references.bib

@article{Nakagawa:2015bn,
author = {Nakagawa, Shinichi and Parker, Timothy H},
title = {{Replicating research in ecology and evolution: feasibility, incentives, and the cost-benefit conundrum}},
journal = {BMC Biology},
year = {2015},
pages = {1--6},
month = oct,
publisher = {BMC Biology},
doi = {10.1186/s12915-015-0196-3},
read = {Yes},
rating = {0},
date-added = {2018-04-06T05:11:34GMT},
date-modified = {2018-04-12T01:12:22GMT},
abstract = {BMC Biology, 2015, doi:10.1186/s12915-015-0196-3},
url = {http://dx.doi.org/10.1186/s12915-015-0196-3},
local-url = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Files/1B/1BAF880C-F056-42FE-9136-EE0F9C9E77B3.pdf},
file = {{1BAF880C-F056-42FE-9136-EE0F9C9E77B3.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Files/1B/1BAF880C-F056-42FE-9136-EE0F9C9E77B3.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1186/s12915-015-0196-3}}
}

@article{Peng:2009vn,
author = {Peng, R D},
title = {{Reproducible research and biostatistics}},
journal = {Biostatistics},
year = {2009},
volume = {10},
number = {3},
pages = {405--408},
rating = {0},
date-added = {2018-05-23T00:14:30GMT},
date-modified = {2018-05-23T00:16:00GMT},
uri = {\url{papers3://publication/uuid/C0AFFB74-07A1-450A-8375-8800918D9744}}
}

@article{Patil:2016tm,
author = {Patil, P and Peng, R D and Leek, J},
title = {{A statistical definition for reproducibility and replicability}},
journal = {bioRxiv},
year = {2016},
read = {Yes},
rating = {0},
date-added = {2016-08-28T23:40:32GMT},
date-modified = {2018-05-23T00:19:39GMT},
abstract = {Abstract Everyone agrees that reproducibility and replicability are fundamental characteristics of scientific studies. These topics are attracting increasing attention, scrutiny, and debate both in the popular press and the scientific literature. But there are no formal ...
},
url = {http://www.biorxiv.org/content/early/2016/07/29/066803.abstract},
local-url = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Files/F7/F7A21265-C793-4F3C-A388-BE87539CC888.pdf},
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uri = {\url{papers3://publication/uuid/AD68935E-F032-43AA-AB38-599D39161F05}}
}

@article{Sutherland:2017hc,
author = {Sutherland, William J and Wordley, Claire F R},
title = {{Evidence complacency hampers conservation}},
journal = {Nature Ecology {\&} Evolution},
year = {2017},
volume = {1},
number = {9},
pages = {1--2},
month = aug,
publisher = {Springer US},
doi = {10.1038/s41559-017-0244-1},
language = {English},
read = {Yes},
rating = {0},
date-added = {2018-05-09T02:17:40GMT},
date-modified = {2018-05-23T01:14:55GMT},
abstract = {Nature Ecology {\&} Evolution, doi:10.1038/s41559-017-0244-1},
url = {http://dx.doi.org/10.1038/s41559-017-0244-1},
local-url = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Files/3B/3B2A8864-83E2-40CC-842B-2B99F3719ECE.pdf},
file = {{3B2A8864-83E2-40CC-842B-2B99F3719ECE.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Files/3B/3B2A8864-83E2-40CC-842B-2B99F3719ECE.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1038/s41559-017-0244-1}}
}



@Article{Nature:un,
  author        = {Baker, Monya},
  title         = {Is there a reproducibility crisis?},
  journal       = {nature.com},
  year          = {2016},
  abstract      = {Failing to reproduce results is a rite of passage, says Marcus Munafo, a biological psychologist at the University of Bristol, UK, who has a long- standing interest in scientific reproducibility . When he was a student, he says, {\textquotedblleft}I tried to replicate what looked simple from the literature, and wasn't able to. Then I had a crisis of confidence, and then I learned that my experience wasn't uncommon.{\textquotedblright} The challenge is not to eliminate problems with reproducibility in published work. Being at the cutting edge of science means that some- times results will not be robust, says~{\ldots}
},
  date-added    = {2018-04-18T01:01:50GMT},
  date-modified = {2018-04-18T01:35:29GMT},
  file          = {{92C5B1DC-6B09-48B0-B3A8-BF29F2FFE2B3.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Files/92/92C5B1DC-6B09-48B0-B3A8-BF29F2FFE2B3.pdf:application/pdf}},
  local-url     = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Files/92/92C5B1DC-6B09-48B0-B3A8-BF29F2FFE2B3.pdf},
  rating        = {0},
  uri           = {\url{papers3://publication/uuid/5901A0BB-064F-4834-9E41-7CDD9FD8E93B}},
  url           = {https://www.nature.com/polopoly_fs/1.19970.1469695948!/menu/main/topColumns/topLeftColumn/pdf/533452a.pdf?origin=ppub},
}

@article{OpenScienceCollaboration:2015cn,
author = {{Open Science Collaboration}},
title = {{Estimating the reproducibility of psychological science}},
journal = {Science (New York, N.Y.)},
year = {2015},
volume = {349},
number = {6251},
pages = {aac4716--aac4716},
month = aug,
keywords = {psychology, replication, reproducibility},
doi = {10.1126/science.aac4716},
language = {English},
read = {Yes},
rating = {0},
date-added = {2018-04-18T02:16:06GMT},
date-modified = {2018-04-18T05:31:35GMT},
url = {http://www.sciencemag.org/cgi/doi/10.1126/science.aac4716},
local-url = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Files/5C/5C3661FB-2CB0-4296-86D5-04BED7CDBB84.pdf},
file = {{5C3661FB-2CB0-4296-86D5-04BED7CDBB84.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Files/5C/5C3661FB-2CB0-4296-86D5-04BED7CDBB84.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1126/science.aac4716}}
}

@article{Fidler:2017he,
author = {Fidler, Fiona and Chee, Yung En and Wintle, Brendan A and Burgman, Mark A and McCarthy, Michael A and Gordon, Ascelin},
title = {{Metaresearch for Evaluating Reproducibility in Ecology and Evolution}},
journal = {BioScience},
year = {2017},
pages = {biw159--8},
month = jan,
keywords = {metaresearch, open science, publication bias, reproducibility, transparency},
doi = {10.1093/biosci/biw159},
language = {English},
read = {Yes},
rating = {0},
date-added = {2017-08-07T05:24:18GMT},
date-modified = {2018-04-12T01:11:05GMT},
url = {https://academic.oup.com/bioscience/article-lookup/doi/10.1093/biosci/biw159},
local-url = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Files/82/82B3D18E-39FC-4B5F-88AD-A58923370E2B.pdf},
file = {{82B3D18E-39FC-4B5F-88AD-A58923370E2B.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Files/82/82B3D18E-39FC-4B5F-88AD-A58923370E2B.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1093/biosci/biw159}}
}

@article{Law:2017ia,
author = {Law, Elizabeth A and Ferraro, Paul J and Arcese, Peter and Bryan, Brett A and Davis, Katrina and Gordon, Ascelin and Holden, Matthew H and Iacona, Gwenllian and Martinez, Raymundo Marcos and McAlpine, Clive A and Rhodes, Jonathan R and Sze, Jocelyne S and Wilson, Kerrie A},
title = {{Projecting the performance of conservation interventions}},
journal = {BIOC},
year = {2017},
volume = {215},
pages = {142--151},
month = sep,
publisher = {Elsevier},
doi = {10.1016/j.biocon.2017.08.029},
read = {Yes},
rating = {0},
date-added = {2017-12-18T01:57:05GMT},
date-modified = {2017-12-21T02:37:34GMT},
abstract = {Biological Conservation, 215 (2017) 142-151. doi:10.1016/j.biocon.2017.08.029},
url = {http://dx.doi.org/10.1016/j.biocon.2017.08.029},
local-url = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Files/38/38D02D3B-3170-4E73-9A3E-6870CD6E2FE9.pdf},
file = {{38D02D3B-3170-4E73-9A3E-6870CD6E2FE9.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Files/38/38D02D3B-3170-4E73-9A3E-6870CD6E2FE9.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1016/j.biocon.2017.08.029}}
}

@article{TorontoInternationalDataReleaseWorkshopAuthors:2009jh,
author = {{Toronto International Data Release Workshop Authors} and Birney, Ewan and Hudson, Thomas J and Green, Eric D and Gunter, Chris and Eddy, Sean and Rogers, Jane and Harris, Jennifer R and Ehrlich, S Dusko and Apweiler, Rolf and Austin, Christopher P and Berglund, Lisa and Bobrow, Martin and Bountra, Chas and Brookes, Anthony J and Cambon-Thomsen, Anne and Carter, Nigel P and Chisholm, Rex L and Contreras, Jorge L and Cooke, Robert M and Crosby, William L and Dewar, Ken and Durbin, Richard and Dyke, Stephanie O M and Ecker, Joseph R and El Emam, Khaled and Feuk, Lars and Gabriel, Stacey B and Gallacher, John and Gelbart, William M and Granell, Antoni and Guarner, Francisco and Hubbard, Tim and Jackson, Scott A and Jennings, Jennifer L and Joly, Yann and Jones, Steven M and Kaye, Jane and Kennedy, Karen L and Knoppers, Bartha Maria and Kyrpides, Nikos C and Lowrance, William W and Luo, Jingchu and MacKay, John J and Mart{\'\i}n-Rivera, Luis and McCombie, W Richard and McPherson, John D and Miller, Linda and Miller, Webb and Moerman, Don and Mooser, Vincent and Morton, Cynthia C and Ostell, James M and Ouellette, B F Francis and Parkhill, Julian and Raina, Parminder S and Rawlings, Christopher and Scherer, Steven E and Scherer, Stephen W and Schofield, Paul N and Sensen, Christoph W and Stodden, Victoria C and Sussman, Michael R and Tanaka, Toshihiro and Thornton, Janet and Tsunoda, Tatsuhiko and Valle, David and Vuorio, Eero I and Walker, Neil M and Wallace, Susan and Weinstock, George and Whitman, William B and Worley, Kim C and Wu, Cathy and Wu, Jiayan and Yu, Jun},
title = {{Prepublication data sharing.}},
journal = {Nature},
year = {2009},
volume = {461},
number = {7261},
pages = {168--170},
month = sep,
doi = {10.1038/461168a},
pmid = {19741685},
language = {English},
read = {Yes},
rating = {0},
date-added = {2018-02-20T02:49:04GMT},
date-modified = {2018-05-15T12:22:48GMT},
abstract = {Rapid release of prepublication data has served the field of genomics well. Attendees at a workshop in Toronto recommend extending the practice to other biological data sets.},
url = {http://www.nature.com/doifinder/10.1038/461168a},
local-url = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Files/1D/1DD57951-50C1-47D5-943A-D90AE3EFF470.pdf},
file = {{1DD57951-50C1-47D5-943A-D90AE3EFF470.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Files/1D/1DD57951-50C1-47D5-943A-D90AE3EFF470.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1038/461168a}}
}

@article{Anonymous:a1kBf1q9,
author = {Ram, Karthik},
title = {{Git can facilitate greater reproducibility and increased transparency in science.}},
journal = {Source code for biology and medicine},
year = {2013},
volume = {8},
number = {1},
pages = {7},
publisher = {BioMed Central},
affiliation = {Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA 94720, USA. karthik.ram@berkeley.edu.},
doi = {10.1186/1751-0473-8-7},
pmid = {23448176},
language = {English},
rating = {0},
date-added = {2018-02-20T02:49:04GMT},
date-modified = {2018-02-20T02:49:06GMT},
abstract = {BACKGROUND:Reproducibility is the hallmark of good science. Maintaining a high degree of transparency in scientific reporting is essential not just for gaining trust and credibility within the scientific community but also for facilitating the development of new ideas. Sharing data and computer code associated with publications is becoming increasingly common, motivated partly in response to data deposition requirements from journals and mandates from funders. Despite this increase in transparency, it is still difficult to reproduce or build upon the findings of most scientific publications without access to a more complete workflow. FINDINGS:Version control systems (VCS), which have long been used to maintain code repositories in the software industry, are now finding new applications in science. One such open source VCS, Git, provides a lightweight yet robust framework that is ideal for managing the full suite of research outputs such as datasets, statistical code, figures, lab notes, and manuscripts. For individual researchers, Git provides a powerful way to track and compare versions, retrace errors, explore new approaches in a structured manner, while maintaining a full audit trail. For larger collaborative efforts, Git and Git hosting services make it possible for everyone to work asynchronously and merge their contributions at any time, all the while maintaining a complete authorship trail. In this paper I provide an overview of Git along with use-cases that highlight how this tool can be leveraged to make science more reproducible and transparent, foster new collaborations, and support novel uses.},
url = {http://www.scfbm.org/content/8/1/7},
local-url = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Unknown/2013/2013.pdf},
file = {{2013.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Unknown/2013/2013.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1186/1751-0473-8-7}}
}

@book{Merali:2010tw,
author = {Merali, Z},
title = {{Error: why scientific programming does not compute}},
publisher = {Nature},
year = {2010},
read = {Yes},
rating = {0},
date-added = {2018-02-20T02:49:04GMT},
date-modified = {2018-05-15T12:37:01GMT},
url = {http://scholar.google.com/scholar?q=related:0nzms2QeCT0J:scholar.google.com/&hl=en&num=20&as_sdt=0,5},
local-url = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Files/C8/C8186CBA-2119-4C1B-AD37-01309BE2ABE1.pdf},
file = {{C8186CBA-2119-4C1B-AD37-01309BE2ABE1.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Files/C8/C8186CBA-2119-4C1B-AD37-01309BE2ABE1.pdf:application/pdf}},
uri = {\url{papers3://publication/uuid/853BACEB-E64F-451D-8007-D207DABB3B4D}}
}

@article{Leisch:2011hf,
author = {Leisch, Friedrich and Eugster, Manuel and Hothorn, Torsten},
title = {{Executable Papers for the R Community: The R2 Platform for Reproducible Research}},
year = {2011},
volume = {4},
pages = {618--626},
month = may,
keywords = {R, Reproducible Research},
doi = {10.1016/j.procs.2011.04.065},
issn = {1877-0509},
read = {Yes},
rating = {0},
date-added = {2018-02-20T02:49:04GMT},
date-modified = {2018-05-15T13:22:17GMT},
url = {http://dx.doi.org/10.1016/j.procs.2011.04.065},
local-url = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Files/96/960A2DCE-F3C7-4E16-8623-8F21C1245301.pdf},
file = {{960A2DCE-F3C7-4E16-8623-8F21C1245301.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Files/96/960A2DCE-F3C7-4E16-8623-8F21C1245301.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1016/j.procs.2011.04.065}}
}

@article{Barnes:2010dn,
author = {Barnes, Nick},
title = {{Publish your computer code: it is good enough.}},
journal = {Nature},
year = {2010},
volume = {467},
number = {7317},
pages = {753--753},
month = oct,
affiliation = {Climate Code Foundation, Sheffield S17 4DL, UK. nb@climatecode.org},
doi = {10.1038/467753a},
pmid = {20944687},
language = {English},
read = {Yes},
rating = {0},
date-added = {2018-02-20T02:49:05GMT},
date-modified = {2018-05-15T13:31:19GMT},
url = {http://www.nature.com/doifinder/10.1038/467753a},
local-url = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Files/7C/7C8B8AAD-35B1-49B8-9EE3-D11E6797DF5A.pdf},
file = {{7C8B8AAD-35B1-49B8-9EE3-D11E6797DF5A.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Files/7C/7C8B8AAD-35B1-49B8-9EE3-D11E6797DF5A.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1038/467753a}}
}

@article{Science:2012hf,
author = {Morin, A and Urban, J and Adams, P D and Foster, I and Sali, A and Baker, D and Sliz, P},
title = {{Shining Light into Black Boxes}},
journal = {Science (New York, N.Y.)},
year = {2012},
volume = {336},
pages = {1--2},
month = apr,
keywords = {code, reproducibility, Reproducible Research},
doi = {10.2139/ssrn.1757982.10.2139/ssrn.1757982},
read = {Yes},
rating = {0},
date-added = {2018-02-20T02:49:05GMT},
date-modified = {2018-05-15T14:00:07GMT},
local-url = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Files/FD/FD02882B-4DE0-4F07-81F6-31BE0E491937.pdf},
file = {{FD02882B-4DE0-4F07-81F6-31BE0E491937.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Files/FD/FD02882B-4DE0-4F07-81F6-31BE0E491937.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.2139/ssrn.1757982.10.2139/ssrn.1757982}}
}



