Man pages for walterxie/ComMA
Community Matrix Analysis

abundancePerSampleabundance (reads, gamme0) per sample return 1-column data...
classificationClassify samples by taxonomic composition
CMStatisticsStatistics to one or multipe community matrix
ComMA-packageComMA R documentation
CommunityComparisonCompare community structure
CommunityPhyloStruCommunity Phylogenetic Structure from 'picante' Package
convertTypeConvert data frame columns to different type, default to...
distanceCalculate various multivariate distance metrics
diverrareRarefaction curves using Jost diversities
EUtilsEUtils NCBI
firstNReturn the first 'n' elements. If 'n' is greater than...
getMethodLinesGet lines containing Java method name. The regular expression...
getPhylorareDFRarefaction curve of Phylogenetic Diversity
getPluralGet plural by adding 's' except special plural.
installAllPackagesInstall all dependent packages.
IOComMAIO functions in 'ComMA'
JostDiversityJost diversity from 'vegetarian' Package
mkdirCreate folder from 'file.path' if not exist.
mvRowsToLastMove rows to the last rows of data frame given a column value
normalizenormalize given vector.
PlotPrioritisationPlot prioritisation
prettyNumbers'prettyNumbers' provide pretty numbers with comma separator...
printXTablePrint data fram (table) as Latex format to either file or...
RDARedundancy Analysis
readCodeCoverageUse 'readHTMLTable' to covert the report of code coverage...
readFileRead a file to a data frame.
readFileLineByLineRead File Line By Line
readMCMCLogReads MCMC log files and return a data frame whose column...
ReadsOTUsTaxaTaxonomy analyses for multiple data sets
richnessPerSamplerichness (OTUs/species) per sample return 1-column data frame
shannonPerSampleShannon index (gamma1) per sample return 1-column data frame
spatialGreat-circle distance calculations in R
splitPathSplit a file path into folder names vector
stringUtilsUtils to deal with strings and characters
TaxaUtilsUtils to preprocess taxa table
TreeUtilsUtils to manipulate or visualise phylogenetic tree
utilsCMUtils to preprocess community matrix
UtilsCombineUtils to combine data frames or matrices into the required...
utilsSeqUtils to manipulate sequences or OTUs
writeTableWrite the data fram (table) to a file.
walterxie/ComMA documentation built on May 3, 2019, 11:51 p.m.