Process Digital Images of a Vegetation Cover

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Documentation for package ‘phenopix’ version 2.4.5

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phenopix-package A package for the processing of images of a vegetation cover
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 estimation
bartlett2009.processed Bartlett 2009 dataset processed by greenExplore function
BeckFit Fit a double logistic equation to a time series according to Beck et al. (2006)
combineUncertainty An evolution of 'greenProcess' for the combination of uncertainty after processing
convert Convert in data.frame a 'zoo' or 'ts' object
convertROI Convert a region of interest object from the old structure to the new (phenopix > 2.4)
CutSeason Cut time series by visual estimation
DrawMULTIROI Draw a Region of Interest
editExposure Change erroneous exposure values by hand
ElmoreFit Fit a double logistic equation to a time series according to Elmore et al. (2012)
extract 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 Fit a double logistic equation to a vector according to Gu et al. (2003)
FitDoubleLogKlHeavy Fit a double logistic function to a vector according to Klosterman et al. (2014)
FitDoubleLogKlLight Fit a double logistic equation to a vector according to Klosterman et al. (2014)
fitted.phenopix Returns predicted values from 'phenopix' objects.
get.options Returns default options for function 'autoFilter'.
getCoords Extract coordinates (in pixels) of the exposure string from a given JPEG image
getExposure Extract exposure from stardot (or similar) images
greenClusters Performs a cluster analysis on data in output from pixel-based phenology
greenExplore Explore all possible fitting and theshold methods from the package phenopix
greenProcess Fit a curve and extract thresholds from vegetation index time series
GuFit Fit a double logistic equation to a time series according to Gu et al. (2003)
hydrodoy Converts from and to hydrological day of year
KlostermanFit Fit a double logistic equation to a vector according to Klosterman et al. (2014)
matchExposure Match exposures retrieved from the header of (stardot) digital images
NDVI Compute NDVI from Phenocam color indices
PasteSeason A plotting facility for seasonal data with multiple cycles
PhenoBP Extract breakpoints on a time series
PhenoDeriv Extract phenophases from a fitted equation with method Derivatives
PhenoExtract Generic function for the extraction of phenological thresholds
PhenoGu Extract phenophases from a fitted equation according to Gu et al. 2009
PhenoKl Extract phenophases from a fitted equation according to Klosterman et al. 2014
phenopix A package for the processing of images of a vegetation cover
PhenoPlot A plotting function for phenological thresholds
PhenoTrs A phenophase method based on fixed thresholds
plot.phenopix Plotting 'phenopix' objects.
plotBP A function to plot results of function 'PhenoBP'
plotExplore Plot an object in output from the greenExplore function
plotSpatial Plot pixel-based analysis results from spatialGreen and extractParameters functions
plotSum A plotting facility to show the combination of uncertainty
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 package phenopix
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 uncertainty after processing
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