ma_ecology_book.bib

@book{xie_bookdown_2019,
	title = {Bookdown: {Authoring} {Books} and {Technical} {Documents} with {R} {Markdown}},
	url = {https://bookdown.org/yihui/bookdown/.},
	publisher = {CRC Press},
	author = {Xie, Yihui},
	year = {2019}
}

@article{crystal-ornelas_cumulative_2020,
	title = {Cumulative meta-analysis identifies when invasive species impacts on richness stabilize},
	journal = {Ecology},
	author = {Crystal-Ornelas, Robert and Lockwood, Julie L.},
	year = {2020},
	keywords = {⛔ No DOI found}
}

@misc{kossmier_metaviz:_2018,
	title = {metaviz: {Forest} plots, funnel plots, and visual funnel plot inference for meta-analysis},
	author = {Kossmier, Michael and Tran, Ulrich S. and Voracek, Martin},
	year = {2018}
}
@article{bai_meta-analysis_2013,
	title = {A meta-analysis of experimental warming effects on terrestrial nitrogen pools and dynamics},
	volume = {199},
	issn = {0028646X},
	url = {http://doi.wiley.com/10.1111/nph.12252},
	doi = {10/gbc88g},
	abstract = {Global warming may have profound effects on terrestrial ecosystems. However, a comprehensive evaluation of the effects of warming on ecosystem nitrogen (N) pools and dynamics is not available.},
	language = {en},
	number = {2},
	urldate = {2020-04-10},
	journal = {New Phytologist},
	author = {Bai, Edith and Li, Shanlong and Xu, Wenhua and Li, Wei and Dai, Weiwei and Jiang, Ping},
	month = jul,
	year = {2013},
	pages = {441--451},
	file = {Bai et al. - 2013 - A meta-analysis of experimental warming effects on.pdf:/Users/robcrystalornelas/Zotero/storage/CN39DT8I/Bai et al. - 2013 - A meta-analysis of experimental warming effects on.pdf:application/pdf}
}
@article{mattingly_disconnects_2020,
	title = {Disconnects between {Communicated} {Impact} and {Ecological} {Impact} of {Biological} {Invasions}},
	volume = {70},
	issn = {0006-3568, 1525-3244},
	url = {https://academic.oup.com/bioscience/article/70/3/252/5716739},
	doi = {10/ggpcz2},
	language = {en},
	number = {3},
	urldate = {2020-03-20},
	journal = {BioScience},
	author = {Mattingly, Kali Z and Pelletier, Tara A and Lanterman, Jessie and Frevola, Danielle and Stucke, Benjamin and Kinney, Kaitlin and Schwartz, Ross and Spacht, Drew and Dixon, Graham and Hovick, Stephen M},
	month = mar,
	year = {2020},
	pages = {252--263},
	file = {Mattingly et al. - 2020 - Disconnects between Communicated Impact and Ecolog.pdf:/Users/robcrystalornelas/Zotero/storage/L4XM9Y2X/Mattingly et al. - 2020 - Disconnects between Communicated Impact and Ecolog.pdf:application/pdf}
}

@book{lockwood_invasion_2013,
	title = {Invasion ecology},
	isbn = {1-118-57082-0},
	publisher = {John Wiley \& Sons},
	author = {Lockwood, Julie L. and Hoopes, Martha F. and Marchetti, Michael P.},
	year = {2013}
}

@book{simberloff_encyclopedia_2011,
	title = {Encyclopedia of biological invasions},
	isbn = {0-520-26421-5},
	publisher = {Univ of California Press},
	author = {Simberloff, Daniel and Rejmánek, Marcel},
	year = {2011}
}

@book{koricheva_handbook_2013,
	title = {Handbook of meta-analysis in ecology and evolution},
	isbn = {1-4008-4618-8},
	publisher = {Princeton University Press},
	author = {Koricheva, Julia and Gurevitch, Jessica and Mengersen, Kerrie},
	year = {2013},
	note = {r},
	keywords = {read}
}

@article{thapa_cover_2018,
	title = {Cover crops reduce nitrate leaching in agroecosystems: {A} global meta-analysis},
	volume = {47},
	issn = {0047-2425},
	shorttitle = {Cover {Crops} {Reduce} {Nitrate} {Leaching} in {Agroecosystems}},
	url = {https://dl.sciencesocieties.org/publications/jeq/abstracts/47/6/1400},
	doi = {10.2134/jeq2018.03.0107},
	language = {en},
	number = {6},
	urldate = {2019-12-10},
	journal = {Journal of Environment Quality},
	author = {Thapa, Resham and Mirsky, Steven B. and Tully, Katherine L.},
	year = {2018},
	pages = {1400},
	file = {1400-supplement1.pdf:/Users/robcrystalornelas/Zotero/storage/PDFFAR84/1400-supplement1.pdf:application/pdf;Thapa et al. - 2018 - Cover Crops Reduce Nitrate Leaching in Agroecosyst.pdf:/Users/robcrystalornelas/Zotero/storage/Q6PY82SX/Thapa et al. - 2018 - Cover Crops Reduce Nitrate Leaching in Agroecosyst.pdf:application/pdf}

}
@article{thapa_biomass_2018,
	title = {Biomass {Production} and {Nitrogen} {Accumulation} by {Hairy} {Vetch}–{Cereal} {Rye} {Mixtures}: {A} {Meta}-{Analysis}},
	volume = {110},
	issn = {0002-1962},
	shorttitle = {Biomass {Production} and {Nitrogen} {Accumulation} by {Hairy} {Vetch}–{Cereal} {Rye} {Mixtures}},
	url = {https://dl.sciencesocieties.org/publications/aj/abstracts/110/4/1197},
	doi = {10.2134/agronj2017.09.0544},
	language = {en},
	number = {4},
	urldate = {2019-12-10},
	journal = {Agronomy Journal},
	author = {Thapa, Resham and Poffenbarger, Hanna and Tully, Katherine L. and Ackroyd, Victoria J. and Kramer, Matt and Mirsky, Steven B.},
	year = {2018},
	pages = {1197},
	file = {Thapa et al. - 2018 - Biomass Production and Nitrogen Accumulation by Ha.pdf:/Users/robcrystalornelas/Zotero/storage/NHGTVFUC/Thapa et al. - 2018 - Biomass Production and Nitrogen Accumulation by Ha.pdf:application/pdf}
}

