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neotoma_bib.bib
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neotoma_bib.bib
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@Manual{grid2012,
Title = {gridExtra: functions in {Grid} graphics},
Author = {Baptiste Auguie},
Note = {R package version 0.9.1},
Year = {2012},
Url = {http://CRAN.R-project.org/package=gridExtra}
}
@Article{banbury2014reol,
Title = {{Reol: R} interface to the {Encyclopedia of Life}},
Author = {Banbury, Barbara L and O'Meara, Brian C},
Journal = {Ecology and Evolution},
Year = {2014},
Publisher = {Wiley Online Library}
}
@InCollection{behrensmeyer2012building,
Title = {Building links between ecology and paleontology using taphonomic studies of recent vertebrate communities},
Author = {Behrensmeyer, Anna K and Miller, Joshua H},
Booktitle = {Paleontology in Ecology and Conservation},
Publisher = {Springer},
Year = {2012},
Pages = {69--91},
Doi = {10.1007/978-3-642-25038-5_5}
}
@Article{blaauw2010methods,
Title = {Methods and code for {``classical'' age-modelling} of radiocarbon sequences},
Author = {Blaauw, Maarten},
Journal = {Quaternary Geochronology},
Year = {2010},
Number = {5},
Pages = {512--518},
Volume = {5},
Doi = {10.1016/j.quageo.2010.01.002},
Publisher = {Elsevier}
}
@Article{blaauw2011flexible,
Title = {Flexible paleoclimate age-depth models using an autoregressive gamma process},
Author = {Blaauw, Maarten and Christen, J Andr{\'e}s},
Journal = {Bayesian Analysis},
Year = {2011},
Number = {3},
Pages = {457--474},
Volume = {6},
Doi = {10.1214/ba/1339616472},
Publisher = {International Society for Bayesian Analysis}
}
@Article{blarquez2014disentangling,
Title = {Disentangling the trajectories of alpha, beta and gamma plant diversity of {North American} boreal ecoregions since {15,500} years},
Author = {Blarquez, Olivier and Carcaillet, Christopher and Frejaville, Thibaut and Bergeron, Yves},
Journal = {Frontiers In Paleoecology},
Year = {2014},
Pages = {6},
Volume = {2},
Doi = {10.3389/fevo.2014.00006},
Publisher = {Frontiers}
}
@Article{blarquez2014paleofire,
Title = {{paleofire}: an {R} package to analyse sedimentary charcoal records from the {Global Charcoal Database} to reconstruct past biomass burning},
Author = {Blarquez, Olivier and Vanni\`{e}re, Boris and Marlon, Jennifer R and Daniau, Anne-Laure and Power, Mitchell J and Brewer, Simon and Bartlein, Patrick J},
Journal = {Computers \& Geosciences},
Year = {2014},
Pages = {255--261},
Volume = {72},
Doi = {10.1016/j.cageo.2014.07.020},
Publisher = {Elsevier}
}
@Article{blois2013modeling,
Title = {Modeling the climatic drivers of spatial patterns in vegetation composition since the {Last Glacial Maximum}},
Author = {Blois, Jessica L and Williams, John W and Fitzpatrick, Matthew C and Ferrier, Simon and Veloz, Samuel D and He, Feng and Liu, Zhengyu and Manion, Glenn and Otto-Bliesner, Bette},
Journal = {Ecography},
Year = {2013},
Number = {4},
Pages = {460--473},
Volume = {36},
Doi = {10.1111/j.1600-0587.2012.07852.x},
Publisher = {Wiley Online Library}
}
@Article{boettiger2012rfishbase,
Title = {rfishbase: exploring, manipulating and visualizing {FishBase} data from {R}},
Author = {Boettiger, C and Lang, DT and Wainwright, PC},
Journal = {Journal of Fish Biology},
Year = {2012},
Number = {6},
Pages = {2030--2039},
Volume = {81},
Doi = {10.1111/j.1095-8649.2012.03464.x},
Publisher = {Wiley Online Library}
}
@Article{brewer2012paleo,
