Files in nmouquet/RLS_AESTHE
Research Compendium
.gitignore
DESCRIPTION
LICENSE
LICENSE.md
R/functions_biodiv.R
R/functions_cons.R
R/functions_elo.R
R/setup.R
R/shadow_text.R
README.md
analyses/biodiversity/01_phylogeny.R
analyses/biodiversity/02_functional_div.R
analyses/conservation/01_conservation_status.R
analyses/deep/01_test_size.py
analyses/deep/02_train_crossval.py
analyses/deep/03_aggregate_species_level.R
analyses/deep/03_train_all.py
analyses/deep/04_inference.py
analyses/deep/05_size_effect.R
analyses/deep/06_prediction_performance.R
analyses/elo/01_group_effect.R
analyses/elo/02_elo_scores.R
analyses/features/cluster.R
analyses/features/features_analysis.R
analyses/features/lumsat.R
analyses/features/momocs.R
data/Data_S4.csv
data/Data_S4.xlsx
data/example_images/jpg/Abudefduf_luridus_A_1.jpg
data/example_images/jpg/Abudefduf_sexfasciatus_A_1.jpg
data/example_images/jpg/Abudefduf_sparoides_2.jpg
data/example_images/jpg/Acanthurus_bahianus_A_1.jpg
data/example_images/jpg/Amphiprion_bicinctus_J_1.jpg
data/example_images/jpg/Amphiprion_perideraion_A_1.jpg
data/example_images/jpg/Anampses_femininus_F_1.jpg
data/example_images/jpg/Apogon_pacificus_A_1.jpg
data/example_images/jpg/Aracana_aurita_M_2.jpg
data/example_images/jpg/Belone_belone_A_1.jpg
data/example_images/jpg/Bodianus_unimaculatus_F_1.jpg
data/example_images/jpg/Cantherhines_dumerilii_J_1.jpg
data/example_images/jpg/Caranx_ignobilis_A_2.jpg
data/example_images/jpg/Cephalopholis_sexmaculata_A_1.jpg
data/example_images/jpg/Chaetodon_lunula_A_1.jpg
data/example_images/jpg/Chromis_acares_A_1.jpg
data/example_images/jpg/Chromis_margaritifer_A_2.jpg
data/example_images/jpg/Chrysiptera_hemicyanea_A_1.jpg
data/example_images/jpg/Cirrhilabrus_temminckii_F_1.jpg
data/example_images/jpg/Coris_aygula_fem_186.jpg
data/example_images/jpg/Coris_bulbifrons_J_1.jpg
data/example_images/jpg/Ctenochaetus_marginatus_A_1.jpg
data/example_images/jpg/Diplodus_annularis_A_1.jpg
data/example_images/jpg/Embiotoca_jacksoni_A_1.jpg
data/example_images/jpg/Epinephelus_multinotatus_A_1.jpg
data/example_images/jpg/Epinephelus_ongus_J_1.jpg
data/example_images/jpg/Gerres_equulus_A_1.jpg
data/example_images/jpg/Gerres_subfasciatus_A_2.jpg
data/example_images/jpg/Gunnellichthys_monostigma_A_2.jpg
data/example_images/jpg/Holacanthus_ciliaris_J_1.jpg
data/example_images/jpg/Istigobius_decoratus_A_2.jpg
data/example_images/jpg/Itycirrhitus_wilhelmi_F_1.jpg
data/example_images/jpg/Kyphosus_bigibbus_A_2.jpg
data/example_images/jpg/Meiacanthus_atrodorsalis_A_2.jpg
data/example_images/jpg/Muraena_argus_A_2.jpg
data/example_images/jpg/Myripristis_amaena_A_2.jpg
data/example_images/jpg/Neoglyphidodon_crossi_J_1.jpg
data/example_images/jpg/Odontoscion_dentex_A_1.jpg
data/example_images/jpg/Opistognathus_aurifrons_A_2.jpg
data/example_images/jpg/Parma_bicolor_A_1.jpg
data/example_images/jpg/Pomacanthus_imperator_J_1.jpg
data/example_images/jpg/Pomacanthus_navarchus_A_1.jpg
data/example_images/jpg/Pomacanthus_semicirculatus_J_1.jpg
data/example_images/jpg/Pseudanthias_huchtii_M_1.jpg
data/example_images/jpg/Pseudobalistes_flavimarginatus_A_1.jpg
