R: Process Digital Images of a Vegetation Cover

# Process Digital Images of a Vegetation Cover

## Documentation for package ‘phenopix’ version 2.4.5

- DESCRIPTION file

## Help Pages

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