metagear
an R package for facilitating systematic reviews,
data extractions, and meta-analysis

ON CRANVIGNETTESON GitHub
OpenMEE
free and open source software for meta-analysis
in ecology and evolution

WEBSITEDOWNLOADON GitHub






Rúa, M.A., Antoninka, A., Antunes, P.M., Chaudhary, V.B., Gehring, C., Lamit, L.J., Piculell, B.J., Bever, J.D., Zabinski, C., Meadow, J.F., Lajeunesse, M.J., Milligan, B.G., Karst, J., and Hoeksema, J.D. (2016) Home-field advantage? Evidence of local adaptation among plants, soil, and arbuscular mycorrhizal fungi through meta-analysis. BMC Evolutionary Biology 16, 122. [PDF] [DOI]

Lajeunesse, M.J. (2016) Facilitating systematic reviews, data extraction and meta-analysis with the metagear package for R. Methods in Ecology and Evolution 7, 323−330. [ [PDF] = article + supp. info. & [PDF] = updated manual ] [DOI] [CRAN]

Liu, L., Wang, X., Lajeunesse, M.J., Miao, G., Piao, S., Wan, S., Wu, Y., Wang, Z., Yang, S., Li, P. and Deng, M. (2016) A cross-biome synthesis of soil respiration and its determinants under simulated precipitation changes. Global Change Biology 22, 1394−1405. [ article = [PDF] & supp. info. = [ZIP] ] [DOI]

Janicke, T., Haederer, I.K, Lajeunesse, M.J. and Anthes, N. (2016) Darwinian sex roles confirmed across the animal kingdom. Science Advances 2, e1500983. [ [PDF] = article + appendices ] [Faculty of 1000] [DOI]

Lajeunesse, M.J. (2015) Bias and correction for the log response ratio in ecological meta-analysis. Ecology 96, 2056−2063. [ [PDF] = article + appendices ] [DOI]

Ferguson, A.R, Huber, D.R., Lajeunesse, M.J. and Motta, P.J. (2015) Feeding performance of king Mackerel, Scomberomorus cavalla. Journal of Experimental Zoology 323A, 399−413. [PDF] [DOI]

Lajeunesse, M.J. and Fox, G.A. (2014) Statistical approaches to the problem of phylogenetically correlated data. In G.A. Fox, S. Negrete-Yankelevitch, and V.J. Sosa, editors. Ecological Statistics: Contemporary Theory and Application (pp. 261−283). Oxford University Press, Oxford, UK. [ [PDF] = chapter + R script ] [DOI]

Lajeunesse, M.J. (2013) Power statistics for meta-analysis: test for mean effects and homogeneity. In J. Koricheva, J. Gurevitch, and K. Mengersen, editors. Handbook of meta-analysis in ecology and evolution (pp. 348−363). Princeton University Press, Princeton, New Jersey, USA. [PDF] [JSTOR]

Lajeunesse, M.J. (2013) Recovering missing or partial data from studies: a survey of conversions and imputations for meta-analysis. In J. Koricheva, J. Gurevitch, and K. Mengersen, editors. Handbook of meta-analysis in ecology and evolution (pp. 195−206). Princeton University Press, Princeton, New Jersey, USA. [PDF] [JSTOR]

Lajeunesse, M.J., Rosenberg, M.R. and Jennions, M.D. (2013) Phylogenetic nonindependence and meta-analysis. In J. Koricheva, J. Gurevitch, and K. Mengersen, editors. Handbook of meta-analysis in ecology and evolution (pp. 284−299). Princeton University Press, Princeton, New Jersey, USA. [PDF] [JSTOR]

Curtis, P.S., Mengersen, K., Lajeunesse, M.J., Rothstein, H.R. and Stewart, G.B. (2013) Extraction and critical appraisal of data. In J. Koricheva, J. Gurevitch, and K. Mengersen, editors. Handbook of meta-analysis in ecology and evolution (pp. 52−60). Princeton University Press, Princeton, New Jersey, USA. [PDF] [JSTOR]

Lortie, C.J., Lau, J. and Lajeunesse, M.J. (2013) Graphical presentation of results. In J. Koricheva, J. Gurevitch, and K. Mengersen, editors. Handbook of meta-analysis in ecology and evolution (pp. 339−347). Princeton University Press, Princeton, New Jersey, USA. [PDF] [JSTOR]

Schmid, C.H., Stewart, G.B., Rothstein, H.R., Lajeunesse, M.J. and Gurevitch, J. (2013) Software for statistical meta-analysis. In J. Koricheva, J. Gurevitch, and K. Mengersen, editors. Handbook of meta-analysis in ecology and evolution (pp. 174−194). Princeton University Press, Princeton, New Jersey, USA. [PDF] [JSTOR]

Robinson, S.A., Lajeunesse, M.J. and Forbes, M.R. (2012) Sex differences in mercury contamination of birds: testing multiple hypotheses with meta-analysis. Environmental Science & Technology 46, 7094−7101. [ [PDF] = article + supp. info. ] [DOI]

Chamberlain, S.A., Hovick, S.M., Dibble, C.J., Rasmussen, N.L., Van Allen, B.G., Maitner, B.S., Ahern, J.R., Bell-Dereske, L.P., Roy, C.L., Meza-Lopez, M, Carrillo, J., Siemann E., Lajeunesse, M.J. and Whitney, K.D. (2012) Does phylogeny matter? Assessing the impact of phylogenetic information in ecological meta-analysis. Ecology Letters 15, 627−636. [ article = [PDF] & supp. info. = [ZIP] ] [DOI]

Parachnowitsch, A.L. and Lajeunesse, M.J. (2012) Adapting with the enemy: local adaptation in plant−herbivore interactions. New Phytologist 193, 294−296. [PDF] [DOI]

