@manual{Rpack:bibtex,
  author = {Romain Francois},
  title = {bibtex: bibtex parser},
  year = {2014},
  note = {R package version 0.4.0},
}

@article{Denny2006,
  author = {M. W. Denny and C. D. G. Harley},
  title = {Hot limpets: predicting body temperature in a conductance-mediated thermal system},
  journal = {Journal of Experimental Biology},
  volume = {209},
  number = {13},
  pages = {2409-2419},
  year = {2006},
  month = {07},
  issn = {0022-0949},
  doi = {10.1242/jeb.02356},
}

@manual{Rpackage:rbibutils,
  title = {rbibutils: Convert Between Bibliography Formats},
  author = {G. N. Boshnakov and C. Putman},
  year = {2020},
  note = {https://CRAN.R-project.org/package=rbibutils},
}

@manual{Blischak,
  title = {Software Carpentry: Programming with R},
  author = {J. Blischak, and D. Chen, and H. Dashnow, and D. Haine},
  year = {2016},
  note = {Version 2016.06, June 2016},
  doi = {10.5281/zenodo.57541},
}


@manual{engingeeringtoolbox,
  title = {Atmospheric Pressure vs. Elevation above Sea Level},
  author = {{Engineering ToolBox}},
  year = {2003},
  note = {https://www.engineeringtoolbox.com/air-altitude-pressure-d_462.html},
}

@manual{parseRd,
  author = {D. Murdoch},
  title = {Parsing Rd files},
  year = {2010},
  url = {https://developer.r-project.org/parseRd.pdf},
}

@manual{ucipm,
  author = {{University of California Integrated Pest Management Program}},
  title = {Degree Days: Methods},
  year = {2016},
  url = {https://ipm.ucanr.edu/WEATHER/ddfigindex.html},
}


@manual{Rdevtools,
  author = {H. Wickham and J. Hester and W. Chang},
  title = {devtools: Tools to Make Developing R Packages Easier},
  year = {2018},
  note = {R package version 1.13.5},
  url = {https://CRAN.R-project.org/package=devtools},
}


@article{Roughgarden1981,
  author = {J. Roughgarden},
  title = {Resource partitioning of space and its relationship to body temperature in Anolis lizard populations},
  year = {1981},
  journal = {Oecologia},
  volume = {50},
  pages = {256 -- 264},
  url = {https://link.springer.com/article/10.1007/BF00348048},
}


@article{Tracy1972,
  author = {Tracy, C. R.},
  title = "{Newton's Law: Its Application for Expressing Heat Losses from Homeotherms}",
  journal = {BioScience},
  volume = {22},
  number = {11},
  pages = {656-659},
  year = {1972},
  month = {11},
  abstract = "{The use of Newton's law in comparative thermobiology and as a predictive ecological model of heat losses from homeotherms does not account for the functional relationship of animal size and ambient wind speed to the overall thermal conductance of homeothermic animals. This paper reports a theoretical examination of some similarities and differences between Newton's law and the thermodynamic energy balance as they have been used to describe heat losses from homeothermic animals in artificial and natural environments.}",
  issn = {0006-3568},
  doi = {10.2307/1296267},
}

@article{Kearney2020,
author = {M. R. Kearney and W. P. Porter},
title = {NicheMapR - an R package for biophysical modelling: the ectotherm and Dynamic Energy Budget models},
journal = {Ecography},
volume = {43},
number = {1},
pages = {85-96},
doi = {10.1111/ecog.04680},
abstract = {Mechanistic niche models characterise the fundamental niche of an organism by determining thermodynamic constraints on its heat, water and nutritional budget, and the consequences of this for growth, development and reproduction. They can thus quantify constraints on survival, activity and, ultimately, the vital rates that determine population growth, given a sequence of environmental conditions and the key morphological, physiological and behavioural functional traits. Here we introduce and document the ectotherm model of NicheMapR, an R package that includes a suite of programs for the mechanistic modelling of heat, water, energy and mass exchange between any kind of ectothermic organism and its environment. The NicheMapR ectotherm model is based on a Fortran program originally developed by Porter, Mitchell and Beckman for predicting core body temperature and evaporative water loss as a function of microclimatic conditions and behavioural thermoregulation. The model includes routines for computing steady state body temperature and evaporative water loss given two extreme microclimates (minimum and maximum shade) as computed by the NicheMapR microclimate model. Behavioural options include posture and colour change, shade-seeking, panting, climbing and retreating underground. Here we configure the program to be called from R as part of the NicheMapR package and describe the model in detail including new functionality for modelling whole life-cycle energy and water budgets using Dynamic Energy Budget theory. We include scripts for core operation of the ectotherm model as well as stand-alone R scripts for running the DEB model. Example applications are provided in the paper and in the associated vignettes. The integrated microclimate and ectotherm models should provide a strong thermodynamic basis for determining the effects of environmental change on the behaviour, distribution and abundance of ectothermic organisms.},
year = {2020},
}



