Integration of TNT in R

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Documentation for package ‘nitro’ version 0.2.0

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AbstractCharacterMatrix Abstract character matrix
AbstractExtension Abstract extension
AbstractResamplingOptions Define options common to resampling analyses
AbstractSectorialSearchOptions Define options common to sectorial searches
BootstrapOptions Set options for bootstrap resampling
BranchBreakingOptions Set options for branch breaking
BranchSupportOptions Set options for branch support calculation
BranchSwappingOptions Define a branch swapping analysis
c.AbstractCharacterMatrix Concatenate character matrices
canale_2022 Canale et al. (2022) matrix
CommandQueue Command Queue
ConstrainedSectorialSearchOptions Set options for a constrained sectorial search
ConstraintBaseOptions Set constraints on monophyly
ContinuousMatrix Continuous character matrix
create_matrix Create a new character matrix
create_new_object Create a new object
DiscreteMatrix Discrete character matrix
DrivenSearchOptions Set options for driven searches
ExclusiveSectorialSearchOptions Set options for an exclusive sectorial search
execute_analysis Execute CommandQueue
ImpliedWeightingOptions Set options for implied weighting
JackknifeOptions Set options for jackknife resampling
MonophylyConstraintOptions Set constraints on monophyly
new_search_config Create a new search configuration
OutputParser Output parser for TNT
print.MultiCharacterMatrix Print MultiCharacterMatrix object
RandomSectorialSearchOptions Set options for a random sectorial search
RatchetOptions Set options for parsimony ratchet
raven_2017 Raven and Maidment (2017) matrix
SymmetricResamplingOptions Set options for symmetric resampling
tnt_attach Register TNT executable
TreeAnalysis Define tree searches
TreeAnalysisResults Results of a tree analyses
TreeDriftingOptions Set options for tree drifting
TreeFusingOptions Set options for tree fusing
TreeHybridizingOptions Set options for tree hybridizing