Programming in Ecology: BAT

This seems to be the best way for me to have a set of files available for my classmates, so the rest of you are just going to have to put up with this…

First, we have the R script provided by the authors of the BAT package (with a few minor additions of my own). Start by copying and pasting this chunk so we can go through and make sure it is working for everyone:

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Stream team Cleanup MacKenzie Creek – 4/18/2015

We met around 9 am in the morning for this cleanup. I believe it was an event organized by the River Des Peres Watershed Coalition. It had been planned a few months out and had a fair number of volunteers.


The area in the black rectangle was the focus of our work. Map by Google

At the start, the group was splitting into two. First, a group of people that were set to get very dirty to go down into the creek. There was trash and tires to find and remove. Corvin and Danelle went to this group.

The second group was for people that were not quite ready to get that dirty, that is where Sonora and I ended up along with about 10 high school girls getting service hours. We headed into a small clearing next to a construction site. There we waded ankle deep into trash that was mostly bottles and cups.


Cleaning up was hard work that required a break half way through. We sat on railroad tracks. Lucky for us, the railroad shut down the tracks for the duration of the cleanup!


Once all the cups were picked up, there were tons of Styrofoam packing peanuts on the ground. Many of us ended up sitting down on the ground and picking them up. It was hard gross work, but the site is significantly improved due to our efforts.

While we were working hard, Corvin found Eric and rode around like a boss with a big smile on his face!


Hogan Haake

Stream Team Cleanup – 2/15/2014

We joined a two day cleanup of the Meramec Bottoms area in south St. Louis. It was a two day event focused on the collection of tires and trash. On the first day, Danelle went out early in the morning and the kids and I met up with her after lunch and Corvin’s basketball game. The weather was around freezing. We all loaded up on layers and coats. I wish I had better photos of the cleanup… After the second day, we had one dumpster completely full of tires with an extra hundred plus tires that wouldn’t fit. The second same sized dumpster was full of trash. We actually had to stop picking up trash the second day as there was no more room to put it!

Two of the things we couldn’t get out were a boat and a truck.

Despite the freezing temperature, we had a great family time and did good!



Eagle Days – 1/18/2014

Each year, the Missouri Department of Conservation celebrates Eagle Days. Its a chance to get out with like minded people and view Eagles in their natural habitat. We have been to official events before, but this year decided to strike out on our own along the river and just see what we saw.

We started out the morning with a visit to a restaurant that the kids have been asking us a lot about recently, IHOP. It was a popular breakfast destination and we had a few minute wait before we were able to get a table. While we were waiting, we noticed a pancake eating challenge. The current record at the location was 22 pancakes. Of course, that got us talking and boasting about how we could easily eat 24 pancakes. Of course, I knew it was unlikely that I could actually beat it or would feel good afterwords whether I beat it or not. Corvin was convinced he could be famous. In the end, we each got normal breakfast.

This is Corvin after trying to eat the 3 pancakes that came with his meal. He didn’t finish them!  From breakfast, we decided to head up Highway 79, on the west side of the Mississippi river.  We made a stop at Lock and Dam #25 (Sandy Chute) and walked out to a point to look. The river was almost completely frozen over upstream of the dam and mostly unfrozen below the dam. The eagles were moving well, but we didn’t get any action shots of them going to the water.

This shot above was taken with an eagle leaving its perch to fly around. While we where there, it started lightly snowing. We decided to pack up and head farther north to Clarksville Missouri. The drive was slow and pleasant. They have another Lock there and we thought we would give it a try.

Clarksville has a very inviting river town. We got a kick out of the riverfront. While Danelle was down at the riverfront taking photos of eagles, I did my best to entertain the kids so she could focus on her photos. She took several hundred photos that all seemed too good to purge. In the end, the album had over 300 photos. There are lots of shots of birds plucking up fish out of the river!

Eventually, the kids and I wandered down to where all the other people were. We found a staircase with seats for looking out on the river. The kids took turns holding onto the railing and kicking ice back into the river.

Eagles were not the only birds catching fish!

This was a perfect way to spend a cold winter day as a family!


Hogan Haake

Another Raingarden – 10/16/2013

Back in August, I purchased a new boat. Yeah, I’m up to 4 now, but who is really counting. This boat may have been a bit expensive, and bound to take up more space in our crowded garage. When I asked Danelle’s permission/agreement to purchase the boat, she asked me “What are you going to get rid of?”. I expected that question, but I surprised myself with my quick reply, “Anything!”. Initially shocked, Danelle replied that she wanted the front yard to which I agreed.

This may not sound like much of a trade, but Danelle is an ecologist at heart. Many things that she does are motivated by her love for protecting the physical world around her. Claiming control over the front yard means removing much of the grass that I like with native plants and more garden areas. Ultimately this will lead to less watering outside and some prevention of flooding by her adding on to her existing rain garden.

So here is what the yard looked like before she got started

Then Danelle got landscaping bricks, her parents, and shovels and went to town. Note that I did some helping, but this is her project that she is excited about!

Work went late into the night but had to stop when it got too dark.

Danelle’s dad carving a new path for the water to fill the new rain garden. The existing garden is mainly fed via a french drain that comes from the side yard and the neighbor’s roof.

There it is with some plants in it. It’ll take a year or more for the plants to truly take hold. In the top left of the photo, you can see some extra plants just past the walk up to the house, this area got a makeover as well, but not as large.


Hogan Haake