phylocomr-inputs: Expected inputs

In phylocomr: Interface to 'Phylocom'

Expected inputs

Description

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:

• ph_bladj()

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:

• ph_comtrait()

• ph_comstruct()

• ph_comdist()

• ph_pd()

• ph_rao()

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:

• ph_comtrait()

• ph_aot()

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()

phylocomr documentation built on April 22, 2023, 1:14 a.m.