phenopix: Process Digital Images of a Vegetation Cover

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A collection of functions to process digital images, depict greennes index trajectories and extract relevant phenological stages.

Author
Gianluca Filippa, Edoardo Cremonese, Mirco Migliavacca, Marta Galvagno, Matthias Folker, Andrew D. Richardson, Enrico Tomelleri
Date of publication
2016-11-23 14:55:14
Maintainer
Gianluca Filippa <gian.filippa@gmail.com>
License
GPL-2
Version
2.3

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Man pages

autoFilter
A multiple-approach filtering procedure
bartlett2009
Bartlett 2009 raw data
bartlett2009.filtered
Bartlett 2009 dataset filtered
bartlett2009.fitted
Bartlett 2009 dataset with computed fitting and uncertainty...
bartlett2009.processed
Bartlett 2009 dataset processed by greenExplore function
BeckFit
A function to fit a double logisitic function to a vector...
combineUncertainty
An evolution of 'greenProcess' for the combination of...
convert
A function to convert in data.frame a 'zoo' or 'ts' objct
CutSeason
A function to cut time series by visual estimation
DrawROI
Draw Region of Interest
editExposure
Change erroneous exposure values by hand
ElmoreFit
A function to fit a double logisitic function to a vector...
extract
A function to extract items from an object of class phenopix
extractDateFilename
Estract dates from filenames
extractParameters
Extract fitting parameters from a pixel-based analysis
extractVIs
Extracts various vegetation indexes in a ROI
FitDoubleLogBeck
A fit
FitDoubleLogElmore
A fit
FitDoubleLogGu
A function to fit a double logisitic function to a vector...
FitDoubleLogKlHeavy
A function to fit a double logisitic function to a vector...
FitDoubleLogKlLight
A function to fit a double logisitic function to a vector...
fitted.phenopix
Returns predicted values from 'phenopix' objects.
getCoords
Extract given coordinates (in pixels) from a given JPEG image
getExposure
Extract exposure from stardot (or similar) images
get.options
Returns default options for function 'autoFilter'.
greenClusters
A function to perform a cluster analysis on data in output...
greenExplore
Explore all possible fitting and theshold methods from the...
greenProcess
A function to fit a curve and extract thresholds from...
GuFit
A function to fit a double logisitic function to a vector...
hydrodoy
Converts from and to hydrological day of year
KlostermanFit
A function to fit a double logisitic function to a vector...
matchExposure
Match exposures retrieved from the header of (stardot)...
NDVI
Compute NDVI
PasteSeason
A plotting facility for seasonal data with multiple cycles
PhenoBP
A function to extract breakpoints on a time series
PhenoDeriv
A function to extract thresholds
PhenoExtract
A function that extracts phenological thresholds
PhenoGu
A function to extract phenological thresholds according to Gu...
PhenoKl
A function to extract phenological thresholds according to...
phenopix-package
A package to process images of a vegetation cover
PhenoPlot
A plotting function for phenological thresholds
PhenoTrs
A fitting function
plotBP
A function to plot results of function 'PhenoBP'
plotExplore
Plot an object in output from the greenExplore function
plot.phenopix
Plotting 'phenopix' objects.
plotSpatial
Plot pixel-based analysis results from spatialGreen and...
plotSum
An evolution of 'greenProcess' for the combination of...
plotVI
Plot RGB DN, RGB indices and brightness
print.phenopix
Print 'phenopix' objects.
PrintROI
Print an already drawn region of interest
resizeImage
Resize an image (and a tROI) to a given pixel resolution
spatialFilter
Explore all possible fitting and theshold methods from the...
spatialGreen
Process pixel-based greenness indexes
SplineFit
A function to fit a smoothed spline to Phenological Data
splitROI
Splits a ROI into multiple subrois for spatial analysis
structureFolder
Fast structuration of a folder for phenopix process
summarizePhases
An evolution of 'greenProcess' for the combination of...
summary.phenopix
Summary of 'phenopix' objects.
trainOCR
Extract a training dataset for OCR procedure
update.phenopix
Update 'phenopix' objects.
updateROI
Update pixels included in a ROI of different pixel size