Title = {Paleoecoinformatics: applying geohistorical data to ecological questions},
Author = {Brewer, Simon and Jackson, Stephen T and Williams, John W},
Journal = {Trends in Ecology \& Evolution},
Year = {2012},
Number = {2},
Pages = {104--112},
Volume = {27},
Doi = {10.1016/j.tree.2011.09.009},
Publisher = {Elsevier}
}
@Article{chamberlain2013taxize,
Title = {taxize: taxonomic search and retrieval in {R}},
Author = {Chamberlain, Scott A and Sz{\"o}cs, Eduard},
Journal = {F1000Research},
Year = {2013},
Volume = {2},
Doi = {10.12688/f1000research.2-191.v2},
Publisher = {Faculty of 1000 Ltd}
}
@InProceedings{C4PExecutive2013,
Title = {Paleobiology Workshop Report},
Author = {C4P Executive Committee},
Booktitle = {EarthCube Collaboration and Cyberinfrastructure for Paleogeosciences {(C4P)}},
Year = {2014},
Month = {May},
Organization = {National Science Foundation EarthCube Research Coordination Network: Cyberinfrastructure for Paleogeoscience},
Owner = {Simon Goring},
Timestamp = {2014.10.04},
Url = {http://workspace.earthcube.org/sites/default/files/files/document-repository/C4P%20Paleogbiology%20Workshop%20Report.pdf}
}
@InCollection{davis1981quaternary,
Title = {Quaternary history and the stability of forest communities},
Author = {Davis, Margaret Bryan},
Booktitle = {Forest succession},
Publisher = {Springer},
Year = {1981},
Pages = {132--153},
Doi = {10.1007/978-1-4612-5950-3_10}
}
@Article{dietl2011conservation,
Title = {Conservation paleobiology: putting the dead to work},
Author = {Dietl, Gregory P and Flessa, Karl W},
Journal = {Trends in Ecology \& Evolution},
Year = {2011},
Number = {1},
Pages = {30--37},
Volume = {26},
Doi = {10.1016/j.tree.2010.09.010},
Publisher = {Elsevier}
}
@Article{fritz2013diversity,
Title = {Diversity in time and space: wanted dead and alive},
Author = {Fritz, Susanne A and Schnitzler, Jan and Eronen, Jussi T and Hof, Christian and B{\"o}hning-Gaese, Katrin and Graham, Catherine H},
Journal = {Trends in Ecology \& Evolution},
Year = {2013},
Number = {9},
Pages = {509--516},
Volume = {28},
Doi = {10.1016/j.tree.2013.05.004},
Publisher = {Elsevier}
}
@Article{gavin2003statistical,
Title = {A statistical approach to evaluating distance metrics and analog assignments for pollen records},
Author = {Gavin, Daniel G and Oswald, W Wyatt and Wahl, Eugene R and Williams, John W},
Journal = {Quaternary Research},
Year = {2003},
Number = {3},
Pages = {356--367},
Volume = {60},
Doi = {10.1016/S0033-5894(03)00088-7},
Publisher = {Elsevier}
}
@article{shuman2005magnitudes,
title={The magnitudes of millennial-and orbital-scale climatic change in eastern North America during the Late Quaternary},
author={Shuman, Bryan and Bartlein, Patrick J and Webb, Thompson},
journal={Quaternary Science Reviews},
volume={24},
number={20},
pages={2194--2206},
year={2005},
publisher={Elsevier}
}
@article{gill2009pleistocene,
title={Pleistocene megafaunal collapse, novel plant communities, and enhanced fire regimes in North America},
author={Gill, Jacquelyn L and Williams, John W and Jackson, Stephen T and Lininger, Katherine B and Robinson, Guy S},
journal={Science},
volume={326},
number={5956},
pages={1100--1103},
year={2009},
publisher={American Association for the Advancement of Science}
}
@Article{gill2013linking,
Title = {Linking abundances of the dung fungus {Sporormiella} to the density of bison: implications for assessing grazing by megaherbivores in palaeorecords},