@article{Baumer:2015hc,
author = {Baumer, Benjamin and Udwin, Dana},
title = {{R Markdown}},
journal = {Wiley Interdisciplinary Reviews: Computational Statistics},
year = {2015},
volume = {7},
number = {3},
pages = {167--177},
month = feb,
doi = {10.1002/wics.1348},
language = {English},
read = {Yes},
rating = {0},
date-added = {2018-02-20T02:49:05GMT},
date-modified = {2018-05-15T13:52:34GMT},
url = {http://doi.wiley.com/10.1002/wics.1348},
local-url = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Files/89/8909C0F9-7F3A-423C-A56D-78EDD4E7D157.pdf},
file = {{8909C0F9-7F3A-423C-A56D-78EDD4E7D157.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Files/89/8909C0F9-7F3A-423C-A56D-78EDD4E7D157.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1002/wics.1348}}
}

@book{Gandrud:2016ux,
author = {Gandrud, Christopher},
title = {{Reproducible Research with R and R Studio, Second Edition}},
publisher = {CRC Press},
year = {2016},
month = jul,
isbn = {1498715389},
language = {English},
rating = {0},
date-added = {2018-02-20T02:49:05GMT},
date-modified = {2018-02-20T02:49:06GMT},
abstract = {All the Tools for Gathering and Analyzing Data and Presenting Results Reproducible Research with R and RStudio, Second Edition brings together the skills and tools needed for doing and presenting computational research. Using straightforward examples, the book takes you through an entire reproducible research workflow. This practical workflow enables you to gather and analyze data as well as dynamically present results in print and on the web. New to the Second Edition The rmarkdown package that allows you to create reproducible research documents in PDF, HTML, and Microsoft Word formats using the simple and intuitive Markdown syntax Improvements to RStudio{\textquoteright}s interface and capabilities, such as its new tools for handling R Markdown documents Expanded knitr R code chunk capabilities The kable function in the knitr package and the texreg package for dynamically creating tables to present your data and statistical results An improved discussion of file organization, enabling you to take full advantage of relative file paths so that your documents are more easily reproducible across computers and systems The dplyr, magrittr, and tidyr packages for fast data manipulation Numerous modifications to R syntax in user-created packages Changes to GitHub{\textquoteright}s and Dropbox{\textquoteright}s interfaces Create Dynamic and Highly Reproducible Research This updated book provides all the tools to combine your research with the presentation of your findings. It saves you time searching for information so that you can spend more time actually addressing your research questions. Supplementary files used for the examples and a reproducible research project are available on the author{\textquoteright}s website.},
url = {http://books.google.com.au/books?id=Ce35CQAAQBAJ&pg=PA10&dq=intitle:Reproducible+Research+with+R+and+RStudio+Second+Edition&hl=&cd=1&source=gbs_api},
local-url = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Files/C9/C997F6E8-2164-413C-9B91-C77AC9217D3D.pdf},
file = {{C997F6E8-2164-413C-9B91-C77AC9217D3D.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Files/C9/C997F6E8-2164-413C-9B91-C77AC9217D3D.pdf:application/pdf}},
uri = {\url{papers3://publication/uuid/2BBE0779-6E05-4EFF-BA46-8D00A5718237}}
}

@book{Stodden:2012ww,
author = {Stodden, V},
title = {{Reproducible research: Tools and strategies for scientific computing}},
publisher = {Computing in Science {\&} Engineering},
year = {2012},
read = {Yes},
rating = {0},
date-added = {2018-02-20T02:49:05GMT},
date-modified = {2018-05-15T14:07:00GMT},
abstract = {... Reproducible Research for Scientific Computing: Tools and Strategies for Changing the Culture Comput. Sci. Eng. 14, 13 (2012); 10.1109 / MCSE . 2012.38 System Testing a Scientific Framework Using a Regression-Test Environment Comput. Sci. Eng. ...},
url = {http://scitation.aip.org/content/aip/journal/cise/14/4/10.1109/MCSE.2012.82},
local-url = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Files/D4/D4C2AA16-687A-4F64-B98C-C4B2FD971EC5.pdf},
file = {{D4C2AA16-687A-4F64-B98C-C4B2FD971EC5.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Files/D4/D4C2AA16-687A-4F64-B98C-C4B2FD971EC5.pdf:application/pdf}},
uri = {\url{papers3://publication/uuid/50EC491F-7869-4338-AD23-8EB58D9B2A2C}}
}

@article{Stodden:2013ho,
author = {Stodden, Victoria and Guo, Peixuan and Ma, Zhaokun},
title = {{Toward Reproducible Computational Research: An Empirical Analysis of Data and Code Policy Adoption by Journals}},
journal = {PLoS One},
year = {2013},
volume = {8},
number = {6},
pages = {e67111--8},
month = jun,
doi = {10.1371/journal.pone.0067111},
language = {English},
read = {Yes},
rating = {0},
date-added = {2018-02-20T02:49:05GMT},
date-modified = {2018-05-15T14:10:38GMT},
url = {http://dx.plos.org/10.1371/journal.pone.0067111},
local-url = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Files/6C/6C78FB31-86ED-4973-82AD-013E52DD95B3.PDF},
file = {{6C78FB31-86ED-4973-82AD-013E52DD95B3.PDF:/Users/Elise/Dropbox/papers3/Library.papers3/Files/6C/6C78FB31-86ED-4973-82AD-013E52DD95B3.PDF:application/pdf}},
uri = {\url{papers3://publication/doi/10.1371/journal.pone.0067111}}
}

@article{Gribbin:2009us,
author = {{Gribbin} and {Simon}},
title = {{Post-publication sharing of data and tools}},
year = {2009},
pages = {1--3},
month = sep,
keywords = {code, open data, open science, Reproducible Research, transparency},
read = {Yes},
rating = {0},
date-added = {2018-02-20T02:49:05GMT},
date-modified = {2018-05-15T14:16:21GMT},
local-url = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Files/78/78634705-480A-4399-8B8C-BBEF3E3B64F7.pdf},
file = {{78634705-480A-4399-8B8C-BBEF3E3B64F7.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Files/78/78634705-480A-4399-8B8C-BBEF3E3B64F7.pdf:application/pdf}},
uri = {\url{papers3://publication/uuid/61610910-2A5A-4746-B3B2-F479B97826C6}}
}

@article{White:2013ea,
author = {White, Ethan and Baldridge, Elita and Brym, Zachary and Locey, Kenneth and McGlinn, Daniel and Supp, Sarah},
title = {{Nine simple ways to make it easier to (re)use your data}},
journal = {Ideas in Ecology and Evolution},
year = {2013},
volume = {6},
number = {2},
pages = {1--10},
doi = {10.4033/iee.2013.6b.6.f},
read = {Yes},
rating = {0},
date-added = {2018-02-20T02:49:05GMT},
date-modified = {2018-05-15T14:20:00GMT},
url = {http://library.queensu.ca/ojs/index.php/IEE/article/view/4608},
local-url = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Files/5D/5D0A891D-A720-4DD8-9CF0-4441592E34C6.pdf},
file = {{5D0A891D-A720-4DD8-9CF0-4441592E34C6.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Files/5D/5D0A891D-A720-4DD8-9CF0-4441592E34C6.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.4033/iee.2013.6b.6.f}}
}

@webpage{Borregaard:2018gu,
author = {Borregaard, Michael K and Hart, E M},
title = {{Towards a more reproducible ecology}},
year = {2018},
month = feb,
doi = {10.1111/ecog.01552/abstract},
read = {Yes},
rating = {0},
date-added = {2018-02-20T08:20:55GMT},
date-modified = {2018-05-15T14:59:03GMT},
local-url = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Files/2C/2C209586-43EE-4B99-8A23-374A11653A26.pdf},
file = {{2C209586-43EE-4B99-8A23-374A11653A26.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Files/2C/2C209586-43EE-4B99-8A23-374A11653A26.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1111/ecog.01552/abstract}}
}

@article{Wilson:2014ck,
author = {Wilson, Greg and Aruliah, D A and Brown, C Titus and Chue Hong, Neil P and Davis, Matt and Guy, Richard T and Haddock, Steven H D and Huff, Kathryn D and Mitchell, Ian M and Plumbley, Mark D and Waugh, Ben and White, Ethan P and Wilson, Paul},
title = {{Best Practices for Scientific Computing}},
journal = {PLoS Biology},
year = {2014},
volume = {12},
number = {1},
pages = {e1001745},
month = jan,
doi = {10.1371/journal.pbio.1001745},
language = {English},
read = {Yes},
rating = {0},
date-added = {2018-02-20T02:49:05GMT},
date-modified = {2018-05-15T14:30:32GMT},
url = {http://dx.plos.org/10.1371/journal.pbio.1001745},
local-url = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Wilson/2014/PLoS_Biol-2014-Wilson.pdf},
file = {{PLoS_Biol-2014-Wilson.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Wilson/2014/PLoS_Biol-2014-Wilson.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1371/journal.pbio.1001745}}
}

@book{BritishEcologicalSociety:2014va,
author = {{British Ecological Society}},
title = {{A Guide to Data Management in Ecology and Evolution}},
publisher = {British Ecological Society},
year = {2014},
month = nov,
rating = {0},
date-added = {2018-02-20T02:49:05GMT},
date-modified = {2018-02-20T02:49:06GMT},
url = {www.britishecologicalsociety.org/publications/journals},
local-url = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Files/70/700B004D-BA1A-4E32-8B19-911AD1BF562E.pdf},
file = {{700B004D-BA1A-4E32-8B19-911AD1BF562E.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Files/70/700B004D-BA1A-4E32-8B19-911AD1BF562E.pdf:application/pdf}},
uri = {\url{papers3://publication/uuid/E4078A2A-EF76-413E-828C-76B1E8FBDCED}}
}

@article{Noble:2009da,
author = {Noble, William Stafford},
title = {{A Quick Guide to Organizing Computational Biology Projects}},
journal = {PLoS Computational Biology},
year = {2009},
volume = {5},
number = {7},
pages = {e1000424},
month = jul,
doi = {10.1371/journal.pcbi.1000424.g001},
language = {English},
read = {Yes},
rating = {0},
date-added = {2018-02-20T02:49:06GMT},
date-modified = {2018-02-20T02:49:06GMT},
url = {http://dx.plos.org/10.1371/journal.pcbi.1000424.g001},
local-url = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Noble/2009/PLoS_Comp_Biol-2009-Noble.pdf},
file = {{PLoS_Comp_Biol-2009-Noble.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Noble/2009/PLoS_Comp_Biol-2009-Noble.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1371/journal.pcbi.1000424.g001}}
}

@article{Jones:2007fv,
author = {Jones, Christopher and Blanchette, Carol and Brooke, Matthew and Harris, John and Jones, Matthew and Schildhauer, Mark},
title = {{A metadata-driven framework for generating field data entry interfaces in ecology}},
journal = {Ecological Informatics},
year = {2007},
volume = {2},
number = {3},
pages = {270--278},
month = oct,
keywords = {data structure, Database, Ecology, EML, Field sampling, informatics},
doi = {10.1016/j.ecoinf.2007.06.005},
language = {English},
read = {Yes},
rating = {0},
date-added = {2016-12-03T00:50:00GMT},
date-modified = {2018-05-16T01:27:05GMT},
url = {http://linkinghub.elsevier.com/retrieve/pii/S1574954107000416},
local-url = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Files/79/79959D1D-C91A-4458-AF87-721090723446.pdf},
file = {{79959D1D-C91A-4458-AF87-721090723446.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Files/79/79959D1D-C91A-4458-AF87-721090723446.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1016/j.ecoinf.2007.06.005}}
}

@article{Madin:2008jv,
author = {Madin, Joshua S and Bowers, Shawn and Schildhauer, Mark P and Jones, Matthew B},
title = {{Advancing ecological research with ontologies}},
journal = {Trends in Ecology {\&} Evolution},
year = {2008},
volume = {23},
number = {3},
pages = {159--168},
month = mar,
doi = {10.1016/j.tree.2007.11.007},
language = {English},
read = {Yes},
rating = {0},
date-added = {2018-05-16T01:19:08GMT},
date-modified = {2018-05-16T01:30:52GMT},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0169534708000384},
local-url = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Files/CB/CB3206D8-49D6-453B-88E5-F7D7F14CFB30.pdf},
file = {{CB3206D8-49D6-453B-88E5-F7D7F14CFB30.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Files/CB/CB3206D8-49D6-453B-88E5-F7D7F14CFB30.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1016/j.tree.2007.11.007}}
}

@article{Culina:2018dn,
author = {Culina, Antica and Baglioni, Miriam and Crowther, Tom W and Visser, Marcel E and Woutersen-Windhouwer, Saskia and Manghi, Paolo},
title = {{Navigating the unfolding open data landscape in ecology and evolution}},
journal = {Nature Ecology {\&} Evolution},
year = {2018},
pages = {1--7},
month = feb,
publisher = {Springer US},
doi = {10.1038/s41559-017-0458-2},
read = {Yes},
rating = {0},
date-added = {2018-04-12T01:32:39GMT},
date-modified = {2018-05-16T04:59:02GMT},
abstract = {Nature Ecology {\&} Evolution, doi:10.1038/s41559-017-0458-2},
url = {http://dx.doi.org/10.1038/s41559-017-0458-2},
local-url = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Files/15/156FF1D6-21B9-479F-B199-4FDC5E598D4A.pdf},
file = {{156FF1D6-21B9-479F-B199-4FDC5E598D4A.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Files/15/156FF1D6-21B9-479F-B199-4FDC5E598D4A.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1038/s41559-017-0458-2}}
}

@article{MoruetaHolme:2018bi,
author = {Morueta-Holme, Naia and Oldfather, Meagan F and Olliff-Yang, Rachael L and Weitz, Andrew P and Levine, Carrie R and Kling, Matthew M and Riordan, Erin C and Merow, Cory and Sheth, Seema N and Thornhill, Andrew H and Ackerly, David D},
title = {{Best practices for reporting climate data in ecology}},
journal = {Nature Climate Change},
year = {2018},
pages = {1--3},
month = jan,
publisher = {Springer US},
doi = {10.1038/s41558-017-0060-2},
rating = {0},
date-added = {2018-05-16T06:29:30GMT},
date-modified = {2018-05-16T06:30:23GMT},
abstract = {Nature Climate Change, doi:10.1038/s41558-017-0060-2},
url = {http://dx.doi.org/10.1038/s41558-017-0060-2},
local-url = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Files/7E/7E0CEFAB-6215-4A94-8F78-23ED3F74352F.pdf},
file = {{7E0CEFAB-6215-4A94-8F78-23ED3F74352F.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Files/7E/7E0CEFAB-6215-4A94-8F78-23ED3F74352F.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1038/s41558-017-0060-2}}
}

@article{Bower:2017im,
author = {Bower, Shannon D and Brownscombe, Jacob W and Birnie-Gauvin, Kim and Ford, Matthew I and Moraga, Andrew D and Pusiak, Ryan J P and Turenne, Eric D and Zolderdo, Aaron J and Cooke, Steven J and Bennett, Joseph R},
title = {{Making Tough Choices: Picking the Appropriate Conservation Decision-Making Tool}},
journal = {Conservation letters},
year = {2017},
volume = {11},
number = {2},
pages = {e12418--7},
month = nov,
doi = {10.1111/conl.12418},
language = {English},
read = {Yes},
rating = {0},
date-added = {2018-05-16T06:31:33GMT},
date-modified = {2018-05-16T07:06:58GMT},
url = {http://doi.wiley.com/10.1111/conl.12418},
local-url = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Files/62/62E68E1E-78D3-4FF9-A759-6053E46BF228.pdf},
file = {{62E68E1E-78D3-4FF9-A759-6053E46BF228.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Files/62/62E68E1E-78D3-4FF9-A759-6053E46BF228.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1111/conl.12418}}
}

@book{Conroy:2013tc,
author = {Conroy, Michael J and Peterson, J T},
title = {{Decision Making in Natural Resource Management: A Structured, Adaptive Approach}},
publisher = {Wiley Blackwell},
year = {2013},
rating = {0},
date-added = {2018-05-16T02:57:44GMT},
date-modified = {2018-05-16T02:57:45GMT},
uri = {\url{papers3://publication/uuid/600E2CAD-2A27-4E19-9F42-10CF7F405A74}}
}

@article{Conroy:2008jg,
author = {Conroy, Michael J and Barker, Richard J and Barker, Richard J and Dillingham, Peter W and Dillingham, Peter W and Fletcher, David and Fletcher, David and Gormley, Andrew M and Gormley, Andrew M and Westbrooke, Ian M and Westbrooke, Ian M},
title = {{Application of decision theory to conservation management: recovery of Hector's dolphin}},
journal = {Wildlife Research},
year = {2008},
volume = {35},
number = {2},
pages = {93},
keywords = {Bayesian Belief Networks},
doi = {10.1071/WR07147},
language = {English},
read = {Yes},
rating = {0},
date-added = {2015-01-17T00:33:01GMT},
date-modified = {2018-05-16T07:42:59GMT},
url = {http://www.publish.csiro.au/?paper=WR07147},
local-url = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Conroy/2008/Wildl._Res.-2008-Conroy.pdf},
file = {{Wildl._Res.-2008-Conroy.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Conroy/2008/Wildl._Res.-2008-Conroy.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1071/WR07147}}
}