@book{harrer_doing_2019,
	title = {Doing {Meta}-{Analysis} in {R}},
	url = {https://bookdown.org/MathiasHarrer/Doing_Meta_Analysis_in_R/},
	language = {en},
	author = {Harrer, Mathias and Cuijpers, P and Furukawa, T.A. and Ebert, D.D.},
	year = {2019},
	file = {Harrer - Doing Meta-Analysis in R.pdf:/Users/robcrystalornelas/Zotero/storage/78FX7IIP/Harrer - Doing Meta-Analysis in R.pdf:application/pdf}
}

@book{schwarzer_meta-analysis_2015,
	title = {Meta-analysis with {R}},
	isbn = {3-319-21415-2},
	publisher = {Springer},
	author = {Schwarzer, Guido and Carpenter, James R. and Rücker, Gerta},
	year = {2015},
	note = {r},
	keywords = {read}
}

@book{gough_introduction_2012,
	address = {London ; Thousand Oaks, Calif},
	title = {An introduction to systematic reviews},
	isbn = {978-1-84920-180-3 978-1-84920-181-0},
	language = {en},
	publisher = {SAGE},
	editor = {Gough, David and Oliver, Sandy and Thomas, James},
	year = {2012},
	note = {OCLC: ocn785989104},
	keywords = {Decision making, Research},
	file = {Gough et al. - 2012 - An introduction to systematic reviews.pdf:/Users/robcrystalornelas/Zotero/storage/5YR8M4EV/Gough et al. - 2012 - An introduction to systematic reviews.pdf:application/pdf}
}

@article{crystal-ornelas_known_2020,
	title = {The ‘known unknowns’ of invasive species impact measurement},
	volume = {22},
	issn = {1387-3547, 1573-1464},
	url = {http://link.springer.com/10.1007/s10530-020-02200-0},
	doi = {10.1007/s10530-020-02200-0},
	language = {en},
	number = {4},
	urldate = {2020-01-22},
	journal = {Biological Invasions},
	author = {Crystal-Ornelas, Robert and Lockwood, Julie L.},
	year = {2020},
	pages = {1513--1525},
	file = {Crystal-Ornelas and Lockwood - 2020 - The ‘known unknowns’ of invasive species impact me.pdf:/Users/robcrystalornelas/Zotero/storage/ENGKK5HU/Crystal-Ornelas and Lockwood - 2020 - The ‘known unknowns’ of invasive species impact me.pdf:application/pdf}
}


@article{Crystal-Ornelas2021-hs,
  title     = "Meta-analysis shows that overabundant deer (Cervidae)
               populations consistently decrease average population abundance
               and species richness of forest birds",
  author    = "Crystal-Ornelas, Robert and Brown, Jeffrey A and Valentin,
               Rafael E and Beardsley, Caroline and Lockwood, Julie L",
  abstract  = "Abstract. Local-scale studies have shown that an overabundance
               of Cervidae species (deer, elk, moose) impacts forest bird
               communities. Through meta-analysis, we",
  journal   = "Ornithological Applications",
  publisher = "Oxford University Press",
  month     =  sep,
  year      =  2021,
  language  = "en"
}


@article{wang_wei_citizen_2016,
	title = {Citizen science and the urban ecology of birds and butterflies - {A} systematic review},
	volume = {11},
	issn = {1932-6203 (Electronic) 1932-6203 (Linking)},
	doi = {10/gbnb34},
	number = {6},
	journal = {PLoS ONE},
	author = {Wang Wei, J. and Lee, B. P. and Bing Wen, L.},
	year = {2016},
	keywords = {*Birds/classification, *Butterflies/classification, *Cities/epidemiology, *Ecology, *Science/methods/trends, *Volunteers, Animals, Data Collection/*methods, Humans, Knowledge, Research/*manpower/organization \& administration, Urban Population/statistics \& numerical data},
	pages = {e0156425}
}

@article{moher_preferred_2009,
	title = {Preferred reporting items for systematic reviews and meta-analyses: the {PRISMA} statement},
	volume = {6},
	issn = {1549-1676},
	doi = {10/bq3jpc},
	number = {7},
	journal = {PLoS Medicine},
	author = {Moher, David and Liberati, Alessandro and Tetzlaff, Jennifer and Altman, Douglas G. and Prisma Group},
	year = {2009},
	pages = {e1000097}
}


@article{hedges_distribution_1981,
	title = {Distribution theory for {Glass}'s estimator of effect size and related estimators.},
	volume = {6},
	language = {en},
	number = {2},
	journal = {Journal of Educational Statistics},
	author = {Hedges, Larry V},
	year = {1981},
	keywords = {⛔ No DOI found},
	pages = {107--128},
	file = {Hedges - Journal oi Educational Statistic SummoA, 1981, Vo.pdf:/Users/robcrystalornelas/Zotero/storage/CHHNISXB/Hedges - Journal oi Educational Statistic SummoA, 1981, Vo.pdf:application/pdf}
}
@article{huang_evaluation_2006,
	title = {Evaluation of {PICO} as a knowledge representation for clinical questions},
	volume = {2006},
	issn = {1942-597X},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1839740/},
	abstract = {The paradigm of evidence-based medicine (EBM) recommends that physicians formulate clinical questions in terms of the problem/population, intervention, comparison, and outcome. Together, these elements comprise a PICO frame. Although this framework was developed to facilitate the formulation of clinical queries, the ability of PICO structures to represent physicians’ information needs has not been empirically investigated. This paper evaluates the adequacy and suitability of PICO frames as a knowledge representation by analyzing 59 real-world primary-care clinical questions. We discovered that only two questions in our corpus contain all four PICO elements, and that 37\% of questions contain both intervention and outcome. Our study reveals prevalent structural patterns for the four types of clinical questions: therapy, diagnosis, prognosis, and etiology. We found that the PICO framework is primarily centered on therapy questions, and is less suitable for representing other types of clinical information needs. Challenges in mapping natural language questions into PICO structures are also discussed. Although we point out limitations of the PICO framework, our work as a whole reaffirms its value as a tool to assist physicians practicing EBM.},
	urldate = {2018-08-28},
	journal = {AMIA Annual Symposium Proceedings},
	author = {Huang, Xiaoli and Lin, Jimmy and Demner-Fushman, Dina},
	year = {2006},
	pmid = {17238363},
	pmcid = {PMC1839740},
	pages = {359--363}
}

