Measurement and Partitioning of Similarity-Sensitive Biodiversity

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Documentation for package ‘rdiversity’ version 2.2.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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