@article{Whitlock:cl,
author = {Whitlock, MC},
year = {2011},
title = {{Data archiving in ecology and evolution: best practices}},
journal = {Elsevier
},
doi = {10.1016/j.tree.2010.11.006},
rating = {0},
date-added = {2018-05-16T08:49:14GMT},
date-modified = {2018-05-16T08:51:25GMT},
abstract = {Many ecology and evolution journals have recently adopted policies requiring that data from their papers be publicly archived. I present suggestions on how data generators, data re- users, and journals can maximize the fairness and scientific value of data archiving. Data should be archived with enough clarity and supporting information that they can be accurately interpreted by others. Re-users should respect their intellectual debt to the originators of data through citation both of the paper and of the data package. In addition~{\ldots}
},
url = {https://www.sciencedirect.com/science/article/pii/S0169534710002697},
local-url = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Files/0A/0A9B67EA-978B-4630-AF37-F42F03E8562C.pdf},
file = {{0A9B67EA-978B-4630-AF37-F42F03E8562C.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Files/0A/0A9B67EA-978B-4630-AF37-F42F03E8562C.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1016/j.tree.2010.11.006}}
}

@article{Michener:2012ho,
author = {Michener, William K and Jones, Matthew B},
title = {{Ecoinformatics: supporting ecology as a data-intensive science}},
journal = {Trends in Ecology {\&} Evolution},
year = {2012},
volume = {27},
number = {2},
pages = {85--93},
month = feb,
publisher = {Elsevier Ltd},
doi = {10.1016/j.tree.2011.11.016},
read = {Yes},
rating = {0},
date-added = {2018-05-16T09:02:25GMT},
date-modified = {2018-05-16T09:08:27GMT},
abstract = {Trends in Ecology {\&} Evolution, 27 (2011) 85-93. 10.1016/j.tree.2011.11.016},
url = {http://dx.doi.org/10.1016/j.tree.2011.11.016},
local-url = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Files/D3/D3232DA5-E4C1-4430-BE19-6F51D8EDB940.pdf},
file = {{D3232DA5-E4C1-4430-BE19-6F51D8EDB940.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Files/D3/D3232DA5-E4C1-4430-BE19-6F51D8EDB940.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1016/j.tree.2011.11.016}}
}

@article{Kim:2016gf,
author = {Kim, Milena Kiatkoski and Evans, Louisa and Scherl, Lea M and Marsh, Helene},
title = {{Applying Governance Principles to Systematic Conservation Decision-Making in Queensland}},
journal = {Environmental Policy and Governance},
year = {2016},
volume = {26},
number = {6},
pages = {452--467},
month = aug,
doi = {10.1002/eet.1731},
language = {English},
rating = {0},
date-added = {2018-05-16T09:47:00GMT},
date-modified = {2018-05-16T09:47:11GMT},
url = {http://doi.wiley.com/10.1002/eet.1731},
local-url = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Files/AA/AAF3233D-D198-4959-B522-42F18EC93CA0.pdf},
file = {{AAF3233D-D198-4959-B522-42F18EC93CA0.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Files/AA/AAF3233D-D198-4959-B522-42F18EC93CA0.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1002/eet.1731}}
}

@article{Morrison:2016cd,
author = {Morrison, Clare and Wardle, Cassandra and Castley, J Guy},
title = {{Repeatability and Reproducibility of Population Viability Analysis (PVA) and the Implications for Threatened Species Management}},
journal = {Frontiers in Ecology and Evolution},
year = {2016},
volume = {4},
pages = {875--7},
month = aug,
doi = {10.3389/fevo.2016.00098},
rating = {0},
date-added = {2018-05-16T09:47:41GMT},
date-modified = {2018-05-16T09:47:53GMT},
abstract = {Conservation triage focuses on prioritizing species, populations or habitats based on urgency, biodiversity benefits, recovery potential as well as cost.Conservation triage focuses on prioritizing species, populations or habitats based on urgency, biodiversity benefits, recovery potential as well as cost.},
url = {http://journal.frontiersin.org/Article/10.3389/fevo.2016.00098/abstract},
local-url = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Files/CC/CCC49064-4976-42DB-BB7E-6E38E7911104.pdf},
file = {{CCC49064-4976-42DB-BB7E-6E38E7911104.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Files/CC/CCC49064-4976-42DB-BB7E-6E38E7911104.pdf:application/pdf;CCC49064-4976-42DB-BB7E-6E38E7911104.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Files/CC/CCC49064-4976-42DB-BB7E-6E38E7911104.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.3389/fevo.2016.00098}}
}

@article{Fanelli:2018je,
author = {Fanelli, Daniele},
title = {{Opinion: Is science really facing a reproducibility crisis, and do we need it to?}},
journal = {Proceedings of the National Academy of Sciences},
year = {2018},
volume = {115},
number = {11},
pages = {2628--2631},
month = mar,
doi = {10.1073/pnas.1708272114},
language = {English},
rating = {0},
date-added = {2018-05-16T10:03:34GMT},
date-modified = {2018-05-16T10:03:54GMT},
url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1708272114},
local-url = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Files/A1/A1180F43-41E0-45B7-B866-AFCB34110320.pdf},
file = {{A1180F43-41E0-45B7-B866-AFCB34110320.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Files/A1/A1180F43-41E0-45B7-B866-AFCB34110320.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1073/pnas.1708272114}}
}

@article{Jamieson:2018kz,
author = {Jamieson, Kathleen Hall},
title = {{Crisis or self-correction: Rethinking media narratives about the well-being of science}},
journal = {Proceedings of the National Academy of Sciences},
year = {2018},
volume = {115},
number = {11},
pages = {2620--2627},
month = mar,
doi = {10.1073/pnas.1708276114},
language = {English},
rating = {0},
date-added = {2018-05-16T10:05:53GMT},
date-modified = {2018-05-16T10:06:03GMT},
url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1708276114},
local-url = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Files/74/74469AAD-92C3-4533-AEBC-2B1A4A666A3D.pdf},
file = {{74469AAD-92C3-4533-AEBC-2B1A4A666A3D.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Files/74/74469AAD-92C3-4533-AEBC-2B1A4A666A3D.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1073/pnas.1708276114}}
}

@article{Williams:2017bg,
author = {Williams, Mary and Bagwell, Jacqueline and Zozus, Meredith Nahm},
title = {{Data management plans, the missing perspective}},
journal = {Journal of Biomedical Informatics},
year = {2017},
volume = {71},
pages = {130--142},
month = jul,
doi = {10.1016/j.jbi.2017.05.004},
rating = {0},
date-added = {2018-05-16T10:10:38GMT},
date-modified = {2018-05-16T10:10:58GMT},
abstract = {Journal of Biomedical Informatics, 71 (2017) 130-142. doi:10.1016/j.jbi.2017.05.004},
url = {http://dx.doi.org/10.1016/j.jbi.2017.05.004},
local-url = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Files/FC/FC9BF49A-634E-4591-9E6A-0D94D667FCC4.pdf},
file = {{FC9BF49A-634E-4591-9E6A-0D94D667FCC4.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Files/FC/FC9BF49A-634E-4591-9E6A-0D94D667FCC4.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1016/j.jbi.2017.05.004}}
}

@article{McIntosh:2011ew,
author = {McIntosh, B S and Ascough II, J C and Twery, M and Chew, J and Elmahdi, A and Haase, D and Harou, J J and Hepting, D and Cuddy, S and Jakeman, A J and Chen, S and Kassahun, A and Lautenbach, S and Matthews, K and Merritt, W and Quinn, N W T and Rodriguez-Roda, I and Sieber, S and Stavenga, M and Sulis, A and Ticehurst, J and Volk, M and Wrobel, M and van Delden, H and El-Sawah, S and Rizzoli, A and Voinov, A},
title = {{Environmental decision support systems (EDSS) development - Challenges and best practices}},
journal = {Environmental Modelling {\&} Software},
year = {2011},
volume = {26},
number = {12},
pages = {1389--1402},
month = dec,
publisher = {Elsevier Ltd},
doi = {10.1016/j.envsoft.2011.09.009},
rating = {0},
date-added = {2018-05-16T10:13:30GMT},
date-modified = {2018-05-16T10:13:36GMT},
abstract = {Environmental Modelling and Software, 26 (2011) 1389-1402. doi:10.1016/j.envsoft.2011.09.009},
url = {http://dx.doi.org/10.1016/j.envsoft.2011.09.009},
local-url = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Files/B1/B1648C61-F754-4630-A288-33E8001620D1.pdf},
file = {{B1648C61-F754-4630-A288-33E8001620D1.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Files/B1/B1648C61-F754-4630-A288-33E8001620D1.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1016/j.envsoft.2011.09.009}}
}

@article{Agnoli:2017kl,
author = {Agnoli, Franca and Wicherts, Jelte M and Veldkamp, Coosje L S and Albiero, Paolo and Cubelli, Roberto},
title = {{Questionable research practices among italian research psychologists}},
journal = {PLoS One},
year = {2017},
volume = {12},
number = {3},
pages = {e0172792--17},
month = mar,
doi = {10.1371/journal.pone.0172792},
language = {English},
rating = {0},
date-added = {2018-05-16T10:16:32GMT},
date-modified = {2018-05-16T10:16:40GMT},
url = {http://dx.plos.org/10.1371/journal.pone.0172792},
local-url = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Files/34/348D9733-A3C4-40C9-9087-1159DBD5B063.pdf},
file = {{348D9733-A3C4-40C9-9087-1159DBD5B063.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Files/34/348D9733-A3C4-40C9-9087-1159DBD5B063.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1371/journal.pone.0172792}}
}

@article{Fidler:2016wv,
author = {Fidler, Fiona and Chee, Yung En and Wintle, Bonnie and Burgman, Mark A and McCarthy, Michael A and Gordon, Ascelin},
title = {{Why and how to evaluate reproducibility of ecological research}},
journal = {BioScience},
year = {2016},
pages = {1--27},
month = jun,
read = {Yes},
rating = {0},
date-added = {2016-10-24T00:45:16GMT},
date-modified = {2018-05-16T23:44:49GMT},
url = {https://osf.io/g7vha/},
local-url = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Files/19/19C43D30-EC24-4388-81A3-DA013D0A24A2.pdf},
file = {{19C43D30-EC24-4388-81A3-DA013D0A24A2.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Files/19/19C43D30-EC24-4388-81A3-DA013D0A24A2.pdf:application/pdf}},
uri = {\url{papers3://publication/uuid/DA36EB55-1B48-4AF5-A1D3-F6184C82D42E}}
}

@article{Crutzen:2017kn,
author = {Crutzen, Rik and Peters, Gjalt-Jorn Y},
title = {{Targeting Next Generations to Change the Common Practice of Underpowered Research}},
journal = {Frontiers in Psychology},
year = {2017},
volume = {8},
pages = {67--4},
month = jul,
doi = {10.3389/fpsyg.2017.01184},
rating = {0},
date-added = {2018-05-18T03:43:38GMT},
date-modified = {2018-05-18T03:58:05GMT},
abstract = {Underpowered studies remain ubiquitous (Maxwell, 2004; Bakker et al., 2012; Button et al., 2013; Turner et al., 2013; Szucs and Ioannidis, 2017) despite strong pleas to change this practice (Cohen, 1988, 1990, 1992).Underpowered studies remain ubiquitous (Maxwell, 2004; Bakker et al., 2012; Button et al., 2013; Turner et al., 2013; Szucs and Ioannidis, 2017) despite strong pleas to change this practice (Cohen, 1988, 1990, 1992).},
url = {http://journal.frontiersin.org/article/10.3389/fpsyg.2017.01184/full},
local-url = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Files/56/56DB8F99-5CCB-4DF0-B578-13860201796D.pdf},
file = {{56DB8F99-5CCB-4DF0-B578-13860201796D.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Files/56/56DB8F99-5CCB-4DF0-B578-13860201796D.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.3389/fpsyg.2017.01184}}
}

@article{OpenScienceCollaboration:2015cn,
author = {{Open Science Collaboration}},
title = {{Estimating the reproducibility of psychological science}},
journal = {Science (New York, N.Y.)},
year = {2015},
volume = {349},
number = {6251},
pages = {aac4716--aac4716},
month = aug,
keywords = {psychology, replication, reproducibility},
doi = {10.1126/science.aac4716},
language = {English},
read = {Yes},
rating = {0},
date-added = {2018-04-18T02:16:06GMT},
date-modified = {2018-05-20T09:15:09GMT},
url = {http://www.sciencemag.org/cgi/doi/10.1126/science.aac4716},
local-url = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Files/5C/5C3661FB-2CB0-4296-86D5-04BED7CDBB84.pdf},
file = {{5C3661FB-2CB0-4296-86D5-04BED7CDBB84.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Files/5C/5C3661FB-2CB0-4296-86D5-04BED7CDBB84.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1126/science.aac4716}}
}

@article{Sutherland:2017hc,
author = {Sutherland, William J and Wordley, Claire F R},
title = {{Evidence complacency hampers conservation}},
journal = {Nature Ecology {\&} Evolution},
year = {2017},
volume = {1},
number = {9},
pages = {1--2},
month = aug,
publisher = {Springer US},
doi = {10.1038/s41559-017-0244-1},
language = {English},
read = {Yes},
rating = {0},
date-added = {2018-05-09T02:17:40GMT},
date-modified = {2018-05-20T10:11:28GMT},
abstract = {Nature Ecology {\&} Evolution, doi:10.1038/s41559-017-0244-1},
url = {http://dx.doi.org/10.1038/s41559-017-0244-1},
local-url = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Files/3B/3B2A8864-83E2-40CC-842B-2B99F3719ECE.pdf},
file = {{3B2A8864-83E2-40CC-842B-2B99F3719ECE.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Files/3B/3B2A8864-83E2-40CC-842B-2B99F3719ECE.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1038/s41559-017-0244-1}}
}

@article{Nakagawa:2015bn,
author = {Nakagawa, Shinichi and Parker, Timothy H},
title = {{Replicating research in ecology and evolution: feasibility, incentives, and the cost-benefit conundrum}},
journal = {BMC Biology},
year = {2015},
pages = {1--6},
month = oct,
publisher = {BMC Biology},
doi = {10.1186/s12915-015-0196-3},
read = {Yes},
rating = {0},
date-added = {2018-04-06T05:11:34GMT},
date-modified = {2018-05-20T11:44:28GMT},
abstract = {BMC Biology, 2015, doi:10.1186/s12915-015-0196-3},
url = {http://dx.doi.org/10.1186/s12915-015-0196-3},
local-url = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Files/1B/1BAF880C-F056-42FE-9136-EE0F9C9E77B3.pdf},
file = {{1BAF880C-F056-42FE-9136-EE0F9C9E77B3.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Files/1B/1BAF880C-F056-42FE-9136-EE0F9C9E77B3.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1186/s12915-015-0196-3}}
}

@article{Mukherjee:2018cb,
author = {Mukherjee, Nibedita and Zabala, Aiora and Huge, Jean and Nyumba, Tobias Ochieng and Adem Esmail, Blal and Sutherland, William J},
title = {{Comparison of techniques for eliciting views and judgements in decision-making}},
journal = {Methods in Ecology and Evolution},
year = {2018},
volume = {9},
number = {1},
pages = {54--63},
month = jan,
doi = {10.1111/2041-210X.12940},
language = {English},
read = {Yes},
rating = {0},
date-added = {2018-05-20T22:50:08GMT},
date-modified = {2018-05-20T23:20:31GMT},
url = {http://doi.wiley.com/10.1111/2041-210X.12940},
local-url = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Files/DC/DCF03737-E4EA-47F8-B4D9-C1AB2C5A330F.pdf},
file = {{DCF03737-E4EA-47F8-B4D9-C1AB2C5A330F.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Files/DC/DCF03737-E4EA-47F8-B4D9-C1AB2C5A330F.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1111/2041-210X.12940}}
}

