Package: phenopix 2.4.4

phenopix: Process Digital Images of a Vegetation Cover

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

Authors:Gianluca Filippa, Edoardo Cremonese, Mirco Migliavacca, Marta Galvagno, Matthias Folker, Andrew D. Richardson, Enrico Tomelleri

phenopix_2.4.4.tar.gz
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phenopix.pdf |phenopix.html✨
phenopix/json (API)

# Install 'phenopix' in R:
install.packages('phenopix', repos = c('https://gianlucafilippa.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.48 score 5 stars 60 scripts 279 downloads 1 mentions 57 exports 23 dependencies

Last updated 10 months agofrom:416d3b64aa. Checks:OK: 5 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 15 2024
R-4.5-winNOTENov 15 2024
R-4.5-linuxNOTENov 15 2024
R-4.4-winOKNov 15 2024
R-4.4-macOKNov 15 2024
R-4.3-winOKNov 15 2024
R-4.3-macOKNov 15 2024

Exports:autoFilterBeckFitcombineUncertaintyconvertconvertROICutSeasonDrawMULTIROIeditExposureElmoreFitextractextractDateFilenameextractParametersextractVIsFitDoubleLogBeckFitDoubleLogElmoreFitDoubleLogGuFitDoubleLogKlHeavyFitDoubleLogKlLightfitted.phenopixget.optionsgetCoordsgetExposuregreenClustersgreenExploregreenProcessGuFithydrodoyKlostermanFitmatchExposureNDVIPasteSeasonPhenoBPPhenoDerivPhenoExtractPhenoGuPhenoKlPhenoPlotPhenoTrsplot.phenopixplotBPplotExploreplotSpatialplotSumplotVIprint.phenopixPrintROIresizeImagespatialFilterspatialGreenSplineFitsplitROIstructureFoldersummarizePhasessummary.phenopixtrainOCRupdate.phenopixupdateROI

Dependencies:clicodetoolsdoParallelforeachgluegtoolsiteratorsjpeglatticelifecyclemagrittrplyrrasterRcpprlangsandwichspstringistringrstrucchangeterravctrszoo

Readme and manuals

Help Manual

Help pageTopics
A package for the processing of images of a vegetation coverphenopix-package phenopix
A multiple-approach filtering procedureautoFilter
Bartlett 2009 raw databartlett2009
Bartlett 2009 dataset filteredbartlett2009.filtered
Bartlett 2009 dataset with computed fitting and uncertainty estimationbartlett2009.fitted
Bartlett 2009 dataset processed by greenExplore functionbartlett2009.processed
Fit a double logistic equation to a time series according to Beck et al. (2006)BeckFit
An evolution of 'greenProcess' for the combination of uncertainty after processingcombineUncertainty
Convert in data.frame a 'zoo' or 'ts' objectconvert
Convert a region of interest object from the old structure to the new (phenopix > 2.4)convertROI
Cut time series by visual estimationCutSeason
Draw a Region of InterestDrawMULTIROI
Change erroneous exposure values by handeditExposure
Fit a double logistic equation to a time series according to Elmore et al. (2012)ElmoreFit
Extract items from an object of class phenopixextract
Estract dates from filenamesextractDateFilename
Extract fitting parameters from a pixel-based analysisextractParameters
Extracts various vegetation indexes in a ROIextractVIs
A fitFitDoubleLogBeck
A fitFitDoubleLogElmore
Fit a double logistic equation to a vector according to Gu et al. (2003)FitDoubleLogGu
Fit a double logistic function to a vector according to Klosterman et al. (2014)FitDoubleLogKlHeavy
Fit a double logistic equation to a vector according to Klosterman et al. (2014)FitDoubleLogKlLight
Returns predicted values from 'phenopix' objects.fitted.phenopix
Returns default options for function 'autoFilter'.get.options
Extract coordinates (in pixels) of the exposure string from a given JPEG imagegetCoords
Extract exposure from stardot (or similar) imagesgetExposure
Performs a cluster analysis on data in output from pixel-based phenologygreenClusters
Explore all possible fitting and theshold methods from the package phenopixgreenExplore
Fit a curve and extract thresholds from vegetation index time seriesgreenProcess
Fit a double logistic equation to a time series according to Gu et al. (2003)GuFit
Converts from and to hydrological day of yearhydrodoy
Fit a double logistic equation to a vector according to Klosterman et al. (2014)KlostermanFit
Match exposures retrieved from the header of (stardot) digital imagesmatchExposure
Compute NDVI from Phenocam color indicesNDVI
A plotting facility for seasonal data with multiple cyclesPasteSeason
Extract breakpoints on a time seriesPhenoBP
Extract phenophases from a fitted equation with method DerivativesPhenoDeriv
Generic function for the extraction of phenological thresholdsPhenoExtract
Extract phenophases from a fitted equation according to Gu et al. 2009PhenoGu
Extract phenophases from a fitted equation according to Klosterman et al. 2014PhenoKl
A plotting function for phenological thresholdsPhenoPlot
A phenophase method based on fixed thresholdsPhenoTrs
Plotting 'phenopix' objects.plot.phenopix
A function to plot results of function 'PhenoBP'plotBP
Plot an object in output from the greenExplore functionplotExplore
Plot pixel-based analysis results from spatialGreen and extractParameters functionsplotSpatial
A plotting facility to show the combination of uncertaintyplotSum
Plot RGB DN, RGB indices and brightnessplotVI
Print 'phenopix' objects.print.phenopix
Print an already drawn region of interestPrintROI
Resize an image (and a tROI) to a given pixel resolutionresizeImage
Explore all possible fitting and theshold methods from the package phenopixspatialFilter
Process pixel-based greenness indexesspatialGreen
A function to fit a smoothed spline to Phenological DataSplineFit
Splits a ROI into multiple subrois for spatial analysissplitROI
Fast structuration of a folder for phenopix processstructureFolder
An evolution of 'greenProcess' for the combination of uncertainty after processingsummarizePhases
Summary of 'phenopix' objects.summary.phenopix
Extract a training dataset for OCR proceduretrainOCR
Update 'phenopix' objects.update.phenopix
Update pixels included in a ROI of different pixel sizeupdateROI