@article{Tracy1976,
  author = {Tracy, C. R.},
  title = {A Model of the Dynamic Exchanges of Water and Energy between a Terrestrial Amphibian and Its Environment},
  journal = {Ecological Monographs},
  volume = {46},
  number = {3},
  pages = {293-326},
  doi = {10.2307/1942256},
  year = {1976}
}



@article{Meiri2010,
  author = {Meiri, S.},
  title = {Length - weight allometries in lizards},
  journal = {Journal of Zoology},
  volume = {281},
  number = {3},
  pages = {218-226},
  doi = {10.1111/j.1469-7998.2010.00696.x},
  year = {2010}
}



@article{Pough1980,
  ISSN = {00030147, 15375323},
  author = {F. H. Pough},
  journal = {The American Naturalist},
  number = {1},
  pages = {92--112},
  publisher = {[University of Chicago Press, American Society of Naturalists]},
  title = {The Advantages of Ectothermy for Tetrapods},
  volume = {115},
  year = {1980}
}



@article{Sample1993,
  ISSN = {00030031, 19384238},
  DOI = {10.2307/2426503},
  author = {B. E. Sample and R. J. Cooper and R. D. Greer and R. C. Whitmore},
  journal = {The American Midland Naturalist},
  number = {2},
  pages = {234--240},
  publisher = {University of Notre Dame},
  title = {Estimation of Insect Biomass by Length and Width},
  volume = {129},
  year = {1993}
}

@article{Muth1977,
  title = {Thermoregulatory Postures and Orientation to the Sun: A Mechanistic Evaluation for the Zebra-Tailed Lizard, Callisaurus draconoides},
  journal = {Copeia},
  volume = {4},
  pages = {710 - 720},
  year = {1977},
  author = {A. Muth},
}

@article{Idso1969,
author = {Idso, S B. and Jackson, R. D.},
title = {Thermal radiation from the atmosphere},
journal = {Journal of Geophysical Research (1896-1977)},
volume = {74},
number = {23},
pages = {5397-5403},
doi = {10.1029/JC074i023p05397},
year = {1969}
}



@article{Helmuth1999,
author = {Helmuth, B.},
title = {Thermal biology of rocky intertidal mussels: quantifying body temperatures using climatological data},
journal = {Ecology},
volume = {80},
number = {1},
pages = {15-34},
keywords = {aerial exposure, body temperature, climate data, environmental averages, fluctuating temperatures, microclimate, Mytilus, physical factors, rocky intertidal, tidal cycle},
doi = {10.2307/176977},
year = {1999}
}

@article{Helmuth1998,
 ISSN = {00129615},
 DOI = {10.2307/2657143},
 author = {B. S. T. Helmuth},
 journal = {Ecological Monographs},
 number = {1},
 pages = {51--74},
 publisher = {Ecological Society of America},
 title = {Intertidal Mussel Microclimates: Predicting the Body Temperature of a Sessile Invertebrate},
 volume = {68},
 year = {1998}
}



@article{Bartlett1967,
  title = {The energy budget of a lizard on a tree trunk},
  author = {P. N. Bartlett and D. M. Gates},
  journal = {Ecology},
  year = {1967},
  volume = {48},
  pages = {316-322}
}


@article{Porter1973,
  author = {W. P. Porter and J. W. Mitchell and A. Bekman and C. B. DeWitt},
  journal = {Oecologia},
  pages = {1-54},
  title = {Behavioral implications of mechanistic ecology: thermal and behavioral modeling of desert ectotherms and their microenvironments},
  volume = {13},
  year = {1973}
}

@article{Pennell1989,
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  pages = {299-302},
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  author = {S. Pennell and J. Deignan},
  doi = {10.1137/1031052}
}

@article{Kingsolver1979,
  title = {Thermal and hydric aspects of environmental hetergeneity in the pitcher plant mosquito},
  journal = {Ecological Monographs},
  volume = {49},
  pages = {357-376},
  year = {1979},
  author = {J. G. Kingsolver}
}

