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data-software-code.qmd
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data-software-code.qmd
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---
title: "Data, software & code"
editor:
markdown:
wrap: 72
---
Many of the links below will take you to content on GitHub
([\@vbaliga](https://github.com/vbaliga)) or Figshare ([see my profile
here](https://figshare.com/authors/Vikram_B_Baliga/4769286)).
## Software packages
### [avinertia](https://cran.r-project.org/web/packages/AvInertia/index.html): 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](https://www.christinaharvey.ca/)
and [Jasmin C.M.
Wong](https://research-information.bris.ac.uk/en/persons/jasmin-wong).
Accompanying paper ([Harvey et al.,
2022](https://doi.org/10.1038/s41586-022-04477-8)) in Nature
------------------------------------------------------------------------
### [pathviewr](https://github.com/ropensci/pathviewr): Tools to import, clean, and visualize animal movement data in R
{fig-alt="pathviewr r package"
style="float:left;" width="100"}
Part of the rOpenSci project (github:
[ropensci/pathviewr](https://github.com/ropensci/pathviewr))
*pathviewr* offers tools to import, clean, and visualize movement data,
particularly from motion capture systems such from [Optitrack's
Motive](https://optitrack.com/products/motive/), the [Straw Lab's
Flydra](https://github.com/strawlab/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](https://melissasarmstrong.com/) and [Eric R.
Press](https://www.grad.ubc.ca/campus-community/meet-our-students/press-eric).
------------------------------------------------------------------------
### [gaussplotR](https://github.com/vbaliga/gaussplotR): Fit, predict, and plot 2D Gaussians in R
{fig-alt="gaussplotR r package"
style="float:left;" width="100"}
gaussplotR provides functions to fit two-dimensional Gaussian functions,
predict values from such functions, and produce plots of predicted data.
Accompanying paper ([Baliga, 2021](https://doi.org/10.21105/joss.03074))
in the Journal of Open Source Software
------------------------------------------------------------------------
### [workloopR](https://github.com/ropensci/workloopR): Analysis of work loops and other data from muscle physiology experiments in R
{fig-alt="workloopR r package"
style="float:left;" width="100"}
Part of the [rOpenSci](https://ropensci.org/) project (github:
[ropensci/workloopR](https://github.com/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](https://www.linkedin.com/in/shreeram-senthivasan-43b0881bb/).
Accompanying paper ([Baliga and Senthivasan,
2019](https://doi.org/10.21105/joss.01856)) in the Journal of Open
Source Software
------------------------------------------------------------------------
### [genbank_downloadR](https://github.com/vbaliga/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](https://doi.org/10.6084/m9.figshare.12980189).
------------------------------------------------------------------------
## Data & code from pubs
Many of these repositories contain phylogenies that we've inferred, but
be sure to see the [Phylogenetic
trees](data-software-code.qmd#phylogenetic-trees) section below for
straightforward access to MCC & ML trees.
- [figshare repository](https://doi.org/10.6084/m9.figshare.23535717)
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](https://doi.org/10.6084/m9.figshare.19425737)
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](https://figshare.com/collections/Supplement_to_Inertia_links_avian_morphology_to_flight_manoeuvrability/5503989)
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](https://figshare.com/authors/Christina_Harvey/4766004))
- [figshare
repository](https://rs.figshare.com/collections/Supplementary_material_from_Gull-inspired_joint-driven_wing_morphing_allows_adaptive_longitudinal_flight_control_/5438933)
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](https://figshare.com/authors/Christina_Harvey/4766004))
- [figshare
repository](https://rs.figshare.com/collections/Supplementary_material_from_Phase_transformation-driven_artificial_muscle_mimics_the_multi-functionality_of_avian_wing_muscle_/5675606)
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](https://rs.figshare.com/authors/_/11598656))
- [figshare
repository](https://figshare.com/articles/dataset/Data_and_code_for_Flight_muscle_power_increases_with_strain_amplitude_and_decreases_with_cycle_frequency_in_zebra_finches_Taeniopygia_guttata_/12520733)
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](https://doi.org/10.6084/m9.figshare.8856161)
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](https://github.com/christiandamsgaard/Evolution-of-air-breathing)
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](https://github.com/christiandamsgaard))
- [figshare repository](https://doi.org/10.6084/m9.figshare.7658597)
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](https://doi.org/10.6084/m9.figshare.c.3977505.v1) 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](https://figshare.com/authors/Christina_Harvey/4766004))
------------------------------------------------------------------------
## 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*):
- Bayesian MCC tree
([download](https://vikram-baliga.squarespace.com/s/Baliga-etal-Science-Advances_222s_Avian_MCCtree.tre))
- Maximum likelihood tree
([download](https://vikram-baliga.squarespace.com/s/Baliga-etal-Science-Advances_222s_Avian_MLtree.tre))
### Gobies (Gobiidae)
- 54 species of Western Atlantic gobies + outgroup; from Baliga and
Mehta 2019 (*Integrative and Comparative Biology*):
- Bayesian MCC tree
([download](https://vikram-baliga.squarespace.com/s/Gobiidae_MCC.tre))
### Marine Angelfishes (Pomacanthidae)
- 72 species of marine angelfishes + outgroup; from Baliga and Mehta
2019 (*Integrative and Comparative Biology*):
- Bayesian MCC tree
([download](https://vikram-baliga.squarespace.com/s/Pomacanthidae_MCC.tre))
### Wrasses & Parrotfishes (Labridae)
- 344 species of wrasses + parrotfishes + outgroup; from Baliga and
Law 2016 (*Molecular Phylogenetics and Evolution*):
- Bayesian MCC tree
([download](https://vikram-baliga.squarespace.com/s/BaligaLaw2016_344SP_MCC.nwk))
- Maximum likelihood tree
([download](https://vikram-baliga.squarespace.com/s/BaligaLaw2016_344SP_MLtree.nwk))
------------------------------------------------------------------------