@article{Dicks:2014gf,
author = {Dicks, Lynn V and Walsh, Jessica C and Sutherland, William J},
title = {{Organising evidence for environmental management decisions: a {\textquoteleft}4S{\textquoteright} hierarchy}},
journal = {Trends in Ecology {\&} Evolution},
year = {2014},
volume = {29},
number = {11},
pages = {607--613},
month = nov,
publisher = {Elsevier Ltd},
keywords = {Decision support, environmental management, Environmental planning},
doi = {10.1016/j.tree.2014.09.004},
language = {English},
read = {Yes},
rating = {0},
date-added = {2015-09-08T01:12:21GMT},
date-modified = {2018-05-21T00:13:17GMT},
abstract = {Trends in Ecology {\&} Evolution, 29 (2014) 607-613. doi:10.1016/j.tree.2014.09.004},
url = {http://dx.doi.org/10.1016/j.tree.2014.09.004},
local-url = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Dicks/2014/Trends_in_Ecology_&_Evolution-2014-Dicks.pdf},
file = {{Trends_in_Ecology_&_Evolution-2014-Dicks.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Dicks/2014/Trends_in_Ecology_&_Evolution-2014-Dicks.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1016/j.tree.2014.09.004}}
}

@article{Baillieul:2018jd,
author = {Baillieul, John and Grenier, Gerry and Setti, Gianluca},
title = {{Reflections on the Future of Research Curation and Research Reproducibility [Point of View]}},
journal = {Proceedings of the IEEE},
year = {2018},
volume = {106},
number = {5},
pages = {779--783},
month = apr,
doi = {10.1109/JPROC.2018.2816618},
read = {Yes},
rating = {0},
date-added = {2018-05-21T00:50:05GMT},
date-modified = {2018-05-21T02:21:49GMT},
url = {https://ieeexplore.ieee.org/document/8347157/},
local-url = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Files/82/825E0838-2DCA-4D8F-8A46-F69706198F93.pdf},
file = {{825E0838-2DCA-4D8F-8A46-F69706198F93.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Files/82/825E0838-2DCA-4D8F-8A46-F69706198F93.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1109/JPROC.2018.2816618}}
}

@article{Bennett:2017jh,
author = {Bennett, Nathan J and Roth, Robin and Klain, Sarah C and Chan, Kai and Christie, Patrick and Clark, Douglas A and Cullman, Georgina and Curran, Deborah and Durbin, Trevor J and Epstein, Graham and Greenberg, Alison and Nelson, Michael P and Sandlos, John and Stedman, Richard and Teel, Tara L and Thomas, Rebecca and Ver{\'\i}ssimo, Diogo and Wyborn, Carina},
title = {{Conservation social science: Understanding and integrating human dimensions to improve conservation}},
journal = {Biological Conservation},
year = {2017},
volume = {205},
number = {C},
pages = {93--108},
month = jan,
publisher = {The Authors},
doi = {10.1016/j.biocon.2016.10.006},
rating = {0},
date-added = {2018-05-22T02:53:08GMT},
date-modified = {2018-05-22T02:53:20GMT},
abstract = {BIOC, 205 (2017) 93-108. doi:10.1016/j.biocon.2016.10.006},
url = {http://dx.doi.org/10.1016/j.biocon.2016.10.006},
local-url = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Files/8D/8DDB2910-8997-44D8-B6A1-587202D3A531.pdf},
file = {{8DDB2910-8997-44D8-B6A1-587202D3A531.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Files/8D/8DDB2910-8997-44D8-B6A1-587202D3A531.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1016/j.biocon.2016.10.006}}
}

@article{Giljohann:2014tv,
author = {Giljohann, K M and Giljohann, K M and McCarthy, M A and McCarthy, M A and Kelly, L T and Kelly, L T},
title = {{Choice of biodiversity index drives optimal fire management decisions}},
journal = {Ecological Modelling},
year = {2014},
read = {Yes},
rating = {0},
date-added = {2015-01-17T00:32:35GMT},
date-modified = {2018-05-22T03:28:33GMT},
abstract = {Preservation of biodiversity is a central goal of conservation management , yet the conditions that promote persistence may differ for the species in the community. For systems subject to stochastic disturbances such as fire , understanding which management practices promote ...
},
url = {http://www.esajournals.org/doi/abs/10.1890/14-0257.1},
local-url = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Giljohann/2014/2014-Giljohann.pdf},
file = {{2014-Giljohann.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Giljohann/2014/2014-Giljohann.pdf:application/pdf}},
uri = {\url{papers3://publication/uuid/F03588C2-BD3E-4E10-9445-EB62C90BFD87}}
}

@article{Gardner:2018dm,
author = {Gardner, Charlie J and Waeber, Patrick O and Razafindratsima, Onja H and Wilm{\'e}, Lucienne},
title = {{Decision complacency and conservation planning}},
journal = {Conservation Biology},
year = {2018},
pages = {1--10},
month = may,
doi = {10.1111/cobi.13124},
language = {English},
read = {Yes},
rating = {0},
date-added = {2018-05-09T01:15:36GMT},
date-modified = {2018-05-22T04:19:27GMT},
url = {http://doi.wiley.com/10.1111/cobi.13124},
local-url = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Files/A6/A638B209-9F4F-4A9A-AD71-E1228A018EC5.pdf},
file = {{A638B209-9F4F-4A9A-AD71-E1228A018EC5.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Files/A6/A638B209-9F4F-4A9A-AD71-E1228A018EC5.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1111/cobi.13124}}
}

@article{Fraser:2018cl,
author = {Fraser, Hannah Stephanie and Parker, Timothy H and Nakagawa, Shinichi and Barnett, A and Fidler, Fiona},
title = {{Questionable Research Practices in Ecology and Evolution}},
year = {2018},
pages = {1--24},
month = mar,
keywords = {QRP, reproducibility},
doi = {10.17605/OSF.IO/AJYQG},
read = {Yes},
rating = {0},
date-added = {2018-05-15T01:23:53GMT},
date-modified = {2018-05-22T14:28:47GMT},
url = {https://osf.io/ajyqg},
local-url = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Files/5E/5E03E199-94B4-439B-9CA4-D658C2EB1E00.pdf},
file = {{5E03E199-94B4-439B-9CA4-D658C2EB1E00.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Files/5E/5E03E199-94B4-439B-9CA4-D658C2EB1E00.pdf:application/pdf;5E03E199-94B4-439B-9CA4-D658C2EB1E00.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Files/5E/5E03E199-94B4-439B-9CA4-D658C2EB1E00.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.17605/OSF.IO/AJYQG}}
}

@book{CEE:M-Sg3G8U,
author = {{Centre for Environmental Evidence}},
editor = {PULLIN, ANDREW S and Frampton, G K and Livoreil, B and Petrokofsky, G},
title = {{\textbf{\emph{Guidelines and Standards for Evidence synthesis in Environmental Management}}}},
edition = {Volume 5},
read = {Yes},
rating = {0},
date-added = {2018-05-23T05:12:20GMT},
date-modified = {2018-05-23T05:21:02GMT},
url = {www.environmentalevidence.org/information-for-authors},
uri = {\url{papers3://publication/uuid/33E4A0DC-6F14-41A5-AA32-2B7EAE35B3BA}}
}

@article{Nakagawa:2012fl,
author = {Nakagawa, Shinichi and Poulin, Robert},
title = {{Meta-analytic insights into evolutionary ecology: an introduction and synthesis}},
journal = {Evolutionary Ecology},
year = {2012},
volume = {26},
number = {5},
pages = {1085--1099},
month = jul,
doi = {10.1007/s10682-012-9593-z},
language = {English},
read = {Yes},
rating = {0},
date-added = {2018-03-14T22:14:55GMT},
date-modified = {2018-05-23T05:32:29GMT},
url = {http://link.springer.com/10.1007/s10682-012-9593-z},
local-url = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Files/01/01761F3D-A23D-4023-8DC6-516837263C69.pdf},
file = {{01761F3D-A23D-4023-8DC6-516837263C69.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Files/01/01761F3D-A23D-4023-8DC6-516837263C69.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1007/s10682-012-9593-z}}
}

@article{Bower:2017im,
author = {Bower, Shannon D and Brownscombe, Jacob W and Birnie-Gauvin, Kim and Ford, Matthew I and Moraga, Andrew D and Pusiak, Ryan J P and Turenne, Eric D and Zolderdo, Aaron J and Cooke, Steven J and Bennett, Joseph R},
title = {{Making Tough Choices: Picking the Appropriate Conservation Decision-Making Tool}},
journal = {Conservation letters},
year = {2017},
volume = {11},
number = {2},
pages = {e12418--7},
month = nov,
doi = {10.1111/conl.12418},
language = {English},
read = {Yes},
rating = {0},
date-added = {2018-05-16T06:31:33GMT},
date-modified = {2018-05-23T06:08:32GMT},
url = {http://doi.wiley.com/10.1111/conl.12418},
local-url = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Files/62/62E68E1E-78D3-4FF9-A759-6053E46BF228.pdf},
file = {{62E68E1E-78D3-4FF9-A759-6053E46BF228.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Files/62/62E68E1E-78D3-4FF9-A759-6053E46BF228.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1111/conl.12418}}
}

@inproceedings{gomez:2010rp,
  title={Replications types in experimental disciplines},
  author={G{\'o}mez, Omar S and Juristo, Natalia and Vegas, Sira},
  booktitle={Proceedings of the 2010 ACM-IEEE international symposium on empirical software engineering and measurement},
  pages={3},
  year={2010},
  organization={ACM}
}

@article{Moore:2012ii,
author = {Moore, Joslin L and Runge, Michael C},
title = {{Combining Structured Decision Making and Value-of-Information Analyses to Identify Robust Management Strategies}},
year = {2012},
volume = {26},
number = {5},
pages = {810--820},
month = aug,
annote = {Veg man.

Weed control optimisation. Salix cinerea

Optimisation that includes budgeting.
------
Two schools of thought about adaptive management:
1. Decision analytic school
2. Resilience experimentalist school},
keywords = {Adaptive management, Decision model, Gray sallow willow, Non-native invasive species, Salix cinerea},
doi = {10.1111/j.1523-1739.2012.01907.x},
language = {English},
read = {Yes},
rating = {0},
date-added = {2015-01-17T00:32:30GMT},
date-modified = {2018-05-28T16:51:55GMT},
url = {http://doi.wiley.com/10.1111/j.1523-1739.2012.01907.x},
local-url = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Moore/2012/2012-Moore-2.pdf},
file = {{2012-Moore-2.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Moore/2012/2012-Moore-2.pdf:application/pdf;2012-Moore-2.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Moore/2012/2012-Moore-2.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1111/j.1523-1739.2012.01907.x}}
}

@article{Converse:2013wp,
author = {Converse, Sarah J and Moore, Clinton T and Folk, Martin J and Runge, Michael C},
title = {{A matter of tradeoffs: Reintroduction as a multiple objective decision.}},
journal = {Journal of Wildlife Management},
year = {2013},
volume = {77},
number = {6},
pages = {1145--1156},
month = aug,
annote = {Accession Number: 89305806; Converse, Sarah J. 1; Moore, Clinton T. 2; Folk, Martin J. 3; Runge, Michael C. 1; Affiliations: 1: U.S. Geological Survey, Patuxent Wildlife Research Center; 2: U.S. Geological Survey, Patuxent Wildlife Research Center Warnell School of Forestry and Natural Resources, University of Georgia; 3: Florida Fish and Wildlife Conservation Commission, 1475 Regal Court; Issue Info: Aug2013, Vol. 77 Issue 6, p1145; Thesaurus Term: BIOTIC communities; Thesaurus Term: WILDLIFE reintroduction; Subject Term: DECISION making; Subject Term: ALLEE effect; Subject Term: WHOOPING crane; Subject Term: COST control; Subject Term: DEMOGRAPHIC research; Subject: FLORIDA; Author-Supplied Keyword: Allee effect; Author-Supplied Keyword: expert elicitation; Author-Supplied Keyword: Florida; Author-Supplied Keyword: Grus americana; Author-Supplied Keyword: model weights; Author-Supplied Keyword: population modeling; Author-Supplied Keyword: structured decision making; Author-Supplied Keyword: whooping cranes; NAICS/Industry Codes: 541720 Research and Development in the Social Sciences and Humanities; Number of Pages: 12p; Illustrations: 1 Diagram, 4 Charts, 2 Graphs; Document Type: Article},
publisher = {Wiley-Blackwell},
keywords = {ALLEE effect, Decision making, Expert elicitation, Grus americana, Population modelling, Structured decision-making, Whooping crane},
read = {Yes},
rating = {0},
date-added = {2015-01-17T00:33:02GMT},
date-modified = {2018-05-28T16:52:32GMT},
abstract = {Decision making in guidance of reintroduction efforts is made challenging by the substantial scientific uncertainty typically involved. However, a less recognized challenge is that the management objectives are often numerous and complex. Decision makers managing reintroduction efforts are often concerned with more than just how to maximize the probability of reintroduction success from a population perspective. Decision makers are also weighing other concerns such as budget limitations, public support and/or opposition, impacts on the ecosystem, and the need to consider not just a single reintroduction effort, but conservation of the entire species. Multiple objective decision analysis is a powerful tool for formal analysis of such complex decisions. We demonstrate the use of multiple objective decision analysis in the case of the Florida non-migratory whooping crane reintroduction effort. In this case, the State of Florida was considering whether to resume releases of captive-reared crane chicks into the non-migratory whooping crane population in that state. Management objectives under consideration included maximizing the probability of successful population establishment, minimizing costs, maximizing public relations benefits, maximizing the number of birds available for alternative reintroduction efforts, and maximizing learning about the demographic patterns of reintroduced whooping cranes. The State of Florida engaged in a collaborative process with their management partners, first, to evaluate and characterize important uncertainties about system behavior, and next, to formally evaluate the tradeoffs between objectives using the Simple Multi-Attribute Rating Technique (SMART). The recommendation resulting from this process, to continue releases of cranes at a moderate intensity, was adopted by the State of Florida in late 2008. Although continued releases did not receive support from the International Whooping Crane Recovery Team, this approach does provide a template for the formal, transparent consideration of multiple, potentially competing, objectives in reintroduction decision making. {\textcopyright} 2013 The Wildlife Society. [ABSTRACT FROM AUTHOR]},
url = {https://search.ebscohost.com/login.aspx?direct=true&db=eih&AN=89305806&site=ehost-live},
local-url = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Converse/2013/2013-Converse.pdf},
file = {{2013-Converse.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Converse/2013/2013-Converse.pdf:application/pdf;2013-Converse.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Converse/2013/2013-Converse.pdf:application/pdf}},
uri = {\url{papers3://publication/uuid/DF43BC21-5D31-4B95-A31C-61699A673107}}
}

@article{Schreiber:2004to,
author = {Schreiber, E Sabine G and Schreiber, E Sabine G and Bearlin, Andrew R and Bearlin, Andrew R and Nicol, Simon J and Nicol, Simon J and Todd, Charles R and Todd, Charles R},
title = {{Adaptive management: a synthesis of current understanding and effective application}},
journal = {Ecological Management {\&} Restoration},
year = {2004},
volume = {5},
number = {3},
pages = {177--182},
publisher = {Wiley Online Library},
keywords = {Adaptive Environmental Assessment, Adaptive management, Modelling, Uncertainty},
read = {Yes},
rating = {0},
date-added = {2015-01-17T00:32:57GMT},
date-modified = {2018-05-28T16:53:07GMT},
url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1442-8903.2004.00206.x/full},
local-url = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Schreiber/2004/Ecological_Management_&_Restoration-2004-Schreiber.pdf},
file = {{Ecological_Management_&_Restoration-2004-Schreiber.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Schreiber/2004/Ecological_Management_&_Restoration-2004-Schreiber.pdf:application/pdf}},
uri = {\url{papers3://publication/uuid/D662FA73-8FFB-488B-9BD8-377F0115EDDA}}
}

@book{BES:tGdddZne,
author = {Croucher, Mike and Graham, Laura and James, Tamora and Krystalli, Anna and Michonneau, Francois},
editor = {Cooper, Natalie and Hsing, Pen-Yuan},
title = {{A Guide to Reproducible Code in Ecology and Evolution}},
publisher = {British Ecological Society},
year = {2017},
month = nov,
read = {Yes},
rating = {0},
date-added = {2018-05-28T02:15:32GMT},
date-modified = {2018-05-28T02:20:47GMT},
local-url = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Files/98/98637134-2E3D-4E7F-B382-87D7E97B4ECE.pdf},
file = {{98637134-2E3D-4E7F-B382-87D7E97B4ECE.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Files/98/98637134-2E3D-4E7F-B382-87D7E97B4ECE.pdf:application/pdf}},
uri = {\url{papers3://publication/uuid/B4675D75-99DE-484A-9032-A1E4FE7A1544}}
}