Author = {Gill, Jacquelyn L and McLauchlan, Kendra K and Skibbe, Adam M and Goring, Simon and Zirbel, Chad R and Williams, John W},
Journal = {Journal of Ecology},
Year = {2013},
Number = {5},
Pages = {1125--1136},
Volume = {101},
Publisher = {Wiley Online Library}
}
@Article{goring2013pollen,
Title = {Pollen assemblage richness does not reflect regional plant species richness: a cautionary tale},
Author = {Goring, Simon and Lacourse, Terri and Pellatt, Marlow G and Mathewes, Rolf W},
Journal = {Journal of Ecology},
Year = {2013},
Number = {5},
Pages = {1137--1145},
Volume = {101},
Doi = {10.1111/1365-2745.12135},
Publisher = {Wiley Online Library}
}
@Article{goring2012depo,
Title = {Deposition times in the northeastern {United States} during the {Holocene:} establishing valid priors for {Bayesian} age models},
Author = {Goring, S and Williams, JW and Blois, JL and Jackson, ST and Paciorek, CJ and Booth, RK and Marlon, JR and Blaauw, M and Christen, JA},
Journal = {Quaternary Science Reviews},
Year = {2012},
Pages = {54--60},
Volume = {48},
Doi = {10.1016/j.quascirev.2012.05.019},
Publisher = {Elsevier}
}
@Article{graham1996spatial,
Title = {Spatial Response of Mammals to Late {Quaternary} Environmental Fluctuations},
Author = {Graham, Russell W and Lundelius Jr, Ernest L and Graham, Mary Ann and Schroeder, Erich K and Toomey III, Rickard S and Anderson, Elaine and Barnosky, Anthony D and Burns, James A and Churcher, Charles S and Grayson, Donald K and others},
Journal = {Science},
Year = {1996},
Pages = {1601--1606},
Volume = {272}
}
@Article{grimm2013databases,
Title = {Pollen databases and their application.},
Author = {Grimm, EC and Bradshaw, RHW and Brewer, S and Flantua, S and Giesecke, T and L{\'e}zine, AM and Takahara, H and JW Jr, Williams},
Year = {2013},
Publisher = {Elsevier}
}
@Book{huntley1988vegetation,
Title = {Vegetation history},
Author = {Huntley, Brian J and Webb, Thompson},
Publisher = {Kluwer Academic Publishers Dordrecht},
Year = {1988}
}
@article{jackson2012representation,
title={Representation of flora and vegetation in Quaternary fossil assemblages: known and unknown knowns and unknowns},
author={Jackson, Stephen T},
journal={Quaternary Science Reviews},
volume={49},
pages={1--15},
year={2012},
publisher={Elsevier}
}
@Manual{rioja2013,
Title = {rioja: Analysis of {Quaternary} Science Data},
Author = {Steve Juggins},
Note = {R package version 0.8-5},
Year = {2013},
Url = {http://www.staff.ncl.ac.uk/staff/stephen.juggins/}
}
@Manual{ggmap2013,
Title = {ggmap: A package for spatial visualization with {Google Maps} and
{OpenStreetMap}},
Author = {David Kahle and Hadley Wickham},
Note = {R package version 2.3},
Year = {2013},
Url = {http://CRAN.R-project.org/package=ggmap}
}
@article{kujawa2016pollen,
title = {The effect of anthropogenic land cover change on pollen-vegetation relationships in the American Midwest},
author = {Kujawa, E and Goring, SJ and Dawson, A and Calcote, R and Grimm, EC and Hotchkiss, SC and Jackson, ST and Lynch, EA and McLachlan, J and St-Jacques, J-M and Umbanhowar, C, Jr. and Williams, JW},
year = {accepted},
journal = {Anthropocene}
}
@article{hotchkiss2007response,
title={Response of vegetation and fire to Little Ice Age climate change: regional continuity and landscape heterogeneity},
author={Hotchkiss, Sara C and Calcote, Randy and Lynch, Elizabeth A},
journal={Landscape Ecology},
volume={22},
number={1},
pages={25--41},
year={2007},
publisher={Springer}