@article{iannone_diagrammer_2018,
	title = {{DiagrammeR}: {Graph}/network visualization},
	volume = {1},
	number = {0},
	journal = {R package},
	author = {Iannone, R.},
	year = {2018},
	keywords = {⛔ No DOI found}
}

@book{hedges_statistical_1985,
	address = {Orlando, FL},
	title = {Statistical {Method} for {Meta}-analysis},
	publisher = {Academic Press},
	author = {Hedges, Larry V. and Olkin, I},
	year = {1985}
}

@article{zavorka_negative_2018,
	title = {The negative ecological impacts of a globally introduced species decrease with time since introduction},
	volume = {24},
	issn = {13541013},
	url = {http://doi.wiley.com/10.1111/gcb.14323},
	doi = {10.1111/gcb.14323},
	language = {en},
	number = {9},
	urldate = {2019-01-14},
	journal = {Global Change Biology},
	author = {Závorka, Libor and Buoro, Mathieu and Cucherousset, Julien},
	month = sep,
	year = {2018},
	keywords = {read},
	pages = {4428--4437}
}
@article{ellis_surface-active_2000,
	title = {Surface-active arthropod communities in native and exotic riparian vegetation in the middle {Rio} {Grande} {Valley}, {New} {Mexico}},
	volume = {45},
	issn = {0038-4909},
	doi = {10.2307/3672594},
	number = {4},
	journal = {Southwestern Naturalist},
	author = {Ellis, L. M. and Molles, M. C. and Crawford, C. S. and Heinzelmann, F.},
	month = dec,
	year = {2000},
	pages = {456--471},
	annote = {Ellis, LM Molles, MC Crawford, CS Heinzelmann, F},
	annote = {The following values have no corresponding Zotero field:accession-num: WOS:000166555500006},
	file = {36026-Ellis-2000:/Users/robcrystalornelas/Zotero/storage/3KYCRDQR/36026-Ellis-2000.pdf:application/pdf}
}

@article{rollin_impacts_2019,
	title = {Impacts of honeybee density on crop yield: {A} meta-analysis},
	issn = {00218901},
	shorttitle = {Impacts of honeybee density on crop yield},
	url = {http://doi.wiley.com/10.1111/1365-2664.13355},
	doi = {10.1111/1365-2664.13355},
	language = {en},
	urldate = {2019-02-04},
	journal = {Journal of Applied Ecology},
	author = {Rollin, Orianne and Garibaldi, Lucas A.},
	month = feb,
	year = {2019},
	file = {Rollin and Garibaldi - 2019 - Impacts of honeybee density on crop yield A meta-.pdf:/Users/robcrystalornelas/Zotero/storage/J3KKPK7D/Rollin and Garibaldi - 2019 - Impacts of honeybee density on crop yield A meta-.pdf:application/pdf}
}

@article{doherty_reptile_2020,
	title = {Reptile responses to anthropogenic habitat modification: {A} global meta-analysis: {Reptile} responses to anthropogenic habitat modification: {A} global meta-analysis},
	issn = {1466822X},
	shorttitle = {Reptile responses to anthropogenic habitat modification},
	url = {http://doi.wiley.com/10.1111/geb.13091},
	doi = {10/ggrbd9},
	abstract = {Aim: The aim was to determine how reptile populations respond to anthropogenic habitat modification and determine whether species traits and environmental factors influence such responses.},
	language = {en},
	urldate = {2020-04-07},
	journal = {Global Ecology and Biogeography},
	author = {Doherty, Tim S. and Balouch, Sara and Bell, Kristian and Burns, Thomas J. and Feldman, Anat and Fist, Charles and Garvey, Timothy F. and Jessop, Tim S. and Meiri, Shai and Driscoll, Don A.},
	editor = {McGill, Brian},
	month = mar,
	year = {2020},
	file = {Doherty et al. - 2020 - Reptile responses to anthropogenic habitat modific.pdf:/Users/robcrystalornelas/Zotero/storage/4U8ADYAQ/Doherty et al. - 2020 - Reptile responses to anthropogenic habitat modific.pdf:application/pdf}
}

