R: Measurement and Partitioning of Similarity-Sensitive Biodiversity

# Measurement and Partitioning of Similarity-Sensitive Biodiversity

## Documentation for package ‘rdiversity’ version 2.2.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

rdiversity-package | rdiversity: diversity measurement in R
as.binary | as binary digit.
binAdd | Binary Addition (+)
binary | Binary digit.
binSeq | Binary sequence
byte | A simple helper function to return the size of one byte
bytesNeeded | Minimum number of "byte" needed to hold n "bit"
chainsaw | Function to cut the phylogeny to a specified depth from the tip with the greatest distance from the root.
dist2sim | Distance to similarity
distance | Generate distance object
distance-class | distance-class
distance-method | Generate distance object
fillUpToBit | Fill up to bit (000..)
fillUpToByte | Fill up to Byte (00000000..)
gen2dist | Genetic distance matrix
inddiv | Calculate individual-level diversity
inddiv-method | Calculate individual-level diversity
is.binary | is Binary Vector
loadAttributes | loadAttributes
metacommunity | Metacommunity
metacommunity-class | metacommunity-class
metacommunity-method | Metacommunity
metadiv | Metacommunity-level diversity
metadiv-method | Metacommunity-level diversity
meta_gamma | Metacommunity gamma diversity
negate | Binary Negation (!)
norm_alpha | Normalised alpha (low level diversity component)
norm_beta | Normalised beta (low level diversity component)
norm_meta_alpha | Normalised metacommunity alpha diversity
norm_meta_beta | Normalised metacommunity beta diversity
norm_meta_rho | Normalised metacommunity rho diversity
norm_rho | Normalised rho (low level diversity component)
norm_sub_alpha | Normalised subcommunity alpha diversity
norm_sub_beta | Normalised subcommunity beta diversity
norm_sub_rho | Normalised subcommunity rho diversity
Ops.binary | Group Generic Ops
phy2branch | Phylogenetic similarity
phy2dist | Phylogenetic pairwise tip distance matrix
phy_abundance | Relative abundance of historical species
phy_struct | Calculate phylogenetic structure matrix
powermean-class | powermean-class
power_mean | Power mean of vector elements
print.binary | Print method for binary number.
raw_alpha | Raw alpha (low level diversity component)
raw_beta | Raw beta (low level diversity component)
raw_gamma | Gamma (low level diversity component)
raw_meta_alpha | Raw metacommunity alpha diversity
raw_meta_beta | Raw metacommunity beta diversity
raw_meta_rho | Raw metacommunity rho diversity
raw_rho | Raw rho (low level diversity component)
raw_sub_alpha | Raw subcommunity alpha diversity
raw_sub_beta | Raw subcommunity beta diversity
raw_sub_rho | Raw subcommunity rho diversity
rdiversity | rdiversity: diversity measurement in R
relativeentropy-class | relativeentropy-class
repartition | Repartition metacommunity
saveAttributes | saveAttributes
show-method | distance-class
show-method | metacommunity-class
show-method | similarity-class
similarity | Generate similarity object
similarity-class | similarity-class
similarity-method | Generate similarity object
subdiv | Calculate subcommunity-level diversity
subdiv-method | Calculate subcommunity-level diversity
sub_gamma | Subcommunity gamma diversity
summary.binary | Summary method for binary number.
switchEndianess | Switch Endianess.
tax2dist | Generate taxonomic distance matrix