Software and Resources

This page links to code, data, and other resources. (In progress).

Data and mathematical corrections

Corrections to Harte (2011), Maximum Entropy and Ecology: A Theory of Abundance, Distribution, and Energetics. Updated September 2019. Link.

Data for: Hembry, D.H., R. Raimundo, E.A. Newman, L. Atkinson, C. Guo, P.R. Guimãraes Jr., R.G. Gillespie (2018) Does biological intimacy shape ecological network structure? A test using a brood pollination mutualism on continental and oceanic islands. Journal of Animal Ecology 87(4): 1160-1171. Link.

Cite as: Hembry, David H. et al. (2019), Data from: Does biological intimacy shape ecological network structure? A test using a brood pollination mutualism on continental and oceanic islands, Dryad, Dataset, https://doi.org/10.5061/dryad.1224pr2

Data for: Newman, E.A., M.Q. Wilber, K.E. Kopper, M.A. Moritz, D.A. Falk, D. McKenzie, J. Harte. Disturbance macroecology: a comparative study of community structure metrics in a high severity disturbance regime. https://doi.org/10.1101/309419. Link.

Cite as: Newman, Erica; Wilber, Mark Q.; Kopper, Karen E.; Moritz, Max A.; Falk, Donald A.; McKenzie, Don; Harte, John. (2019): Disturbance Macroecology: Bishop Pine tree coring and location information from Point Reyes National Seashore, California, USA. figshare. Dataset. https://doi.org/10.6084/m9.figshare.11363051.v1

Data for: Newman, E.A., J.B. Potts, M.W. Tingley, C.E. Vaughn, S.L. Stephens (2018) Chaparral bird community responses to prescribed fire and mastication in three management seasons. Journal of Applied Ecology 52(3). Link.

Cite as: Newman, Erica A.; Potts, Jennifer B.; Tingley, Morgan W.; Vaughn, Charles; Stephens, Scott L. (2018): Newman et al, 2017. California chaparral bird community responses to wildfire management. Dryad. Dataset. https://doi.org/10.5061/dryad.mt3tr/1

Data for: Newman, E.A., C.A Winkler, and D.H. Hembry. (2018) Effects of anthropogenic wildfire activity in low elevation Pacific island vegetation communities in French Polynesia. PeerJ 6 (2018): e5114.. Link.

Cite as: Newman, Erica A.; Hembry, David H.; Winkler, Carlea (2017): Plant species and abundance records for burned and unburned areas. figshare. Dataset. https://doi.org/10.6084/m9.figshare.5718325.v1

Data for: Newman, E.A., L. Eisen, R. Eisen, N. Fedorova, J.M. Hasty, C.E. Vaughn, R.S. Lane (2015) Borrelia burgdorferi sensu lato spirochetes in wild birds in northwestern California: Associations with ecological factors, bird behavior and tick infestation. PLOS ONE 10(2): e0118146. Link.

Cite as: A. Newman, Erica; Eisen, Lars; J. Eisen, Rebecca; Fedorova, Natalia; M. Hasty, Jeomhee; Vaughn, Charles; et al. (2015): Data from: Borrelia burgdorferi sensu lato spirochetes in wild birds in northwestern California: associations with ecological factors, bird behavior and tick infestation. Dryad. Collection. https://doi.org/10.5061/dryad.p3b61

Software packages and code

EcoNetGen in R: Simulate and Sample from Ecological Interaction Networks. Link to R package in CRAN.

Cite as: de Aguiar, M.A.M., E.A. Newman, M. Pires, & C. Boettiger. (2018, April 4). EcoNetGen: an R package to Simulate and Sample from Ecological Interaction Networks.

EcoNetGen in Python. Link.

EcoNetGen examples from Carl Boettiger.

Large collaborations

I am a member of a National Institute of Mathematical and Biological Synthesis (NIMBioS) working group Ecological Network Dynamics: Spatiotemporal variation and dynamics in ecological networks)

I am also a contributing developer on the Botanical Information and Ecology Network, BIEN. We recently released BIEN version 4.1.

More collaborations

I have multiple ongoing collaborations in various topic areas. Some are listed below.

Chaparral management effects on California bird communities

Scott Stephens, Department of Environmental Science, Policy, and Management. University of California, Berkeley

Justin Brashares, Department of Environmental Science, Policy, and Management. University of California, Berkeley

Morgan Tingley, Ecology and Evolutionary Biology, University of Connecticut

Fire ecology in French Polynesia

Jean-Yves Meyer, Délégation à la Recherche. Papeete, Tahiti, French Polynesia

Pascal Ortéga, Université de la Polynésie française. Punaauia, Tahiti, French Polynesia

Ecological interaction networks

David Hembry, Department of Entomology, Cornell University

Paulo R. Guimarães, Universidade de São Paulo, São Paulo, Brazil

Marcus A.M. de Aguiar, Universidade Esatudal de Campinas, São Paulo, Brazil