Friday, May 3, 2013

Reordering columns/rows in a shapefile in ArcGIS

I recently created a shapefile in ArcGIS of my oceanic transform fault data. I started off with two separate files: a shapefile of points that simply contained a latitude/longitude and name for each fault; and a polyline shape file that contained the length measurements and the start/end points. I combined these two shapefiles in ArcMap using the "Join Data" command, and selecting to join the data based on spatial location. The result was a single polyline shapefile, that included all the original polyline attributes as well as all the related attributes (name, center lat/long) from the point file.

The problem was that the shapefile was not ordered the way I wanted it. In ArcMap you can reorder rows by ascending/descending values by double-clicking on the column header, or move columns simply by clicking on the header and dragging it over. The problem is that this only applies to your view of the shapefile attribute table, and the reordering is not actually saved to the shapefile itself. If you close out ArcMap, open a new map, reimport the shapefile, everything is back to the original order.

There is a free plugin tool for ArcGIS that is quite powerful and can solve these issues for you: ET GeoWizards. There are both free and paid versions of this toolbox, but I found the free version did exactly what I need. This toolbox is pretty impressive, and includes tools for feature translation, where shapefile objects are moved by a user-specified distance, filling holes in polygons, generalizing features, creating clusters from points, and a whole suite of other functions.

In order to reorder the columns and sort the rows in your shapefile, you can find the necessary commands under "Basic." The "Order Fields" command lets you select which fields you want to use from your original shapefile and specify the order in which they should appear. The "Sort Shapes" command lets you select which columns you want to sort the data by (you can select more than one), and whether you want them in ascending or descending order.

Another great toolbox plugin for ArcMap is Jenness Enterprises' Tools for Graphics and Shapes.  If you are looking for a tool to calculate spheroidal (geodesic) length of features in your shapefile, this is the tool for you. While this toolbox includes many of the same functions as the GeoWizards plugin, it also has many unique tools as well.  I have found that having both toolboxes has made working in ArcMap a much more pleasant experience. I wrote up a blogpost on the Tools for Graphics and Shapes plug-in back in 2010.

Thursday, May 2, 2013

Negotiating a Postdoc Position

UPDATE: The webinar link has now been posted. You can view the webinar yourself here.

On Tuesday evening, April 30th, COSEE (Centers for Ocean Sciences Education Excellence) and IBP (Institute for Broadening Participation) co-hosted a webinar :

“How to Negotiate Your Postdoc Position”

The panel speakers included Dr. Ashanti Johnson (Pyrtle), the executive director of IBP, whom I know from the University of South Florida, where she was faculty member when I was a master's student, and Dr. Edward Krug, Assistant Dean for Postdoctoral Affairs and an associate professor at the Medical University of South Carolina.

The webinar focused on how to negotiate your postdoctoral position in order to make your experience the best one possible. This does not just include salary negotiation, which is frequently a moot point anyway since funding is often provided by grants and is fixed, but also start date/end date, teaching load, student advising, publications, expectations, etc.

I took notes during the webinar and thought I would post them here in case they might be a benefit to others. The webinar also mentioned a few online documents and resources for students to help them in finding and negotiating a postdoctoral position, which I will post below.


2) Pathways to Science, an IBP program that seeks to help connect underrepresented groups to careers in STEM fields, lists a whole bunch of programs from K-8 grade levels all the way through faculty positions. Their listing of postdoc programs is quite extensive. They also provide tips on how to prepare and enhance your application, questions to ask before you start, and links to past webinars (the webinar I just attended should be posted there within the next week). While the primary aim of the program is to help bridge the gender/race/ethnicity gap in science, the website is a great resource for everyone.

3) The National Postdoctoral Association, which seeks to provide a "national voice and seeking positive change for postdoctoral scholars." The website provides a lot of resources to students and current postdocs, including listings of current and upcoming positions, guidelines for responsible conduct in research, and access to a network of current and former postdocs and mentors, research universities, and industry companies. Membership is required to access the majority of their content, and the annual dues amount varies according to your position (student, post doc faulty member, etc.).

Below are the notes I took while each presenter was speaking. I have also included a summary of the  questions and answer portion of the webinar.

