phenopix (version 2.4.5)

Process Digital Images of a Vegetation Cover

Description

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

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Version

Install

install.packages('phenopix')

Monthly Downloads

352

Version

2.4.5

License

GPL-2

Maintainer

Gianluca Filippa

Last Published

February 13th, 2025

Functions in phenopix (2.4.5)

combineUncertainty

An evolution of greenProcess for the combination of uncertainty after processing

bartlett2009.fitted

Bartlett 2009 dataset with computed fitting and uncertainty estimation

PhenoPlot

A plotting function for phenological thresholds

PhenoExtract

Generic function for the extraction of phenological thresholds

PhenoDeriv

Extract phenophases from a fitted equation with method Derivatives

bartlett2009.processed

Bartlett 2009 dataset processed by greenExplore function

bartlett2009.filtered

Bartlett 2009 dataset filtered

extractDateFilename

Estract dates from filenames

extractParameters

Extract fitting parameters from a pixel-based analysis

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

fitted.phenopix

Returns predicted values from phenopix objects.

bartlett2009

Bartlett 2009 raw data

autoFilter

A multiple-approach filtering procedure

extractVIs

Extracts various vegetation indexes in a ROI

convertROI

Convert a region of interest object from the old structure to the new (phenopix > 2.4)

convert

Convert in data.frame a zoo or ts object

matchExposure

Match exposures retrieved from the header of (stardot) digital images

hydrodoy

Converts from and to hydrological day of year

PhenoTrs

A phenophase method based on fixed thresholds

editExposure

Change erroneous exposure values by hand

phenopix-package

A package for the processing of images of a vegetation cover

plot.phenopix

Plotting phenopix objects.

extract

Extract items from an object of class phenopix

plotVI

Plot RGB DN, RGB indices and brightness

KlostermanFit

Fit a double logistic equation to a vector according to Klosterman et al. (2014)

PrintROI

Print an already drawn region of interest

SplineFit

A function to fit a smoothed spline to Phenological Data

NDVI

Compute NDVI from Phenocam color indices

summarizePhases

An evolution of greenProcess for the combination of uncertainty after processing

structureFolder

Fast structuration of a folder for phenopix process

get.options

Returns default options for function autoFilter.

splitROI

Splits a ROI into multiple subrois for spatial analysis

spatialGreen

Process pixel-based greenness indexes

print.phenopix

Print phenopix objects.

plotBP

A function to plot results of function PhenoBP

plotExplore

Plot an object in output from the greenExplore function

updateROI

Update pixels included in a ROI of different pixel size

update.phenopix

Update phenopix objects.

trainOCR

Extract a training dataset for OCR procedure

summary.phenopix

Summary of phenopix objects.

greenClusters

Performs a cluster analysis on data in output from pixel-based phenology

getExposure

Extract exposure from stardot (or similar) images

resizeImage

Resize an image (and a tROI) to a given pixel resolution

plotSpatial

Plot pixel-based analysis results from spatialGreen and extractParameters functions

spatialFilter

Explore all possible fitting and theshold methods from the package phenopix

plotSum

A plotting facility to show the combination of uncertainty

getCoords

Extract coordinates (in pixels) of the exposure string from a given JPEG image

greenProcess

Fit a curve and extract thresholds from vegetation index time series

greenExplore

Explore all possible fitting and theshold methods from the package phenopix

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)

GuFit

Fit a double logistic equation to a time series according to Gu et al. (2003)

FitDoubleLogBeck

A fit

BeckFit

Fit a double logistic equation to a time series according to Beck et al. (2006)

FitDoubleLogElmore

A fit

CutSeason

Cut time series by visual estimation

DrawMULTIROI

Draw a Region of Interest

ElmoreFit

Fit a double logistic equation to a time series according to Elmore et al. (2012)

FitDoubleLogKlLight

Fit a double logistic equation to a vector according to Klosterman et al. (2014)

PhenoBP

Extract breakpoints on a time series

PasteSeason

A plotting facility for seasonal data with multiple cycles