skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: An integrated phenology modelling framework in r

ORCiD logo [1];  [2];  [3];  [4];  [5];
  1. INRAUMR ISPA Villenave d'Ornon France, Department of Applied Ecology and Environmental BiologyGhent University Aquitaine Belgium, Department of Organismic and Evolutionary BiologyHarvard University Cambridge MA USA
  2. Department of Organismic and Evolutionary BiologyHarvard University Cambridge MA USA
  3. Earth Systems Research CenterUniversity of New Hampshire Durham NH USA
  4. Department of Earth &, EnvironmentBoston University Boston MA USA
  5. Department of Organismic and Evolutionary BiologyHarvard University Cambridge MA USA, School of Informatics, Computing and Cyber SystemsNorthern Arizona University Flagstaff AZ USA, Center for Ecosystem Science and SocietyNorthern Arizona University Flagstaff AZ USA
Publication Date:
Sponsoring Org.:
OSTI Identifier:
Resource Type:
Publisher's Accepted Manuscript
Journal Name:
Methods in Ecology and Evolution (Online)
Additional Journal Information:
Journal Name: Methods in Ecology and Evolution (Online) Journal Volume: 9 Journal Issue: 5; Journal ID: ISSN 2041-210X
Country of Publication:
United Kingdom

Citation Formats

Hufkens, Koen, Basler, David, Milliman, Tom, Melaas, Eli K., Richardson, Andrew D., and Goslee, ed., Sarah. An integrated phenology modelling framework in r. United Kingdom: N. p., 2018. Web. doi:10.1111/2041-210X.12970.
Hufkens, Koen, Basler, David, Milliman, Tom, Melaas, Eli K., Richardson, Andrew D., & Goslee, ed., Sarah. An integrated phenology modelling framework in r. United Kingdom. doi:10.1111/2041-210X.12970.
Hufkens, Koen, Basler, David, Milliman, Tom, Melaas, Eli K., Richardson, Andrew D., and Goslee, ed., Sarah. Tue . "An integrated phenology modelling framework in r". United Kingdom. doi:10.1111/2041-210X.12970.
title = {An integrated phenology modelling framework in r},
author = {Hufkens, Koen and Basler, David and Milliman, Tom and Melaas, Eli K. and Richardson, Andrew D. and Goslee, ed., Sarah},
abstractNote = {},
doi = {10.1111/2041-210X.12970},
journal = {Methods in Ecology and Evolution (Online)},
number = 5,
volume = 9,
place = {United Kingdom},
year = {2018},
month = {2}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1111/2041-210X.12970

Citation Metrics:
Cited by: 7 works
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

Evaluating remote sensing of deciduous forest phenology at multiple spatial scales using PhenoCam imagery
journal, January 2014

  • Klosterman, S. T.; Hufkens, K.; Gray, J. M.
  • Biogeosciences Discussions, Vol. 11, Issue 2
  • DOI: 10.5194/bgd-11-2305-2014

Greenness indices from digital cameras predict the timing and seasonal dynamics of canopy-scale photosynthesis
journal, January 2015

  • Toomey, Michael; Friedl, Mark A.; Frolking, Steve
  • Ecological Applications, Vol. 25, Issue 1
  • DOI: 10.1890/14-0005.1

MODISTools - downloading and processing MODIS remotely sensed data in R
journal, December 2014

  • Tuck, Sean L.; Phillips, Helen R. P.; Hintzen, Rogier E.
  • Ecology and Evolution, Vol. 4, Issue 24
  • DOI: 10.1002/ece3.1273

Apple Fruit Bud Development and Growth; Analysis and an Empirical Model
journal, November 1974

Productivity of North American grasslands is increased under future climate scenarios despite rising aridity
journal, February 2016

  • Hufkens, Koen; Keenan, Trevor F.; Flanagan, Lawrence B.
  • Nature Climate Change, Vol. 6, Issue 7
  • DOI: 10.1038/nclimate2942

Generalized simulated annealing
journal, November 1996

  • Tsallis, Constantino; Stariolo, Daniel A.
  • Physica A: Statistical Mechanics and its Applications, Vol. 233, Issue 1-2
  • DOI: 10.1016/S0378-4371(96)00271-3