@article{Parker:2016hc,
author = {Parker, Timothy H and Forstmeier, Wolfgang and Koricheva, Julia and Fidler, Fiona and Hadfield, Jarrod D and Chee, Yung En and Kelly, Clint D and Gurevitch, Jessica and Nakagawa, Shinichi},
title = {{Transparency in Ecology and Evolution: Real Problems, Real Solutions}},
journal = {Trends in Ecology {\&} Evolution},
year = {2016},
volume = {31},
number = {9},
pages = {711--719},
month = sep,
publisher = {Elsevier},
doi = {10.1016/j.tree.2016.07.002},
language = {English},
read = {Yes},
rating = {0},
date-added = {2016-10-06T04:03:47GMT},
date-modified = {2018-05-28T11:05:29GMT},
abstract = {To make progress scientists need to know what other researchers have found and how they found it. However, transparency is often insufficient across much of ecology and evolution. Researchers often fail to report results and methods in detail sufficient to permit interpretation and meta-analysis, and many results go entirely unreported. Further, these unreported results are often a biased subset. Thus the conclusions we can draw from the published literature are themselves often biased and sometimes might be entirely incorrect.},
url = {http://www.cell.com/article/S0169534716300957/fulltext},
local-url = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Files/F5/F5801508-B0B5-45B1-959E-281AB436C46C.pdf},
file = {{F5801508-B0B5-45B1-959E-281AB436C46C.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Files/F5/F5801508-B0B5-45B1-959E-281AB436C46C.pdf:application/pdf;F5801508-B0B5-45B1-959E-281AB436C46C.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Files/F5/F5801508-B0B5-45B1-959E-281AB436C46C.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1016/j.tree.2016.07.002}}
}

@article{Stewart:2010fh,
author = {Stewart, G},
title = {{Meta-analysis in applied ecology}},
journal = {Biology Letters},
year = {2010},
volume = {6},
number = {1},
pages = {78--81},
month = jan,
doi = {10.1098/rsbl.2009.0546},
language = {English},
rating = {0},
date-added = {2018-05-28T03:17:39GMT},
date-modified = {2018-05-28T03:17:48GMT},
url = {http://rsbl.royalsocietypublishing.org/cgi/doi/10.1098/rsbl.2009.0546},
local-url = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Files/E8/E8336303-CAB8-4214-A27E-75EE62AE7DE9.pdf},
file = {{E8336303-CAB8-4214-A27E-75EE62AE7DE9.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Files/E8/E8336303-CAB8-4214-A27E-75EE62AE7DE9.pdf:application/pdf;E8336303-CAB8-4214-A27E-75EE62AE7DE9.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Files/E8/E8336303-CAB8-4214-A27E-75EE62AE7DE9.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1098/rsbl.2009.0546}}
}

@article{Nature:2018ud,
title = {{A checklist for our community}},
journal = {Nature Ecology {\&} Evolution},
year = {2018},
volume = {2},
number = {6},
pages = {913--913},
month = jun,
publisher = {Nature Publishing Group},
doi = {10.1038/s41559-018-0574-7},
language = {English},
read = {Yes},
rating = {0},
date-added = {2018-05-28T04:03:28GMT},
date-modified = {2018-05-28T04:10:23GMT},
abstract = {A new Nature journal checklist for authors is tailored specifically to ecology and evolution research, and is the product of feedback from the scientific community.},
url = {https://www-nature-com.ezp.lib.unimelb.edu.au/articles/s41559-018-0574-7},
local-url = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Files/EA/EACBDDE1-2606-4E76-8638-CF8A1EB7EEDC.pdf},
file = {{EACBDDE1-2606-4E76-8638-CF8A1EB7EEDC.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Files/EA/EACBDDE1-2606-4E76-8638-CF8A1EB7EEDC.pdf:application/pdf;EACBDDE1-2606-4E76-8638-CF8A1EB7EEDC.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Files/EA/EACBDDE1-2606-4E76-8638-CF8A1EB7EEDC.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1038/s41559-018-0574-7}}
}

@article{Fidler:2018ho,
author = {Fidler, Fiona and Fraser, Hannah and McCarthy, Michael A and Game, Edward T},
title = {{Improving the transparency of statistical reporting in Conservation Letters}},
journal = {Conservation letters},
year = {2018},
volume = {11},
number = {2},
pages = {e12453--4},
month = apr,
publisher = {Wiley/Blackwell (10.1111)},
doi = {10.1111/conl.12453},
language = {English},
read = {Yes},
rating = {0},
date-added = {2018-05-28T04:14:07GMT},
date-modified = {2018-05-28T11:31:16GMT},
url = {http://doi.wiley.com/10.1111/conl.12453},
local-url = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Files/8E/8E1979A6-B3B6-47A7-AE6B-106EEA8FDBBA.pdf},
file = {{8E1979A6-B3B6-47A7-AE6B-106EEA8FDBBA.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Files/8E/8E1979A6-B3B6-47A7-AE6B-106EEA8FDBBA.pdf:application/pdf;8E1979A6-B3B6-47A7-AE6B-106EEA8FDBBA.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Files/8E/8E1979A6-B3B6-47A7-AE6B-106EEA8FDBBA.pdf:application/pdf}},
uri = {\url{papers3://publication/doi/10.1111/conl.12453}}
}

@article{Regan:2005wn,
author = {Regan, H M and Ben-Haim, Y and Langford, B and al, et},
title = {{Robust decision-making under severe uncertainty for conservation management}},
journal = {Ecological Applications},
year = {2005},
volume = {15},
number = {4},
pages = {1471--1477},
publisher = {Eco Soc America},
keywords = {Conservation management, Decision theory, Dicerorhinus sumatrensis, Information gap, Robustness of decisions, Sumatran Rhino, Uncertainty},
read = {Yes},
rating = {0},
date-added = {2015-01-17T00:32:07GMT},
date-modified = {2018-05-28T16:57:41GMT},
abstract = {In conservation biology it is necessary to make management decisions for endangered and threatened species under severe uncertainty . Failure to acknowledge and treat uncertainty can lead to poor decisions. To illustrate the importance of considering uncertainty , we  ...},
url = {http://www.esajournals.org/doi/abs/10.1890/03-5419},
local-url = {file://localhost/Users/Elise/Dropbox/papers3/Library.papers3/Regan/2005/Ecological_Applications-2005-Regan.pdf},
file = {{Ecological_Applications-2005-Regan.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Regan/2005/Ecological_Applications-2005-Regan.pdf:application/pdf;Ecological_Applications-2005-Regan.pdf:/Users/Elise/Dropbox/papers3/Library.papers3/Regan/2005/Ecological_Applications-2005-Regan.pdf:application/pdf}},
uri = {\url{papers3://publication/uuid/F9E6CA0A-6E8C-4FAE-9DFC-4BCB0271FDB7}}
}

@article{Moher:2015,
author = {Moher, David and Shamseer, Larissa and Clarke, Mike and Ghersi, Davina and Liberati, Alessandro and Petticrew, Mark and Shekelle, Paul and Stewart, Lesley A},
title = {{Preferred reporting items for systematic review and meta-analysis protocols (PRISMA-P) 2015 statement}},
journal = {Systematic reviews},
year = {2015},
volume = {4},
number = {1},
pages = {1},
month = jan,
doi = {10.1186/2046-4053-4-1},
rating = {0},
date-added = {2018-05-28T14:28:58GMT},
date-modified = {2018-05-28T14:29:09GMT},
abstract = {Systematic reviews should build on a protocol that describes the rationale, hypothesis, and planned methods of the review; few reviews report whether a protocol exists. Detailed, well-described protocols can facilitate the understanding and appraisal of the review methods, as well as the detection of modifications to methods and selective reporting in completed reviews. We describe the development of a reporting guideline, the Preferred Reporting Items for Systematic reviews and Meta-Analyses for Protocols 2015 (PRISMA-P 2015). PRISMA-P consists of a 17-item checklist intended to facilitate the preparation and reporting of a robust protocol for the systematic review. Funders and those commissioning reviews might consider mandating the use of the checklist to facilitate the submission of relevant protocol information in funding applications. Similarly, peer reviewers and editors can use the guidance to gauge the completeness and transparency of a systematic review protocol submitted for publication in a journal or other medium.},
doi = {10.1186/2046-4053-4-1},
uri = {\url{papers3://publication/doi/10.1186/2046-4053-4-1}}
}

@Article{Parker2019,
author = {Parker, T and Fraser, H and Nakagawa, S},
title = {Making conservation science more reliable with preregistration and registered reports.},
journal = {Conserv Biol},
volume = {},
number = {},
pages = {},
year = {2019},
abstract = {},
location = {Biology Department, Whitman College, 345 Boyer Ave., Walla Walla, WA, 99362, U.S.A. School of BioSciences, University of Melbourne, Grattan Street, Parkville, Victoria, 3010, Australia. Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Randwick, New South Wales, 2052, Australia.},
keywords = {}}


@Article{Wicherts2016,
author = {Wicherts, JM and Veldkamp, CL and Augusteijn, HE and Bakker, M and van Aert, RC and van Assen, MA},
title = {Degrees of Freedom in Planning, Running, Analyzing, and Reporting Psychological Studies: A Checklist to Avoid p-Hacking.},
journal = {Front Psychol},
volume = {7},
number = {},
pages = {1832},
year = {2016},
abstract = {The designing, collecting, analyzing, and reporting of psychological studies entail many choices that are often arbitrary. The opportunistic use of these so-called researcher degrees of freedom aimed at obtaining statistically significant results is problematic because it enhances the chances of false positive results and may inflate effect size estimates. In this review article, we present an extensive list of 34 degrees of freedom that researchers have in formulating hypotheses, and in designing, running, analyzing, and reporting of psychological research. The list can be used in research methods education, and as a checklist to assess the quality of preregistrations and to determine the potential for bias due to (arbitrary) choices in unregistered studies.},
location = {Methodology and Statistics, Tilburg University Tilburg, Netherlands.},
keywords = {questionable research practice; experimental design; significance testing; p-hacking; bias; significance chasing; research methods education}}


@Article{Simmons:2011iw,
author = {Simmons, Joseph P and Nelson, Leif D and Simonsohn, Uri},
title = {False-Positive Psychology},
journal = {Psychological Science},
volume = {22},
number = {11},
pages = {1359–1366},
year = {2011},
abstract = {In this article, we accomplish two things. First, we show that despite empirical psychologists’ nominal endorsement of a low rate of false-positive findings (≤.05), flexibility in data collection, analysis, and reporting dramatically increases actual false-positive rates. In many cases, a researcher is more likely to falsely find evidence that an effect exists than to correctly find evidence that it does not. We present computer simulations and a pair of actual experiments that demonstrate how unacceptably easy it is to accumulate (and report) statistically significant evidence for a false hypothesis. Second, we suggest a simple, low-cost, and straightforwardly effective disclosure-based solution to this problem. The solution involves six concrete requirements for authors and four guidelines for reviewers, all of which impose a minimal burden on the publication process.},
location = {},
keywords = {disclosure; methodology; publication; Questionable Research Practices; transparency; undisclosed flexibility; researcher degrees of freedom}}

@Article{Seaman:2015gv,
author = {Seaman, Christopher Scott and Weber, Rene},
title = {Undisclosed Flexibility in Computing and Reporting Structural Equation Models in Communication Science},
journal = {Communication Methods and Measures},
volume = {9},
number = {4},
pages = {208–232},
year = {2015},
abstract = {Communication Methods and Measures, 2015. doi:10.1080/19312458.2015.1096329},
location = {},
keywords = {causal modelling; cherry picking; HARKing; Questionable Research Practices; reproducibility; research flexibilities; researcher degrees of freedom; structural equation modelling}}


@Article{Earp:2015bl,
author = {Earp, Brian D and Trafimow, David},
title = {Replication, falsification, and the crisis of confidence in social psychology},
journal = {Frontiers in Psychology},
volume = {6},
number = {781},
pages = {108–111},
year = {2015},
abstract = {The (latest) crisis in confidence in social psychology has generated much heated discussion about the importance of replication, including how it should be carried out as well as interpreted by scholars in the field.The (latest) crisis in confidence in social psychology has generated much heated discussion about the importance of replication, including how it should be carried out as well as interpreted by scholars in the field.},
location = {},
keywords = {replication, falsification, falsifiability, crisis of confidence, social psychology, priming, philosophy of science, Karl Popper}}


@Proceedings{Gould:2019ebg,
author = {Gould, E. and Fraser, H. and Rumpff, L. and Fidler, F.},
editor = {},
title = {Questionable Research Practices in non-hypothesis testing research: Ecological models for conservation decision-making},
booktitle = {Questionable Research Practices in non-hypothesis testing research: Ecological models for conservation decision-making},
volume = {},
publisher = {},
address = {},
pages = {},
year = {2019},
abstract = {Recent metaresearch studying the prevalence, types, causes and solutions to Questionable Research Practices (QRPs) has almost exclusively focussed on frequentist hypothesis-testing. However, within Conservation Science, modellers routinely conduct non-hypothesis testing research; building models that generate anticipatory predictions to guide policy and decision makers in managing threatened ecosystems and species. We expand the scope of current QRP work by proposing a conceptual framework for defining and understanding the emergence of QRPs within model-centric research. We surveyed the literature to construct ‘roadmaps’ identifying the type and location of plausible QRPs within the model development process. There are many opportunities for undisclosed researcher degrees of freedom in ecological modelling. While there are direct analogues between NHST and non-NHST research, there are domain and context-specific nuances that influence the emergence of QRPs in model-centric research.},
keywords = {metascience; ecology; applied ecology; modeling}}

@Article{Gould:2020ebg,
author = {Gould, E., Fraser, H., Rumpff, L., Fidler, F.},
title = {Questionable Research Practices in Ecological Modelling},
journal = {},
volume = {},
number = {},
pages = {},
year = {In prep.},
abstract = {},
location = {},
keywords = {}}


@Article{Cruwell2019b,
author = {Crüwell, Sophia and Evans, Nathan J.},
title = {Preregistration in Complex Contexts: A Preregistration Template for the Application of Cognitive Models},
journal = {},
volume = {},
number = {},
pages = {},
year = {2019},
abstract = {In recent years, open science practices have become increasingly popular in psychology and related sciences. These practices aim to increase rigour and transparency in science as a potential response to the challenges posed by the replication crisis. Many of these reforms -- including the highly influential preregistration -- have been designed for experimental work that tests simple hypotheses with standard statistical analyses, such as assessing whether an experimental manipulation has an effect on a variable of interest. However, psychology is a diverse field of research, and the somewhat narrow focus of the prevalent discussions surrounding and templates for preregistration has led to debates on how appropriate these reforms are for areas of research with more diverse hypotheses and more complex methods of analysis, such as cognitive modelling research within mathematical psychology. Our article attempts to bridge the gap between open science and mathematical psychology, focusing on the type of cognitive modelling that Crüwell, Stefan, & Evans (2019) labelled model application, where researchers apply a cognitive model as a measurement tool to test hypotheses about parameters of the cognitive model. Specifically, we (1) discuss several potential researcher degrees of freedom within model application, (2) provide the first preregistration template for model application, and (3) provide an example of a preregistered model application using our preregistration template. More broadly, we hope that our discussions and proposals constructively advance the debate surrounding preregistration in cognitive modelling, and provide a guide for how preregistration templates may be developed in other diverse or complex research contexts.},
location = {},
keywords = {}}


@Article{Saltelli2017a,
author = {Saltelli, Andrea and Giampietro, Mario},
title = {What is wrong with evidence based policy, and how can it be improved},
journal = {Futures},
volume = {91},
number = {},
pages = {62–71},
year = {2017},
abstract = {},
location = {},
keywords = {}}

@Article{Powers2018,
author = {Powers, Stephen M. and Hampton, Stephanie E.},
title = {Open science, reproducibility, and transparency in ecology},
journal = {Ecological Applications},
volume = {},
number = {},
pages = {},
year = {2018},
abstract = {Reproducibility is a key tenet of the scientific process that dictates the reliability and generality of results and methods. The complexities of ecological observations and data present novel challenges in satisfying needs for reproducibility, and also transparency. Ecological systems are dynamic and heterogeneous, interacting with numerous factors that sculpt natural history and that investigators cannot completely control. Observations may be highly dependent on spatial and temporal context, making them very difficult to reproduce, but computational reproducibility still can be achieved. Computational reproducibility often refers to the ability to produce equivalent analytical outcomes from the same data set using the same code and software as the original study. When coded workflows are shared, authors and editors provide transparency for readers and allow other researchers to build directly and efficiently on primary work. These qualities may be especially important in ecological applications that have important or controversial implications for science, management, and policy. Expectations for computational reproducibility and transparency are shifting rapidly in the sciences. In this work we highlight many of the unique challenges for ecology along with practical guidelines for reproducibility and transparency, as ecologists continue to participate in the stewardship of critical environmental information and ensure that research methods demonstrate integrity.},
location = {},
keywords = {reproducibility, transparency, open science, data policy, environmental science, ecoinformatics, ecosystem engineering, replicability, repeatability, data science, collaborative tools, workflows}}

