Expected inputs
Ages data
A file or data.frame, with 2 columns:
(character) node taxonomic name
(numeric) age estimate for the node
If a file path is used, the table must not have headers
Applies to:
Sample data
A file or data.frame, with 3 columns, sorted by column 1, one row per taxon:
(character) sample plot/quadrat/trap/etc. name (no spaces, must begin with a letter, not a number or symbol)
(integer) abundance (leave as 1 for presence/absence data)
(character) species code (same as in the phylogeny, must begin with a letter, not a number or symbol)
If a file path is used, the table must not have headers, and must be tab-delimited
Applies to:
Traits data
A tab-delimited file with the first line as
type<TAB>n<TAB>n<TAB>... [up to the number of traits], for example:
type<TAB>3<TAB>3<TAB>3<TAB>0
where n indicates the type of trait in each of the four columns. Types:
0: binary (only one binary trait may be included, and it must be in the first column) 1 for unordered multistate (no algorithms currently implemented)2: ordered multistate (currently treated as continuous)3: continuous
Optional: The second line can start with the word name (lower case only) and then list the names of the traits in order. These will appear in the full output file
Subsequent lines should have the taxon name, which must be identical to
its appearance in phylo, and the data columns separated by tabs. For
example: sp1<TAB>1<TAB>1<TAB>1<TAB>0
OR -
A data.frame, where the first column called name has each taxon, followed by
any number of columns with traits. The first column name must be name, and
the following columns should be named using the name of the trait.
Applies to:
Phylogenies
Phylocom expects trees in Newick format. The basic Newick format used by
Phylocom is: ((A,B),C);. See the Phylocom manual
(https://phylodiversity.net/phylocom/) for more details on what they expect.
Applies to: all functions except ph_phylomatic() and ph_ecovolve()