endophyte: Foliar endophytic fungi across the Hawaiian Archipelago
In darcyj/specificity: Calculate Environmental or Host Phylogenetic Specificity
endophyte R Documentation
Foliar endophytic fungi across the Hawaiian Archipelago
Description
A dataset containing an OTU table (species-by-site), environmental
metadata, and host plant phylogeny.
Usage
endophyte
Format
A list containing 4 objects:
- otutable:
-
data.frame object where each row is a sample and each column is a
fungal OTU (actually ASV from DADA2). Rownames are sample IDs.
- metadata:
-
data.frame object containing environmental metadata for samples in
otutable. SampleID column of metadata matches rownames of otutable.
- supertree:
-
Phylogenetic tree containing all host plant genera in PlantGenus
column of metadata.
- taxonomy:
-
UNITE (v8) taxonomy for OTUs in otutable. Assigned using BLAST, e-value (eval) and UNITE best hit (hit) are given as well.
Source
Darcy et al. (2020) Fungal communities living within leaves
of native Hawaiian dicots are structured by landscape‐scale
variables as well as by host plants. Mol Ecol 29:3102-3115
https://doi.org/10.1111/mec.15544
darcyj/specificity documentation built on Aug. 1, 2023, 8 a.m.
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| endophyte | R Documentation |
Foliar endophytic fungi across the Hawaiian Archipelago
Description
A dataset containing an OTU table (species-by-site), environmental metadata, and host plant phylogeny.
Usage
endophyte
Format
A list containing 4 objects:
- otutable:
-
data.frame object where each row is a sample and each column is a fungal OTU (actually ASV from DADA2). Rownames are sample IDs.
- metadata:
-
data.frame object containing environmental metadata for samples in otutable. SampleID column of metadata matches rownames of otutable.
- supertree:
-
Phylogenetic tree containing all host plant genera in PlantGenus column of metadata.
- taxonomy:
-
UNITE (v8) taxonomy for OTUs in otutable. Assigned using BLAST, e-value (eval) and UNITE best hit (hit) are given as well.
Source
Darcy et al. (2020) Fungal communities living within leaves of native Hawaiian dicots are structured by landscape‐scale variables as well as by host plants. Mol Ecol 29:3102-3115 https://doi.org/10.1111/mec.15544
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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