pick_base: pick_base
In adw96/DivNet: Diversity Estimation in Networked Ecological Communities
pick_base R Documentation
pick_base
Description
Picks the base taxon to be used in divnet fit. If no taxon is detected
in all samples, returns error; in this case, we recommend manually choosing
a few taxa fairly abundant across samples and for each such taxon
fitting divnet specifying this taxon as the base taxon.
Usage
pick_base(W, detection_cutoff = NULL, automatic_cutoff = FALSE)
Arguments
W
A taxon abundance matrix (taxa as columns)
detection_cutoff
The proportion of samples base taxon must be detected
in. Default is NULL in which case base taxon must be detected in all samples
unless automatic_cutoff is set to TRUE.
automatic_cutoff
Choose detection cutoff automatically? Default is
FALSE. If TRUE, detection_cutoff will be set equal to the maximum proportion
of samples any taxon is detected in.
Author(s)
Amy Willis
adw96/DivNet documentation built on Oct. 2, 2023, 11:49 a.m.
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| pick_base | R Documentation |
pick_base
Description
Picks the base taxon to be used in divnet fit. If no taxon is detected in all samples, returns error; in this case, we recommend manually choosing a few taxa fairly abundant across samples and for each such taxon fitting divnet specifying this taxon as the base taxon.
Usage
pick_base(W, detection_cutoff = NULL, automatic_cutoff = FALSE)
Arguments
W |
A taxon abundance matrix (taxa as columns) |
detection_cutoff |
The proportion of samples base taxon must be detected in. Default is NULL in which case base taxon must be detected in all samples unless automatic_cutoff is set to TRUE. |
automatic_cutoff |
Choose detection cutoff automatically? Default is FALSE. If TRUE, detection_cutoff will be set equal to the maximum proportion of samples any taxon is detected in. |
Author(s)
Amy Willis
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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