Predicting the start and peak dates of the Poaceae pollen season in Spain using process-based models
journal, February 2009

Climatic determinants of budburst seasonality in four temperate-zone tree species
journal, August 1999

Genetic Optimization Using Derivatives: The rgenoud Package for R
journal, January 2011

  • Mebane, Walter R.; Sekhon, Jasjeet S.
  • Journal of Statistical Software, Vol. 42, Issue 11
  • DOI: 10.18637/jss.v042.i11

Chilling outweighs photoperiod in preventing precocious spring development
journal, October 2013

  • Laube, Julia; Sparks, Tim H.; Estrella, Nicole
  • Global Change Biology, Vol. 20, Issue 1
  • DOI: 10.1111/gcb.12360

Modelling of weather variability effect on fitophenology
journal, March 2006

Influence of spring and autumn phenological transitions on forest ecosystem productivity
journal, October 2010

  • Richardson, Andrew D.; Andy Black, T.; Ciais, Philippe
  • Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 365, Issue 1555
  • DOI: 10.1098/rstb.2010.0102

Changes in autumn senescence in northern hemisphere deciduous trees: a meta-analysis of autumn phenology studies
journal, May 2015

  • Gill, Allison L.; Gallinat, Amanda S.; Sanders-DeMott, Rebecca
  • Annals of Botany, Vol. 116, Issue 6
  • DOI: 10.1093/aob/mcv055

A Critique of the Heat Unit Approach to Plant Response Studies
journal, October 1960

Seasonal patterns and environmental control of carbon dioxide and water vapour exchange in an ecotonal boreal forest
journal, December 1999

Digital repeat photography for phenological research in forest ecosystems
journal, January 2012

Multiscale modeling of spring phenology across Deciduous Forests in the Eastern United States
journal, January 2016

  • Melaas, Eli K.; Friedl, Mark A.; Richardson, Andrew D.
  • Global Change Biology, Vol. 22, Issue 2
  • DOI: 10.1111/gcb.13122

On the uncertainty of phenological responses to climate change, and implications for a terrestrial biosphere model
journal, January 2012

Predicting the Timing of Budburst in Temperate Trees
journal, January 1992

  • Hunter, Alison F.; Lechowicz, Martin J.
  • The Journal of Applied Ecology, Vol. 29, Issue 3
  • DOI: 10.2307/2404467

Thermal Time, Chill Days and Prediction of Budburst in Picea sitchensis
journal, December 1983

  • Cannell, M. G. R.; Smith, R. I.
  • The Journal of Applied Ecology, Vol. 20, Issue 3
  • DOI: 10.2307/2403139

The ERA-Interim reanalysis: configuration and performance of the data assimilation system
journal, April 2011

  • Dee, D. P.; Uppala, S. M.; Simmons, A. J.
  • Quarterly Journal of the Royal Meteorological Society, Vol. 137, Issue 656
  • DOI: 10.1002/qj.828

Detecting leaf area and surface resistance during transition seasons
journal, April 1997

  • Sakai, Ricardo K.; Fitzjarrald, David R.; Moore, Kathleen E.
  • Agricultural and Forest Meteorology, Vol. 84, Issue 3-4
  • DOI: 10.1016/S0168-1923(96)02359-3

Implementing a U.S. National Phenology Network
journal, January 2005

  • Betancourt, Julio L.; Schwartz, Mark D.; Breshears, David D.
  • Eos, Transactions American Geophysical Union, Vol. 86, Issue 51
  • DOI: 10.1029/2005EO510005

Intercomparison, interpretation, and assessment of spring phenology in North America estimated from remote sensing for 1982-2006
journal, October 2009

Plant Modelling Framework: Software for building and running crop models on the APSIM platform
journal, December 2014

Phenology model from surface meteorology does not capture satellite-based greenup estimations
journal, March 2007

Tree phenology responses to winter chilling, spring warming, at north and south range limits
journal, July 2014

Selecting models to predict the timing of flowering of temperate trees: implications for tree phenology modelling
journal, January 1999