@article{blakey_importance_2018,
	title = {Importance of wetlands to bats on a dry continent: a review and meta-analysis},
	abstract = {Australia has diverse landscapes ranging from wet tropical regions in the North to temperate regions in the South and a vast arid interior. This variety has given rise to not only a speciose bat fauna, but also a variety of wetland ecosystems. The relationship between bats and wetlands is influenced by a range of environmental gradients including: aridity and climate variability, hydrological, structural, productivity and salinity. However, little is known about how these gradients influence bats in Australian wetland systems. Our aim was to determine whether wetlands were important for Australia’s bat communities, identify the environmental gradients influencing this importance, and review the threats to wetland bat communities combining a review and meta-analysis. We reviewed the literature on bats within wetland ecosystems in six ecoregions (arid, semi-arid floodplain, temperate, tropics, estuarine/saline and urban) in Australia. We used a meta-analysis to estimate relative wetland importance across ecoregions by calculating the effect size of the difference in bat activity between 43 paired wet and dry habitats. Bats were significantly more active in wet than surrounding dry habitats in arid and semi-arid floodplain. Urban wetlands also hosted greater bat activity than surrounding dry areas in 4 out of 7 sites. Wetlands were generally less important for bats in warm, wet tropical areas, and more important for bats in dry landscapes where landscape woody cover and productivity were low. Relative to dry areas within each region assessed, wetlands were most important for bats in semi-arid floodplain and urban regions. These regions are also under greatest threats from vegetation clearing, modification of flow regimes, development pressures, pollution and climate change.},
	language = {en},
	journal = {Hystrix},
	author = {Blakey, R V and Law, B S and Straka, T M and Kingsford, R T and Milne, D J},
	year = {2018},
	keywords = {read},
	pages = {13},
	annote = {compared bat activity across 43 paired plots of habitat. In more urban and arid areas, wetlands were important for increasing bat activity (blakey et al., 2018)Used Mean, SD and N to compare. (blakey et al., 2018)13 studies total. (blakey et al., 2018)The authors used Log of the response ratio to compare mean of wet and dry sites. (blakey et al., 2018)},
	file = {Blakey et al. - 2018 - Importance of wetlands to bats on a dry continent.pdf:/Users/robcrystalornelas/Zotero/storage/99MPULAR/Blakey et al. - 2018 - Importance of wetlands to bats on a dry continent.pdf:application/pdf}
}

@ARTICLE{Murphy2014-nt,
  title    = "A meta-analysis of declines in local species richness from human
              disturbances",
  author   = "Murphy, G E and Romanuk, T N",
  abstract = "There is high uncertainty surrounding the magnitude of current
              and future biodiversity loss that is occurring due to human
              disturbances. Here, we present a global meta-analysis of
              experimental and observational studies that report 327 measures
              of change in species richness between disturbed and undisturbed
              habitats across both terrestrial and aquatic biomes. On average,
              human-mediated disturbances lead to an 18.3\% decline in species
              richness. Declines in species richness were highest for
              endotherms (33.2\%), followed by producers (25.1\%), and
              ectotherms (10.5\%). Land-use change and species invasions had
              the largest impact on species richness resulting in a 24.8\% and
              23.7\% decline, respectively, followed by habitat loss (14\%),
              nutrient addition (8.2\%), and increases in temperature (3.6\%).
              Across all disturbances, declines in species richness were
              greater for terrestrial biomes (22.4\%) than aquatic biomes
              (5.9\%). In the tropics, habitat loss and land-use change had the
              largest impact on species richness, whereas in the boreal forest
              and Northern temperate forests, species invasions had the largest
              impact on species richness. Along with revealing trends in
              changes in species richness for different disturbances, biomes,
              and taxa, our results also identify critical knowledge gaps for
              predicting the effects of human disturbance on Earth's biomes.",
  journal  = "Ecol. Evol.",
  volume   =  4,
  number   =  1,
  pages    = "91--103",
  month    =  jan,
  year     =  2014
}


@ARTICLE{Cameron2016-yj,
  title    = "Global meta-analysis of the impacts of terrestrial invertebrate
              invaders on species, communities and ecosystems",
  author   = "Cameron, E K and Vil{\`a}, M and Cabeza, M",
  abstract = "Aim Terrestrial invertebrates comprise a large proportion of
              alien species world-wide, yet a quantitative global synthesis of
              their effects on native species and ecosystems has not been
              explored. We conducted a meta-analysis to examine the ecological
              impacts of terrestrial invertebrate invaders and to test how
              impacts are modulated by the invader's trophic position, habitat
              attributes (i.e. insularity and disturbance) and the study
              methodology (observational versus experimental). LocationGlobal.
              MethodsWe investigated the effects of terrestrial invertebrate
              invaders on populations, communities and ecosystems by conducting
              a random effects meta-analysis using 112 articles reporting data
              from 710 field and laboratory studies. The analysis included 16
              insect, 11 earthworm, 7 slug and 1 nematode invaders. Results On
              average, across invaders, the presence of invaders reduced plant
              fitness (52\%), animal diversity (33\%) and animal abundance
              (29\%). Leaf litter decomposition was 41\% higher in the presence
              of invaders, while other ecosystem-level variables such as
              nutrient cycling were not affected in a consistent direction.
              Invasive predators and detritivores decreased animal abundance,
              whereas herbivores and omnivores had limited impacts. Single
              invaders increased soil nitrogen pools while multiple species did
              not. Insularity and disturbance did not affect the magnitude of
              the impacts significantly, mainly because there was a large
              variation among studies. Main conclusionsOverall, our study
              indicates that terrestrial invertebrate invaders have significant
              consistent effects on populations, communities and ecosystems,
              with islands and disturbed sites not being more prone to impacts.
              However, effects vary considerably depending on the type of
              impact being examined and the trophic position of the invader.
              There is no evidence that invaders cause larger impacts when
              multiple species of invaders, rather than single invaders, are
              involved.",
  journal  = "Glob. Ecol. Biogeogr.",
  volume   =  25,
  number   =  5,
  pages    = "596--606",
  month    =  may,
  year     =  2016,
  language = "English"
}


