Gentry forest transect dataset as a phyloseq object
gentry.RdA dataset containing species abundance data, phylogenetic tree, sample metadata, and taxonomy
information for forest plots from the Gentry dataset. This dataset has been processed to
aggregate species counts by unique trinomial names, mapped onto a phylogenetic tree using
the S.PhyloMaker tool, and organized into a phyloseq-class object.
Format
A phyloseq-class object containing:
- OTU table
Species abundance counts, with rows as samples (sites) and columns as species identified by their trinomial names.
- phylogenetic tree
A phylo object representing the evolutionary relationships among species in the dataset.
- sample data
Metadata for each forest plot site, including geographic coordinates and other site attributes.
- taxonomy table
Taxonomic classifications (family, genus, species) matched using the
taxonlookuppackage.
Source
Raw data originally from: https://github.com/zdealveindy/anadat-r/tree/master/data
Phylogenetic tree and nodes from: https://github.com/jinyizju/S.PhyloMaker
Taxonomic lookups performed using the taxonlookup package.
Details
This dataset was constructed by combining raw species presence data from the Gentry forest plot dataset with phylogenetic information and cleaned taxonomic names. The species names were standardized by removing uncertain annotations such as "cf." and "aff." and mapped to a phylogenetic tree using S.PhyloMaker with scenario S1. Species not matched to the phylogeny (less than 2% of counts) were removed from the final dataset.
The data can be used for analyses involving phylogenetic diversity, community ecology, and evolutionary relationships among species in forest plots.
Examples
library(phyloseq)
data(gentry)
# view the OTU table (species counts)
otu_table(gentry)[1:5, 1:20]
#> OTU Table: [20 taxa and 5 samples]
#> taxa are columns
#> Abies_lasiocarpa Abies_amabilis Picea_sitchensis Picea_abies
#> ankarif 0 0 0 0
#> banyong 0 0 0 0
#> beza1 0 0 0 0
#> beza2 0 0 0 0
#> brisefer 0 0 0 0
#> Pinus_sylvestris Fitzroya_cupressoides Juniperus_communis
#> ankarif 0 0 0
#> banyong 0 0 0
#> beza1 0 0 0
#> beza2 0 0 0
#> brisefer 0 0 0
#> Juniperus_virginiana Agathis_microstachys Allocasia_macrorhiza
#> ankarif 0 0 0
#> banyong 0 0 0
#> beza1 0 0 0
#> beza2 0 0 0
#> brisefer 0 0 0
#> Rhodopspatha_m1 Rhodospatha_m1 Rhodospatha_latifolia
#> ankarif 0 0 0
#> banyong 0 0 0
#> beza1 0 0 0
#> beza2 0 0 0
#> brisefer 0 0 0
#> Symplocarpus_purpusii Anthurium_weberbaueri Anthurium_giganteum
#> ankarif 0 0 0
#> banyong 0 0 0
#> beza1 0 0 0
#> beza2 0 0 0
#> brisefer 0 0 0
#> Anthurium_formosum Anthurium_dolichostachyum Anthurium_cordiforme
#> ankarif 0 0 0
#> banyong 0 0 0
#> beza1 0 0 0
#> beza2 0 0 0
#> brisefer 0 0 0
#> Anthurium_argyrostachyum
#> ankarif 0
#> banyong 0
#> beza1 0
#> beza2 0
#> brisefer 0
# the phylogenetic tree
phy_tree(gentry)
#>
#> Phylogenetic tree with 585 tips and 349 internal nodes.
#>
#> Tip labels:
#> Abies_lasiocarpa, Abies_amabilis, Picea_sitchensis, Picea_abies, Pinus_sylvestris, Fitzroya_cupressoides, ...
#> Node labels:
#> Spermatophyta, , Pinales, , , , ...
#>
#> Rooted; includes branch length(s).
# view the sample data
sample_data(gentry) |> head()
#> Lat Long Elev Precip
#> ankarif -16.32 46.82 85 1400
#> banyong 5.00 9.17 420 2600
#> beza1 -23.63 44.57 150 600
#> beza2 -23.63 44.57 175 600
#> brisefer -20.38 57.43 550 2400
#> korup 5.73 8.70 100 5460
# extract taxonomic classifications
tax_table(gentry) |> head()
#> Taxonomy Table: [6 taxa by 4 taxonomic ranks]:
#> genus family order group
#> Abies_lasiocarpa "Abies" "Pinaceae" "Pinales" "Gymnosperms"
#> Abies_amabilis "Abies" "Pinaceae" "Pinales" "Gymnosperms"
#> Picea_sitchensis "Picea" "Pinaceae" "Pinales" "Gymnosperms"
#> Picea_abies "Picea" "Pinaceae" "Pinales" "Gymnosperms"
#> Pinus_sylvestris "Pinus" "Pinaceae" "Pinales" "Gymnosperms"
#> Fitzroya_cupressoides "Fitzroya" "Cupressaceae" "Pinales" "Gymnosperms"