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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"