Ashanti Johnson:

  • you are encouraged to negotiate your first salary 
  • can negotiate full compensation package including research support, benefits, etc., not just salary
  • always start off by responding how pleased you are to receive the offer and ask for a written confirmation of the offer. Confirm with them how long you have to make your decision as to whether or not to accept
  • You should convey enthusiasm the whole time, especially throughout the negotiation process
  • Get final offer in writing after all compensations have been made
  • If you reject the position, remember that these are still potential future colleagues and maintain professionalism and enthusiasm throughout

Edward Krug:

  • Grad school versus Post Doc
    • grad school is really focused on how to address problems while postdoctoral positions show you how to identify and address critical gaps in current knowledge. Survival skills for scientists
  • Fundamental science post docs - NSF is primary funding agency
  • National Postdoctoral Association - professional tools - - helps develop core competencies that postdocs should learn during their tenure:
    • Discipline-specific conceptual knowledge
    • research skill development
    • communication skills
    • professionalism
    • leadership and management
    • responsible conduct of research
  • NIGMS IRACDA Program - for biomedical/behavioral scientists. You apply to the program, not a specific person. You teach 25% of your time. Good for want-to-be academics. Includes a yearly conference. Typically 2 - 3 years
  • MyIDP - My Individual Development Plan - aims to help you find the ideal career position once you have completed your PhD. The website gives you means of self-assesment and then fits you with a possible career match (e.g. being a PI). Once matched, the program:
    • provides you with a list of strategic goals to help you achieve your desired career path
    • help you identify possible your weak points towards achieving your goals
    • gives you access support groups of people with similar goals/challenges
  • Publications are the currency of academia. The majority of postdocs end up in some type of publication disputs with their advisor. So what makes a coauthor versus first author?
    • you should discuss this openly and agree on set guidelines with your advisor from the get-go
    • ask about authorship BEFORE joining a lab. Don't assume your mentor will put you first

Questions from the crowd:

   Q: Can you do something else while doing a post doc - non-profit work that fits in with your career?
        A: maybe 25% of time, but don't let it compromise your Post Doc

   Q: If you want to pursue an Industry position, should you pursue a post doc?
        A: Yes. NSF has an industry/academic program. Post docs can really help you get the ideal position.

   Q: Are salaries generally negotiable?
        A: If funding is through a grant, it may be fixed. You need to research the funding source before trying to negotiate a salary. Some institutions have a post doc office that can help you negotiate your post doc salary.

   Q: Can you take your post doc research with you?
        A: Yes, under some circumstances. You can discuss this with your mentor at the beginning. It may also depend on who the funding was awarded to.

   Q: What are the options for foreign post docs studying at US institutions?
        A: NSF and some institutions have foreign postdoc positions, but not NIH

   Q: When do you inform your advisor of your post doc plans?
        A: It really depends on the relationship you have with your advisor and whether or not you can have an informal conversation about it. Remember, they decide when you're done, not you

   Q: Can you apply for a post doc doing the same thing as your PhD?
        A: Similar is fine, but having a post doc that is different is advantageous to learn new skills. NSF actually encourages you to pursue different, but related topics

   Q: If papers are submitted, but not published, can you still look for a post doc?
         A: Yes! Do not wait. Look often and look early.

   Q: What kind of negotiating power do I have as a first time post doc?
         A: Depends on the position, but you should definitely be your own advocate. There is a new government recommendation of starting salary of 42K for postdoctoral scholars, so use that as a starting off point if you are going to negotiate salary

   Q: How many publications per year is expected?
        A: 1 - 1.5 per year is good, at least in biomedical research fields. Some clinical positions expect 3 - 4 publications per year. Expectations are really dependent on the specific field you are in.

   Q: How does research vary between post doc and PhD
         A: You are now a professional, and this should be reflected in the quality of your work and publications. There is less structure, more self-guided. You have one primary mentor, not a whole committee.
               It is what you make of it, so you need to be able to productive on your own and not be dependent on others. Do not be afraid to go out and seek more mentors that can help coach you professionally and personally as you move through your career. These mentors can help you throughout your post doc and beyond.

    Q: So how do you find those other mentors?
         A: Professional societies can be a great source
              Your PhD advisor can become a lifelong mentor. You are now part of their lineage, and they want you to succeed. If there is someone whose work you are interested in, talk to them. They can become a mentor. Networking is key.