@Article{Nilsen2020,
author = {Nilsen, Erlend B. and Bowler, Diana E. and Linnell, John D. C.},
title = {Exploratory and confirmatory research in the open science era},
journal = {Journal of Applied Ecology},
volume = {},
number = {},
pages = {},
year = {2020},
abstract = {1. Applied ecological research is increasingly inspired by the open science movement. However, new challenges about how we define our science when biodiversity data are being shared and re-used are not solved. Among these challenges is the risk associated with blurring the distinction between research that mainly seeks to explore patterns with no a-priori articulated hypotheses (exploratory research), and research that explicitly tests a-priori formulated hypotheses (confirmatory research).
2. A rapid screening of a random selection of the peer-reviewed literature suggests that neither experimental protocols nor hypothesis-testing sensu stricto are com- mon in applied ecological research. In addition, most experiments are carried out on small spatial scales, which contrast with current global policy needs and research trends towards addressing large spatial and temporal scales. This latter trend makes it unfeasible for policy to rely mainly on insights gained from experimental research.
3. To solve fundamental local, regional and global societal challenges, we need both exploratory and confirmatory research. However, the fundamental roles that con- firmatory research testing a-priori hypothesis play in establishing causal relation- ships need to be revaluated in applied ecological research.
4. A clearer distinction between exploratory and confirmatory research is currently needed, and could be facilitated by allocating journal sections to different types of research; by embracing new tools offered by the open science era, such as pre- registration of hypothesis; by establishing new systems where post-hoc hypoth- eses emerging through exploration can also be registered for later testing; and by more broad adoption of causal inference methods that foster more structured test- ing of hypotheses about causal mechanisms from observational biodiversity data.
5. Synthesis and applications. To gain the full benefits of the open science era, re- searchers, funding bodies and journal editors should explicitly consider approaches and incentives that encourage openness about methods and approaches, as well as value the plurality of scientific approaches needed to address questions in applied ecology and conservation science.},
location = {},
keywords = {}}


@Article{Augusiak:2014gz,
author = {Augusiak, Jacqueline and Van den Brink, Paul J and Grimm, Volker},
title = {Merging validation and evaluation of ecological models to ‘evaludation’: A review of terminology and a practical approach},
journal = {Ecological Modelling},
volume = {280},
number = {},
pages = {117–128},
year = {2014},
abstract = {Confusion about model validation is one of the main challenges in using ecological models for decision support, such as the regulation of pesticides. Decision makers need to know whether a model is a suffi- ciently good representation of its real counterpart and what criteria can be used to answer this question. Unclear terminology is one of the main obstacles to a good understanding of what model validation is, how it works, and what it can deliver. Therefore, we performed a literature review and derived a standard set of terms. ‘Validation’ was identified as a catch-all term, which is thus useless for any practical pur- pose. We introduce the term ‘evaludation’, a fusion of ‘evaluation’ and ‘validation’, to describe the entire process of assessing a model’s quality and reliability. Considering the iterative nature of model develop- ment, the modelling cycle, we identified six essential elements of evaludation: (i) ‘data evaluation’ for scrutinising the quality of numerical and qualitative data used for model development and testing; (ii) ‘conceptual model evaluation’ for examining the simplifying assumptions underlying a model’s design; (iii) ‘implementation verification’ for testing the model’s implementation in equations and as a computer programme; (iv) ‘model output verification’ for comparing model output to data and patterns that guided model design and were possibly used for calibration; (v) ‘model analysis’ for exploring the model’s sensi- tivity to changes in parameters and process formulations to make sure that the mechanistic basis of main behaviours of the model has been well understood; and (vi) ‘model output corroboration’ for comparing model output to new data and patterns that were not used for model development and parameterisation. Currently, most decision makers require ‘validating’ a model by testing its predictions with new exper- iments or data. Despite being desirable, this is neither sufficient nor necessary for a model to be useful for decision support. We believe that the proposed set of terms and its relation to the modelling cycle can help to make quality assessments and reality checks of ecological models more comprehensive and transparent.},
doi = {10.1016/j.ecolmodel.2013.11.009},
location = {},
keywords = {Model validation; terminology; decision support; documentation; ecological models; risk assessment}}


@Article{Grimm:2014es,
author = {Grimm, Volker and Augusiak, Jacqueline and Focks, Andreas and Frank, Béatrice M and Gabsi, Faten and Johnston, Alice S A and Liu, Chun and Martin, Benjamin T and Meli, Mattia and Radchuk, Viktoriia and Thorbek, Pernille and Railsback, Steven F},
title = {Towards better modelling and decision support: Documenting model development, testing, and analysis using TRACE},
journal = {Ecological Modelling},
volume = {280},
number = {},
pages = {129–139},
year = {2014},
abstract = {Ecological Modelling, 280 (2014) 129-139. doi:10.1016/j.ecolmodel.2014.01.018},
location = {},
keywords = {Standardization; Good modelling practice; Risk assessment; Decision support; Model documentation; Reporting practices}}


@Article{Jakeman:2006ii,
author = {Jakeman, A J and Letcher, R A and Norton, J P},
title = {Ten iterative steps in development and evaluation of environmental models},
journal = {Environmental Modelling & Software},
volume = {21},
number = {5},
pages = {602–614},
year = {2006},
abstract = {},
location = {},
doi = {10.1016/j.envsoft.2006.01.004},
keywords = {Integrated assessment; Model testing; Sensitivity; System identification; Uncertainty; Verification}}


@Article{Moallemi2019,
author = {Moallemi, Enayat A. and Elsawah, Sondoss and Ryan, Michael J.},
title = {Strengthening ‘good’ modelling practices in robust decision support: A reporting guideline for combining multiple model-based methods},
journal = {Mathematics and Computers in Simulation},
volume = {},
number = {},
pages = {},
year = {2019},
abstract = {},
location = {},
doi = {10.1016/j.matcom.2019.05.002},
keywords = {}}


@Article{Holzkamper:2012je,
author = {Holzkämper, Annelie and Kumar, Vikas and Ben, W J Surridge and Paetzold, Achim and Lerner, David N},
title = {Bringing diverse knowledge sources together - A meta-model for supporting integrated catchment management},
journal = {Journal of Environmental Management},
volume = {96},
number = {1},
pages = {116–127},
year = {2012},
abstract = {Journal of Environmental Management, 96 (2012) 116-127. doi:10.1016/j.jenvman.2011.10.016},
location = {},
keywords = {Bayesian Network; Decision support; Integrated catchment management; Integrated modelling; Meta-model; Water framework directive; Papers_flagged}}


@Article{Cartwright:2016kr,
author = {Cartwright, Samantha J and Bowgen, Katharine M and Collop, Catherine and Hyder, Kieran and Nabe-Nielsen, Jacob and Stafford, Richard and Stillman, Richard A and Thorpe, Robert B and Sibly, Richard M},
title = {Communicating complex ecological models to non-scientist end users},
journal = {Ecological Modelling},
volume = {338},
number = {},
pages = {51–59},
year = {2016},
abstract = {Complex computer models are used to predict how ecological systems respond to changing environ- mental conditions or management actions. Communicating these complex models to non-scientists is challenging, but necessary, because decision-makers and other end users need to understand, accept, and use the models and their predictions. Despite the importance of communicating effectively with end users, there is little guidance available as to how this may be achieved. Here, we review the challenges typically encountered by modellers attempting to communicate complex models and their outputs to managers and other non-scientist end users. We discuss the implications of failing to communicate effec- tively in each case. We then suggest a general approach for communicating with non-scientist end users. We detail the specific elements to be communicated using the example of individual-based models, which are widely used in ecology. We demonstrate that despite their complexity, individual-based models have characteristics that can facilitate communication with non-scientists. The approach we propose is based on our experiences and methods used in other fields, but which until now have not been synthesised or made broadly available to ecologists. Our aim is to facilitate the process of communicating with end users of complex models and encourage more modellers to engage in it by providing a structured approach to the communication process. We argue that developing measures of the effectiveness of communication with end users will help increase the impact of complex models in ecology.},
location = {},
doi = {10.1016/j.ecolmodel.2016.07.012},
keywords = {participatory modelling; stakeholder; non-expert; individual-based model; environmental management; communication}}


@Article{Moon2019,
author = {Moon, Katie and Guerrero, Angela M. and Adams, Vanessa. M. and Biggs, Duan and Blackman, Deborah A. and Craven, Luke and Dickinson, Helen and Ross, Helen},
title = {Mental models for conservation research and practice},
journal = {Conservation Letters},
volume = {12},
number = {3},
pages = {e12642},
year = {2019},
abstract = {},
location = {},
doi = {10.1111/conl.12642},
keywords = {}}


@Article{Yates2018,
author = {Yates, KL and Bouchet, PJ and Caley, MJ and Mengersen, K and Randin, CF and Parnell, S and Fielding, AH and Bamford, AJ and Ban, S and Barbosa, AM and Dormann, CF and Elith, J and Embling, CB and Ervin, GN and Fisher, R and Gould, S and Graf, RF and Gregr, EJ and Halpin, PN and Heikkinen, RK and Heinänen, S and Jones, AR and Krishnakumar, PK and Lauria, V and Lozano-Montes, H and Mannocci, L and Mellin, C and Mesgaran, MB and Moreno-Amat, E and Mormede, S and Novaczek, E and Oppel, S and Ortuño Crespo, G and Peterson, AT and Rapacciuolo, G and Roberts, JJ and Ross, RE and Scales, KL and Schoeman, D and Snelgrove, P and Sundblad, G and Thuiller, W and Torres, LG and Verbruggen, H and Wang, L and Wenger, S and Whittingham, MJ and Zharikov, Y and Zurell, D and Sequeira, AMM},
title = {Outstanding Challenges in the Transferability of Ecological Models.},
journal = {Trends Ecol. Evol. (Amst.)},
volume = {33},
number = {10},
pages = {790–802},
year = {2018},
abstract = {Predictive models are central to many scientific disciplines and vital for informing management in a rapidly changing world. However, limited understanding of the accuracy and precision of models transferred to novel conditions (their ‘transferability’) undermines confidence in their predictions. Here, 50 experts identified priority knowledge gaps which, if filled, will most improve model transfers. These are summarized into six technical and six fundamental challenges, which underlie the combined need to intensify research on the determinants of ecological predictability, including species traits and data quality, and develop best practices for transferring models. Of high importance is the identification of a widely applicable set of transferability metrics, with appropriate tools to quantify the sources and impacts of prediction uncertainty under novel conditions.},
location = {},
doi = {10.1016/j.tree.2018.08.001},
keywords = {}}


@Article{Araujo2019,
author = {Araújo, MB and Anderson, RP and Márcia Barbosa, A and Beale, CM and Dormann, CF and Early, R and Garcia, RA and Guisan, A and Maiorano, L and Naimi, B and O’Hara, RB and Zimmermann, NE and Rahbek, C},
title = {Standards for distribution models in biodiversity assessments.},
journal = {Sci Adv},
volume = {5},
number = {1},
pages = {eaat4858},
year = {2019},
abstract = {Demand for models in biodiversity assessments is rising, but which models are adequate for the task? We propose a set of best-practice standards and detailed guidelines enabling scoring of studies based on species distribution models for use in biodiversity assessments. We reviewed and scored 400 modeling studies over the past 20 years using the proposed standards and guidelines. We detected low model adequacy overall, but with a marked tendency of improvement over time in model building and, to a lesser degree, in biological data and model evaluation. We argue that implementation of agreed-upon standards for models in biodiversity assessments would promote transparency and repeatability, eventually leading to higher quality of the models and the inferences used in assessments. We encourage broad community participation toward the expansion and ongoing development of the proposed standards and guidelines.},
doi = {10.1126/sciadv.aat4858},
location = {},
keywords = {}}


@Article{Mahmoud2009,
author = {Mahmoud, Mohammed and Liu, Yuqiong and Hartmann, Holly and Stewart, Steven and Wagener, Thorsten and Semmens, Darius and Stewart, Robert and Gupta, Hoshin and Dominguez, Damian and Dominguez, Francina and Hulse, David and Letcher, Rebecca and Rashleigh, Brenda and Smith, Court and Street, Roger and Ticehurst, Jenifer and Twery, Mark and van Delden, Hedwig and Waldick, Ruth and White, Denis and Winter, Larry},
title = {A formal framework for scenario development in support of environmental decision-making},
journal = {Environmental Modelling & Software},
volume = {24},
number = {7},
pages = {798–808},
year = {2009},
abstract = {},
location = {},
doi = {10.1016/j.envsoft.2008.11.010},
keywords = {}}


@Article{Saltelli2019,
author = {Saltelli, Andrea and Aleksankina, Ksenia and Becker, William and Fennell, Pamela and Ferretti, Federico and Holst, Niels and Li, Sushan and Wu, Qiongli},
title = {Why so many published sensitivity analyses are false: A systematic review of sensitivity analysis practices},
journal = {Environmental Modelling & Software},
volume = {114},
number = {},
pages = {29–39},
year = {2019},
abstract = {},
location = {},
doi = {10.1016/j.envsoft.2019.01.012},
keywords = {}}

@Article{Fraser:2017jf,
author = {Fraser, Hannah and Rumpff, Libby and Yen, Jian D L and Robinson, Doug and Wintle, Brendan A},
title = {Integrated models to support multiobjective ecological restoration decisions},
journal = {Conservation Biology},
volume = {31},
number = {6},
pages = {1418–1427},
year = {2017},
abstract = {},
location = {},
doi = {10.1111/cobi.12939},
keywords = {}}

@Article{McDonald-Madden2008,
author = {McDonald-Madden, Eve and Baxter, Peter W.J. and Possingham, Hugh P.},
title = {Making robust decisions for conservation with restricted money and knowledge},
journal = {Journal of Applied Ecology},
volume = {45},
number = {6},
pages = {1630–1638},
year = {2008},
abstract = {1. In conservation decision-making, we operate within the confines of limited funding. Furthermore, we often assume particular relationships between management impact and our investment in management. The structure of these relationships, however, is rarely known with certainty – there is model uncertainty. We investigate how these two fundamentally limiting factors in conservation management, money and knowledge, impact optimal decision-making.
2. We use information-gap decision theory to find strategies for maximizing the number of extant subpopulations of a threatened species that are most immune to failure due to model uncertainty. We thus find a robust framework for exploring optimal decision-making.
3. The performance of every strategy decreases as model uncertainty increases.
4. The strategy most robust to model uncertainty depends not only on what performance is perceived to be acceptable but also on available funding and the time horizon over which extinction is considered.
5. Synthesis and applications. We investigate the impact of model uncertainty on robust decision- making in conservation and how this is affected by available conservation funding. We show that subpopulation triage can be a natural consequence of robust decision-making. We highlight the need for managers to consider triage not as merely giving up, but as a tool for ensuring species persistence in light of the urgency of most conservation requirements, uncertainty and the poor state of conservation funding. We illustrate this theory by a specific application to allocation of funding to reduce poaching impact on the Sumatran tiger Panthera tigris sumatrae in Kerinci Seblat National Park.},
location = {},
doi = {10.1111/j.1365-2664.2008.01553.x},
keywords = {conservationfunding; decisiontheory; info-gap; model uncertainty; resource allocation; Sumatran tiger; triage}}


@Article{Grimm:2014es,
author = {Grimm, Volker and Augusiak, Jacqueline and Focks, Andreas and Frank, Béatrice M and Gabsi, Faten and Johnston, Alice S A and Liu, Chun and Martin, Benjamin T and Meli, Mattia and Radchuk, Viktoriia and Thorbek, Pernille and Railsback, Steven F},
title = {Towards better modelling and decision support: Documenting model development, testing, and analysis using TRACE},
journal = {Ecological Modelling},
volume = {280},
number = {},
pages = {129–139},
year = {2014},
abstract = {Ecological Modelling, 280 (2014) 129-139. doi:10.1016/j.ecolmodel.2014.01.018},
location = {},
doi = {10.1016/j.ecolmodel.2014.01.018},
keywords = {Standardization; Good modelling practice; Risk assessment; Decision support; Model documentation; Reporting practices}}

@Article{White2019a,
author = {White, Craig R and Marshall, Dustin J},
title = {Should We Care If Models Are Phenomenological or Mechanistic},
journal = {Trends in ecology & evolution},
volume = {34},
number = {4},
pages = {276–278},
year = {2019},
abstract = {A recent meta-analysis of published data demonstrated that reproductive output increases disproportionately with size in fish [1]. Building on this observation, we hypothesised that growth slows as animals increase in size because of an increasing allocation of energy to reproduction, and we demonstrated that this hypothesis is plausible by fitting a simple model of energy allocation to growth, reproduction, and maintenance to weight-for-age data for a selection of fish species [2]. The fit of our model to growth data was indistinguishable from …},
location = {},
doi = {10.1016/j.tree.2019.01.006},
keywords = {}}


