Files in katiesaund/hogwash
Three Bacterial Genome-Wide Association Study Methods
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
LICENSE
NAMESPACE
NEWS.md
R/ancestral_reconstruction.R
R/continuous_algorithm.R
R/convergence.R
R/data.R
R/discrete_algorithm.R
R/formatting.R
R/genotype.R
R/group_genotypes_for_both_methods.R
R/group_genotypes_post_ancetral_reconstruction.R
R/group_genotypes_pre_ancestral_reconstruction.R
R/high_confidence.R
R/hogwash.R
R/non_plot_outputs.R
R/output_generation.R
R/phenotype.R
R/plotting.R
R/read_format_inputs.R
R/run_continuous.R
R/run_phyc.R
R/run_synchronous.R
R/select_test_type.R
R/transition_edges.R
R/tree_manipulation.R
R/validation.R
README
README.md
codecov.yml
cran-comments.md
data/antibiotic_resistance.rda
data/growth.rda
data/snp_gene_key.rda
data/snp_genotype.rda
data/tree.rda
hogwash.Rproj
inst/CITATION
inst/wiki_images/0_to_1_transition_edge.png
inst/wiki_images/2019-06-16_fqR_roary_convergence_test.png
inst/wiki_images/Genotype_transitions.png
inst/wiki_images/KS_null_distribution.png
inst/wiki_images/ancestral_reconstruction.png
inst/wiki_images/both_bad_reconstructions.png
inst/wiki_images/both_transition_edges.png
inst/wiki_images/continuous_algorithm_demo.png
inst/wiki_images/continuous_phenotype_ancestral_reconstruction.png
inst/wiki_images/convergence_for_wiki.png
inst/wiki_images/convergence_genotype_reconstruction.png
inst/wiki_images/convergence_null_distribution.png
inst/wiki_images/delta_phenotype_by_edge_type.png
inst/wiki_images/er_good_ard_bad_reconstruction.png
inst/wiki_images/good_correlation_beta_e.png
inst/wiki_images/good_correlation_eta_p.png
inst/wiki_images/good_correlation_p_e.png
inst/wiki_images/good_looking_reconstruction.png
inst/wiki_images/hogwash_phyc_phyc_discrete_pheno_BM_tree_1_pheno_1_genotype.png
inst/wiki_images/hogwash_phyc_phyc_discrete_pheno_BM_tree_1_pheno_1_heatmap.png
inst/wiki_images/hogwash_phyc_phyc_discrete_pheno_BM_tree_1_pheno_1_manhattan.png
inst/wiki_images/hogwash_phyc_phyc_discrete_pheno_BM_tree_1_pheno_1_null_dist.png
inst/wiki_images/hogwash_phyc_phyc_discrete_pheno_BM_tree_1_pheno_1_phenotype.png
inst/wiki_images/hogwash_synchronous_dummy_tree_has_low_confidence_tips_just_phenotype_for_wiki.pdf
inst/wiki_images/hogwash_synchronous_dummy_tree_has_low_confidence_tips_just_phenotype_for_wiki.png
inst/wiki_images/ordered_by_tree_edge.png
inst/wiki_images/overlong_edge_example.pdf
inst/wiki_images/overlong_edge_example.png
inst/wiki_images/phenotype_binary_reconstruction.png
inst/wiki_images/poor_correlation_beta_e.png
inst/wiki_images/poor_correlation_beta_p.png
inst/wiki_images/poor_correlation_p_e.png
inst/wiki_images/poor_correlation_p_e_genotypes_of_interest.png
inst/wiki_images/post_AR_geno_recon_and_trans.png
inst/wiki_images/pre_AR_geno_recon_and_trans.png
inst/wiki_images/sim162_geno_trans.png
inst/wiki_images/sim25149_geno_trans.png
inst/wiki_images/synchronous_genotype_transition.png
inst/wiki_images/synchronous_grouped_genotype_summary_heatmap.png
inst/wiki_images/synchronous_null_distribution.png
inst/wiki_images/synchronous_phenotype_transitio.png
inst/wiki_images/transition_edges.png
inst/wiki_images/tree_for_wiki.jpg
inst/wiki_images/tree_with_nomenclature_for_wiki.png
man/antibiotic_resistance.Rd
man/growth.Rd
man/hogwash.Rd
man/report_phylogenetic_signal.Rd
man/snp_gene_key.Rd
man/snp_genotype.Rd
man/tree.Rd
tests/testthat.R
tests/testthat/test-hogwash.R
tests/testthat/test_ancestral_reconstruction.R
tests/testthat/test_continuous_algorithm.R
tests/testthat/test_convergence.R
tests/testthat/test_discrete_algorithm.R
tests/testthat/test_formatting.R
tests/testthat/test_genotype.R
tests/testthat/test_group_genotypes.R
tests/testthat/test_high_confidence.R
tests/testthat/test_non_plot_outputs.R
tests/testthat/test_output_generation.R
tests/testthat/test_phenotype.R
tests/testthat/test_plotting.R
tests/testthat/test_read_format_inputs.R
tests/testthat/test_run_continuous.R
tests/testthat/test_run_phyc.R
tests/testthat/test_run_synchronous.R
tests/testthat/test_select_test_type.R
tests/testthat/test_transition_edges.R
tests/testthat/test_tree_manipulation.R
tests/testthat/test_validation.R
