# Methods for Continuous Flow Cytometry

## Documentation for package ‘flowPhyto’ version 1.6.0

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.
- Package NEWS.

## Help Pages

census | Cross tabulate a consensus vector
censusFile | Create a consensus from several classification vector files and cross tabulate the population composition
CHANNEL.CLMNS | Seaflow detector column names
CHANNEL.CLMNS.SM | Seaflow detector column names
classify | Cluster the different Phytoplankton Populations
classifyFile | Cluster the different Phytoplankton Populations
cleanupLogs | Remove R Batch Output Files.
clearOutputs | Clear the output files from particular flowPhyto pipeline steps.
combineCensusFiles | Combine the Census Files.
combineSdsFiles | Combine the SDS files.
consensus | create a consensus vector from several classification vectors
consensusFile | Create a consensus from several classification vector files and cross tabulate the population composition
createResamplingScheme | Generate the Population Resampling scheme.
EVT.HEADER | Seaflow File Headers
filter | Filter Optimally Positioned Particles from an EVT dataframe
filterFile | Filter an EVT file and output an Optimally Positioned Particles (OPP) file
getCruiseFiles | Get all of the files from a cruise.
getCruisePath | Get the Cruise Directory.
getFileNumber | Get the (original) integer file number of any seaflow repository file.
joinSDS | join this dataframe to the corresponding SDS log file entry.
pipeline | Run the SeaFlow Pipeline
plotCruiseStats | Plot a seaflow cruise statistics
plotCytogram | Plot a Phytoplankton Cytogram
plotLatLongMap | plot file location on a map
plotStatMap | plot the stat.tab file on a map
POP.DEF | population definition table
readConsensusFile | Read a Consensus File.
readPopDef | Read the Population Definition File.
readSeaflow | Read a SeaFlow File
REPO.PATH | Seaflow Data directory
summarize | Summarize phytoplankon event & log parameters
summarizeFile | Compute aggregate statistics on a collection of opp or fcs files.
validatePopDef | Validate a Population Definition Dataframe.
writeSeaflow | Write A SeaFlow File