Analysis of Numerical Plankton Images

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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