@book{Campbell1998,
  publisher = {Springer},
  isbn = {0387949372},
  year = {1998},
  title = {Introduction to environmental biophysics},
  edition = {2nd ed.},
  language = {eng},
  address = {New York},
  author = {G. S. Campbell and J. M Norman},
  keywords = {Biophysics; Ecology},
  lccn = {97015706},
}

@book{Rosenberg1974,
  publisher = {Wiley},
  year = {1974},
  title = {Microclimate: the biological environment},
  language = {eng},
  address = {New York},
  author = {N. J. Rosenberg},
}


@article{Kingsolver1983,
  author = {J. G. Kingsolver},
  title = {Thermoregulation and Flight in Colias Butterflies: Elevational Patterns and Mechanistic Limitations},
  journal = {Ecology},
  volume = {64},
  number = {3},
  pages = {534-545},
  doi = {10.2307/1939973},
  year = {1983}
}

@article{Buckley2012,
  author = {L. B. Buckley and J. G. Kingsolver},
  title = {The demographic impacts of shifts in climate means and extremes on alpine butterflies},
  journal = {Functional Ecology},
  volume = {26},
  number = {4},
  pages = {969-977},
  keywords = {biophysical model, climate change, Colias, egg viability, elevation gradient, flight activity time, local adaptation, phenotype, thermal stress},
  doi = {10.1111/j.1365-2435.2012.01969.x},
  year = {2012}
}



@article{Anderson1979,
  doi = {10.1007/BF00345194},
  author = {R. V. Anderson and C. R. Tracy and Z. Abramsky},
  journal = {Oecologia},
  number = {3},
  pages = {359--374},
  publisher = {Springer},
  title = {Habitat Selection in Two Species of Short-Horned Grasshoppers. The Role of Thermal and Hydric Stresses},
  volume = {38},
  year = {1979}
}

@article{Galushko2005,
	doi = {10.1088/0268-1242/20/3/005},
	year = 2005,
	month = {feb},
	publisher = {{IOP} Publishing},
	volume = {20},
	number = {3},
	pages = {286--289},
	author = {D. Galushko and N. Ermakov and M. Karpovski and A. Palevski and J. S. Ishay and D. J. Bergman},
	title = {Electrical, thermoelectric and thermophysical properties of hornet cuticle},
	journal = {Semiconductor Science and Technology},
}

@article{Mitchell1976,
  title = {Heat transfer from spheres and other animal forms},
  journal = {Biophysical Journal},
  volume = {16},
  number = {6},
  pages = {561-569},
  year = {1976},
  issn = {0006-3495},
  doi = {10.1016/S0006-3495(76)85711-6},
  author = {J.W. Mitchell},
  abstract = {A general predictive relation for the convection heat transfer from animal forms is developed. This relation is based on the convection equation for a sphere, and employs a simple, unique characteristic dimension to represent the animal which is the cube root of the animal volume. The accuracy of this relation is established through comparison with available convection results from animal shapes ranging in size and shape from spiders to cows. This relation allows an extrapolation to animal shapes for which data are not available. Results are also presented for the enhancement of convection heat transfer due to natural turbulence. A procedure is outlined for estimating the convecture heat loss from an animal in the natural outdoor environment.}
}


@article{Samietz2005,
  author = {Samietz, J. and Salser, M. A. and Dingle, H.},
  title = {Altitudinal variation in behavioural thermoregulation: local adaptation vs. plasticity in California grasshoppers},
  journal = {Journal of Evolutionary Biology},
  volume = {18},
  number = {4},
  pages = {1087-1096},
  keywords = {altitude, behaviour, ectotherm, life history, local adaptation, temperature, thermoregulation, thermoregulatory behaviour},
  doi = {10.1111/j.1420-9101.2005.00893.x},
  year = {2005}
}



@article{Lactin1998,
  title = {Convective heat loss and change in body temperature of grasshopper and locust nymphs: Relative importance of wind speed, insect size and insect orientation},
  journal = {Journal of Thermal Biology},
  number = {1},
  volume = {23},
  pages = {5-13},
  year = {1998},
  issn = {0306-4565},
  doi = {10.1016/S0306-4565(97)00037-5},
  url = {https://www.sciencedirect.com/science/article/pii/S0306456597000375},
  author = {D. J. Lactin and D. L. Johnson},
  keywords = {Convection, insect, grasshopper, locust, Orthoptera, Acrididae, body temperature, Newton's law of cooling, convective heat-transfer coefficient, biophysics}
}

@article{Wong2001,
  title = {Solar radiation model},
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  volume = {69},
  number = {3},
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  year = {2001},
  issn = {0306-2619},
  doi = {10.1016/S0306-2619(01)00012-5},
  url = {https://www.sciencedirect.com/science/article/pii/S0306261901000125},
  author = {L.T. Wong and W.K. Chow},
}