data/example_images/jpg/Pterois_miles_A_2.jpg
data/example_images/jpg/Pygoplites_diacanthus_A_2.jpg
data/example_images/jpg/Sarda_australis_A_1.jpg
data/example_images/jpg/Scarus_ferrugineus_M_1.jpg
data/example_images/jpg/Scomberomorus_commerson_A_1.jpg
data/example_images/jpg/Seriolella_brama_A_1.jpg
data/example_images/jpg/Sillago_schomburgkii_A_2.jpg
data/example_images/jpg/Suezichthys_devisi_J_1.jpg
data/example_images/jpg/Thyrsites_atun_A_2.jpg
data/example_images/jpg/Zebrasoma_scopas_A_1.jpg
data/example_images/jpg_mask/Abudefduf_luridus_A_1.jpg
data/example_images/jpg_mask/Abudefduf_sexfasciatus_A_1.jpg
data/example_images/jpg_mask/Abudefduf_sparoides_2.jpg
data/example_images/jpg_mask/Acanthurus_bahianus_A_1.jpg
data/example_images/jpg_mask/Amphiprion_bicinctus_J_1.jpg
data/example_images/jpg_mask/Amphiprion_perideraion_A_1.jpg
data/example_images/jpg_mask/Anampses_femininus_F_1.jpg
data/example_images/jpg_mask/Apogon_pacificus_A_1.jpg
data/example_images/jpg_mask/Aracana_aurita_M_2.jpg
data/example_images/jpg_mask/Belone_belone_A_1.jpg
data/example_images/jpg_mask/Bodianus_unimaculatus_F_1.jpg
data/example_images/jpg_mask/Cantherhines_dumerilii_J_1.jpg
data/example_images/jpg_mask/Caranx_ignobilis_A_2.jpg
data/example_images/jpg_mask/Cephalopholis_sexmaculata_A_1.jpg
data/example_images/jpg_mask/Chaetodon_lunula_A_1.jpg
data/example_images/jpg_mask/Chromis_acares_A_1.jpg
data/example_images/jpg_mask/Chromis_margaritifer_A_2.jpg
data/example_images/jpg_mask/Chrysiptera_hemicyanea_A_1.jpg
data/example_images/jpg_mask/Cirrhilabrus_temminckii_F_1.jpg
data/example_images/jpg_mask/Coris_aygula_fem_186.jpg
data/example_images/jpg_mask/Coris_bulbifrons_J_1.jpg
data/example_images/jpg_mask/Ctenochaetus_marginatus_A_1.jpg
data/example_images/jpg_mask/Diplodus_annularis_A_1.jpg
data/example_images/jpg_mask/Embiotoca_jacksoni_A_1.jpg
data/example_images/jpg_mask/Epinephelus_multinotatus_A_1.jpg
data/example_images/jpg_mask/Epinephelus_ongus_J_1.jpg
data/example_images/jpg_mask/Gerres_equulus_A_1.jpg
data/example_images/jpg_mask/Gerres_subfasciatus_A_2.jpg
data/example_images/jpg_mask/Gunnellichthys_monostigma_A_2.jpg
data/example_images/jpg_mask/Holacanthus_ciliaris_J_1.jpg
data/example_images/jpg_mask/Istigobius_decoratus_A_2.jpg
data/example_images/jpg_mask/Itycirrhitus_wilhelmi_F_1.jpg
data/example_images/jpg_mask/Kyphosus_bigibbus_A_2.jpg
data/example_images/jpg_mask/Meiacanthus_atrodorsalis_A_2.jpg
data/example_images/jpg_mask/Muraena_argus_A_2.jpg
data/example_images/jpg_mask/Myripristis_amaena_A_2.jpg
data/example_images/jpg_mask/Neoglyphidodon_crossi_J_1.jpg
data/example_images/jpg_mask/Odontoscion_dentex_A_1.jpg
data/example_images/jpg_mask/Opistognathus_aurifrons_A_2.jpg
data/example_images/jpg_mask/Parma_bicolor_A_1.jpg
data/example_images/jpg_mask/Pomacanthus_imperator_J_1.jpg
data/example_images/jpg_mask/Pomacanthus_navarchus_A_1.jpg
data/example_images/jpg_mask/Pomacanthus_semicirculatus_J_1.jpg
data/example_images/jpg_mask/Pseudanthias_huchtii_M_1.jpg
data/example_images/jpg_mask/Pseudobalistes_flavimarginatus_A_1.jpg
data/example_images/jpg_mask/Pterois_miles_A_2.jpg