@Article{Boets:2015gl,
author = {Boets, Pieter and Landuyt, Dries and Everaert, Gert and Broekx, Steven and Goethals, Peter L M},
title = {Evaluation and comparison of data-driven and knowledge-supported Bayesian Belief Networks to assess the habitat suitability for alien macroinvertebrates},
journal = {},
volume = {74},
number = {},
pages = {92–103},
year = {2015},
abstract = {},
location = {},
doi = {10.1016/j.envsoft.2015.09.005},
keywords = {#comparison; #write-up; Bayesian Belief Networks; BN documentation}}


@Article{Liu2018b,
author = {Liu, Zelin and Peng, Changhui and Work, Timothy and Candau, Jean-Noel and DesRochers, Annie and Kneeshaw, Daniel},
title = {Application of machine-learning methods in forest ecology: recent progress and future challenges},
journal = {Environmental Reviews},
volume = {26},
number = {4},
pages = {339–350},
year = {2018},
abstract = {Machine learning, an important branch of artificial intelligence, is increasingly being applied in sciences such as forest ecology. Here, we review and discuss three commonly used methods of machine learning (ML) including decision-tree learning, artificial neural network, and support vector machine and their applications in four different aspects of forest ecology over the last decade. These applications include:(i) species distribution models,(ii) carbon cycles,(iii) hazard assessment and prediction, and (iv) other applications in forest …},
location = {},
doi = {10.1139/er-2018-0034},
keywords = {}}


@Article{Barnard2019,
author = {Barnard, David M. and Germino, Matthew J. and Pilliod, David S. and Arkle, Robert S. and Applestein, Cara and Davidson, Bill E. and Fisk, Matthew R.},
title = {Can’t see the random forest for the decision trees: selecting predictive models for restoration ecology},
journal = {Restoration Ecology},
volume = {},
number = {},
pages = {},
year = {2019},
abstract = {},
location = {},
doi = {10.1111/rec.12938},
keywords = {}}


@Article{Yenni2019,
author = {Yenni, GM and Christensen, EM and Bledsoe, EK and Supp, SR and Diaz, RM and White, EP and Ernest, SKM},
title = {Developing a modern data workflow for regularly updated data.},
journal = {PLoS Biol},
volume = {17},
number = {1},
pages = {e3000125},
year = {2019},
abstract = {Over the past decade, biology has undergone a data revolution in how researchers collect data and the amount of data being collected. An emerging challenge that has received limited attention in biology is managing, working with, and providing access to data under continual active collection. Regularly updated data present unique challenges in quality assurance and control, data publication, archiving, and reproducibility. We developed a workflow for a long-term ecological study that addresses many of the challenges associated with managing this type of data. We do this by leveraging existing tools to 1) perform quality assurance and control; 2) import, restructure, version, and archive data; 3) rapidly publish new data in ways that ensure appropriate credit to all contributors; and 4) automate most steps in the data pipeline to reduce the time and effort required by researchers. The workflow leverages tools from software development, including version control and continuous integration, to create a modern data management system that automates the pipeline.},
location = {Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, Florida, United States of America. School of Natural Resources and the Environment, University of Florida, Gainesville, Florida, United States of America. Data Analytics Program, Denison University, Granville, Ohio, United States of America. School of Natural Resources and the Environment, University of Florida, Gainesville, Florida, United States of America. Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, Florida, United States of America. Informatics Institute, University of Florida, Gainesville, Florida, United States of America. Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, Florida, United States of America. Biodiversity Institute, University of Florida, Gainesville, Florida, United States of America.},
keywords = {}}


@Article{Conn:2018hd,
author = {Conn, Paul B and Johnson, Devin S and Williams, Perry J and Melin, Sharon R and Hooten, Mevin B},
title = {A guide to Bayesian model checking for ecologists},
journal = {Ecological monographs},
volume = {9},
number = {},
pages = {341–317},
year = {2018},
abstract = {},
location = {},
doi = {10.1002/ecm.1314},
keywords = {Bayesian; Bayesian P value; goodness-of-fit; hierarchical model; model checking; model diagnostics; Model evaluation; posterior checks}}

@Article{Blischak:2016kr,
author = {Blischak, John D and Davenport, Emily R and Wilson, Greg},
title = {A Quick Introduction to Version Control with Git and GitHub},
journal = {PLoS Computational Biology},
volume = {12},
number = {1},
pages = {e1004668–18},
year = {2016},
abstract = {},
location = {},
keywords = {git; GitHub; open data; open science; version control}}


@Article{Simmons:2011iw,
author = {Simmons, Joseph P and Nelson, Leif D and Simonsohn, Uri},
title = {False-Positive Psychology},
journal = {Psychological Science},
volume = {22},
number = {11},
pages = {1359–1366},
year = {2011},
abstract = {In this article, we accomplish two things. First, we show that despite empirical psychologists’ nominal endorsement of a low rate of false-positive findings (≤.05), flexibility in data collection, analysis, and reporting dramatically increases actual false-positive rates. In many cases, a researcher is more likely to falsely find evidence that an effect exists than to correctly find evidence that it does not. We present computer simulations and a pair of actual experiments that demonstrate how unacceptably easy it is to accumulate (and report) statistically significant evidence for a false hypothesis. Second, we suggest a simple, low-cost, and straightforwardly effective disclosure-based solution to this problem. The solution involves six concrete requirements for authors and four guidelines for reviewers, all of which impose a minimal burden on the publication process.},
location = {},
keywords = {disclosure; methodology; publication; Questionable Research Practices; transparency; undisclosed flexibility; researcher degrees of freedom}}


@Article{Seaman:2015gv,
author = {Seaman, Christopher Scott and Weber, Rene},
title = {Undisclosed Flexibility in Computing and Reporting Structural Equation Models in Communication Science},
journal = {Communication Methods and Measures},
volume = {9},
number = {4},
pages = {208–232},
year = {2015},
abstract = {Communication Methods and Measures, 2015. doi:10.1080/19312458.2015.1096329},
location = {},
keywords = {causal modelling; cherry picking; HARKing; Questionable Research Practices; reproducibility; research flexibilities; researcher degrees of freedom; structural equation modelling}}


@Book{Kitzes2018vn,
author = {Kitzes, J and Turek, D and Deniz, F},
title = {The Practice of Reproducible Research: Case Studies and Lessons from the Data-Intensive Sciences.},
volume = {},
pages = {1-319},
editor = {Kitzes, J and Turek, D and Deniz, F},
publisher = {University of California Press},
address = {Oakland, CA},
year = {2018},
abstract = {},
keywords = {}}

@Article{BenBondLamberty:2018by,
author = {Ben, Bond-Lamberty and Smith, A Peyton and Bailey, Vanessa},
title = {Running an open experiment: transparency and reproducibility in soil and ecosystem science},
journal = {Environmental Research Letters},
volume = {11},
number = {8},
pages = {1–7},
year = {2018},
abstract = {Environmental Research Letters, 11(2016) 084004. doi:10.1088/1748-9326/11/8/084004},
location = {},
keywords = {git; GitHub; open data; reproducibility; Reproducible Research; transparency}}


@Article{Fraser:2018cl,
author = {Fraser, Hannah and Parker, Tim and Nakagawa, Shinichi and Barnett, Ashley and Fidler, Fiona},
title = {Questionable research practices in ecology and evolution.},
journal = {PLoS One},
volume = {13},
number = {7},
pages = {e0200303},
year = {2018},
abstract = {We surveyed 807 researchers (494 ecologists and 313 evolutionary biologists) about their use of Questionable Research Practices (QRPs), including cherry picking statistically significant results, p hacking, and hypothesising after the results are known (HARKing). We also asked them to estimate the proportion of their colleagues that use each of these QRPs. Several of the QRPs were prevalent within the ecology and evolution research community. Across the two groups, we found 64% of surveyed researchers reported they had at least once failed to report results because they were not statistically significant (cherry picking); 42% had collected more data after inspecting whether results were statistically significant (a form of p hacking) and 51% had reported an unexpected finding as though it had been hypothesised from the start (HARKing). Such practices have been directly implicated in the low rates of reproducible results uncovered by recent large scale replication studies in psychology and other disciplines. The rates of QRPs found in this study are comparable with the rates seen in psychology, indicating that the reproducibility problems discovered in psychology are also likely to be present in ecology and evolution.},
location = {School of BioSciences, University of Melbourne, Parkville, VIC, Australia.},
keywords = {QRP; questionable research practice; reproducibility}}


@Article{Fidler:2017he,
author = {Fidler, Fiona and Chee, Yung En and Wintle, Brendan A and Burgman, Mark A and McCarthy, Michael A and Gordon, Ascelin},
title = {Metaresearch for Evaluating Reproducibility in Ecology and Evolution},
journal = {BioScience},
volume = {},
number = {},
pages = {biw159–8},
year = {2017},
abstract = {},
location = {},
keywords = {metaresearch; open science; publication bias; reproducibility; transparency}}


@Article{Srivastava2018,
author = {Srivastava, Sanjay},
title = {Sound Inference in Complicated Research: A Multi-Strategy Approach},
journal = {},
volume = {},
number = {},
pages = {},
year = {2018},
abstract = {Researchers are increasingly paying attention to practices that can capitalize on chance. Capitalizing on chance can lead to unreplicable results in the form of false-positive tests, biased estimates, or overfit models. Preregistration of analysis plans, where a researcher anticipates all analysis decisions in advance and makes a plan for each one, has been promoted as one way to make inferences more sound and findings more replicable. Preregistration works by creating decision independence: analytic decisions are the same regardless of the potentially spurious features of the specific dataset being analyzed, instead of being overfit to them. But preregistration can be difficult in practice for some complicated research paradigms, including longitudinal studies, statistical modeling, machine learning, and other large multivariate designs and analyses where key decisions may be difficult to anticipate or make in advance. When simple preregistration is not practical, other strategies that create decision independence can be incorporated into it or used in place of it. This manuscript describes six such strategies: standardization, blind analysis, data partitioning, supporting studies, coordinated analysis, and multiverse analysis. All of them can be used to create adaptive preregistrations, and several can also be used when decisions arise that were not anticipated. Used together, they can form an integrative, multi-strategy approach to drawing sound inferences in a wide range of research.},
location = {},
keywords = {}}


@Article{Raemaekers2017,
author = {Raemaekers, S. and van Deursen, A. and Visser, J.},
title = {Semantic versioning and impact of breaking changes in the Maven repository},
journal = {Journal of Systems and Software},
volume = {129},
number = {},
pages = {140–158},
year = {2017},
abstract = {},
location = {},
keywords = {}}


@Article{Wicherts2016,
author = {Wicherts, JM and Veldkamp, CL and Augusteijn, HE and Bakker, M and van Aert, RC and van Assen, MA},
title = {Degrees of Freedom in Planning, Running, Analyzing, and Reporting Psychological Studies: A Checklist to Avoid p-Hacking.},
journal = {Front Psychol},
volume = {7},
number = {},
pages = {1832},
year = {2016},
abstract = {The designing, collecting, analyzing, and reporting of psychological studies entail many choices that are often arbitrary. The opportunistic use of these so-called researcher degrees of freedom aimed at obtaining statistically significant results is problematic because it enhances the chances of false positive results and may inflate effect size estimates. In this review article, we present an extensive list of 34 degrees of freedom that researchers have in formulating hypotheses, and in designing, running, analyzing, and reporting of psychological research. The list can be used in research methods education, and as a checklist to assess the quality of preregistrations and to determine the potential for bias due to (arbitrary) choices in unregistered studies.},
location = {Methodology and Statistics, Tilburg University Tilburg, Netherlands.},
keywords = {questionable research practice; experimental design; significance testing; p-hacking; bias; significance chasing; research methods education}}


@Article{Powers2018,
author = {Powers, Stephen M. and Hampton, Stephanie E.},
title = {Open science, reproducibility, and transparency in ecology},
journal = {Ecological Applications},
volume = {},
number = {},
pages = {},
year = {2018},
abstract = {Reproducibility is a key tenet of the scientific process that dictates the reliability and generality of results and methods. The complexities of ecological observations and data present novel challenges in satisfying needs for reproducibility, and also transparency. Ecological systems are dynamic and heterogeneous, interacting with numerous factors that sculpt natural history and that investigators cannot completely control. Observations may be highly dependent on spatial and temporal context, making them very difficult to reproduce, but computational reproducibility still can be achieved. Computational reproducibility often refers to the ability to produce equivalent analytical outcomes from the same data set using the same code and software as the original study. When coded workflows are shared, authors and editors provide transparency for readers and allow other researchers to build directly and efficiently on primary work. These qualities may be especially important in ecological applications that have important or controversial implications for science, management, and policy. Expectations for computational reproducibility and transparency are shifting rapidly in the sciences. In this work we highlight many of the unique challenges for ecology along with practical guidelines for reproducibility and transparency, as ecologists continue to participate in the stewardship of critical environmental information and ensure that research methods demonstrate integrity.},
location = {},
keywords = {reproducibility, transparency, open science, data policy, environmental science, ecoinformatics, ecosystem engineering, replicability, repeatability, data science, collaborative tools, workflows}}


@Article{Cruwell2019,
author = {Crüwell, Sophia and Stefan, Angelika M. and Evans, Nathan J.},
title = {Robust Standards in Cognitive Science},
journal = {Computational Brain & Behavior},
volume = {},
number = {},
pages = {},
year = {2019},
abstract = {},
location = {},
keywords = {}}


@Proceedings{Gould:2019ebg,
author = {Gould, E., Fraser, H., Rumpff, L., Fidler, F.},
editor = {},
title = {Questionable Research Practices in non-hypothesis testing research: Ecological models for conservation decision-making},
booktitle = {Questionable Research Practices in non-hypothesis testing research: Ecological models for conservation decision-making},
volume = {},
publisher = {},
address = {},
pages = {},
year = {2019},
abstract = {Recent metaresearch studying the prevalence, types, causes and solutions to Questionable Research Practices (QRPs) has almost exclusively focussed on frequentist hypothesis-testing. However, within Conservation Science, modellers routinely conduct non-hypothesis testing research; building models that generate anticipatory predictions to guide policy and decision makers in managing threatened ecosystems and species. We expand the scope of current QRP work by proposing a conceptual framework for defining and understanding the emergence of QRPs within model-centric research. We surveyed the literature to construct ‘roadmaps’ identifying the type and location of plausible QRPs within the model development process. There are many opportunities for undisclosed researcher degrees of freedom in ecological modelling. While there are direct analogues between NHST and non-NHST research, there are domain and context-specific nuances that influence the emergence of QRPs in model-centric research.},
keywords = {metascience; ecology; applied ecology; modeling}}

@Article{Parker2019,
author = {Parker, T and Fraser, H and Nakagawa, S},
title = {Making conservation science more reliable with preregistration and registered reports.},
journal = {Conserv Biol},
volume = {},
number = {},
pages = {},
year = {2019},
abstract = {},
location = {Biology Department, Whitman College, 345 Boyer Ave., Walla Walla, WA, 99362, U.S.A. School of BioSciences, University of Melbourne, Grattan Street, Parkville, Victoria, 3010, Australia. Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Randwick, New South Wales, 2052, Australia.},
keywords = {}}


@Article{Gould:2020ebg,
author = {Gould, E., Fraser, H., Rumpff, L., Fidler, F.},
title = {Questionable Research Practices in Ecological Modelling},
journal = {},
volume = {},
number = {},
pages = {},
year = {In prep.},
abstract = {},
location = {},
keywords = {}}


@Article{MacEachern2019,
author = {MacEachern, Steven N and Van Zandt, Trisha},
title = {Preregistration of Modeling Exercises May Not Be Useful},
journal = {Comput Brain Behav},
volume = {2},
number = {3-4},
pages = {179–182},
year = {2019},
abstract = {},
location = {},
keywords = {}}


@Article{Pu2019,
author = {Pu, Xiaoying and Zhu, Licheng and Kay, Matthew and Conrad, Frederick},
title = {Designing for preregistration in practice: Multiple norms and purposes},
journal = {},
volume = {},
number = {},
pages = {},
year = {2019},
abstract = {The replication crisis—a failure to replicate foundational studies—has sparked a conversation in psychology, HCI, and beyond about scientific reliability. To address the crisis, researchers increasingly adopt preregistration: the practice of documenting research plans before conducting a study. Done properly, preregistration reduces bias from taking exploratory findings as confirmatory. It is crucial to treat preregistration, often an online form/template, as a user-centered design problem to ensure preregistration achieves its …},
location = {},
keywords = {}}


