├── .gitignore ├── LICENSE ├── README.html ├── README.md ├── entire_network └── entire.graphml ├── script ├── Net_construction.R ├── bray_bootstrap_matrix.R ├── bray_dist.R ├── bray_p_matrix.R ├── bray_p_value.R ├── bray_perm_matrix.R ├── bs_test.R ├── dataset.R ├── fitness_new.R ├── generalist.R ├── graph_growth_ba.R ├── hub.R ├── hub_01.R ├── modular_connection.R ├── molecular_dating.R ├── morandi.R ├── negative.R ├── netinfer.R ├── nettopo.R ├── network_growth_random.R ├── node_age.R ├── null_model.R ├── os.R ├── otu_detect.R ├── otutable_subset.R ├── overpresension_module.R ├── overrepresentation.R ├── p_cal.R ├── perm_test.R ├── pre_general.R ├── sintax.R ├── spearman_bootstrap_matrix.R ├── spearman_p.R ├── spearman_p_matrix.R ├── spearman_perm_matrix.R ├── spearman_permutation_matrix.R ├── subnet_topology.R ├── taxa_combine.R ├── toy_example.R ├── tree_growth.R ├── trim.R └── trim_01.R ├── subnetwork_original ├── animal_corpus.graphml ├── animal_dgut.graphml ├── animal_pgut.graphml ├── animal_secretion.graphml ├── animal_surface.graphml ├── plant_corpus.graphml ├── plant_surface.graphml ├── rhizosphere.graphml ├── sediment_nonsaline.graphml ├── sediment_saline.graphml ├── soil.graphml ├── surface_nonsaline.graphml ├── water_nonsaline.graphml └── water_saline.graphml └── subnetwork_trimmed ├── animal_dgut.graphml ├── animal_pgut.graphml ├── animal_secretion.graphml ├── animal_surface.graphml ├── plant_surface.graphml ├── rhizosphere.graphml ├── sediment_nonsaline.graphml ├── sediment_saline.graphml ├── soil.graphml ├── surface_nonsaline.graphml ├── water_nonsaline.graphml └── water_saline.graphml /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/LICENSE -------------------------------------------------------------------------------- /README.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/README.html -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/README.md -------------------------------------------------------------------------------- /entire_network/entire.graphml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/entire_network/entire.graphml -------------------------------------------------------------------------------- /script/Net_construction.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/script/Net_construction.R -------------------------------------------------------------------------------- /script/bray_bootstrap_matrix.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/script/bray_bootstrap_matrix.R -------------------------------------------------------------------------------- /script/bray_dist.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/script/bray_dist.R -------------------------------------------------------------------------------- /script/bray_p_matrix.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/script/bray_p_matrix.R -------------------------------------------------------------------------------- /script/bray_p_value.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/script/bray_p_value.R -------------------------------------------------------------------------------- /script/bray_perm_matrix.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/script/bray_perm_matrix.R -------------------------------------------------------------------------------- /script/bs_test.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/script/bs_test.R -------------------------------------------------------------------------------- /script/dataset.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/script/dataset.R -------------------------------------------------------------------------------- /script/fitness_new.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/script/fitness_new.R -------------------------------------------------------------------------------- /script/generalist.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/script/generalist.R -------------------------------------------------------------------------------- /script/graph_growth_ba.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/script/graph_growth_ba.R -------------------------------------------------------------------------------- /script/hub.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/script/hub.R -------------------------------------------------------------------------------- /script/hub_01.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/script/hub_01.R -------------------------------------------------------------------------------- /script/modular_connection.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/script/modular_connection.R -------------------------------------------------------------------------------- /script/molecular_dating.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/script/molecular_dating.R -------------------------------------------------------------------------------- /script/morandi.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/script/morandi.R -------------------------------------------------------------------------------- /script/negative.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/script/negative.R -------------------------------------------------------------------------------- /script/netinfer.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/script/netinfer.R -------------------------------------------------------------------------------- /script/nettopo.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/script/nettopo.R -------------------------------------------------------------------------------- /script/network_growth_random.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/script/network_growth_random.R -------------------------------------------------------------------------------- /script/node_age.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/script/node_age.R -------------------------------------------------------------------------------- /script/null_model.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/script/null_model.R -------------------------------------------------------------------------------- /script/os.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/script/os.R -------------------------------------------------------------------------------- /script/otu_detect.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/script/otu_detect.R -------------------------------------------------------------------------------- /script/otutable_subset.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/script/otutable_subset.R -------------------------------------------------------------------------------- /script/overpresension_module.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/script/overpresension_module.R -------------------------------------------------------------------------------- /script/overrepresentation.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/script/overrepresentation.R -------------------------------------------------------------------------------- /script/p_cal.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/script/p_cal.R -------------------------------------------------------------------------------- /script/perm_test.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/script/perm_test.R -------------------------------------------------------------------------------- /script/pre_general.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/script/pre_general.R -------------------------------------------------------------------------------- /script/sintax.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/script/sintax.R -------------------------------------------------------------------------------- /script/spearman_bootstrap_matrix.