216217, + "monthly_target": { + "January": 0.07422722870986138, + "February": 0.07957950777159611, + "March": 0.2105025628841274, + "April": 0.5644268966925725, + "May": 0.3921727401649599, + "June": 0.10995920906456151, + "July": 0.070917609229015, + "August": 0.02999907403653956, + "September": 0.0170083831345786, + "October": 0.0, + "November": 7.933652477110464e-05, + "December": 0.12975488273023664 + } + }, + "parameter_evidence": { + "INITIAL_Y": 0.111, + "GROWTH_RATE": 2.368, + "DECAY_RATE": 4.173, + "SUMMER_DECAY_BOOST": 4.058, + "PRE_SUMMER_DECAY_REDUCTION": 0.341, + "PRE_SUMMER_DECAY_END": 6.92, + "PRE_SUMMER_DECAY_SHARPNESS": 9.036, + "SPRING_CARRYOVER_WEIGHT": 0.044, + "SPRING_CARRYOVER_END": 7.13, + "SPRING_CARRYOVER_SHARPNESS": 18.654, + "BASELINE": 0.03, + "WINTER_WEIGHT": 0.515, + "AUTUMN_WEIGHT": 0.026, + "WINTER_PEAK": 4.24, + "AUTUMN_PEAK": 10.915, + "AUTUMN_ONSET": 11.355, + "AUTUMN_GATE_SHARPNESS": 6.38, + "WINTER_WIDTH": 12.236, + "WINTER_RISE_WIDTH": 12.376, + "WINTER_FALL_WIDTH": 12.084, + "AUTUMN_WIDTH": 6.683, + "AUTUMN_RISE_WIDTH": 6.649, + "AUTUMN_FALL_WIDTH": 7.014, + "SUMMER_DIP": 0.08, + "SUMMER_LOW": 9.855, + "SUMMER_ONSET": 8.65, + "SUMMER_GATE_SHARPNESS": 4.684, + "SUMMER_DECAY_ONSET": 7.08, + "SUMMER_DECAY_GATE_SHARPNESS": 17.865, + "SUMMER_WIDTH": 21.75, + "SUMMER_RISE_WIDTH": 32.464, + "SUMMER_FALL_WIDTH": 9.921, + "SCALE": 1.078, + "YEAR_END_WEIGHT": 0.124, + "YEAR_END_PEAK": 12.188, + "YEAR_END_WIDTH": 75.754, + "YEAR_END_RISE_WIDTH": 140.262, + "YEAR_END_FALL_WIDTH": 11.506 + }, + "fit": { + "score": 0.356 + }, + "warnings": [], + "summary": "Greylag 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 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/greylag_goose_consensus.json b/modelling/data/thrupp-lake-birds/resident/greylag_goose_consensus.json new file mode 100644 index 0000000..7a5c12d --- /dev/null +++ b/modelling/data/thrupp-lake-birds/resident/greylag_goose_consensus.json @@ -0,0 +1,42 @@ +{ + "SCORE": "0.356", + "INITIAL_Y": "0.111", + "GROWTH_RATE": "2.368", + "DECAY_RATE": "4.173", + "SUMMER_DECAY_BOOST": "4.058", + "PRE_SUMMER_DECAY_REDUCTION": "0.341", + "PRE_SUMMER_DECAY_END": "6.92", + "PRE_SUMMER_DECAY_SHARPNESS": "9.036", + "SPRING_CARRYOVER_WEIGHT": "0.044", + "SPRING_CARRYOVER_END": "7.13", + "SPRING_CARRYOVER_SHARPNESS": "18.654", + "BASELINE": "0.03", + "WINTER_WEIGHT": "0.515", + "AUTUMN_WEIGHT": "0.026", + "WINTER_PEAK": "4.24", + "AUTUMN_PEAK": "10.915", + "AUTUMN_ONSET": "11.355", + "AUTUMN_GATE_SHARPNESS": "6.38", + "WINTER_WIDTH": "12.236", + "WINTER_RISE_WIDTH": "12.376", + "WINTER_FALL_WIDTH": "12.084", + "AUTUMN_WIDTH": "6.683", + "AUTUMN_RISE_WIDTH": "6.649", + "AUTUMN_FALL_WIDTH": "7.014", + "SUMMER_DIP": "0.08", + "SUMMER_LOW": "9.855", + "SUMMER_ONSET": "8.65", + "SUMMER_GATE_SHARPNESS": "4.684", + "SUMMER_DECAY_ONSET": "7.08", + "SUMMER_DECAY_GATE_SHARPNESS": "17.865", + "SUMMER_WIDTH": "21.75", + "SUMMER_RISE_WIDTH": "32.464", + "SUMMER_FALL_WIDTH": "9.921", + "SCALE": "1.078", + "YEAR_END_WEIGHT": "0.124", + "YEAR_END_PEAK": "12.188", + "YEAR_END_WIDTH": "75.754", + "YEAR_END_RISE_WIDTH": "140.262", + "YEAR_END_FALL_WIDTH": "11.506", + "SPECIES": "Greylag Goose" +} diff --git a/modelling/data/thrupp-lake-birds/seasonal/greylag_goose_observed.csv b/modelling/data/thrupp-lake-birds/resident/greylag_goose_observed.csv similarity index 100% rename from modelling/data/thrupp-lake-birds/seasonal/greylag_goose_observed.csv rename to modelling/data/thrupp-lake-birds/resident/greylag_goose_observed.csv diff --git a/modelling/data/thrupp-lake-birds/resident/greylag_goose_parameters.csv b/modelling/data/thrupp-lake-birds/resident/greylag_goose_parameters.csv new file mode 100644 index 0000000..046ca11 --- /dev/null +++ b/modelling/data/thrupp-lake-birds/resident/greylag_goose_parameters.csv @@ -0,0 +1,201 @@ 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a/modelling/data/thrupp-lake-birds/resident/greylag_goose_simulated.png b/modelling/data/thrupp-lake-birds/resident/greylag_goose_simulated.png new file mode 100644 index 