# Analysis of Numerical Plankton Images

## Documentation for package ‘zooimage’ version 5.5.2

- DESCRIPTION file.

## Help Pages

A C D E F G H I J L M N O P R S T U V Z

zooimage-package | ZooImage: analysis of digital plankton images

## -- A --

aboutZI | The ZooImage GUI (Graphical User Interface)
acquireImg | The ZooImage GUI (Graphical User Interface)
activeLearning | The ZooImage error correction (manual validation) tools
activeLearningGUI | The ZooImage GUI (Graphical User Interface)
addClass | Various utility functions used by ZooImage
addItemsToTrain | The ZooImage error correction (manual validation) tools
addToTest | Manipulate training and testsets 'ZITrain'/'ZITest' objects
addToTrain | Manipulate training and testsets 'ZITrain'/'ZITest' objects
addVigsToTrain | The ZooImage GUI (Graphical User Interface)
analyzeClass | The ZooImage GUI (Graphical User Interface)

## -- C --

calcVars | Various utility functions used by ZooImage
calib | The ZooImage GUI (Graphical User Interface)
calibrate | Various utility functions used by ZooImage
cellCompute | Manipulate training and testsets 'ZITrain'/'ZITest' objects
cellCount | Manipulate training and testsets 'ZITrain'/'ZITest' objects
cellModel | Manipulate training and testsets 'ZITrain'/'ZITest' objects
checkDirExists | Various file utility functions used by ZooImage
checkEmptyDir | Various file utility functions used by ZooImage
checkFileExists | Various file utility functions used by ZooImage
checkFirstLine | Various file utility functions used by ZooImage
closeAssistant | The ZooImage GUI (Graphical User Interface)
closeZooImage | The ZooImage GUI (Graphical User Interface)
collectTrain | The ZooImage GUI (Graphical User Interface)
compTrain | The ZooImage GUI (Graphical User Interface)
confusion.ZIClass | Create and manipulate 'ZIClass' objects
contextSelection | Manipulate training and testsets 'ZITrain'/'ZITest' objects
correctError | The ZooImage error correction (manual validation) tools
countCellsGUI | The ZooImage GUI (Graphical User Interface)
createThreshold | Various GUI utility functions used by ZooImage

## -- D --

dropItemsToTrain | The ZooImage error correction (manual validation) tools
dropVars | Various utility functions used by ZooImage

## -- E --

ecd | Various utility functions used by ZooImage
editDescription | The ZooImage GUI (Graphical User Interface)
exitZI | The ZooImage GUI (Graphical User Interface)
exportResults | The ZooImage GUI (Graphical User Interface)
extensionPattern | Various file utility functions used by ZooImage

## -- F --

focusGraph | The ZooImage GUI (Graphical User Interface)
focusR | The ZooImage GUI (Graphical User Interface)
forceDirCreate | Various file utility functions used by ZooImage

## -- G --

getDec | Various utility functions used by ZooImage
getTest | Manipulate training and testsets 'ZITrain'/'ZITest' objects
getTrain | Manipulate training and testsets 'ZITrain'/'ZITest' objects

## -- H --

hasExtension | Various file utility functions used by ZooImage

## -- I --

imageViewer | Various GUI utility functions used by ZooImage
importFlowCAM | Function to import data from the FlowCAM
importImg | The ZooImage GUI (Graphical User Interface)
isZim | Manipulate .zim files (ZooImage Metadata/Measurements)

## -- J --

jpgList | Various file utility functions used by ZooImage

## -- L --

listFilesExt | Various file utility functions used by ZooImage
listObjects | The ZooImage GUI (Graphical User Interface)
listSamples | Various utility functions used by ZooImage
loadObjects | The ZooImage GUI (Graphical User Interface)

## -- M --

makeClass | The ZooImage GUI (Graphical User Interface)
makeId | Various utility functions used by ZooImage
makeTrain | The ZooImage GUI (Graphical User Interface)
makeZid | The ZooImage GUI (Graphical User Interface)
makeZidb | The ZooImage GUI (Graphical User Interface)
makeZidbFlowCAM | The ZooImage GUI (Graphical User Interface)
makeZIVignettes | Various utility functions used by ZooImage
modalAssistant | Various GUI utility functions used by ZooImage

## -- N --

noExtension | Various file utility functions used by ZooImage

## -- O --

optInOutDecimalSep | The ZooImage GUI (Graphical User Interface)

## -- P --

parseIni | Various utility functions used by ZooImage
pngList | Various file utility functions used by ZooImage
predict.ZIClass | Create and manipulate 'ZIClass' objects
prepareTest | Manipulate training and testsets 'ZITrain'/'ZITest' objects
prepareTrain | Manipulate training and testsets 'ZITrain'/'ZITest' objects
print.ZIClass | Create and manipulate 'ZIClass' objects
print.ZIE | ZIE (ZooImage Extension) manipulate .zie files to add custom import, export, etc. routines to ZooImage
print.ZIRes | Various function to calculate results ('ZIRes' object)
processImg | The ZooImage GUI (Graphical User Interface)
processSample | Various function to calculate results ('ZIRes' object)
processSampleAll | Various function to calculate results ('ZIRes' object)
processSamples | The ZooImage GUI (Graphical User Interface)
processSamplesWithCells | The ZooImage GUI (Graphical User Interface)