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/script/spearman_bootstrap_matrix.R -------------------------------------------------------------------------------- /script/spearman_p.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/script/spearman_p.R -------------------------------------------------------------------------------- /script/spearman_p_matrix.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/script/spearman_p_matrix.R -------------------------------------------------------------------------------- /script/spearman_perm_matrix.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/script/spearman_perm_matrix.R -------------------------------------------------------------------------------- /script/spearman_permutation_matrix.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/script/spearman_permutation_matrix.R -------------------------------------------------------------------------------- /script/subnet_topology.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/script/subnet_topology.R -------------------------------------------------------------------------------- /script/taxa_combine.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/script/taxa_combine.R -------------------------------------------------------------------------------- /script/toy_example.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/script/toy_example.R -------------------------------------------------------------------------------- /script/tree_growth.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/script/tree_growth.R -------------------------------------------------------------------------------- /script/trim.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/script/trim.R -------------------------------------------------------------------------------- /script/trim_01.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/script/trim_01.R -------------------------------------------------------------------------------- /subnetwork_original/animal_corpus.graphml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/subnetwork_original/animal_corpus.graphml -------------------------------------------------------------------------------- /subnetwork_original/animal_dgut.graphml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/subnetwork_original/animal_dgut.graphml -------------------------------------------------------------------------------- /subnetwork_original/animal_pgut.graphml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/subnetwork_original/animal_pgut.graphml -------------------------------------------------------------------------------- /subnetwork_original/animal_secretion.graphml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/subnetwork_original/animal_secretion.graphml -------------------------------------------------------------------------------- /subnetwork_original/animal_surface.graphml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/subnetwork_original/animal_surface.graphml -------------------------------------------------------------------------------- /subnetwork_original/plant_corpus.graphml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/subnetwork_original/plant_corpus.graphml -------------------------------------------------------------------------------- /subnetwork_original/plant_surface.graphml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/subnetwork_original/plant_surface.graphml -------------------------------------------------------------------------------- /subnetwork_original/rhizosphere.graphml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/subnetwork_original/rhizosphere.graphml -------------------------------------------------------------------------------- /subnetwork_original/sediment_nonsaline.graphml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/subnetwork_original/sediment_nonsaline.graphml -------------------------------------------------------------------------------- /subnetwork_original/sediment_saline.graphml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/subnetwork_original/sediment_saline.graphml -------------------------------------------------------------------------------- /subnetwork_original/soil.graphml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/subnetwork_original/soil.graphml -------------------------------------------------------------------------------- /subnetwork_original/surface_nonsaline.graphml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/subnetwork_original/surface_nonsaline.graphml -------------------------------------------------------------------------------- /subnetwork_original/water_nonsaline.graphml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/subnetwork_original/water_nonsaline.graphml -------------------------------------------------------------------------------- /subnetwork_original/water_saline.graphml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/subnetwork_original/water_saline.graphml -------------------------------------------------------------------------------- /subnetwork_trimmed/animal_dgut.graphml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/subnetwork_trimmed/animal_dgut.graphml -------------------------------------------------------------------------------- /subnetwork_trimmed/animal_pgut.graphml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/subnetwork_trimmed/animal_pgut.graphml -------------------------------------------------------------------------------- /subnetwork_trimmed/animal_secretion.graphml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/subnetwork_trimmed/animal_secretion.graphml -------------------------------------------------------------------------------- /subnetwork_trimmed/animal_surface.graphml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/subnetwork_trimmed/animal_surface.graphml -------------------------------------------------------------------------------- /subnetwork_trimmed/plant_surface.graphml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/subnetwork_trimmed/plant_surface.graphml -------------------------------------------------------------------------------- /subnetwork_trimmed/rhizosphere.graphml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/subnetwork_trimmed/rhizosphere.graphml -------------------------------------------------------------------------------- /subnetwork_trimmed/sediment_nonsaline.graphml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/subnetwork_trimmed/sediment_nonsaline.graphml -------------------------------------------------------------------------------- /subnetwork_trimmed/sediment_saline.graphml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/subnetwork_trimmed/sediment_saline.graphml -------------------------------------------------------------------------------- /subnetwork_trimmed/soil.graphml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/subnetwork_trimmed/soil.graphml -------------------------------------------------------------------------------- /subnetwork_trimmed/surface_nonsaline.graphml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/subnetwork_trimmed/surface_nonsaline.graphml -------------------------------------------------------------------------------- /subnetwork_trimmed/water_nonsaline.graphml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/subnetwork_trimmed/water_nonsaline.graphml -------------------------------------------------------------------------------- /subnetwork_trimmed/water_saline.graphml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/microbma/earthnetwork/HEAD/subnetwork_trimmed/water_saline.graphml --------------------------------------------------------------------------------