0000000..13f3218 Binary files /dev/null and b/modelling/data/thrupp-lake-birds/resident/greylag_goose_simulated.png differ diff --git a/modelling/data/thrupp-lake-birds/resident/greylag_goose_synthesised.csv b/modelling/data/thrupp-lake-birds/resident/greylag_goose_synthesised.csv new file mode 100644 index 0000000..07fd1df --- /dev/null +++ b/modelling/data/thrupp-lake-birds/resident/greylag_goose_synthesised.csv @@ -0,0 +1,13 @@ +month,observed,simulated_raw,synthesised +1,1,0.08872489,2.6411537089143766 +2,2,0.09284811,2.7638933121493867 +3,8,0.2565472,7.636871556466266 +4,19,0.5045381,15.019040024773348 +5,5,0.3455072,10.285023996497728 +6,4,0.12620506,3.7568596850642635 +7,2,0.05123282,1.5250934947469943 +8,2,0.02980957,0.8873683175785592 +9,1,0.0073469188,0.21870234877397718 +10,0,7.26746928e-06,0.00021633730335752789 +11,0,0.015620679919,0.4649948475994861 +12,2,0.11122625,3.310971957430859 diff --git a/modelling/data/thrupp-lake-birds/resident/greylag_goose_synthesised.png b/modelling/data/thrupp-lake-birds/resident/greylag_goose_synthesised.png new file mode 100644 index 0000000..e6a9a72 Binary files /dev/null and b/modelling/data/thrupp-lake-birds/resident/greylag_goose_synthesised.png differ diff --git a/modelling/data/thrupp-lake-birds/seasonal/greylag_goose_classification.json b/modelling/data/thrupp-lake-birds/seasonal/greylag_goose_classification.json deleted file mode 100644 index e04a50d..0000000 --- a/modelling/data/thrupp-lake-birds/seasonal/greylag_goose_classification.json +++ /dev/null @@ -1,52 +0,0 @@ -{ - "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 deleted file mode 100644 index 3a696ab..0000000 --- a/modelling/data/thrupp-lake-birds/seasonal/greylag_goose_consensus.json +++ /dev/null @@ -1,13 +0,0 @@ -{ - "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_parameters.csv b/modelling/data/thrupp-lake-birds/seasonal/greylag_goose_parameters.csv deleted file mode 100644 index 8723a90..0000000 --- a/modelling/data/thrupp-lake-birds/seasonal/greylag_goose_parameters.csv +++ 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deleted file mode 100644 index fbcb70e..0000000 Binary files a/modelling/data/thrupp-lake-birds/seasonal/greylag_goose_simulated.png and /dev/null 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 deleted file mode 100644 index b05fb7c..0000000 --- a/modelling/data/thrupp-lake-birds/seasonal/greylag_goose_synthesised.csv +++ /dev/null @@ -1,13 +0,0 @@ -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 deleted file mode 100644 index 3adb692..0000000 Binary files a/modelling/data/thrupp-lake-birds/seasonal/greylag_goose_synthesised.png and /dev/null differ diff --git a/modelling/scripts/run-similarity.sh b/modelling/scripts/run-similarity.sh index 3d91893..62dfb30 100755 --- a/modelling/scripts/run-similarity.sh +++ b/modelling/scripts/run-similarity.sh @@ -1,8 +1,8 @@ #!/usr/bin/env bash -if (( $# < 1 )); then +if (( $# < 2 )); then scriptname=$(basename -- "$0") - echo Usage: $scriptname PROJECT [WRITE-CSV] + echo Usage: $scriptname PROJECT CLUSTERS [WRITE-CSV] exit 1 fi @@ -36,9 +36,9 @@ fi # Set the arguments to write the CSV file WRITE_CSV="" -if (( $# == 2 )); then +if (( $# == 3 )); then # Get the first argument in lowercase - value=$(printf '%s' "$2" | tr '[:upper:]' '[:lower:]') + value=$(printf '%s' "$3" | tr '[:upper:]' '[:lower:]') # If it's truthy, set the CSV output arguments. Otherwise, make them blank case "$value" in @@ -49,7 +49,7 @@ if (( $# == 2 )); then WRITE_CSV="" ;; *) - echo "'$2' is not a valid value for WRITE-CSV" + echo "'$3' is not a valid value for WRITE-CSV" exit 1 ;; esac @@ -62,6 +62,7 @@ python "$MODELLING_ROOT/src/feature-matrix.py" \ --similarity "$ANALYSIS_FOLDER/species_similarity.json" \ --similarity-summary "$ANALYSIS_FOLDER/species_similarity.txt" \ --heatmap "$ANALYSIS_FOLDER/species_similarity_heatmap.png" \ + --number-of-clusters $2 \ --clusters "$ANALYSIS_FOLDER/cluster_analysis.json" \ --cluster-summary "$ANALYSIS_FOLDER/cluster_summary.txt" \ --dendrogram "$ANALYSIS_FOLDER/cluster_dendrogram.png"$WRITE_CSV