}
@article{davis1991detecting,
title={Detecting a species limit from pollen in sediments},
author={Davis, Margaret B and Schwartz, Mark W and Woods, Kerry},
journal={Journal of Biogeography},
pages={653--668},
year={1991},
publisher={JSTOR}
}
@article{jacobson1981selection,
title={The selection of sites for paleovegetational studies},
author={Jacobson, George L and Bradshaw, Richard HW},
journal={Quaternary research},
volume={16},
number={1},
pages={80--96},
year={1981},
publisher={Elsevier}
}
@article{grimm1984fire,
title={Fire and Other Factors Controlling the Big Woods Vegetation of Minnesota in the Mid-Nineteenth Century},
author={Grimm, Eric C},
journal={Ecological Monographs},
volume={54},
number={3},
pages={291--311},
year={1984},
publisher={Wiley Online Library}
}
@Article{macdonald1991post,
Title = {Post-glacial population growth rates of \textit{Pinus contorta} ssp. \textit{latifolia} in western {Canada}},
Author = {MacDonald, GM and Cwynar, Les C},
Journal = {The Journal of Ecology},
Year = {1991},
Pages = {417--429},
Doi = {10.2307/2260723},
Publisher = {JSTOR}
}
@Article{marlon2013global,
Title = {Global biomass burning: a synthesis and review of Holocene paleofire records and their controls},
Author = {Marlon, Jennifer R and Bartlein, Patrick J and Daniau, Anne-Laure and Harrison, Sandy P and Maezumi, Shira Y and Power, Mitchell J and Tinner, Willy and Vanni{\'e}re, Boris},
Journal = {Quaternary Science Reviews},
Year = {2013},
Pages = {5--25},
Volume = {65},
Doi = {10.1016/j.quascirev.2012.11.029},
Publisher = {Elsevier}
}
@Article{mathewes1973palynological,
Title = {A palynological study of postglacial vegetation changes in the {University Research Forest}, southwestern {British Columbia}},
Author = {Mathewes, Rolf W},
Journal = {Canadian Journal of Botany},
Year = {1973},
Number = {11},
Pages = {2085--2103},
Volume = {51},
Doi = {10.1139/b73-271},
Publisher = {NRC Research Press}
}
@article{overpeck1985quantitative,
title={Quantitative interpretation of fossil pollen spectra: dissimilarity coefficients and the method of modern analogs},
author={Overpeck, JT and Webb, TIII and Prentice, IC},
journal={Quaternary Research},
volume={23},
number={1},
pages={87--108},
year={1985},
publisher={Elsevier}
}
@Manual{bchron2014,
Title = {Bchron: Radiocarbon dating, age-depth modelling, relative sea level rate
estimation, and non-parametric phase modelling},
Author = {Andrew Parnell},
Note = {R package version 4.1.1},
Year = {2014},
Url = {http://CRAN.R-project.org/package=Bchron}
}
@Article{pellatt1997holocene,
Title = {Holocene tree line and climate change on the {Queen Charlotte Islands, Canada}},
Author = {Pellatt, Marlow G and Mathewes, Rolf W},
Journal = {Quaternary Research},
Year = {1997},
Number = {1},
Pages = {88--99},
Volume = {48},
Doi = {10.1006/qres.1997.1903},
Publisher = {Elsevier}
}
@Article{peters2001biodiversity,
Title = {Biodiversity in the {Phanerozoic:} a reinterpretation},
Author = {Peters, Shanan E and Foote, Michael},
Journal = {Paleobiology},
Year = {2001},
Number = {4},
Pages = {583--601},
Volume = {27},
Publisher = {Paleontological Soc}
}
@Manual{RCoreTeam2014,
Title = {R: A Language and Environment for Statistical Computing},
Address = {Vienna, Austria},
Author = {{R Core Team}},
Organization = {R Foundation for Statistical Computing},
Year = {2014},
Url = {http://www.R-project.org/}
}
@Article{raup1984periodicity,
Title = {Periodicity of extinctions in the geologic past},