Files in this package

phenopix/DESCRIPTION
phenopix/NAMESPACE
phenopix/R
phenopix/R/BeckFit.R
phenopix/R/CutSeason.R
phenopix/R/DrawROI.R
phenopix/R/ElmoreFit.R
phenopix/R/FitDoubleLogBeck.R
phenopix/R/FitDoubleLogElmore.R
phenopix/R/FitDoubleLogGu.R
phenopix/R/FitDoubleLogKlHeavy.R
phenopix/R/FitDoubleLogKlLight.R
phenopix/R/GuFit.R
phenopix/R/KlostermanFit.R
phenopix/R/NDVI.R
phenopix/R/PasteSeason.R
phenopix/R/PhenoBP.R
phenopix/R/PhenoDeriv.R
phenopix/R/PhenoExtract.R
phenopix/R/PhenoGu.R
phenopix/R/PhenoKl.R
phenopix/R/PhenoPlot.R
phenopix/R/PhenoTrs.R
phenopix/R/PrintROI.R
phenopix/R/SplineFit.R
phenopix/R/autoFilter.R
phenopix/R/combineUncertainty.R
phenopix/R/convert.R
phenopix/R/editExposure.R
phenopix/R/extract.R
phenopix/R/extractDateFilename.R
phenopix/R/extractParameters.R
phenopix/R/extractVIs.R
phenopix/R/fitted.phenopix.R
phenopix/R/get.options.R
phenopix/R/getCoords.R
phenopix/R/getExposure.R
phenopix/R/greenClusters.R
phenopix/R/greenExplore.R
phenopix/R/greenProcess.R
phenopix/R/hydrodoy.R
phenopix/R/matchExposure.R
phenopix/R/plot.phenopix.R
phenopix/R/plotBP.R
phenopix/R/plotExplore.R
phenopix/R/plotSpatial.R
phenopix/R/plotSum.R
phenopix/R/plotVI.R
phenopix/R/print.phenopix.R
phenopix/R/resizeImage.R
phenopix/R/spatialFilter.R
phenopix/R/spatialGreen.R
phenopix/R/splitROI.R
phenopix/R/structureFolder.R
phenopix/R/summarizePhases.R
phenopix/R/summary.phenopix.R
phenopix/R/trainOCR.R
phenopix/R/update.phenopix.R
phenopix/R/updateROI.R
phenopix/build
phenopix/build/vignette.rds
phenopix/data
phenopix/data/bartlett2009.filtered.rda
phenopix/data/bartlett2009.fitted.rda
phenopix/data/bartlett2009.processed.rda
phenopix/data/bartlett2009.rda
phenopix/inst
phenopix/inst/doc
phenopix/inst/doc/OCR.Rnw
phenopix/inst/doc/OCR.pdf
phenopix/inst/doc/base.Rnw
phenopix/inst/doc/base.pdf
phenopix/inst/doc/spatial.Rnw
phenopix/inst/doc/spatial.pdf
phenopix/man
phenopix/man/BeckFit.Rd
phenopix/man/CutSeason.Rd
phenopix/man/DrawROI.Rd
phenopix/man/ElmoreFit.Rd
phenopix/man/FitDoubleLogBeck.Rd
phenopix/man/FitDoubleLogElmore.Rd
phenopix/man/FitDoubleLogGu.Rd
phenopix/man/FitDoubleLogKlHeavy.Rd
phenopix/man/FitDoubleLogKlLight.Rd
phenopix/man/GuFit.Rd
phenopix/man/KlostermanFit.Rd
phenopix/man/NDVI.Rd
phenopix/man/PasteSeason.Rd
phenopix/man/PhenoBP.Rd
phenopix/man/PhenoDeriv.Rd
phenopix/man/PhenoExtract.Rd
phenopix/man/PhenoGu.Rd
phenopix/man/PhenoKl.Rd
phenopix/man/PhenoPlot.Rd
phenopix/man/PhenoTrs.Rd
phenopix/man/PrintROI.Rd
phenopix/man/SplineFit.Rd
phenopix/man/autoFilter.Rd
phenopix/man/bartlett2009.Rd
phenopix/man/bartlett2009.filtered.Rd
phenopix/man/bartlett2009.fitted.Rd
phenopix/man/bartlett2009.processed.Rd
phenopix/man/combineUncertainty.Rd
phenopix/man/convert.Rd
phenopix/man/editExposure.Rd
phenopix/man/extract.Rd
phenopix/man/extractDateFilename.Rd
phenopix/man/extractParameters.Rd
phenopix/man/extractVIs.Rd
phenopix/man/fitted.phenopix.Rd
phenopix/man/get.options.Rd
phenopix/man/getCoords.Rd
phenopix/man/getExposure.Rd
phenopix/man/greenClusters.Rd
phenopix/man/greenExplore.Rd
phenopix/man/greenProcess.Rd
phenopix/man/hydrodoy.Rd
phenopix/man/matchExposure.Rd
phenopix/man/phenopix-package.Rd
phenopix/man/plot.phenopix.Rd
phenopix/man/plotBP.Rd
phenopix/man/plotExplore.Rd
phenopix/man/plotSpatial.Rd
phenopix/man/plotSum.Rd
phenopix/man/plotVI.Rd
phenopix/man/print.phenopix.Rd
phenopix/man/resizeImage.Rd
phenopix/man/spatialFilter.Rd
phenopix/man/spatialGreen.Rd
phenopix/man/splitROI.Rd
phenopix/man/structureFolder.Rd
phenopix/man/summarizePhases.Rd
phenopix/man/summary.phenopix.Rd
phenopix/man/trainOCR.Rd
phenopix/man/update.phenopix.Rd
phenopix/man/updateROI.Rd
phenopix/vignettes
phenopix/vignettes/OCR.Rnw
phenopix/vignettes/base.Rnw
phenopix/vignettes/spatial.Rnw