Shortcomings of classical phenological forcing models and a way to overcome them
journal, October 2012

Changing Environmental Effects on Frost Hardiness of Scots Pine During Dehardening
journal, February 1997

A framework for modelling the annual cycle of trees in boreal and temperate regions
journal, January 2007

  • Hänninen, Heikki; Kramer, Koen
  • Silva Fennica, Vol. 41, Issue 1
  • DOI: 10.14214/sf.313

Modeling grassland spring onset across the Western United States using climate variables and MODIS-derived phenology metrics
journal, May 2015

MODIS Collection 5 global land cover: Algorithm refinements and characterization of new datasets
journal, January 2010

  • Friedl, Mark A.; Sulla-Menashe, Damien; Tan, Bin
  • Remote Sensing of Environment, Vol. 114, Issue 1
  • DOI: 10.1016/j.rse.2009.08.016

Predicting Climate Change Impacts on the Amount and Duration of Autumn Colors in a New England Forest
journal, March 2013

Physiology-based phenology models for forest tree species in Germany
journal, August 2003

Monitoring vegetation phenology using MODIS
journal, March 2003

Grape ripening as a past climate indicator
journal, November 2004

  • Chuine, Isabelle; Yiou, Pascal; Viovy, Nicolas
  • Nature, Vol. 432, Issue 7015
  • DOI: 10.1038/432289a

Tracking vegetation phenology across diverse North American biomes using PhenoCam imagery
journal, March 2018

  • Richardson, Andrew D.; Hufkens, Koen; Milliman, Tom
  • Scientific Data, Vol. 5, Issue 1
  • DOI: 10.1038/sdata.2018.28

Terrestrial biosphere models need better representation of vegetation phenology: results from the North American Carbon Program Site Synthesis
journal, November 2011

A Unified Model for Budburst of Trees
journal, December 2000

Selecting a Model to Predict the Onset of Growth of Fagus sylvatica
journal, February 1994

  • Kramer, Koen
  • The Journal of Applied Ecology, Vol. 31, Issue 1
  • DOI: 10.2307/2404609

Does humidity trigger tree phenology? Proposal for an air humidity based framework for bud development in spring
journal, January 2014

  • Laube, Julia; Sparks, Tim H.; Estrella, Nicole
  • New Phytologist, Vol. 202, Issue 2
  • DOI: 10.1111/nph.12680

Climate change, phenology, and phenological control of vegetation feedbacks to the climate system
journal, February 2013

Models of the spring phenology of boreal and temperate trees: is there something missing?
journal, September 2006

Foliar stage in wheat correlates better to photothermal time than to thermal time
journal, April 1989

Tracking forest phenology and seasonal physiology using digital repeat photography: a critical assessment
journal, September 2014

  • Keenan, T. F.; Darby, B.; Felts, E.
  • Ecological Applications, Vol. 24, Issue 6
  • DOI: 10.1890/13-0652.1

A European daily high-resolution gridded data set of surface temperature and precipitation for 1950–2006
journal, January 2008

  • Haylock, M. R.; Hofstra, N.; Klein Tank, A. M. G.
  • Journal of Geophysical Research, Vol. 113, Issue D20
  • DOI: 10.1029/2008JD010201

Macroscale prediction of autumn leaf coloration throughout the continental United States: Scaling and predicting autumn phenology
journal, July 2014

  • Jeong, Su-Jong; Medvigy, David
  • Global Ecology and Biogeography, Vol. 23, Issue 11
  • DOI: 10.1111/geb.12206

Date of Budburst of Fifteen Tree Species in Britain Following Climatic Warming
journal, August 1989

  • Murray, M. B.; Cannell, M. G. R.; Smith, R. I.
  • The Journal of Applied Ecology, Vol. 26, Issue 2
  • DOI: 10.2307/2404093

Generalized Simulated Annealing for Global Optimization: The GenSA Package
journal, January 2013

  • Xiang, Yang; Gubian, Sylvain; Suomela, Brian
  • The R Journal, Vol. 5, Issue 1
  • DOI: 10.32614/RJ-2013-002