Trans: Latin prefix implying "across" or "Beyond", often used in gender nonconforming situations – Scend: Archaic word describing a strong "surge" or "wave", originating with 15th century english sailors – Survival: 15th century english compound word describing an existence only worth transcending.

Category: Birding (Page 1 of 4)

The eBird API & regionCode

get this script and other GIS bits here on github

The Ebird dataset is awesome. While directly handling data as a massive delimited file- as distributed by the eBird people- is cumbersome at best, the ebird api offers a fairly straightforward and efficient alternative for a few choice bits and batches of data.

  • The eBird AWK tool for filtering the actual delimited data can be found over here:

    install.packages("auk")

It is worth noting R + auk (or frankly any R centered filtering method) will quickly become limited by the single-threaded approach of R, and how you're managing memory as you iterate. Working and querying the data from a proper database quickly becomes necessary.

Most conveniently, the eBird API already exists- snag an key over here.

...The API package for R is over here:
install.packages("rebird")

...There is also a neat Python wrapper over here:
pip3 install ebird-api

Region Codes:

I'm not sure why, but some methods use normal latitude / longitude in decimal degrees while some others use "regionCode", which seems to be some kind of eBird special. Only ever seen this format in ebird data.

For example, recent observations uses regionCode:

# GET Recent observations in a region:
# https://api.ebird.org/v2/data/obs/{{regionCode}}/recent

...But nearby recent observations uses latitude / longitude:

# GET Recent nearby observations:
# https://api.ebird.org/v2/data/obs/geo/recent?lat={{lat}}&lng={{lng}}

Regardless, lets just write a function to convert decimal degrees to this regionCode thing. Here's mine:

#!/usr/bin/env python3
"""
# provide latitude & longitude, return eBird "regionCode"
Written by Jess Sullivan
@ https://transscendsurvival.org/
available at: 
https://raw.githubusercontent.com/Jesssullivan/GIS_Shortcuts/master/regioncodes.py
"""
import requests
import json

def get_regioncode(lat, lon):

    # this municipal api is a publicly available, no keys needed afaict
    census_url = str('https://geo.fcc.gov/api/census/area?lat=' +
                     str(lat) +
                     '&lon=' +
                     str(lon) +
                     '&format=json')

    # send out a GET request:
    payload = {}
    get = requests.request("GET", census_url, data=payload)

    # parse the response, all api values are contained in list 'results':
    response = json.loads(get.content)['results'][0]

    # use the last three digits from the in-state fips code as the "subnational 2" identifier:
    fips = response['county_fips']

    # assemble and return the "subnational type 2" code:
    regioncode = 'US-' + response['state_code'] + '-' + fips[2] + fips[3] + fips[4]
    print('formed region code: ' + regioncode)
    return regioncode

Warbler Trillers of the Charles

The first ones to arrive in MA, brush up!

 

Palm warbler

songs

 

This is usually the first one to arrive.  Gold bird, medium sized warbler, rufus hat.  When they arrive in MA they are often found lower than usual / on the ground looking for anything they can munch on.  Song is a rapid trill. More “musical / pleasant” than a fast chipping sparrow, faster than many Junco trills.

 

Pine warbler

songs

 

Slimmer than palm, no hat, very slim beak, has streaks on the breast usually.  Also a triller. They remain higher in the trees on arrival.

 

Yellow-rumped warbler

songs

 

Spectacular bird, if it has arrived you can’t miss it- also they will arrive by the dozen so worth waiting for a good visual.  These also trill, which is another reason it is good to get a visual. The trill is slow, very “sing-song”, and has a downward inflection at the end.  If there are a bunch sticking around for the summer, try to watch some sing- soon enough you will be able to pick out this trill from the others.

 

-- Yellow warbler says “sweet sweet sweet, I’m so Sweet!” and can get a bit confusing with Yellow-rumped warbler

-- Chestnut-sided warbler says “very very pleased to meet ya!” and can get a bit confusing with Yellow warbler

 

Black-and-white warbler

songs

 

Looks like a zebra - always acts like a nuthatch (clings to trunk and branches).  This one trills like a rusty wheel. It can easily be distinguished after a bit of birding with some around.  

 

American Redstart

songs

 

Adult males look like a late 50’s hot-rodded American muscle car: long, low, two tone paint job.  Matte/luster black with flame accents. Can’t miss it. The females and young males are buff (chrome, to keep in style I guess) with yellow accents.  Look for behavior- if a “female” is getting beaten up while trying to sing a song in the same area, it is actually a first year male failing to establish a territory due to obviously being a youth.

 

Cheers,

- Jess

How to Query KML point data as CSV using QGIS and R

How to Query KML point data as CSV using QGIS and R

Here you can see more than 800 points, each describing an observation of an individual bird.  This data is in the form of KML, a sort of XML document from Google for spatial data.

 

I want to know which points have “pair” or “female” in the description text nodes using R.  This way, I can quickly make and update a .csv in Excel of only the paired birds (based on color bands).

