Data, software & code

Many of the links below will take you to content on GitHub (@vbaliga) or Figshare (see my profile here).

Software packages

avinertia: Calculate the inertial properties of a flying bird

avinertia provides tools to compute the center of gravity and moment of inertia tensor of any flying bird. The tools function by modeling a bird as a composite structure of simple geometric objects. This requires detailed morphological measurements of bird specimens although those obtained for the associated paper have been included in the package for use. Written with Christina A. Harvey and Jasmin C.M. Wong.

Accompanying paper (Harvey et al., 2022) in Nature

pathviewr: Tools to import, clean, and visualize animal movement data in R

pathviewr r package

Part of the rOpenSci project (github: ropensci/pathviewr)

pathviewr offers tools to import, clean, and visualize movement data, particularly from motion capture systems such from Optitrack’s Motive, the Straw Lab’s Flydra, or from other sources. We provide functions to remove artifacts, standardize tunnel position and tunnel axes, select a region of interest, isolate specific trajectories, fill gaps in trajectory data, and calculate 3D and per-axis velocity. For experiments of visual guidance, we also provide functions that use subject position to estimate perception of visual stimuli. Written with Melissa S. Armstrong and Eric R. Press.

gaussplotR: Fit, predict, and plot 2D Gaussians in R

gaussplotR r package

gaussplotR provides functions to fit two-dimensional Gaussian functions, predict values from such functions, and produce plots of predicted data.

Accompanying paper (Baliga, 2021) in the Journal of Open Source Software

workloopR: Analysis of work loops and other data from muscle physiology experiments in R

workloopR r package

Part of the rOpenSci project (github: ropensci/workloopR)

workloopR (pronounced “work looper”) provides functions for the import, transformation, and analysis of muscle physiology experiments in R. Over the course of developing the package, we expanded this goal to also cover experiments that are often complementary to the work loop technique. Written with Shree Senthivasan.

Accompanying paper (Baliga and Senthivasan, 2019) in the Journal of Open Source Software

genbank_downloadR: Batch downloading of DNA or protein sequences from GenBank

written as a standalone R script rather than as a full-blown package. Stable releases also available on Figshare.

Data & code from pubs

Some of these repositories contain phylogenies that we’ve inferred, but see the Phylogenetic trees section below for straightforward access to MCC & ML trees.

  • figshare repository for: Dash S, Baliga VB, Lapsansky AB, Wylie DR, and Altshuler DL. 2024. Encoding of global visual motion in the avian pretectum shifts from a bias for temporal-to-nasal selectivity to omnidirectional excitation across speeds. eNeuro.

  • figshare repository for: Baliga VB, Dakin R, Wylie DR, and Altshuler DL. 2024. Hummingbirds use distinct control strategies for forward and hovering flight. Proceedings of the Royal Society B: Biological Sciences.

  • figshare repository for: Smyth G, Baliga VB, Gaede AH, Wylie DR, and Altshuler DL. 2022. Specializations in optic flow encodingin the pretectum of hummingbirds and zebra finches. Current Biology.

  • figshare repository for: Harvey, CA, Baliga VB, Wong JCM, Altshuler DL, and Inman DJ. 2022. Birds can transition between stable and unstable states via wing morphing. Nature. (repository arranged & maintained by Christina Harvey)

  • figshare repository for: Harvey C, Baliga VB, Goates CD, Hunsaker D, and Inman DJ. 2021. Gull-inspired joint-driven wing morphing allows adaptive longitudinal flight control. Journal of the Royal Society Interface. (repository arranged & maintained by Christina Harvey)

  • figshare repository for: Leal PBC, Cabral-Seanez M, Baliga VB, Altshuler DL, and Hartl DJ. 2021. Phase transformation-driven artificial muscle mimics the multifunctionality of avian wing muscle. Journal of the Royal Society Interface. (repository arranged & maintained by Pedro Leal)

  • figshare repository for: Bahlman JW, Baliga VB, and Altshuler DL. 2020. Flight muscle power increases with strain amplitude and decreases with cycle frequency in zebra finches (Taeniopygia guttata). Journal of Experimental Biology.

  • figshare repository for: Baliga VB, Szabo I, and Altshuler DL. 2019. Range of motion in the avian wing is strongly associated with flight behavior and body mass. Science Advances.

  • github repository for: Damsgaard C, Baliga VB, Bates E, Burggren W, McKenzie DJ, Taylor E, and Wright PA. 2019. Evolutionary and Cardio-Respiratory Physiology of Air-breathing and Amphibious Fishes. Acta Physiologica. (repository arranged & maintained by Christian Damsgaard)

  • figshare repository for: Baliga VB and Mehta RS. 2019. Morphology, ecology, and biogeography of independent origins of cleaning behavior around the world. Integrative and Comparative Biology.

  • figshare repository for: Harvey C, Baliga VB, Lavoie P, and Altshuler DL. 2019. Wing morphing allows gulls to modulate static pitch stability during gliding. Journal of the Royal Society Interface. (repository arranged & maintained by Christina Harvey)

Phylogenetic trees

I am generally happy to share trees from posterior distributions — just shoot me an email

Birds (Aves)

  • 222 taxa across Aves + outgroup; from Baliga et al. 2019 (Science Advances):

Gobies (Gobiidae)

  • 54 species of Western Atlantic gobies + outgroup; from Baliga and Mehta 2019 (Integrative and Comparative Biology):

Marine Angelfishes (Pomacanthidae)

  • 72 species of marine angelfishes + outgroup; from Baliga and Mehta 2019 (Integrative and Comparative Biology):

Wrasses & Parrotfishes (Labridae)

  • 344 species of wrasses + parrotfishes + outgroup; from Baliga and Law 2016 (Molecular Phylogenetics and Evolution):