Files in BPerezLamarque/HOME

Phylogenetic Models of HOst-Microbiota Evolution

.gitignore

DESCRIPTION

HOME.Rproj

NAMESPACE

R/HOME_model.R R/LL.R R/LL_tree.R R/L_computation.R R/RcppExports.R R/example_great_apes_microbiota.R R/fit_HOME.R R/get_tip_label.R R/independent_evolution.R R/inference_switches.R R/inference_vertical_transmission.R R/model_selection_HOME.R R/output_results_HOME.R R/plot_simulated_switches.R R/prepare_data_HOME.R R/rescale_tree.R R/resume_PHS_random.R R/resume_switches.R R/resume_switches_all.R R/selection_vertical_transmission.R R/sim_duplications_tree.R R/sim_microbiota.R R/simul_bank_tree.R R/simulate_OTU_alignment.R R/simulate_alignment.R R/simulate_uniform_PHS.R R/tree_change.R R/tree_change_geo_dependent.R R/tree_change_given_switches.R R/tree_change_host_dependent.R R/tree_change_temporal.R R/tree_slice.R R/tree_switch.R README.md

data/.DS_Store

data/great_apes_microbiota.rda

man/HOME_model.Rd man/example_great_apes_microbiota.Rd man/fit_HOME.Rd man/great_apes_microbiota.Rd man/model_selection_HOME.Rd man/output_results_HOME.Rd man/prepare_data_HOME.Rd man/sim_microbiota.Rd man/simul_bank_tree.Rd man/simulate_alignment.Rd

src/.DS_Store

src/RcppExports.cpp

src/llpruning.cpp

tutorial_HOME/OTU_contingency_table.py

tutorial_HOME/add_host_tips.R tutorial_HOME/example_run_HOME_empirical.R

tutorial_HOME/fasta_extract.py

tutorial_HOME/figures/host_tree_simul_C1_S65.png

tutorial_HOME/figures/independent_evolution_bootstrap_simul_C1_S124.png

tutorial_HOME/figures/independent_evolution_bootstrap_simul_C1_S5.png

tutorial_HOME/figures/independent_evolution_bootstrap_simul_C1_S65.png

tutorial_HOME/figures/profil_model_switches_mu_simul_C1_S124.png

tutorial_HOME/figures/profil_model_switches_mu_simul_C1_S5.png

tutorial_HOME/figures/profil_model_switches_mu_simul_C1_S65.png

tutorial_HOME/figures/profil_model_switches_simul_C1_S124.png

tutorial_HOME/figures/profil_model_switches_simul_C1_S5.png

tutorial_HOME/figures/profil_model_switches_simul_C1_S65.png

tutorial_HOME/figures/pure_vertical_transmission_simul_C1_S124.png

tutorial_HOME/figures/pure_vertical_transmission_simul_C1_S5.png

tutorial_HOME/figures/pure_vertical_transmission_simul_C1_S65.png

tutorial_HOME/make_clusters_OTU_pipeline1.sh

tutorial_HOME/make_clusters_OTU_pipeline2.sh

tutorial_HOME/make_clusters_OTU_pipeline3.sh

tutorial_HOME/make_stats.py

tutorial_HOME/map2qiime.py

tutorial_HOME/samples.txt

tutorial_HOME/select_core_OTUs.R

tutorial_HOME/seqs.fna

BPerezLamarque/HOME documentation built on May 17, 2023, 7:02 a.m.