Parker, J.D., Burkepile, D.E., Lajeunesse, M.J. and Lind, E.M. (2012) Phylogenetic isolation increases plant success despite increasing susceptibility to generalist herbivores. Diversity and Distributions 18, 1−9. [ [PDF] = article + appendix] [DOI]

Lajeunesse, M.J. (2011) On the meta-analysis of response ratios for studies with correlated and multi-group designs. Ecology 92, 2049−2055. [ [PDF] = article + appendix ] [DOI]

Lajeunesse, M.J. (2011) phyloMeta: a program for phylogenetic comparative analyses with meta-analysis. Bioinformatics 27, 2603−2604. [PDF] [ PHYLOMETA [link] | software for meta-analysis ] [DOI]

Carmona, D., Lajeunesse, M.J. and Johnson, M.T.J. (2011) Plant traits that predict resistance to herbivores. Functional Ecology 25, 358−367. [ article = [PDF] & supp. info. = [ZIP] ] [DOI]

Lajeunesse, M.J. (2010) Achieving synthesis with meta-analysis by combining and comparing all available studies. Ecology 91, 2561−2564. [PDF] [DOI]

Garamszegi, L.Z., Calhim, S., Dochtermann, N., Hegyi, G., Hurd, P.L., Jørgensen, C., Kutsukake, N., Lajeunesse, M.J., Pollard, K.A., Schielzeth, H., Symonds, M.R.E. and Nakagawa, S. (2009) Changing philosophies and tools for statistical inferences in behavioral ecology. Behavioral Ecology 20, 1363−1375. [PDF] [DOI]

Lajeunesse, M.J. (2009) Meta-analysis and the comparative phylogenetic method. American Naturalist 174, 369−381. [ [PDF] = article + appendix ] [ PHYLOMETA [link] | software for meta-analysis ] [DOI]

Agrawal, A.A., Lajeunesse, M.J. and Fishbein, M. (2008) Evolution of latex and its constituent defensive chemistry in milkweeds (Asclepias): a phylogenetic test of plant defense escalation. Entomologia Experimentalis et Applicata 128, 126−138. [PDF] [DOI]

Lajeunesse, M.J. (2007) Ectoparasitism of damselflies by water mites in Central Florida. Florida Entomologist 90, 643−649. [PDF] [DOI]

Beirinckx, K., Van Gossum, H., Lajeunesse, M.J. and Forbes, M.R. (2006) Sex biases in dispersal and philopatry: insights from a meta-analysis based on capture-mark-recapture studies of damselflies. Oikos 113, 539−547. [PDF] [DOI]

Johnson, M.T.J., Lajeunesse, M.J. and Agrawal, A.A. (2006) Additive and interactive effects of plant genotypic diversity on arthropod communities and plant fitness. Ecology Letters 9, 24−34. [ [PDF] = article + appendix ] [Faculty of 1000] [DOI]

Lajeunesse, M.J., Forbes, M.R. and Smith, B.P. (2004) Species and sex biases in ectoparasitism of dragonflies by mites. Oikos 106, 501−508. [PDF] [DOI]

Lajeunesse, M.J. and Forbes, M.R. (2003) A comparison of structural size and condition in two female morphs of the damselfly Nehalennia irene (Hagen) (Zygoptera : Coenagrionidae). Odonatologica 32, 281−287. [PDF]

Lajeunesse, M.J. and Forbes, M.R. (2003) Variable reporting and quantitative reviews: a comparison of three meta-analytical techniques. Ecology Letters 6, 448−454. [PDF] [DOI]

Lajeunesse, M.J. and Forbes, M.R. (2002) Host range and local parasite adaptation. Proceedings of the Royal Society of London, Series B. 269, 703−710. [PDF] [DOI]



ODDS & SODS



Patel, B.B., Andrade, C.M., Lajeunesse, M.J. and Geerken, R. (2014) Unusual finding of an intact moth during routine colonoscopy. ACG Case Reports Journal 1(3), 119. [PDF] [DOI]







OpenMEE beta

OpenMEE is a user-friendly, open-source program for carrying out meta-analysis in ecology and evolution. Our aim is to make newly developed statistical approaches easily accessible to all. These statistics include: multi-factor meta-analysis, meta-regression, and phylogenetic meta-analysis. NOTE: this software is still in beta development, but new functionalities are added almost daily! Give it a try and any feedback is welcome (lajeunesse@usf.edu)!




PHYLOMETA 1.3 beta

PhyloMeta is a program for integrating a phylogeny (in NEWICK format) into traditional meta-analysis. All the familiar statistics of meta-analysis are calculated (e.g., pooled effect sizes with 95%CI and homogeneity tests) and paired with the phylogenetically-independent equivalents to these statistics. PhyloMeta is currently only available as a console program for WINDOWS. Details of these statistics were reported in Lajeunesse (2009) Am. Nat. 174: 369-381 [link].


DOWNLOAD [ [ZIP] ]



PRUNETREE 5.0

Prunetree is a program for trimming taxa off phylogenies. You can make subtrees by either including (or excluding) a specific group of taxa. In addition, it also has options to arbitrarily transform internode branch lengths (BL) following a speciational model (all BL = 1) or following Pagel?s method (all taxa aligned and all internode BL = 1). Prunetree is currently only available for WINDOWS.


DOWNLOAD [ [ZIP] ]



PHYLOSTAT 1.0 beta

Phylostat calculates several statistics from your phylogenetic tree (e.g., number of polytomies, total tree distance, etc.). Phylostat is currently only available for WINDOWS.


DOWNLOAD [ [ZIP] ]


design by M. J. Lajeunesse | ver. 5.1, updated 2010.06.11 ~