Project Phases - Where are we now?

If this project were to be broken down into phases it would be as follows:

Field Work Phase
Lab Work Phase
Data Analysis Phase
Writing Phase

Field Work Phase

The Field Work Phase was wonderful. It was full of sunrises, bird banding, and sound recordings. Easily my favorite among the Phases. I got to work with wonderful people and learn so much about the white-crowned sparrows of San Francisco.

Lab Work Phase

Not my favorite but a lot was learned in this phase - both about laboratory techniques and about the parasites. It was in this phase that my thesis took on a new direction. After extracting all of the parasite DNA from my blood samples and running PCR, it turned out that only 5 total birds were infected. Of the 103 individuals captured over the two field seasons only 5 were infected! Statistically speaking this is not a large enough sample size to come to any solid conclusions about the effects of parasites on song. Unfortunately I had to put this portion of my investigation aside.

The good thing is I have plenty of other data to work with to investigate the factors influencing song performance in Nuttall's white-crowned sparrows. These factors include things such as morphology, weather, proximity to competitors, and anthropogenic noise.

Data Analysis/Writing Phases

While these phases are heavy on the indoor/computer work, they are critical to any scientific study. It is important to get the results of a study published and accessible to the scientific community and the public at large. From there the results are added to the general body of knowledge and can inspire future work so that the inertia of learning is carried on.

For me these phases have encompassed becoming familiar with several new computer programs. Here's a few that I have relied on most heavily lately:

Audacity

viewing and analyzing song spectrograms

This program allows me to visualize and annotate various features of a bird's song. It is how I generated song performance measures such as song rate, song length, trill number and trill rate.

ArcGIS

creating maps and analyzing relationships among various features

This program is fantastic! I took a course at SFSU called "Intro to GIS" (GIS = Geographic Information Systems) where I just scratched the surface on all the features this program has to offer. I'll write a separate post about all the cool analyses I did with ArcGIS.

RStudio 

statistical analysis

RStudio is a really helpful graphical user interface for the R statistics program, which is just raw coding. I am using this program to compare song performance between different study sites and attempt to tease out which factors seem to be most significant in influencing performance.

Mendeley 

storing and organizing primary literature

This program is an essential organization tool during writing. It stores all relevant publications and allows one to highlight, annotate, tag, and extract citations. Every professor I've had in graduate school has recommended this program or something like it.





Stay tuned because I have some exciting things to share in upcoming posts! I'll share some of the maps I've created and interesting differences I've seen in the sonograms of the white-crowns within and among the study sites. For now it's back to the statistics!