data/example_images/jpg_mask/Pygoplites_diacanthus_A_2.jpg
data/example_images/jpg_mask/Sarda_australis_A_1.jpg
data/example_images/jpg_mask/Scarus_ferrugineus_M_1.jpg
data/example_images/jpg_mask/Scomberomorus_commerson_A_1.jpg
data/example_images/jpg_mask/Seriolella_brama_A_1.jpg
data/example_images/jpg_mask/Sillago_schomburgkii_A_2.jpg
data/example_images/jpg_mask/Suezichthys_devisi_J_1.jpg
data/example_images/jpg_mask/Thyrsites_atun_A_2.jpg
data/example_images/jpg_mask/Zebrasoma_scopas_A_1.jpg
data/example_images/png/Abudefduf_luridus_A_1.png
data/example_images/png/Abudefduf_sexfasciatus_A_1.png
data/example_images/png/Abudefduf_sparoides_2.png
data/example_images/png/Acanthurus_bahianus_A_1.png
data/example_images/png/Amphiprion_bicinctus_J_1.png
data/example_images/png/Amphiprion_perideraion_A_1.png
data/example_images/png/Anampses_femininus_F_1.png
data/example_images/png/Apogon_pacificus_A_1.png
data/example_images/png/Aracana_aurita_M_2.png
data/example_images/png/Belone_belone_A_1.png
data/example_images/png/Bodianus_unimaculatus_F_1.png
data/example_images/png/Cantherhines_dumerilii_J_1.png
data/example_images/png/Caranx_ignobilis_A_2.png
data/example_images/png/Cephalopholis_sexmaculata_A_1.png
data/example_images/png/Chaetodon_lunula_A_1.png
data/example_images/png/Chromis_acares_A_1.png
data/example_images/png/Chromis_margaritifer_A_2.png
data/example_images/png/Chrysiptera_hemicyanea_A_1.png
data/example_images/png/Cirrhilabrus_temminckii_F_1.png
data/example_images/png/Coris_aygula_fem_186.png
data/example_images/png/Coris_bulbifrons_J_1.png
data/example_images/png/Ctenochaetus_marginatus_A_1.png
data/example_images/png/Diplodus_annularis_A_1.png
data/example_images/png/Embiotoca_jacksoni_A_1.png
data/example_images/png/Epinephelus_multinotatus_A_1.png
data/example_images/png/Epinephelus_ongus_J_1.png
data/example_images/png/Gerres_equulus_A_1.png
data/example_images/png/Gerres_subfasciatus_A_2.png
data/example_images/png/Gunnellichthys_monostigma_A_2.png
data/example_images/png/Holacanthus_ciliaris_J_1.png
data/example_images/png/Istigobius_decoratus_A_2.png
data/example_images/png/Itycirrhitus_wilhelmi_F_1.png
data/example_images/png/Kyphosus_bigibbus_A_2.png
data/example_images/png/Meiacanthus_atrodorsalis_A_2.png
data/example_images/png/Muraena_argus_A_2.png
data/example_images/png/Myripristis_amaena_A_2.png
data/example_images/png/Neoglyphidodon_crossi_J_1.png
data/example_images/png/Odontoscion_dentex_A_1.png
data/example_images/png/Opistognathus_aurifrons_A_2.png
data/example_images/png/Parma_bicolor_A_1.png
data/example_images/png/Pomacanthus_imperator_J_1.png
data/example_images/png/Pomacanthus_navarchus_A_1.png
data/example_images/png/Pomacanthus_semicirculatus_J_1.png
data/example_images/png/Pseudanthias_huchtii_M_1.png
data/example_images/png/Pseudobalistes_flavimarginatus_A_1.png
data/example_images/png/Pterois_miles_A_2.png
data/example_images/png/Pygoplites_diacanthus_A_2.png
data/example_images/png/Sarda_australis_A_1.png
data/example_images/png/Scarus_ferrugineus_M_1.png
data/example_images/png/Scomberomorus_commerson_A_1.png
data/example_images/png/Seriolella_brama_A_1.png