@ARTICLE{Crystal-Ornelas2021-sg,
  title    = "Soil organic carbon is affected by organic amendments,
              conservation tillage, and cover cropping in organic farming
              systems: A meta-analysis",
  author   = "Crystal-Ornelas, Robert and Thapa, Resham and Tully, Katherine L",
  abstract = "Meta-analysis is often used to compare how soil health differs
              between organic and conventional farming systems. However, the
              burgeoning primary literature on organic farming now allows
              direct evaluation of the best management practices (BMPs) within
              organic farming systems on soil health improvements. Therefore,
              the main objective of this meta-analysis was to investigate the
              effect of BMPs, such as organic amendments, conservation tillage,
              and cover cropping, on soil health within organic farming
              systems. We focused on two principal soil health metrics: soil
              organic carbon (SOC) and microbial biomass carbon (MBC)
              concentrations. On average, adoption of BMPs increased
              depth-weighted SOC and MBC concentrations by 18 and 30 \%,
              respectively, relative to organically-managed control groups.
              Among BMPs, organic amendments and conservation tillage practices
              showed net positive effect on soil health with 24 and 14 \%
              increase in depth-weighted SOC concentrations, respectively.
              Although cover cropping did not have an overall influence on SOC
              concentrations, we found a temporal trend such that cover
              cropping significantly increased SOC concentrations after 5 years
              of its adoption. This indicates that the soil health benefits
              from BMPs accrue over time and highlights the need of long-term
              adoptability of BMPs to achieve agricultural sustainability.
              Future primary articles that focus on under-researched cropping
              practices in organic systems (e.g., crop rotation length and
              diversity, biochar addition) and the additive effects of multiple
              BMPs on soil health, will add to the synthesizable evidence base.
              Therefore, this meta-analysis confirms the soil health benefits
              of adopting BMPs within organic farming systems, identifies
              critical knowledge gaps, and provides directions for future
              organic farming research.",
  journal  = "Agric. Ecosyst. Environ.",
  volume   =  312,
  pages    = "107356",
  month    =  jun,
  year     =  2021,
  keywords = "Soil health; Soil organic carbon; Microbial biomass carbon;
              Organic amendments; Conservation tillage; Cover crops; Organic
              farming"
}


@ARTICLE{Nakagawa2017-hz,
  title    = "Meta-evaluation of meta-analysis: ten appraisal questions for
              biologists",
  author   = "Nakagawa, S and Noble, D W and Senior, A M and Lagisz, M",
  abstract = "Meta-analysis is a statistical procedure for analyzing the
              combined data from different studies, and can be a major source
              of concise up-to-date information. The overall conclusions of a
              meta-analysis, however, depend heavily on the quality of the
              meta-analytic process, and an appropriate evaluation of the
              quality of meta-analysis (meta-evaluation) can be challenging. We
              outline ten questions biologists can ask to critically appraise a
              meta-analysis. These questions could also act as simple and
              accessible guidelines for the authors of meta-analyses. We focus
              on meta-analyses using non-human species, which we term
              'biological' meta-analysis. Our ten questions are aimed at
              enabling a biologist to evaluate whether a biological
              meta-analysis embodies 'mega-enlightenment', a 'mega-mistake', or
              something in between.",
  journal  = "BMC Biol.",
  volume   =  15,
  number   =  1,
  pages    = "18",
  month    =  mar,
  year     =  2017
}


@ARTICLE{Nakagawa2012-lc,
  title    = "Methodological issues and advances in biological meta-analysis",
  author   = "Nakagawa, Shinichi and Santos, Eduardo S A",
  abstract = "Meta-analysis has changed the way researchers conduct literature
              reviews not only in medical and social sciences but also in
              biological sciences. Meta-analysis in biological sciences,
              especially in ecology and evolution (which we refer to as
              `biological' meta-analysis) faces somewhat different
              methodological problems from its counterparts in medical and
              social sciences, where meta-analytic techniques were originally
              developed. The main reason for such differences is that
              biological meta-analysis often integrates complex data composed
              of multiple strata with, for example, different measurements and
              a variety of species. Here, we review methodological issues and
              advancements in biological meta-analysis, focusing on three
              topics: (1) non-independence arising from multiple effect sizes
              obtained in single studies and from phylogenetic relatedness, (2)
              detecting and accounting for heterogeneity, and (3) identifying
              publication bias and measuring its impact. We show how the
              marriage between mixed-effects (hierarchical/multilevel) models
              and phylogenetic comparative methods has resolved most of the
              issues under discussion. Furthermore, we introduce the concept of
              across-study and within-study metaanalysis, and propose how the
              use of within-study meta-analysis can improve many empirical
              studies typical of ecology and evolution.",
  journal  = "Evol. Ecol.",
  volume   =  26,
  number   =  5,
  pages    = "1253--1274",
  year     =  2012,
  language = "en"
}


@ARTICLE{Salerno2021-oc,
  title    = "Microplastics and the functional traits of fishes: A global
              meta-analysis",
  author   = "Salerno, Martina and Berlino, Manuel and Mangano, M Cristina and
              Sar{\`a}, Gianluca",
  abstract = "Over the years, concern about the effects of microplastics has
              grown. Here, we answered the main question ``What are the impacts
              of microplastics on the functional traits of fish species?''
              through a meta-analysis. The general impact of microplastic
              exposure on the functional traits of fishes and specifically on
              eight variables, namely, behaviour, development, fecundity,
              feeding, growth, health, hatching and survival was explored.
              Subgroup analyses were performed to detect correlations between
              the impact of microplastics and the following factors: species,
              life stage, habitat, water column habitat, day of exposure to
              microplastics and microplastic size, type and shape. A
              meta-regression analysis allowed understanding the correlation
              between the impact of microplastics and the size of organisms.
              Generally, microplastics have a negative effect on the functional
              traits of fishes. Feeding and behaviour, followed by growth
              showed the greatest impact. Among the subgroup analysis, four of
              the eight variables considered showed a significant difference
              between groups: species, life stage, microplastic shape and days
              of exposure to microplastics. Depending on their life stage,
              organisms may be more sensitive to microplastic pollution.
              Changes in growth rates, development of early life stage and
              behavioural patterns in fishes may have a negative effect on the
              structure and functions of aquatic ecosystem in the long term and
              consequently affect the ability of aquatic ecosystems to provide
              ecosystem services and sustain human communities.",
  journal  = "Glob. Chang. Biol.",
  month    =  feb,
  year     =  2021,
  keywords = "effects size; fishes; functional traits; meta-analysis;
              microplastics",
  language = "en"
}