@Article{Lupia2014,
author = {Lupia, Arthur and Elman, Colin},
title = {Openness in Political Science: Data Access and Research Transparency},
journal = {PS: Political Science & Politics},
volume = {47},
number = {01},
pages = {19–42},
year = {2014},
abstract = {<jats:p>In 2012, the American Political Science Association (APSA) Council adopted new policies guiding data access and research transparency in political science. The policies appear as a revision to APSA’s<jats:italic>Guide to Professional Ethics in Political Science</jats:italic>. The revisions were the product of an extended and broad consultation with a variety of APSA committees and the association’s membership.</jats:p},
location = {},
keywords = {}}

@Article{Schmolke:2010fd,
author = {Schmolke, Amelie et al.},
title = {Ecological models supporting environmental decision making: a strategy for the future},
journal = {Trends in Ecology & Evolution},
volume = {25},
number = {8},
pages = {479–486},
year = {2010},
abstract = {},
location = {},
keywords = {Decision making; Decision support; Ecological modelling; Good modelling practice; Model description; Model development; model documentation; transparency}}

@Proceedings{deVos:2011uk,
author = {de Vos, M G et al.},
editor = {},
title = {Are environmental models transparent and reproducible enough},
booktitle = {Are environmental models transparent and reproducible enough},
volume = {},
publisher = {},
address = {Perth, Australia},
pages = {},
year = {2011},
abstract = {Environmental computer models are considered essential tools in supporting environmental decision making, but their main value is that they allow a better understanding of our complex environment. Environmental models are in fact applications of shared theories on how real-world systems are functioning. Just like the underlying scientific theories they need to be evaluated and discussed among peers. To allow proper assessment of the quality and suitability of environmental models peers should be able to trace their results and insights.},
keywords = {Good modelling practice; Model evaluation; model quality; Peer review; reproducibility; transparency}}

@Article{Alexandrov:2011iv,
author = {Alexandrov, G A et al.},
title = {Technical assessment and evaluation of environmental models and software: Letter to the Editor},
journal = {Environmental Modelling & Software},
volume = {26},
number = {3},
pages = {328–336},
year = {2011},
abstract = {Environmental Modelling and Software, 26 (2011) 328-336. doi:10.1016/j.envsoft.2010.08.004},
location = {},
keywords = {}}

@Article{Feng2019,
author = {Feng, X et al.},
title = {A checklist for maximizing reproducibility of ecological niche models.},
journal = {Nat Ecol Evol},
volume = {3},
number = {10},
pages = {1382–1395},
year = {2019},
abstract = {Reporting specific modelling methods and metadata is essential to the reproducibility of ecological studies, yet guidelines rarely exist regarding what information should be noted. Here, we address this issue for ecological niche modelling or species distribution modelling, a rapidly developing toolset in ecology used across many aspects of biodiversity science. Our quantitative review of the recent literature reveals a general lack of sufficient information to fully reproduce the work. Over two-thirds of the examined studies neglected to report the version or access date of the underlying data, and only half reported model parameters. To address this problem, we propose adopting a checklist to guide studies in reporting at least the minimum information necessary for ecological niche modelling reproducibility, offering a straightforward way to balance efficiency and accuracy. We encourage the ecological niche modelling community, as well as journal reviewers and editors, to utilize and further develop this framework to facilitate and improve the reproducibility of future work. The proposed checklist framework is generalizable to other areas of ecology, especially those utilizing biodiversity data, environmental data and statistical modelling, and could also be adopted by a broader array of disciplines.},
location = {Institute of the Environment, University of Arizona, Tucson, AZ, USA. fengxiao@e-mail.arizona.edu. School of Natural Resources and the Environment, University of Arizona, Tucson, AZ, USA. fengxiao@e-mail.arizona.edu. Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA. Department of Integrative Biology, Oklahoma State University, Stillwater, OK, USA. Biodiversity Institute, University of Kansas, Lawrence, KS, USA. Ecology and Evolutionary Biology, University of Connecticut, Storss, CT, USA. Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, USA.},
keywords = {}}

@Article{Addison:2013wa,
author = {Addison, Prue FE et al.},
title = {Practical solutions for making models indispensable in conservation decision-making},
journal = {Diversity and Distributions},
volume = {19},
number = {5-6},
pages = {490–502},
year = {2013},
abstract = {},
location = {},
keywords = {Communication; Conservation; Modelling; Structured decision-making; Trust; Uncertainty; Papers_flagged}}

@Article{Pavelin2012,
author = {Pavelin, K et al.},
title = {Bioinformatics meets user-centred design: a perspective.},
journal = {PLoS Comput Biol},
volume = {8},
number = {7},
pages = {e1002554},
year = {2012},
abstract = {Designers have a saying that “the joy of an early release lasts but a short time. The bitterness of an unusable system lasts for years.” It is indeed disappointing to discover that your data resources are not being used to their full potential. Not only have you invested your time, effort, and research grant on the project, but you may face costly redesigns if you want to improve the system later. This scenario would be less likely if the product was designed to provide users with exactly what they need, so that it is fit for purpose before its launch. We work at EMBL-European Bioinformatics Institute (EMBL-EBI), and we consult extensively with life science researchers to find out what they need from biological data resources. We have found that although users believe that the bioinformatics community is providing accurate and valuable data, they often find the interfaces to these resources tricky to use and navigate. We believe that if you can find out what your users want even before you create the first mock-up of a system, the final product will provide a better user experience. This would encourage more people to use the resource and they would have greater access to the data, which could ultimately lead to more scientific discoveries. In this paper, we explore the need for a user-centred design (UCD) strategy when designing bioinformatics resources and illustrate this with examples from our work at EMBL-EBI. Our aim is to introduce the reader to how selected UCD techniques may be successfully applied to software design for bioinformatics.},
location = {EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.},
keywords = {}}

@Article{Nosek:2018eg,
author = {Nosek, Brian A et al.},
title = {The preregistration revolution.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {115},
number = {11},
pages = {2600–2606},
year = {2018},
abstract = {Progress in science relies in part on generating hypotheses with existing observations and testing hypotheses with new observations. This distinction between postdiction and prediction is appreciated conceptually but is not respected in practice. Mistaking generation of postdictions with testing of predictions reduces the credibility of research findings. However, ordinary biases in human reasoning, such as hindsight bias, make it hard to avoid this mistake. An effective solution is to define the research questions and analysis plan before observing the research outcomes-a process called preregistration. Preregistration distinguishes analyses and outcomes that result from predictions from those that result from postdictions. A variety of practical strategies are available to make the best possible use of preregistration in circumstances that fall short of the ideal application, such as when the data are preexisting. Services are now available for preregistration across all disciplines, facilitating a rapid increase in the practice. Widespread adoption of preregistration will increase distinctiveness between hypothesis generation and hypothesis testing and will improve the credibility of research findings.},
location = {Center for Open Science, Charlottesville, VA 22903; nosek@virginia.edu.},
keywords = {}}

@Article{Mertens2019,
author = {Mertens, G and Krypotos, AM},
title = {Preregistration of Analyses of Preexisting Data.},
journal = {Psychol Belg},
volume = {59},
number = {1},
pages = {338–352},
year = {2019},
abstract = {The preregistration of a study’s hypotheses, methods, and data-analyses steps is becoming a popular psychological research practice. To date, most of the discussion on study preregistration has focused on the preregistration of studies that include the collection of original data. However, much of the research in psychology relies on the (re-)analysis of preexisting data. Importantly, this type of studies is different from original studies as researchers cannot change major aspects of the study (e.g., experimental manipulations, sample size). Here, we provide arguments as to why it is useful to preregister analyses of preexisting data, discuss practical considerations, consider potential concerns, and introduce a preregistration template tailored for studies focused on the analyses of preexisting data. We argue that the preregistration of hypotheses and data-analyses for analyses of preexisting data is an important step towards more transparent psychological research.},
location = {},
keywords = {}}

@Proceedings{deVos:2011,
author = {de Vos, M G et al.},
editor = {},
title = {Are environmental models transparent and reproducible enough},
booktitle = {Are environmental models transparent and reproducible enough},
volume = {},
publisher = {},
address = {Perth, Australia},
pages = {},
year = {2011},
abstract = {Environmental computer models are considered essential tools in supporting environmental decision making, but their main value is that they allow a better understanding of our complex environment. Environmental models are in fact applications of shared theories on how real-world systems are functioning. Just like the underlying scientific theories they need to be evaluated and discussed among peers. To allow proper assessment of the quality and suitability of environmental models peers should be able to trace their results and insights.},
keywords = {Good modelling practice; Model evaluation; model quality; Peer review; reproducibility; transparency}}


@article{braga2023,
	title = {Not just for programmers: How GitHub can accelerate collaborative and reproducible research in ecology and evolution},
	author = {Braga, Pedro Henrique Pereira and {Hébert}, Katherine and Hudgins, Emma J. and Scott, Eric R. and Edwards, Brandon P. M. and {Sánchez Reyes}, Luna L. and Grainger, Matthew J. and Foroughirad, Vivienne and Hillemann, Friederike and Binley, Allison D. and Brookson, Cole B. and Gaynor, Kaitlyn M. and Shafiei Sabet, Saeed and {Güncan}, Ali and Weierbach, Helen and Gomes, Dylan G. E. and Crystal-Ornelas, Robert},
	year = {2023},
	date = {2023},
	journal = {Methods in Ecology and Evolution},
	pages = {1364--1380},
	volume = {14},
	number = {6},
	doi = {10.1111/2041-210X.14108},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/2041-210X.14108},
	note = {{\_}eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/2041-210X.14108},
	langid = {en}
}

@article{Bryan:2008en,
	title = {Systematic regional planning for multiple objective natural resource management},
	author = {Bryan, Brett A. and Crossman, Neville D.},
	year = {2008},
	month = {09},
	date = {2008-09},
	journal = {Journal of Environmental Management},
	pages = {1175--1189},
	volume = {88},
	number = {4},
	doi = {10.1016/j.jenvman.2007.06.003},
	note = {Citation Key: Bryan:2008en},
	langid = {English}
}

@article{Gelman2013,
	title = {The garden of forking paths: Why multiple comparisons can be a problem, even when there is no {\textquotedblleft}fishing expedition{\textquotedblright} or {\textquotedblleft}p-hacking{\textquotedblright} and the research hypothesis was posited ahead of time},
	author = {Gelman, Andrew and Loken, Eric},
	year = {2013},
	date = {2013},
	journal = {Department of Statistics, Columbia University},
	note = {Citation Key: Gelman2013}
}

@inproceedings{Liu2020,
	title = {Proceedings of the 2020 CHI Conference on Human Factors in Computing Systems},
	author = {Liu, Yang and Althoff, Tim and Heer, Jeffrey},
	year = {2020},
	date = {2020},
	publisher = {ACM},
	doi = {10.1145/3313831.3376533},
	note = {Citation Key: Liu2020}
}

@article{gould,
	title = {A Roadmap of Questionable Research Practices in Ecological Modelling},
	author = {Gould, Elliot and {Fraser, Hannah},  and {Rumpff, Libby},  and {Fidler, Fiona}, }
}

@article{Baldwin2022a,
	title = {Protecting against researcher bias in secondary data analysis: challenges and potential solutions.},
	author = {Baldwin, J. R. and Pingault, J. B. and Schoeler, T. and Sallis, H. M. and {Munafò}, M. R.},
	year = {2022},
	month = {01},
	date = {2022-01},
	journal = {Eur J Epidemiol},
	pages = {1--10},
	volume = {37},
	number = {1},
	doi = {10.1007/s10654-021-00839-0},
	note = {Citation Key: Baldwin2022a}
}

@article{ivimey2023,
	title = {Implementing code review in the scientific workflow: Insights from ecology and evolutionary biology},
	author = {Ivimey, Edward R and Pick, Joel L and Bairos, Kevin R and Culina, Antica and Gould, Elliot and Grainger, Matthew and Marshall, Benjamin M and Moreau, David and Paquet, Matthieu and {Royauté}, {Raphaël} and {Sánchez}, Alfredo and Silva, {Inês} and Windecker, Saras M},
	year = {2023},
	date = {2023},
	journal = {Journal of Evolutionary Biology},
	doi = {10.1111/jeb.14230},
	langid = {en}
}

@article{Liu2008,
	title = {Bayes factors: Prior sensitivity and model generalizability},
	author = {Liu, Charles C. and Aitkin, Murray},
	year = {2008},
	date = {2008},
	journal = {Journal of Mathematical Psychology},
	pages = {362--375},
	volume = {52},
	number = {6},
	doi = {10.1016/j.jmp.2008.03.002},
	note = {Citation Key: Liu2008}
}

@article{Grimm2016,
	title = {Structural realism, emergence, and predictions in next-generation ecological modelling: Synthesis from a special issue},
	author = {Grimm, Volker and Berger, Uta},
	year = {2016},
	date = {2016},
	journal = {Ecological Modelling},
	pages = {177--187},
	volume = {326},
	doi = {10.1016/j.ecolmodel.2016.01.001},
	note = {Citation Key: Grimm2016}
}

@article{Dwork2015,
	title = {The reusable holdout: Preserving validity in adaptive data analysis},
	author = {Dwork, Cynthia and Feldman, Vitaly and Hardt, Moritz and Pitassi, Toniann and Reingold, Omer and Roth, Aaron},
	year = {2015},
	date = {2015},
	journal = {Science},
	pages = {636--638},
	volume = {349},
	number = {6248},
	doi = {10.1126/science.aaa9375},
	note = {Citation Key: Dwork2015},
	langid = {eng}
}

@article{McCarthy2011,
	title = {Designing nature reserves in the face of uncertainty},
	author = {McCarthy, Michael A. and Thompson, Colin J. and Moore, Alana L. and Possingham, Hugh P.},
	year = {2011},
	month = {03},
	date = {2011-03},
	journal = {Ecology Letters},
	pages = {470--475},
	volume = {14},
	number = {5},
	doi = {10.1111/j.1461-0248.2011.01608.x},
	note = {Citation Key: McCarthy:2011ha},
	langid = {English}
}

@book{Gould2026a,
	title = {EcoConsPreReg: A Guide to Adaptive Preregistration for Model-Based Research in Ecology and Conservation},
	author = {Gould, Elliot and Jones, Christopher and Yen, J.D.L. and Fraser, Hannah and Wootton, Henry and Good, Megan and Duncan, David and Rumpff, Libby and Fidler, Fiona},
	year = {2026},
	doi = {10.5281/ZENODO.10807029},
	url = {https://zenodo.org/doi/10.5281/zenodo.10807029},
	note = {DOI: 10.5281/ZENODO.10807029
Citation Key: Gould2026a}
}

@article{Boettiger2022,
	title = {The forecast trap.},
	author = {Boettiger, C.},
	year = {2022},
	month = {05},
	date = {2022-05-30},
	journal = {Ecol Lett},
	doi = {10.1111/ele.14024},
	note = {Citation Key: Boettiger2022},
	langid = {eng}
}

@article{Gould2026,
	title = {A Framework for Questionable Research Practices in Ecological Modelling},
	author = {Gould, Elliot and Fraser, Hannah and Wintle, Bonnie and Rumpff, Libby and Fidler, Fiona},
	doi = {10.32942/X2DQ0K},
	year = {2026},
	publisher = {EcoEvoArXiv}
}

@article{Kapoor2023,
	title = {Leakage and the reproducibility crisis in machine-learning-based science},
	author = {Kapoor, Sayash and Narayanan, Arvind},
	year = {2023},
	month = {09},
	date = {2023-09},
	journal = {Patterns},
	pages = {100804},
	volume = {4},
	number = {9},
	doi = {10.1016/j.patter.2023.100804},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S2666389923001599},
	note = {TLDR: A survey of literature in fields that have adopted ML methods finds 17 fields where leakage has been found, collectively affecting 294 papers and, in some cases, leading to wildly overoptimistic conclusions.},
	langid = {en}
}

@article{Campbell2021,
	title = {The consequences of checking for zero{-}inflation and overdispersion in the analysis of count data},
	author = {Campbell, Harlan},
	editor = {{O'Hara}, Robert B.},
	year = {2021},
	date = {2021},
	journal = {Methods in Ecology and Evolution},
	pages = {665--680},
	volume = {12},
	number = {4},
	doi = {10.1111/2041-210x.13559}
}

@article{Arnqvist2020,
	title = {Mixed Models Offer No Freedom from Degrees of Freedom},
	author = {Arnqvist, {Göran}},
	year = {2020},
	date = {2020},
	journal = {Trends in Ecology & Evolution},
	pages = {329--335},
	volume = {35},
	number = {4},
	doi = {10.1016/j.tree.2019.12.004},
	note = {TLDR: Here, I draw attention to a classic flaw in inferential statistics that has resurfaced in a new flavor as a result of increased reliance on complex linear mixed models - the multifaceted and disturbingly persistent problem of pseudoreplication.}
}