Help for Scientists Who Code

More and more, research requires some level of computing to analyze data, whether retrieving a large dataset from a repository, using R and WinBUGS to perform occupancy modeling analyses, or writing Python scripts to run spatial analyses. However, most researchers and students have limited exposure to programming techniques. We often "hack" something together, leaving the potential for undetected errors in increasingly complex analyses. One popular reference source is stackoverflow, a robust, crowd-based resource for answering basic questions like "how to create a data frame from a matrix in R" or "how to create a loop". While this can be effective in completing a particular problem, it does not address best practices for programming, resulting in code that is inefficient, and difficult to share and incorporate into subsequent analyses. A small investment honing programming skills can pay dividends in efficiency down the road.

Enter Software Carpentry, a volunteer network focused on teaching coding principles to scientists, allowing computers to fulfill the promise of enabling analyses too tedious to tackle otherwise. The most useful section of the website are the lesson plans, whose topics include:

  • Version Control with Git -> keep track of changes and prevent data loss
  • Programming with Python
  • Programming with R

By increasing the quality of scientific code and sharing it on sites like figshare, we can make greater strides in taking advantage of large datasets and computing-intensive statistical techniques while lowering barriers to powerful analyses within and across disciplines.



Joint Northeast-Southeast Bird Conference 2014 - Reminders & Updates

As mentioned in a previous newsletter, a Joint Northeast-Southeast Partners in Flight Conference will take place Oct 6-9 in Virgina Beach, VA. Below are some reminders and updates:


The deadline for early-bird registration for the Conference on  October 6-9, 2014, has been extended to Friday, September 5.  If you are intending to register, please consider doing so before the registration costs increase!

The deadline for reserving guest rooms at the conference rate of $94/night at the conference hotel is September 15.   Please make your lodging reservations soon if you are thinking about attending the conference.

Seeking raffle/auction items

To all who would like to support the Northeast and Southeast Partners in Flight groups for organizing the conference , donations are being sought for items to be used in the raffle and silent auction to be held during the conference.  All proceeds from these two events will be used to help offset the costs of the conference.  If you or your organization can contribute any items, please contact Becky Gwynn at <>.  Items that need to be mailed may be sent to: Becky Gwynn, Virginia Department of Game and Inland Fisheries, 3801 John Tyler Memorial Highway, Charles City, VA 23030, and should arrive no later than Friday, October 3.  Be sure to include a note referencing the donor/donating organization so that we can be sure to recognize your contribution. Thanks!

Updated Conference Schedule

Please note that the conference schedule for Thursday, October 9, has been updated from what was originally posted on the conference website.  Thursday morning will be a continuation of the Conservation Business Planning breakouts from Wednesday, with Thursday afternoon devoted to contributed oral presentations and organized sessions.

Invitation for additional poster presentations

Did you miss the deadline for submitting an abstract for the conference but have study results or a conservation accomplishment that you would still like to share with conference participants? Due to fewer than anticipated submissions of abstracts for poster presentations, space is still available for additional posters.  Additional abstracts for poster presentations will be accepted through Friday, September 12.  Please send a <350 word abstract with name and affiliation of authors to Troy Wilson <> or Randy Dettmers <> but September 12.


Linda Pearsall Receives Prestigious Wildlife Conservation Award

Please join me in congratulating Linda Pearsall for her selection to recieve the Thomas L. Quay Wildlife Diversity Award. Most recently, Linda was the leader of the NC Natural Heritage Program for over two decades. From the NC Wildlife Resources Commission Press Release:

Linda Pearsall, a life-long conservationist and architect of partnerships benefitting wildlife, received the Thomas L. Quay Wildlife Diversity Award, one of the most prestigious awards given by the N.C. Wildlife Resources Commission.

The Commission presents the award annually to individuals who make outstanding contributions to wildlife diversity in North Carolina and who are considered leaders in wildlife resources conservation. 

Pearsall, of Raleigh, accepted the award, along with a framed print, from Commission Executive Director Gordon Myers at the agency’s business meeting in Raleigh on August 28.