@ARTICLE{Sohn2016-xe,
  title    = "Potential of forest thinning to mitigate drought stress: A
              meta-analysis",
  author   = "Sohn, Julia A and Saha, Somidh and Bauhus, J{\"u}rgen",
  abstract = "Increasing frequency of extremely dry and hot summers in some
              regions emphasise the need for silvicultural approaches to
              increase the drought tolerance of existing forests in the short
              term, before long-term adaptation through species changes may be
              possible. The aim of this meta-analysis was to assess the
              potential of thinning for improving tree performance during and
              after drought. We used results from 23 experiments that employed
              different thinning intensities including an unthinned control and
              focused on the response variables: radial growth, carbon- and
              oxygen-isotopes in tree-rings and pre-dawn leaf-water potential.
              We found that thinning effects on the growth response to drought
              differed between broadleaves and conifers, although these
              findings are based on few studies only in broadleaved forests.
              Thinning helped to mitigate growth reductions during drought in
              broadleaves, most likely via increases of soil water
              availability. In contrast, in conifers, comparable
              drought-related growth reductions and increases of water-use
              efficiency were observed in all treatments but thinning improved
              the post-drought recovery and resilience of radial growth.
              Results of meta-regression analysis indicate that benefits of
              both moderate and heavy thinning for growth performance following
              drought (recovery and resilience) decrease with time since the
              last intervention. Further, growth resistance during drought
              became smaller with stand age while the rate of growth recovery
              following drought increased over time irrespective of treatment.
              Heavy but not moderate thinning helped to avoid an age-related
              decline in medium-term growth resilience to drought. For both
              closed and very open stands, growth performance during drought
              improved with increasing site aridity but for the same stands
              growth recovery and resilience following drought was reduced with
              increasing site aridity. This synthesis of experiments from a
              wide geographical range has demonstrated that thinning, in
              particular heavy thinning, is a suitable approach to improve the
              growth response of remaining trees to drought in both conifers
              and broadleaves but the underlying processes differ and need to
              be considered.",
  journal  = "For. Ecol. Manage.",
  volume   =  380,
  pages    = "261--273",
  month    =  nov,
  year     =  2016,
  keywords = "Stand density; Water stress; Radial growth; Stable carbon and
              oxygen isotopes; Water potential; Resilience"
}


@ARTICLE{Ferreira2016-ap,
  title    = "A meta-analysis on the effects of changes in the composition of
              native forests on litter decomposition in streams",
  author   = "Ferreira, V and Koricheva, J and Pozo, J and Graca, M A S",
  abstract = "Native forest replacement by plantations and invasions by exotic
              plant species are occurring worldwide. We conducted a
              meta-analysis of studies reporting the effects of these forest
              changes on litter decomposition in streams. Overall, forest
              change significantly inhibited litter decomposition rate by ca
              18\%. However, only the replacement of native forests by
              deciduous broadleaf or eucalyptus (Eucalyptus globulus)
              plantations resulted in significant inhibition of litter
              decomposition (26\% and 22\%, respectively) whereas conifer
              plantations or the invasion by exotic species did not
              significantly affect litter decomposition. The replacement of
              native forests by eucalyptus plantations was the most common type
              of forest change in our database. The effect of eucalyptus
              plantations on litter decomposition was significant when they
              were present simultaneously at the catchment and riparian scales
              and when native litter input was replaced by eucalyptus litter
              input in a manipulative experiment at the stream reach level.
              This suggests that a strong effect of eucalyptus plantations on
              ecosystem functioning is mediated by changes on litter inputs to
              streams. Eucalyptus plantations significantly inhibited the
              decomposition of high quality litter and total leaf litter
              decomposition but not the decomposition of wood and low quality
              leaves, or microbial-driven leaf litter decomposition. This
              indicates that eucalyptus plantations inhibit (likely through
              changes in litter inputs) litter decomposition by affecting
              detritivores. Eucalyptus plantations may thus have stronger
              negative effects on decomposition rates in streams receiving high
              quality litter and where detritivores are abundant. The presence
              of native tree species in the riparian area may mitigate the
              negative effects of eucalyptus plantations on stream processes.
              The inhibitory effect of deciduous broadleaf plantations on
              litter decomposition was likely due to beech (Fagus sylvatica)
              being used in the majority of the plantations, and beech litter
              is of low quality for detritivores and decomposers. The lack of
              significant effects of conifer plantations and invasions might be
              due to contrasting effects of the different conifer or invasive
              species on decomposers. This meta-analysis also identified
              several research gaps that may guide future studies on the effect
              of forest change on stream functioning. (C) 2016 Elsevier B.V.
              All rights reserved.",
  journal  = "For. Ecol. Manage.",
  volume   =  364,
  pages    = "27--38",
  month    =  mar,
  year     =  2016
}


@ARTICLE{Blouin2019-xu,
  title    = "Vermicompost significantly affects plant growth. A meta-analysis",
  author   = "Blouin, Manuel and Barrere, Julien and Meyer, Nicolas and
              Lartigue, Sil{\`e}ne and Barot, S{\'e}bastien and Mathieu,
              J{\'e}r{\^o}me",
  abstract = "Food production and waste management are two increasing issues
              ensuing from the growing world population. Recycling organic
              residues into amendment for food production seems to appear as an
              opportunity to partially solve this double challenge.
              Vermicomposting is a process whereby earthworms transform organic
              residues into compost that can be used as a substrate for plant
              growth. Many studies have evaluated the effect of vermicompost on
              plant growth, but a quantitative summary of these studies is
              still missing. This is the first meta-analysis providing a
              quantitative summary of the effect size of vermicompost on plant
              growth. We found that vermicompost brought about average
              increases of 26\% in commercial yield, 13\% in total biomass,
              78\% in shoot biomass, and 57\% in root biomass. The positive
              effect of vermicompost on plant growth reached a maximum when
              vermicompost represented 30 to 50\% of the soil volume. The best
              original material to be used for vermicompost production was
              cattle manure. The effect was stronger when no fertilizer was
              added, and lower when the standard Metro-Mix 360 substratum
              recommended by some authors was used as a growing medium in
              greenhouse or climatic chambers. Herbs (especially Cucurbitaceae
              and Asteraceae) and legumes exhibited the largest biomass
              increase in the presence of vermicompost. These results are
              discussed through an analysis of potential publication biases
              showing an over-representation of studies with a high effect
              size. We finally recommend authors of primary research to provide
              a minimum set of statistical parameters, output variables, and
              experimental condition parameters to make it easier to include
              their work in meta-analyses. Overall, our study provides
              synthetic information on the beneficial effects of vermicompost
              for plant growth, which could help bring waste management and
              agriculture together towards a society with a more circular
              economy.",
  journal  = "Agron. Sustain. Dev.",
  volume   =  39,
  number   =  4,
  pages    = "34",
  month    =  aug,
  year     =  2019,
  keywords = "read"
}


