remove.TRAMP.match: Mark a TRAMP Match as Ignored

In richfitz/TRAMPR: 'TRFLP' Analysis and Matching Package for R

Mark a TRAMP Match as Ignored

Description

Mark a match in a TRAMP object as ignored; when this is set, a match will be ignored when producing presence/absence matrices (see summary.TRAMP) or when plotting (plot.TRAMP) when ignore is TRUE. update.TRAMP provides an interactive interface for doing this, but remove.TRAMP.match may be useful directly.

Usage

remove.TRAMP.match(x, sample.fk, knowns.fk)

Arguments

x	A TRAMP object.
sample.fk, knowns.fk	Key of sample and known, respectively. See TRAMPsamples and TRAMPknowns for more information.

Value

A modified TRAMP object.

Warning

This should be regarded as experimental. There is currently no mechanism for restoring ignored matches, aside from recreating the TRAMP object, or through editing x$presence.ign directly (the format of that table is self-explanatory, but is not guaranteed not to change between TRAMP versions). Note that by default, summary.TRAMP and plot.TRAMP will not remove matches; you must specify ignore=TRUE to enable this.

Note

This function returns a modified object - the TRAMP object is not modified in place. You must do:

x <- remove.TRAMP.match(x, sample.fk, knowns.fk)

to mark a match as ignored in the object x.

richfitz/TRAMPR documentation built on July 16, 2025, 1:46 p.m.