checkValidPhylo


  This function takes as single argument an object (phy), checks its
  elements, and prints a diagnostic. All problems are printed with a
  label: FATAL (will likely cause an error or a crash) or MODERATE (may
  cause some problems).<p></p><p>  This function is mainly intended for developers creating
  <code>"phylo"</code> objects from scratch.
</p>

manip

Functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from DNA sequences, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood, dating trees with non-contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle, MAFFT) whose results are returned into R.

Emmanuel Paradis

Analyses of Phylogenetics and Evolution

checkValidPhylo function


  This function takes as single argument an object (phy), checks its
  elements, and prints a diagnostic. All problems are printed with a
  label: FATAL (will likely cause an error or a crash) or MODERATE (may
  cause some problems).

  This function is mainly intended for developers creating
  <code>"phylo"</code> objects from scratch.


checkValidPhylo: Check the Structure of a "phylo" Object

Description

Usage

Arguments

Value

Examples