@ARTICLE{Vila2011-tl,
  title    = "Ecological impacts of invasive alien plants: A meta-analysis of
              their effects on species, communities and ecosystems",
  author   = "Vil{\`a}, M and Espinar, J L and Hejda, M and Hulme, P E and
              Jarosik, V and Maron, J L and Pergl, J and Schaffner, U and Sun,
              Y and Py{\v s}ek, P",
  abstract = "Biological invasions cause ecological and economic impacts across
              the globe. However, it is unclear whether there are strong
              patterns in terms of their major effects, how the vulnerability
              of different ecosystems varies and which ecosystem services are
              at greatest risk. We present a global meta-analysis of 199
              articles reporting 1041 field studies that in total describe the
              impacts of 135 alien plant taxa on resident species, communities
              and ecosystems. Across studies, alien plants had a significant
              effect in 11 of 24 different types of impact assessed. The
              magnitude and direction of the impact varied both within and
              between different types of impact. On average, abundance and
              diversity of the resident species decreased in invaded sites,
              whereas primary production and several ecosystem processes were
              enhanced. While alien N-fixing species had greater impacts on
              N-cycling variables, they did not consistently affect other
              impact types. The magnitude of the impacts was not significantly
              different between island and mainland ecosystems. Overall, alien
              species impacts are heterogeneous and not unidirectional even
              within particular impact types. Our analysis also reveals that by
              the time changes in nutrient cycling are detected, major impacts
              on plant species and communities are likely to have already
              occurred.",
  journal  = "Ecol. Lett.",
  volume   =  14,
  number   =  7,
  pages    = "702--708",
  month    =  jul,
  year     =  2011
}

@ARTICLE{Iacarella2015-ii,
  title    = "Negative competitive effects of invasive plants change with time
              since invasion",
  author   = "Iacarella, J C and Mankiewicz, P S and Ricciardi, A",
  abstract = "Competitive impacts of invasive species may vary across invaded
              ranges, owing to spatio-temporal gradients in adapted traits and
              abundance levels. Higher levels of interspecific competition in
              recently invaded areas may lead invaders to be more competitive.
              Here, using meta-analysis and home range estimation techniques,
              we examine how negative competitive effects of invasive species
              vary across different spatio-temporal invasion contexts. We
              conducted a meta-analysis of 26 studies that used greenhouse
              microcosm and common garden pairwise experiments to measure the
              growth response of native plants in the presence of terrestrial
              plant invaders (totaling 36 species), and compared this to the
              time since invasion at the collection site (number of years
              between the estimated year of initial invasion, by spread of the
              invader, and the time of collection for the study). We show that
              negative competitive effects decline across sites that had been
              invaded for longer periods of time, with effects of invasive
              grasses declining more rapidly over time than forbs, herbs and
              shrubs. To our knowledge, only two studies have directly measured
              competitive or consumptive effects of invaders across a gradient
              of time since invasion; our study is the first to identify a
              general pattern of temporal variation of competitive effects that
              may be attributed to intraspecific trait differences. Management
              efforts may be guided by such spatio-temporal patterns of invader
              impact, particularly for grasses.",
  journal  = "Ecosphere",
  volume   =  6,
  number   =  7,
  month    =  jul,
  year     =  2015,
  language = "English"
}


@ARTICLE{Lortie2007-yn,
  title    = "Publication bias and merit in ecology",
  author   = "Lortie, C J and Aarssen, L W and Budden, A E and Koricheva, J K
              and Leimu, R and Tregenza, T",
  journal  = "Oikos",
  volume   =  116,
  number   =  7,
  year     =  2007,
  language = "en"
}

@MISC{Jennions2013-mt,
  title   = "Publication and Related Biases",
  author  = "Jennions, Michael D and Lortie, Christopher J and Rosenberg,
             Michael S and Rothstein, Hannah R",
  journal = "Handbook of Meta-analysis in Ecology and Evolution",
  year    =  2013
}

@BOOK{Rothstein2006-iq,
  title     = "Publication bias in meta-analysis: Prevention, assessment and
               adjustments",
  author    = "Rothstein, Hannah R and Sutton, Alexander J and Borenstein,
               Michael",
  publisher = "John Wiley \& Sons",
  year      =  2006
}