@article{Erbs1982,
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  volume = {28},
  pages = {293-302}
}

@article{Olyphant1984,
  title = {Insolation Topoclimates and Potential Ablation in Alpine Snow Accumulation Basins: Front Range, Colorado},
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  volume = {20},
  number = {4},
  pages = {491-498},
  year = {1984},
  author = {G. Olyphant},
}


@article{Porter1979,
  ISSN = {00458511, 19385110},
  DOI = {10.2307/1443867},
  abstract = {The daily and seasonal activity of the African rainbow lizard, Agama agama is predicted in terms of heat transfer models for the microenvironment and the lizard. The models, originally developed for the temperate Mohave Desert and for the desert iguana, Dipsosaurus dorsalis (Porter et al., 1973), have been refined and are applicable to a tropical area and a tropical species. Field microclimate measurements and observations of lizard activity and food consumption by different sizes of lizards are consistent with these models. Environmental constraints on activity times, sun vs shade locations, height above the ground and postures are described. The sensitivity of the metabolic predictions to different maximum temperature preferences and behavioral options are discussed. The balance between maintenance energy savings via lower thermoregulatory temperatures and time available in different parts of the microenvironment are examined. A simple predator-prey interaction illustrates the substantial effect of climate in modifying amount of time both prey and predator would be expected to be active simultaneously in the tropics vs a temperate desert. Comparisons are made between A. agama and the desert iguana, D. dorsalis for daily and seasonal maintenance requirements and their implications for seasonal changes in growth and reproductive potential.},
  author = {W. P. Porter and F. C. James},
  journal = {Copeia},
  number = {4},
  pages = {594--619},
  publisher = {[American Society of Ichthyologists and Herpetologists (ASIH), Allen Press]},
  title = {Behavioral Implications of Mechanistic Ecology II: The African Rainbow Lizard, Agama agama},
  volume = {1979},
  year = {1979}
}




@incollection{Norris1965,
  title = {Color adaptation in desert reptiles and its thermal relationships},
  author = {K. S. Norris},
  year = {1965},
  booktitle = {Symposium on Lizard Ecology},
  publisher = {U. Missouri Press},
  pages = {162- 229}
}



@article{Riddell2017,
  author = {Riddell, E. A. and Apanovitch, E. K. and Odom, J. P. and Sears, M. W.},
  title = {Physical calculations of resistance to water loss improve predictions of species range models},
  journal = {Ecological Monographs},
  volume = {87},
  number = {1},
  pages = {21-33},
  keywords = {biophysics, energy budget, physiological ecology, salamander, skin resistance, species distribution models, water loss},
  doi = {10.1002/ecm.1240},
  year = {2017}
}


@article{OConnor1999,
  title = {Physiological and ecological implications of a simple model of heating and cooling in reptiles},
  author = {M. O'Connor},
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  year = {1999},
  volume = {24},
  pages = {113-136}
}




@article{Fei2012,
  title = {A body temperature model for lizards as estimated from the thermal environment},
  journal = {Journal of Thermal Biology},
  volume = {37},
  number = {1},
  pages = {56-64},
  year = {2012},
  issn = {0306-4565},
  doi = {10.1016/j.jtherbio.2011.10.013},
  url = {https://www.sciencedirect.com/science/article/pii/S0306456511001513},
  author = {T. Fei and A. K. Skidmore and V. Venus and T. Wang and M. Schlerf and B. Toxopeus and S. {van Overjijk} and M. Bian and Y. Liu},
  keywords = {Lizard, Transient body temperature modeling, Thermal environment, },
}

@article{Whitford1967,
  author = {W. G. Whitford and V. H. Hutchison},
  title = {Body Size and Metabolic Rate in Salamanders},
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  number = {2},
  pages = {127-133},
  year = {1967},
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  URL = {https://doi.org/10.1086/physzool.40.2.30152447}
}
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  title = {Leaf temperature and energy exchange},
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  year = {1962},
  journal = {Archiv fur Meteorologie, Geophysik und Bioklimatologie, Serie B volume},
  volume = {12},
  pages = {321-336}
}
@book{Gates1980,
  title = {Biophysical Ecology},
  author = {D. M. Gates},
  year = {1980},
  publisher = {Springer-Verlag},
  address = {New York, NY, USA},
}