 

 

Even if there was a description string search function in Google Earth Pro (or other organization-centric GIS/waypoint software), this method is more

robust, as I can work immediately with the output as a data frame in R, rather than a list of results.

 

First, open an instance of QGIS.  I am running ~2.8 on OSX.  Add a vector layer of your KML.

“Command-A” in the point dialog to select all before import!

Next, under “Vector”, select “Merge vector layers” via Data Management Tools.

 

Select CSV and elect to save the file instead of use a temporary/scratch file (this is a common error).

Open your csv in Excel for verification! 

 

 

 

 

 

 

The R bit:

# query for paired birds

#EDIT:  Libraries
library(data.table)
library(tidyverse)

data <- data.frame(fread("Bird_CSV.csv"))

pair_rows <- contains("pair", vars = data$description)

fem_rows <- contains("fem", vars = data$description)

result <- combine(pair_rows, fem_rows)

result <- data[result,]

write_csv(result, "Paired_Birds.csv")

Tada!

 

 

 

 

 

 

 

 

-Jess

Visual NH Research Update :)

Olive-sided Flycatcher (Is Says, "Three Beers!! [please]"

Walking to work in the morning

Work

Song Sparrow

Common Yellowthroat Warbler

I'll let the photos to the talking:  welcome to my world! 🙂 !!!!

 

-Jess

 

 

Solar upgrades!

Solar upgrades!

Incredibly, the hut we are working from actually had another solar panel just laying around.  🙂
This 50w square panel had a junction box with MC4 connectors, the standard for small scale solar installations.  As I was unsure how to know when we are running low on electricity reserves, I decided to make some adjustments.

Additional 50w solar panel

(Everything is still solder, hot glue, alligator clips, and zip-ties I’m afraid…)
I traded my NEMA / USA two-prong connection with two MC4 splitters, such that both panels can run in parallel (into a standard USA 110v extension cord that goes into our hut).  This way we should make well over one of the two 35ah batteries-worth of electricity a day.

Dual MC4 splitters to extension cord

I also added a cheap 12v battery level indicator.  It is not very accurate (as it fluctuates with solar input) but it does give us some insight about how much "juice" we have available.  (I also wired and glued the remote-on switch to the back of the input for stability.)

Added battery indicator and button

🙂
-Jess

Research Year Two: Three Photos

Male Common Yellowthroat Warbler

The field season has officially started in Northern NH!

Male Common Yellowthroat warbler (COYE):   This fellow is defending a small territory in a patch of open thicket.   These warblers rely on early succession forest- patches of substrate that haven't  really grown in yet- to build cryptic, ground-level nests.  They develop complex systems to divert/confuse predators away from their nests.

 

Female Black-throated Blue Warbler (BTBW):  I was lucky to see this female.   She is paired with a male who defends a large mature forest territory.   They have quite a few BTBW neighbors, which makes for a lot of skirmishes among the males over land.  The females are often silent and move very fast...

Male Mourning Warbler (MOWA):  This is a rare bird here.   Even more amazing, it is defending a territory in our research site- and trying to chase out a male COYE while doing so.  The two species "share" resources, which means thy can't stand each other.   🙂   Each time the male COYE sings near the MOWA, it gets berated and chased away- and vice versa.   It appears the COYE isn't budging either, probably because it hasn't had this domestic, neighborly problem before.

-Jess

Female Black-throated Blue Warbler

Male Mourning Warbler

Gathering point data using Compass 55 on Apple iOS

Keeping track of birds is tricky!

Attached is our team's workflow with Compass 55.    From the Kml, we go into Google Earth Pro - ArcGIS Desktop (arcmap).   QGIS is sometimes used too.

 

Cheers,

-Jess

 

840 Watts of Solar Power!

Equipment used:

Inverter/PWM Controller:  http://a.co/fdl9YzI

2x 35ah Batteries: http://a.co/5JBIxTC

100w solar panel:  http://a.co/5JBIxTC

We need power!  While doing bird research in the wilds of northern NH, it became evident we needed electricity to power computers, big cameras, and phones/GPS units.

Below is a table of the system and our expected electricity needs:

System Solar 100w 35ah universal (x2)
Ah per day: 33.33333333 35 TOTAL Ah Reserve: 70
V 12 12 Parallel wiring: 12v
Wh in: 400 420 TOTAL Wh Reserve: 840
W 100
Cost $105.00 $64.00
ah/$ 2
Sun Hour / Multiplier 4 2
Need/Day Wh multiplier consump. in Wh = 259.36
Computer 100 2.5 250
iPhone 1.7 2 3.4
AAs 11.2 0.3 3.36
Camera 2.6 1 2.6

*The milk crate system below can charge a 100 watt MacBook Pro around 8-9 times from being completely empty.  

**Remember:  V*A=W,  W/V=A, and Watts over time is Wh.  

-Jess

+/- relates to size of standard prongs

Parallel maintains 12v but doubles Ah. (Series would go to 24v at 35ah)

 

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