“Linda has made countless contributions to wildlife and their habitats, many of which directly benefit imperiled species,” Myers said during the presentation. “Also under her leadership, numerous partnerships have been developed with other agencies, NGOs and landowners. Each of these partnerships has accrued long-lasting conservation benefits to North Carolina.”

Pearsall retired earlier this year after more than two decades as director of the North Carolina Natural Heritage Program in the Department of Environment and Natural Resources. The NCNHP identifies ecologically significant natural areas in the state and facilitates their protection through registry and dedication, including conservation agreements between NCNHP and landowners.

As NCNHP director, Pearsall oversaw a professional staff of 25 and advised politically appointed boards to help shape conservation legislation, policy and practice.

She supervised field staff who conducted Natural Areas Inventories in 93 of 100 counties in North Carolina, leading to the conservation of countless populations of threatened and endangered flora and fauna. During her tenure at NCNHP, Pearsall worked with scientists across the state to create electronic records of the state’s rare species through development of a computer database, GIS maps and online N.C. Conservation Planning Tool. These records are shared with hundreds of conservation agencies, local and state governments, regional planning organizations and non-profit organizations throughout the state to help them make decisions about conservation and other land-use planning efforts.

Pearsall is well known throughout conservation circles for forging strong partnerships with state, federal and private organizations, including the Wildlife Resources Commission, to share resources and conduct projects that have conserved thousands of acres in biologically significant areas like Chimney Rock, Grandfather Mountain, South Mountains Game Land and many other game lands, state parks and natural areas, through Natural Heritage Trust Fund grants.

“When I was informed about receiving the Quay Award, I was astonished to hear my name was being added to the list of winners,” Pearsall said. “It is an amazing honor. … and I hope the award continues to foster good relationships and partnerships in conservation across North Carolina.”

Pearsall is the ninth person to receive the honor. The first recipient was Dr. Quay himself, a former professor of zoology at N.C. State University and self-described “full-time volunteer and unpaid environmental activist.” Quay, who passed away in April 2012, served on a variety of conservation boards while lobbying state agencies for various environmental causes. 


Recent Paper: Refining Estimates of Bird Collision and Electrocution Mortality at Power Lines in the United States

A recent literature review and analysis paper estimates the effects of powerlines on bird mortality from the Smithsonian Conservation Biology Institute.
Citation: Loss SR, Will T, Marra PP (2014) Refining Estimates of Bird Collision and Electrocution Mortality at Power Lines in the United States. PLoS ONE 9(7): e101565. doi:10.1371/journal.pone.0101565
Collisions and electrocutions at power lines are thought to kill large numbers of birds in the United States annually. However, existing estimates of mortality are either speculative (for electrocution) or based on extrapolation of results from one study to all U.S. power lines (for collision). Because national-scale estimates of mortality and comparisons among threats are likely to be used for prioritizing policy and management strategies and for identifying major research needs, these estimates should be based on systematic and transparent assessment of rigorously collected data. We conducted a quantitative review that incorporated data from 14 studies meeting our inclusion criteria to estimate that between 12 and 64 million birds are killed each year at U.S. power lines, with between 8 and 57 million birds killed by collision and between 0.9 and 11.6 million birds killed by electrocution. Sensitivity analyses indicate that the majority of uncertainty in our estimates arises from variation in mortality rates across studies; this variation is due in part to the small sample of rigorously conducted studies that can be used to estimate mortality. Little information is available to quantify species-specific vulnerability to mortality at power lines; the available literature over-represents particular bird groups and habitats, and most studies only sample and present data for one or a few species. Furthermore, additional research is needed to clarify
whether, to what degree, and in what regions populations of different bird species are affected by power line-related mortality. Nonetheless, our data-driven analysis suggests that the amount of bird mortality at U.S. power lines is substantial and that conservation management and policy is necessary to reduce this mortality.

USFWS Communication Position Open

Outreach and Education Specialist in the Migratory Bird Program, Division of Bird Habitat Conservation. The position is based at the US Fish & Wildlife Service Headquarters in Falls Church, Virginia.

GS 9/11 (all qualified candidates) 

GS 12/13 (FWS candidates only)