Author = {Raup, David M and Sepkoski, J John},
Journal = {Proceedings of the National Academy of Sciences},
Year = {1984},
Number = {3},
Pages = {801--805},
Volume = {81},
Publisher = {National Acad Sciences}
}
@Article{reichman2011challenges,
Title = {Challenges and opportunities of open data in ecology},
Author = {Reichman, OJ and Jones, Matthew B and Schildhauer, Mark P},
Journal = {Science(Washington)},
Year = {2011},
Number = {6018},
Pages = {703--705},
Volume = {331},
Doi = {10.1126/science.1197962},
Publisher = {American Association for the Advancement of Science, 1200 New York Avenue, NW Washington DC 20005 USA}
}
@Article{schroeder1996spatial,
Title = {Spatial response of mammals to late {Quaternary} environmental fluctuations},
Author = {Schroeder, Erich K and Ill, Rickard S Toomey and Anderson, Elaine and Barnosky, Anthony D and Burns, James A and Churcher, Charles S and Grayson, Donald K and Guthrie, R Dale and Harington, CR and Jefferson, George T and others},
Journal = {Science},
Year = {1996},
Number = {14},
Volume = {272}
}
@Article{sepkoski1997biodiversity,
Title = {Biodiversity: past, present, and future},
Author = {Sepkoski, J John},
Journal = {Journal of Paleontology},
Year = {1997},
Pages = {533--539},
Publisher = {JSTOR}
}
@Article{analogue2007,
Title = {Analogue Methods in Palaeoecology: Using the analogue Package},
Author = {G. L. Simpson},
Journal = {Journal of Statistical Software},
Year = {2007},
Number = {2},
Pages = {1--29},
Volume = {22}
}
@Manual{analogue2014,
Title = {analogue: Analogue and weighted averaging methods for palaeoecology},
Author = {G. L. Simpson and J. Oksanen},
Note = {R package version 0.14-0},
Year = {2014},
Url = {http://cran.r-project.org/package=analogue}
}
@Article{strong2013holocene,
Title = {Holocene migration of lodgepole pine (\textit{Pinus contorta} var. \textit{latifolia}) in southern {Yukon, Canada}},
Author = {Strong, Wayne L and Hills, Leonard V},
Journal = {The Holocene},
Year = {2013},
Number = {9},
Pages = {1340--1349},
Volume = {23},
Doi = {10.1177/0959683613484614},
Publisher = {Sage Publications}
}
@Article{szeicz1995late,
Title = {Late {Quaternary} vegetation history of the central {Mackenzie Mountains, Northwest Territories, Canada}},
Author = {Szeicz, Julian M and MacDonald, Glen M and Duk-Rodkin, Alejandra},
Journal = {Palaeogeography, Palaeoclimatology, Palaeoecology},
Year = {1995},
Number = {2},
Pages = {351--371},
Volume = {113},
Publisher = {Elsevier}
}
@Article{tzedakis1994vegetation,
Title = {Vegetation change through glacial-interglacial cycles: a long pollen sequence perspective},
Author = {Tzedakis, PC},
Journal = {Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences},
Year = {1994},
Number = {1314},
Pages = {403--432},
Volume = {345},
Doi = {10.1098/rstb.1994.0118},
Publisher = {The Royal Society}
}
@Article{uhen2013card,
Title = {From card catalogs to computers: databases in vertebrate paleontology},
Author = {Uhen, Mark D and Barnosky, Anthony D and Bills, Brian and Blois, Jessica and Carrano, Matthew T and Carrasco, Marc A and Erickson, Gregory M and Eronen, Jussi T and Fortelius, Mikael and Graham, Russell W and others},
Journal = {Journal of Vertebrate Paleontology},
Year = {2013},
Number = {1},
Pages = {13--28},
Volume = {33},
Doi = {10.1080/02724634.2012.716114},
Publisher = {Taylor \& Francis}
}
@Article{whitmore2005modern,
