Man pages for walterxie/ComMA
Community Matrix Analysis
| abundancePerSample | abundance (reads, gamme0) per sample return 1-column data... |
| classification | Classify samples by taxonomic composition |
| CMStatistics | Statistics to one or multipe community matrix |
| ComMA-package | ComMA R documentation |
| CommunityComparison | Compare community structure |
| CommunityPhyloStru | Community Phylogenetic Structure from 'picante' Package |
| convertType | Convert data frame columns to different type, default to... |
| distance | Calculate various multivariate distance metrics |
| diverrare | Rarefaction curves using Jost diversities |
| enterotype | Enterotype |
| EUtils | EUtils NCBI |
| firstN | Return the first 'n' elements. If 'n' is greater than... |
| getMethodLines | Get lines containing Java method name. The regular expression... |
| getPhylorareDF | Rarefaction curve of Phylogenetic Diversity |
| getPlural | Get plural by adding 's' except special plural. |
| installAllPackages | Install all dependent packages. |
| IOComMA | IO functions in 'ComMA' |
| JostDiversity | Jost diversity from 'vegetarian' Package |
| mkdir | Create folder from 'file.path' if not exist. |
| mvRowsToLast | Move rows to the last rows of data frame given a column value |
| normalize | normalize given vector. |
| PlotPrioritisation | Plot prioritisation |
| prettyNumbers | 'prettyNumbers' provide pretty numbers with comma separator... |
| printXTable | Print data fram (table) as Latex format to either file or... |
| RDA | Redundancy Analysis |
| readCodeCoverage | Use 'readHTMLTable' to covert the report of code coverage... |
| readFile | Read a file to a data frame. |
| readFileLineByLine | Read File Line By Line |
| readMCMCLog | Reads MCMC log files and return a data frame whose column... |
| ReadsOTUsTaxa | Taxonomy analyses for multiple data sets |
| richnessPerSample | richness (OTUs/species) per sample return 1-column data frame |
| shannonPerSample | Shannon index (gamma1) per sample return 1-column data frame |
| spatial | Great-circle distance calculations in R |
| splitPath | Split a file path into folder names vector |
| stringUtils | Utils to deal with strings and characters |
| TaxaUtils | Utils to preprocess taxa table |
| TreeUtils | Utils to manipulate or visualise phylogenetic tree |
| utilsCM | Utils to preprocess community matrix |
| UtilsCombine | Utils to combine data frames or matrices into the required... |
| utilsSeq | Utils to manipulate sequences or OTUs |
| writeTable | Write the data fram (table) to a file. |
