Package index • phyloAMR

All functions

AIC_stepwise_regression(): Logistic regression using stepwise Akaike information criteria selection

asr(): Ancestral state reconstruction wrapper function

asr_cluster_analysis(): Analysis of trait clustering on a phylogeny

asr_cluster_detection(): Identification of trait emergence and clustering of trait across the phylogeny using transition data

asr_transition_analysis(): Enumeration of trait transitions using ancestral state reconstruction

characterize_asr_model(): Characterize ancestral state reconstruction model

df: Dataframe with relevant data

downstream_permutation_test(): downstream_permutation_test: Permutation test for downstream analysis

downstream_transitions(): Analysis of downstream transitions of comparitor traits

find_best_asr_model(): Determine best model for ancestral state reconstruction

genotype_mat: Genotype matrix

get_continuation_data(): Annotate parent child data from ancestral state reconstruction with transition data

get_parent_child_data(): Get parent child data from ancestral state reconstruction

nearest_neighbor_algorithm(): Identify the phylogenetic nearest neighbor of a tip

nearest_neighbor_analysis(): nearest_neighbor_analysis: Generate nearest neighbor comparisons for isolate pairs

nearest_neighbor_summary_statistics(): nearest_neighbor_summary_statistics: Generate summary statistics of nearest neighbor comparisons for isolate pairs

paint_tree_with_states(): Paint a phylogenetic tree with ancestral and tip states

phyloaware_dataset_curation(): Dataset curation for phylogenetically aware regression

phyloaware_regression(): Phylogenetically aware regression of genome-influenced traits

purposeful_selection_algorithm(): Logistic regression using purposeful selection

pvalue_informed_regression(): Logistic regression using p-values to select final model

synchronous_permutation_test(): Synchronous permutation test

synchronous_transitions(): Analysis of synchronous transitions of two traits

tr: Phylogenetic tree