DivE: Diversity Estimator
Version 1.0

R-package DivE contains functions for the DivE estimator (Laydon, D. et al., Quantification of HTLV-1 clonality and TCR diversity, PLOS Comput. Biol. 2014). The DivE estimator is a heuristic approach to estimate the number of classes or the number of species (species richness) in a population.

Browse man pages Browse package API and functions Browse package files

AuthorDaniel Laydon, Aaron Sim, Charles Bangham, Becca Asquith
Date of publication2014-04-14 19:07:04
MaintainerDaniel Laydon <d.laydon@imperial.ac.uk>
LicenseGPL (>= 2)
Version1.0
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("DivE")

Man pages

Bact1: Count of Medically Important Bacteria Species in a Sample
comb.dm: comb.dm
Curvature: Curvature
DivE-internal: Internal functions
DiveMaster: DiveMaster
DivE-package: Diversity Estimator
divsamplenum: divsamplenum
divsubsamples: divsubsamples
fitsinglemod: fitsinglemod
ModelSet: List of 58 candidate models to fit to data
ParamRanges: List of 58 sets of upper and lower bounds for models...
ParamSeeds: List of 58 matrices of model seeding parameters.
popdiversity: popdiversity
scoresinglemod: scoresinglemod

Functions

BBprop Man page Source code
Bact1 Man page
Bact2 Man page
Bfunprop Man page Source code
BinFunk Man page Source code
BinFunkSingleNumber Man page Source code
Curvature Man page Source code
DivE Man page
DivE-internal Man page
DivE-package Man page
DiveMaster Man page Source code
DiveMaster.default Man page Source code
IsWholeNumber Man page Source code
ModelSet Man page
ParamRanges Man page
ParamSeeds Man page
comb.dm Man page Source code
combine.criteria Man page Source code
combined.fit Man page Source code
convert.ranges Man page Source code
crossings Man page Source code
div.count Man page Source code
divsamplenum Man page Source code
divsamplenum.default Man page Source code
divsubsamples Man page Source code
divsubsamples.default Man page Source code
divsubsamples_nested Man page Source code
fitallSubs Man page Source code
fitsample Man page Source code
fitsinglemod Man page Source code
fitsinglemod.default Man page Source code
format.input Man page Source code
gen.rarefac.div Man page Source code
gen.rarefac.lengths Man page Source code
gen.subsamp.lengths Man page Source code
geo.mean Man page Source code
global.fit Man page Source code
is.mono Man page Source code
is.slowing Man page Source code
local.fit Man page Man page Source code
model.cost Man page Source code
model.cost.abs Man page Source code
msr.curves Man page Source code
multiple.scoring Man page Source code
plot.fitsingleMod Man page Source code
popdiversity Man page Source code
pred.div Man page Source code
print.DiversityMaster Man page Source code
print.divsubsamples Man page Source code
print.fitsingleMod Man page Source code
print.scoresingleMod Man page Source code
print.summary.DiversityMaster Man page Source code
print.summary.divsubsamples Man page Source code
print.summary.fitsingleMod Man page Source code
print.summary.scoresingleMod Man page Source code
ref.area Man page Source code
scoresinglemod Man page Source code
scoresinglemod.default Man page Source code
simm Man page Source code
single.mod.score Man page Source code
single.var Man page Source code
summary.DiversityMaster Man page Source code
summary.divsubsamples Man page Source code
summary.fitsingleMod Man page Source code
summary.scoresingleMod Man page Source code

Files

NAMESPACE
demo
demo/00Index
demo/Example_Script.R
data
data/ModelSet.rda
data/Bact1.RData
data/ParamRanges.rda
data/ParamSeeds.rda
data/datalist
R
R/DivE.R
MD5
DESCRIPTION
man
man/scoresinglemod.Rd
man/comb.dm.Rd
man/DiveMaster.Rd
man/ParamRanges.Rd
man/Bact1.Rd
man/Curvature.Rd
man/ModelSet.Rd
man/popdiversity.Rd
man/fitsinglemod.Rd
man/divsamplenum.Rd
man/divsubsamples.Rd
man/DivE-package.Rd
man/ParamSeeds.Rd
man/DivE-internal.Rd
DivE documentation built on May 19, 2017, 2:32 p.m.