Title = {Modern pollen data from {North America and Greenland} for multi-scale paleoenvironmental applications},
Author = {Whitmore, J and Gajewski, K and Sawada, M and Williams, JW and Shuman, B and Bartlein, PJ and Minckley, T and Viau, AE and Webb III, T and Shafer, S and others},
Journal = {Quaternary Science Reviews},
Year = {2005},
Number = {16},
Pages = {1828--1848},
Volume = {24},
Doi = {10.1016/j.quascirev.2005.03.005},
Publisher = {Elsevier}
}
@Article{plyr2011,
Title = {The Split-Apply-Combine Strategy for Data Analysis},
Author = {Hadley Wickham},
Journal = {Journal of Statistical Software},
Year = {2011},
Number = {1},
Pages = {1--29},
Volume = {40},
Url = {http://www.jstatsoft.org/v40/i01/}
}
@Book{ggplot2009,
Title = {ggplot2: elegant graphics for data analysis},
Author = {Hadley Wickham},
Publisher = {Springer New York},
Year = {2009},
ISBN = {978-0-387-98140-6},
Url = {http://had.co.nz/ggplot2/book}
}
@Book{wickham2009ggplot2,
Title = {ggplot2: elegant graphics for data analysis},
Author = {Wickham, Hadley},
Publisher = {Springer},
Year = {2009}
}
@Article{reshape2007,
Title = {Reshaping Data with the {reshape} Package},
Author = {Hadley Wickham},
Journal = {Journal of Statistical Software},
Year = {2007},
Number = {12},
Pages = {1--20},
Volume = {21},
Url = {http://www.jstatsoft.org/v21/i12/}
}
@article{williams2007novel,
title={Novel climates, no-analog communities, and ecological surprises},
author={Williams, John W and Jackson, Stephen T},
journal={Frontiers in Ecology and the Environment},
volume={5},
number={9},
pages={475--482},
year={2007},
publisher={Wiley Online Library}
}
@article{williams2001dissimilarity,
title={Dissimilarity analyses of late-Quaternary vegetation and climate in eastern North America},
author={Williams, John W and Shuman, Bryan N and Webb, Thompson},
journal={Ecology},
volume={82},
number={12},
pages={3346--3362},
year={2001},
publisher={Wiley Online Library}
}
@Article{williams2008obtaining,
Title = {Obtaining accurate and precise environmental reconstructions from the modern analog technique and {North American} surface pollen dataset},
Author = {Williams, JW and Shuman, B},
Journal = {Quaternary Science Reviews},
Year = {2008},
Number = {7},
Pages = {669--687},
Volume = {27},
Doi = {10.1016/j.quascirev.2008.01.004},
Publisher = {Elsevier}
}
@Article{williams2010rapid,
Title = {Rapid, time-transgressive, and variable responses to early {Holocene} midcontinental drying in {North America}},
Author = {Williams, John W and Shuman, Bryan and Bartlein, Patrick J and Diffenbaugh, Noah S and Webb, Thompson},
Journal = {Geology},
Year = {2010},
Number = {2},
Pages = {135--138},
Volume = {38},
Publisher = {Geological Society of America}
}
@Article{williams2004late,
Title = {{Late-Quaternary} vegetation dynamics in {North America:} scaling from taxa to biomes},
Author = {Williams, John W and Shuman, Bryan N and Webb III, Thompson and Bartlein, Patrick J and Leduc, Phillip L},
Journal = {Ecological Monographs},
Year = {2004},
Number = {2},
Pages = {309--334},
Volume = {74},
Doi = {10.1890/02-4045},
Publisher = {Eco Soc America}
}
@Article{wolkovich2012advances,
Title = {Advances in global change research require open science by individual researchers},
Author = {Wolkovich, Elizabeth M and Regetz, James and O'Connor, Mary I},
Journal = {Global Change Biology},
Year = {2012},
Number = {7},
Pages = {2102--2110},
Volume = {18},
Doi = {10.1111/j.1365-2486.2012.02693.x},
Publisher = {Wiley Online Library}
}