miguelfortuna/birdmigrationnetworks

Data set and R code used in the following study: "Phylogenetically-conserved bird migration networks determine the distribution of avian flu", which has been recently submitted (2020).

Phylogenetically-conserved bird migration networks determine the distribution of avian flu

Data set and R code used in this study:

folder "raw_data"

We provide the following files:

• "species_135.csv"
• "ibas_135_species.csv"
• "links_135_species.csv"

folder "working_data"

We provide the following files:

• "species_84.csv"
• "ibas_84_species.csv"
• "links_84_species.csv"

folder "avian_flu_data"

We provide the following files:

• "avian_flu_raw_dataset.csv"
• "avian_flu_working_dataset.csv"
• "mapping_avian_flu.R"

Additional files are created after running "mapping_avian_flu.R":

• "flu_data.csv"
• "flu_locations_mapped.csv"
• "flu_mapped_species_list.csv"
• "flu_data_working.csv"
• "flu_mapped_species_list_working.csv"
• "flu_nodes.csv"

folder "pca_and_predictions"

We provide the following files:

• "pca.R"

Additional files and folders are created after running "pca.R": folder "84_species_networks"

• "data_pc1.csv"
• "nodes_100_list.csv"
• "nodes_100_list_84_species.csv"

folder "glmer"

We provide the following files:

• "glmer_flu.R"

Additional files and folders are created after running "glmer_flu.R":

• "flu_incidence.csv"
• "df_flu.csv"

folder "ecological_distance_matrix"

We provide the following files:

• "get_ecological_distances.R"

Additional files are created after running "get_ecological_distances.R":

• "ecological_distance_edgelist.csv"
• "ecological_distance_matrix_OS.csv"
• "ecological_distance_matrix_rel_OS.csv"
• "ecological_distance_matrix_rel_ST.csv"
• "ecological_distance_matrix_S.csv"
• "ecological_distance_matrix_ST.csv"
• "ecological_distance_matrix_WN.csv"

folder "phylogenetic_distance_matrix"

We provide the following files:

• "phylogeny.tre"
• "body_mass.csv"
• "get_phylogenetic_distances.R"

Additional files are created after running "get_phylogenetic_distances.R":

• "transformedPagel.tre"
• "phylogenetic_distance_matrix.csv"
• "phylogenetic_distance_edgelist.csv"

folder "get_correlation_phylo_eco"

We provide the following files:

• "get_correlation_phylo_eco.R"

folder "maps"

We provide the following folders and files:

• "get_maps.R"

Additional folders and figures are created after running "get_maps.R":

• folder "species_networks"
• figures (Fig. 1 and Fig. 2)

folder "sampling_effort"

We provide the following files:

• "sampling_effort.csv"
• "sampling_effort.R"