data/example_images/png/Sillago_schomburgkii_A_2.png
data/example_images/png/Suezichthys_devisi_J_1.png
data/example_images/png/Thyrsites_atun_A_2.png
data/example_images/png/Zebrasoma_scopas_A_1.png
data/fonctio_table.csv
data/image_table.csv
data/table_all_judge.RData
data/table_elo_judge.RData
figures_tables/Extended_table_2.csv
figures_tables/FIGURE_1b.jpg
figures_tables/FIGURE_2a.jpg
figures_tables/FIGURE_2b.png
figures_tables/FIGURE_3.jpg
figures_tables/FIGURE_4.jpg
figures_tables/FIGURE_5.jpg
figures_tables/FIGURE_A.jpg
figures_tables/FIGURE_A.png
figures_tables/FIGURE_B.jpg
figures_tables/FIGURE_E.jpg
figures_tables/FIGURE_H.jpg
figures_tables/FIGURE_I.png
figures_tables/FIGURE_J.jpg
figures_tables/FIGURE_K.jpg
figures_tables/FIGURE_M.jpg
figures_tables/FIGURE_N.jpg
figures_tables/FIGURE_O.jpg
figures_tables/FIGURE_P_abc.jpg
figures_tables/FIGURE_P_d.jpg
figures_tables/FIGURE_Q.jpg
figures_tables/FIGURE_R.jpg
figures_tables/FIGURE_S.jpg
figures_tables/FIGURE_T.jpg
figures_tables/Figure_Ga.jpg
figures_tables/Figure_Gb.jpg
figures_tables/Figure_P_efgh.jpg
figures_tables/Figure_SGa.jpg
figures_tables/Figure_SGb.jpg
figures_tables/TABLE_A_S1.csv
figures_tables/TABLE_B_S1.csv
make.R
results/biodiversity/01_classification.csv
results/biodiversity/01_nb_sp_fam.csv
results/biodiversity/01_pagel_all.csv
results/biodiversity/01_pagel_mean.csv
results/biodiversity/01_set100.RData
results/biodiversity/01_sptable_phylo.csv
results/biodiversity/02_disTraits.RData
results/biodiversity/02_funk_nona.RData
results/biodiversity/02_sptable_biodiv.csv
results/conservation/01_data_imp_raw.csv
results/conservation/01_sp_table_cons.csv
results/conservation/01_sptable_all.csv
results/deep/01_resnet18.csv
results/deep/01_resnet50.csv
results/deep/01_test.txt
results/deep/01_train.txt
results/deep/01_val.txt
results/deep/02_run1/train.csv
results/deep/02_run1/val.csv
results/deep/02_run2/train.csv
results/deep/02_run2/val.csv
results/deep/02_run3/train.csv
results/deep/02_run3/val.csv
results/deep/02_run4/train.csv
results/deep/02_run4/val.csv
results/deep/02_run5/train.csv
results/deep/02_run5/val.csv
results/deep/03_species_table.csv
results/deep/03_train_all/all.pth
results/deep/04_esthe_pred50.csv
results/deep/06_esthe_focus.csv
results/deep/training/run1.csv
results/deep/training/run2.csv
results/deep/training/run3.csv
results/deep/training/run4.csv
results/deep/training/run5.csv
results/deep/validation_score/validation_score1.txt
results/deep/validation_score/validation_score2.txt
results/deep/validation_score/validation_score3.txt
results/deep/validation_score/validation_score4.txt
results/deep/validation_score/validation_score5.txt
results/deep/weight/all.pth
results/deep/weight/run1.pth
results/deep/weight/run2.pth
results/deep/weight/run3.pth
results/deep/weight/run4.pth
results/deep/weight/run5.pth
results/elo/01_nogroupeffect.csv
results/elo/02_deep_train.csv
results/elo/02_eloscores_fisheyes.csv
results/elo/02_esthe_focus.csv
results/elo/02_stabilization_elo.csv
results/features/cluster.csv
results/features/fig_pca.png
results/features/lumsat.csv
results/features/momocs.csv