## -- R --

rbind.ZIRes | Various function to calculate results ('ZIRes' object)
readFlowCAMctx | Function to import data from the FlowCAM
readFlowCAMlst | Function to import data from the FlowCAM
recode | Manipulate training and testsets 'ZITrain'/'ZITest' objects
recode.ZITest | Manipulate training and testsets 'ZITrain'/'ZITest' objects
recode.ZITrain | Manipulate training and testsets 'ZITrain'/'ZITest' objects
removeObjects | The ZooImage GUI (Graphical User Interface)

## -- S --

sampleInfo | Various utility functions used by ZooImage
saveObjects | The ZooImage GUI (Graphical User Interface)
selectFile | Various GUI utility functions used by ZooImage
selectGroups | Various GUI utility functions used by ZooImage
selectList | Various GUI utility functions used by ZooImage
selectObject | Various GUI utility functions used by ZooImage
startPgm | Various GUI utility functions used by ZooImage
summary.ZIClass | Create and manipulate 'ZIClass' objects

## -- T --

template | Manipulate training and testsets 'ZITrain'/'ZITest' objects
template.default | Manipulate training and testsets 'ZITrain'/'ZITest' objects
trimString | Various utility functions used by ZooImage

## -- U --

underscoreToSpace | Various utility functions used by ZooImage
unzipImg | Zip and unzip raw .tif images for ZooImage and embed metadata
unzipImgAll | Zip and unzip raw .tif images for ZooImage and embed metadata

## -- V --

validClass | The ZooImage GUI (Graphical User Interface)
viewFrenchManual | The ZooImage GUI (Graphical User Interface)
viewManual | The ZooImage GUI (Graphical User Interface)
viewResults | The ZooImage GUI (Graphical User Interface)
vignettesClass | The ZooImage GUI (Graphical User Interface)

## -- Z --

zicCheck | Check .zic files (ZooImage Categories)
ZIClass | Create and manipulate 'ZIClass' objects
zidbDatRead | Manage .zidb files (ZooImage Databases)
zidbDrawVignette | Manage .zidb files (ZooImage Databases)
zidbLink | Manage .zidb files (ZooImage Databases)
zidbList | Various file utility functions used by ZooImage
zidbMake | Manage .zidb files (ZooImage Databases)
zidbMakeAll | Manage .zidb files (ZooImage Databases)
zidbPlotNew | Manage .zidb files (ZooImage Databases)
zidbPlotPage | Manage .zidb files (ZooImage Databases)
zidbSampleRead | Manage .zidb files (ZooImage Databases)
zidbSummary | Manage .zidb files (ZooImage Databases)
zidbToZid | Manage .zidb files (ZooImage Databases)
zidbToZidAll | Manage .zidb files (ZooImage Databases)
zidClean | Manage .zid files (ZooImage Data)
zidCompress | Manage .zid files (ZooImage Data)
zidCompressAll | Manage .zid files (ZooImage Data)
zidDatMake | Manage .zid files (ZooImage Data)
zidDatRead | Manage .zid files (ZooImage Data)
ZIDlg | The ZooImage GUI (Graphical User Interface)
zidList | Various file utility functions used by ZooImage
zidToZidb | Manage .zidb files (ZooImage Databases)
zidToZidbAll | Manage .zidb files (ZooImage Databases)
zidUncompress | Manage .zid files (ZooImage Data)
zidUncompressAll | Manage .zid files (ZooImage Data)
zidVerify | Manage .zid files (ZooImage Data)
zidVerifyAll | Manage .zid files (ZooImage Data)
ZIE | ZIE (ZooImage Extension) manipulate .zie files to add custom import, export, etc. routines to ZooImage
zieCompile | ZIE (ZooImage Extension) manipulate .zie files to add custom import, export, etc. routines to ZooImage
zieCompileFlowCAM | ZIE (ZooImage Extension) manipulate .zie files to add custom import, export, etc. routines to ZooImage
zieMake | ZIE (ZooImage Extension) manipulate .zie files to add custom import, export, etc. routines to ZooImage
zimCreate | Manipulate .zim files (ZooImage Metadata/Measurements)
zimDatList | Various file utility functions used by ZooImage
zimDatMakeFlowCAM | Manipulate .zim files (ZooImage Metadata/Measurements)
zimDatMakeFlowCAMAll | Manipulate .zim files (ZooImage Metadata/Measurements)
zimEdit | Manipulate .zim files (ZooImage Metadata/Measurements)
zimExtractAll | Manipulate .zim files (ZooImage Metadata/Measurements)
zimList | Various file utility functions used by ZooImage
zimMake | Manipulate .zim files (ZooImage Metadata/Measurements)
zimUpdateAll | Manipulate .zim files (ZooImage Metadata/Measurements)
zimVerify | Manipulate .zim files (ZooImage Metadata/Measurements)
zipImg | Zip and unzip raw .tif images for ZooImage and embed metadata
zipImgAll | Zip and unzip raw .tif images for ZooImage and embed metadata
zipList | Various file utility functions used by ZooImage
zipNoteAdd | Various utility functions used by ZooImage
zipNoteGet | Various utility functions used by ZooImage
zisCreate | Manipulate .zis files (ZooImage Samples description)
zisEdit | Manipulate .zis files (ZooImage Samples description)
zisRead | Manipulate .zis files (ZooImage Samples description)
ZIUI | The ZooImage GUI (Graphical User Interface)
zooimage | ZooImage: analysis of digital plankton images