calc_alpha_div: Calculate common alpha-diversity metrics You need the "vegan"...
In leylabmpi/LeyLabRMisc: Ley Lab misc R functions, rmd templates, etc.
calc_alpha_div R Documentation
Calculate common alpha-diversity metrics
You need the "vegan" package installed to your R project and loaded for this code to run
Description
Faith's Phylogenetic Diversity ("PD") can be calculated only
if a tree is provided. The tree can have extra tips, but there
must be tip labels for all taxa in the provided table.
Usage
calc_alpha_div(df, tree = NULL, index = c("nobs", "shannon", "PD"))
Arguments
df
sample x taxon abundance table (usual format for vegan)
tree
tree with tips matching taxa in the abundance table (only needed for PD)
index
which of the indices to calculate? (nobs = no. of observations, shannon = Shannon Index, PD = Faith's PD)
Value
a data.frame of alpha diversity values (and sample names)
leylabmpi/LeyLabRMisc documentation built on Nov. 3, 2022, 3:45 p.m.
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| calc_alpha_div | R Documentation |
Calculate common alpha-diversity metrics You need the "vegan" package installed to your R project and loaded for this code to run
Description
Faith's Phylogenetic Diversity ("PD") can be calculated only if a tree is provided. The tree can have extra tips, but there must be tip labels for all taxa in the provided table.
Usage
calc_alpha_div(df, tree = NULL, index = c("nobs", "shannon", "PD"))
Arguments
df |
sample x taxon abundance table (usual format for vegan) |
tree |
tree with tips matching taxa in the abundance table (only needed for PD) |
index |
which of the indices to calculate? (nobs = no. of observations, shannon = Shannon Index, PD = Faith's PD) |
Value
a data.frame of alpha diversity values (and sample names)
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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