@ARTICLE{Song2010-ff,
  title    = "Dissemination and publication of research findings: an updated
              review of related biases",
  author   = "Song, F and Parekh, S and Hooper, L and Loke, Y K and Ryder, J
              and Sutton, A J and Hing, C and Kwok, C S and Pang, C and Harvey,
              I",
  abstract = "OBJECTIVES: To identify and appraise empirical studies on
              publication and related biases published since 1998; to assess
              methods to deal with publication and related biases; and to
              examine, in a random sample of published systematic reviews,
              measures taken to prevent, reduce and detect dissemination bias.
              DATA SOURCES: The main literature search, in August 2008, covered
              the Cochrane Methodology Register Database, MEDLINE, EMBASE, AMED
              and CINAHL. In May 2009, PubMed, PsycINFO and OpenSIGLE were also
              searched. Reference lists of retrieved studies were also
              examined. REVIEW METHODS: In Part I, studies were classified as
              evidence or method studies and data were extracted according to
              types of dissemination bias or methods for dealing with it.
              Evidence from empirical studies was summarised narratively. In
              Part II, 300 systematic reviews were randomly selected from
              MEDLINE and the methods used to deal with publication and related
              biases were assessed. RESULTS: Studies with significant or
              positive results were more likely to be published than those with
              non-significant or negative results, thereby confirming findings
              from a previous HTA report. There was convincing evidence that
              outcome reporting bias exists and has an impact on the pooled
              summary in systematic reviews. Studies with significant results
              tended to be published earlier than studies with non-significant
              results, and empirical evidence suggests that published studies
              tended to report a greater treatment effect than those from the
              grey literature. Exclusion of non-English-language studies
              appeared to result in a high risk of bias in some areas of
              research such as complementary and alternative medicine. In a few
              cases, publication and related biases had a potentially
              detrimental impact on patients or resource use. Publication bias
              can be prevented before a literature review (e.g. by prospective
              registration of trials), or detected during a literature review
              (e.g. by locating unpublished studies, funnel plot and related
              tests, sensitivity analysis modelling), or its impact can be
              minimised after a literature review (e.g. by confirmatory
              large-scale trials, updating the systematic review). The
              interpretation of funnel plot and related statistical tests,
              often used to assess publication bias, was often too simplistic
              and likely misleading. More sophisticated modelling methods have
              not been widely used. Compared with systematic reviews published
              in 1996, recent reviews of health-care interventions were more
              likely to locate and include non-English-language studies and
              grey literature or unpublished studies, and to test for
              publication bias. CONCLUSIONS: Dissemination of research findings
              is likely to be a biased process, although the actual impact of
              such bias depends on specific circumstances. The prospective
              registration of clinical trials and the endorsement of reporting
              guidelines may reduce research dissemination bias in clinical
              research. In systematic reviews, measures can be taken to
              minimise the impact of dissemination bias by systematically
              searching for and including relevant studies that are difficult
              to access. Statistical methods can be useful for sensitivity
              analyses. Further research is needed to develop methods for
              qualitatively assessing the risk of publication bias in
              systematic reviews, and to evaluate the effect of prospective
              registration of studies, open access policy and improved
              publication guidelines.",
  journal  = "Health Technol. Assess. Rep.",
  volume   =  14,
  number   =  8,
  pages    = "iii, ix--xi, 1--193",
  month    =  feb,
  year     =  2010
}

@ARTICLE{Sanchez-Tojar2018-ri,
  title   = "Meta-analysis challenges a textbook example of status signalling:
             evidence for publication bias",
  author  = "Sanchez-Tojar, Alfredo and Nakagawa, Shinichi and Sanchez-Fortun,
             Moises and Martin, Dominic A and Ramani, Sukanya and Girndt, Antje
             and Bokony, Veronika and Kempenaers, Bart and Liker, Andras and
             Westneat, David",
  journal = "bioRxiv",
  pages   = "283150",
  year    =  2018
}


@INCOLLECTION{Trikalinos2005-jm,
  title     = "Assessing the evolution of effect sizes over time",
  booktitle = "Publication Bias in {Meta-Analysis}",
  author    = "Trikalinos, Thomas A and Ioannidis, John P A",
  editor    = "Rothstein, Hannah R and Sutton, A and Borenstein, M",
  publisher = "John Wiley \& Sons",
  pages     = "241--259",
  year      =  2005
}


@ARTICLE{Sterne2001-vv,
  title    = "Funnel plots for detecting bias in meta-analysis: Guidelines on
              choice of axis",
  author   = "Sterne, Jonathan A C and Egger, Matthias",
  abstract = "Asymmetry in funnel plots may indicate publication bias in
              meta-analysis, but the shape of the plot in the absence of bias
              depends on the choice of axes. We evaluated standard error,
              precision (inverse of standard error), variance, inverse of
              variance, sample size and log sample size (vertical axis) and log
              odds ratio, log risk ratio and risk difference (horizontal axis).
              Standard error is likely to be the best choice for the vertical
              axis: the expected shape in the absence of bias corresponds to a
              symmetrical funnel, straight lines to indicate 95\% confidence
              intervals can be included and the plot emphasises smaller studies
              which are more prone to bias. Precision or inverse of variance is
              useful when comparing meta-analyses of small trials with
              subsequent large trials. The use of sample size or log sample
              size is problematic because the expected shape of the plot in the
              absence of bias is unpredictable. We found similar evidence for
              asymmetry and between trial variation in a sample of 78 published
              meta-analyses whether odds ratios or risk ratios were used on the
              horizontal axis. Different conclusions were reached for risk
              differences and this was related to increased between-trial
              variation. We conclude that funnel plots of meta-analyses should
              generally use standard error as the measure of study size and
              ratio measures of treatment effect. \copyright{} 2001 Elsevier
              Science Inc. All rights reserved.",
  journal  = "J. Clin. Epidemiol.",
  pages    = "10",
  year     =  2001,
  language = "en"
}


@MISC{Viechtbauer2017-xj,
  title  = "Metafor: meta-analysis package for {R}",
  author = "Viechtbauer, Wolfgang",
  year   =  2017
}


@ARTICLE{Ioannidis2007-kw,
  title    = "The appropriateness of asymmetry tests for publication bias in
              meta-analyses: a large survey",
  author   = "Ioannidis, J P A and Trikalinos, T A",
  abstract = "Background: Statistical tests for funnel-plot asymmetry are
              common in meta-analyses. Inappropriate application can generate
              misleading inferences about publication bias. We aimed to
              measure, in a survey of meta-analyses, how frequently the
              application of these tests would be not meaningful or
              inappropriate.",
  journal  = "Can. Med. Assoc. J.",
  volume   =  176,
  number   =  8,
  pages    = "1091--1096",
  month    =  apr,
  year     =  2007,
  language = "en"
}



@ARTICLE{Lau2006-mt,
  title    = "The case of the misleading funnel plot",
  author   = "Lau, Joseph and Ioannidis, John P A and Terrin, Norma and Schmid,
              Christopher H and Olkin, Ingram",
  abstract = "Evidence based medicine insists on rigorous standards to appraise
              clinical interventions. Failure to apply the same rules to its
              own tools could be equally damaging",
  journal  = "Br. Med. J.",
  volume   =  333,
  number   =  7568,
  pages    = "597--600",
  month    =  sep,
  year     =  2006
}