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}

@article{Swinbank1963,
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  title = {Long-wave radiation from clear skies},
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@article{Lactin1997,
  author = {D. J. Lactin and D. L. Johnson},
  title = {Response of body temperature to solar radiation in restrained nymphal migratory grasshoppers (Orthoptera: Acrididae): influences of orientation and body size},
  journal = {Physiological Entomology},
  volume = {22},
  number = {2},
  pages = {131-139},
  keywords = {Melanoplus sanguinipes, grasshopper, thermoregulation, body temperature, biophysics, solar radiation, insolation, convection, greybody radiation, simulation model},
  doi = {10.1111/j.1365-3032.1997.tb01150.x},
  year = {1997}
}

@article{McClanahan1969,
  title = {Rate of water uptake through the integument of the desert toad, Bufo punctatus},
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}

@incollection{deVries1963,
  title = {Thermal Properties of Soils},
  journal = {W. R. Van Wijk},
  booktitle = {Physics of Plant Environment},
  publisher = {North Holland Publishing Company},
  Chapter = {2},
  year = {1963},
  doi = {10.1002/qj.49709038628},
  author = {D. A. deVries}
}

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}

@article{Beckman1973,
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  year = {1973},
  number = {2},
  pages = {257-262},
  doi = {10.1115/1.3450037}
}

@article{Deutsch2008,
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  title = {Impacts of climate warming on terrestrial ectotherms across latitude},
  journal = {Proceedings of the National Academy of Science of the United States of America},
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  year = {2008}
}

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}

@article{Kingsolver2015,
  author = {J. G. Kingsolver and L. B. Buckley},
  title = {Climate variability slows evolutionary responses of Colias butterflies to recent climate change},
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  number = {1802},
  doi = {10.1098/rspb.2014.2470},
  year = {2015}
}

@book{Sellers1965,
  title = {Physical climatology},
  author = {W. D. Sellers},
  year = {1965},
  publisher = {University of Chicago Press},
  address = {Chicago, IL, USA},
}

@article{Kearney2017,
  author = {M. R. Kearney and W. P. Porter},
  title = {NicheMapR - an R package for biophysical modelling: the microclimate model},
  journal = {Ecography},
  volume = {40},
  pages = {664-674},
  doi = {10.1111/ecog.02360},
  year = {2017}
}

@article{Tracy1983,
  author = {C. R. Tracy and K. A. Hammond and R. A. Lechleitner and W. J. Smith II and D. B. Thompson and A. D. Whicker and S. C. Williamson},
  title = {Estimating clear-day solar radiation: an evaluation of three models},
  journal = {Journal of Thermal Biology},
  volume = {8},
  number = {3},
  pages = {247-251},
  year = {1983},
  doi = {10.1016/0306-4565(83)90003-7},
}

@article{McCullough1971,
  author = {E. C. McCullough and W. P. Porter},
  title = {Computing Clear Day Solar Radiation Spectra for the Terrestrial Ecological Environment},
  journal = {Ecology},
  volume = {52},
  number = {6},
  pages = {1008-1015},
  year = {1971},
  doi = {10.2307/1933806}
}

@article{Tham2010,
  author = {Y. Tham and T. Muneer and B. Davison},
  title = {Estimation of hourly averaged solar irradiation: evaluation of models},
  journal = {Building Services Engingeering Research Technology},
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  number = {1},
  year = {2010},
  doi = {10.1177/0143624409350547},
}

@article{AlRawahi2011,
  author = {Y. Tham and T. Muneer and B. Davison},
  title = {Prediction of hourly solar radiation on horizontal and inclined surfaces for Muscat/Oman},
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  year = {2011},
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@article{Nikolov1992,
  author = {N. T. Nikolov and K. Zeller},
  title = {A solar radiation algorithm for ecosystem dynamic models},
  journal = {Ecological Modelling},
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  number = {3-4},
  pages = {149-168},
  year = {1992},
  doi = {10.24200/tjer.vol8iss2pp19-31}
}

@article{Parton1981,
  author = {W. J. Parton and J. A. Logan},
  title = {A model for diurnal variation in soil and air temperature},
  journal = {Agricultural Meteorology},
  volume = {23},
  pages = {205-216},
  year = {1981},
  doi = {10.1016/0002-1571(81)90105-9},
  url = {https://www.sciencedirect.com/science/article/abs/pii/0002157181901059}
}

@article{Wann1985,
  author = {M. Wann and D. Yen and H. J. Gold},
  title = {Evaluation and calibration of three models for daily cycle of air temperature},
  journal = {Agricultural and Forest Meteorology},
  volume = {34},
  pages = {121-128},
  year = {1985},
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