First Impressions of Shiny, an R Package

Today I wanted to try something new; so instead of discussing a project, let’s briefly take a look at an R Package I’ve recently discovered. Before we being let me just mention that I realize not everyone uses R or have even used it before, instead my focus here will be on the technology, innovation, and utility of the package. Hopefully there are analogs libraries or packages in other languages, and if not then perhaps you’ll want to write it! Shiny, quite simply, is an R package that allows a user to write R code and generates an interactive webpage....

The benefits of interdisciplinarity: residence time

The so-called residence time of a system is both an immensely useful and highly intuitive conception which provides a relevant timescale for processes. For example, the residence time of nutrients flowing into a pond would be the average ‘lifetime’ of the nutrients before being taking up by the pond creatures. If it is a small number, then the nutrients are taken up very quickly compared to if is a large number. Here is the “traditional” formula for calculating residency time of a conservative tracer:     The more mass that’s in the system the longer the residence time becomes; and...

Julia Language for Scientists

Today I wanted to take a moment and introduce a programming language to my friends and colleagues. While certainly not a common topic, I do so because I believe that it is well worth your time. Rather than trying to get non-programmers into a language, I write this for the already initiated such as those who use Matlab, R or Python (amongst others) since the real benefits of learning one language rather than another comes when the tasks at hand are limited by the language itself. For example, consider if you’re problem or task (such as a model) was required...

Getting Started in 3D Printing

As someone who enjoys working on projects and tinkering with everything from computer systems to welders, I’ve always had a passive interest in 3d printing technology; yet I never seriously considered getting a one for myself. 3d printers work in much the same way a normal printer does, except instead of ejecting ink out of the nozzle it extrudes molten plastic. By layering these thin layers of plastic (typically 50-500 microns) over and over again it can build up entire objects in a matter of minutes to hours. It’s a simple technology which seems to have only recently gained the critical mass...

Remote Sensing Part 2

In a previous article I described a technique to determine the dye concentration from drone images, and I hope it sounded like a reasonable plan. Nevertheless, this plan did go ary when less than ideal conditions arose and the results got jumbled with the imperfections of the real world. So to make amends, I will layout a new pipeline that–with any luck–will work better in practice than the previous one. (more…)

Working with HYCOM

So far this week I’ve been focusing my energies on getting the Hybrid Coordinate Ocean Model (HYCOM) up and running on my computer. For those of you who don’t know what HYCOM is a modeling platform sponsored by the National Ocean Partnership Program which includes–among others–FSU. Simply put, the HYCOM platform is a powerful ocean-atmospheric model for use in climatological and oceanographical research and prediction studies. (more…)

How Twitter Improved my Ecological Model

For a last couple weeks I’ve been working on a marine ecosystem model using a technique called Inverse Modeling(1)I’ll be sure to do a writeup on what Inverse Modeling is and what makes it interesting in the future.; and while there’s been lots of progress, I’m starting to get to the point where the model takes some time to run. As you can imagine, there’s a lot of waiting-around time associated with having a model run for an hour or more at a time. As fate would have it I thought up a pretty fun way to keep updated on the progress...

Announcing my new Misc directory

I’ve started yet another endeavor to get my work organized into some system–or rather system of systems as it most often turns out to be. Recently the solutions for which I’m looking to find have to solve a problem that most people have and don’t realize. Most of my files and works were done by me for me, but few of them should be so limited as that. Most of the code I’ve written should be available by others so that some of the frustration that I worked through might be curtailed for others(1)For example, see my post of Finite...

Finite Difference Implementation

For my numerical methods course–a course centered around the tools and techniques used in modeling ocean systems–we have been tasked with programing a 1D model of a differential equation with simple initial conditions. Our implementation has to be in Fortran, a computer language with a long history, which has been a bit of a learning curve to say the least. Nevertheless, I wanted to take couple minutes and share my preliminary results here. (more…)

Ray Tracing, or Why I bite off more than I can chew

I’ve spent countless hours and a considerable about of energy on getting my ray tracer up and running, and this is what I have achieved: While it may look like modern art(1)Actually, since art exists independent of intent and as a result of a observer-entity interaction, this picture would be “art”. Whether it is modern art rather than some other school I hazard no guess., it is actually a rendering of two triangles in 3D space complete with color gradients and perspective. And I’m pretty proud of this, but let me provide a modecum of background before we continue. (more…)...

Paper of Note: Fast, Minimum Storage Ray-Triangle Intersection

Introduction Raytracing is modern computer graphics technique used to render life-like images for videos and animations. While it’s a relatively modern technique–coinciding with the birth of digital modeling–the inspiration for the methods can be traced back to ancient Greece. While some Greeks truly believed that our eye’s emit the ability to see and not that our eyes collect the light, Ray Tracers actually work on that very principle. Starting from the camera or ‘eye’, the ray tracer sends out ‘light’ rays and monitors their interactions with the objects in the scene. At the end of the trace, an image is compiled based...

If I were a farmer…

While checking out the latest headlines and otherwise perusing the PLOSONE site in search of some new and interesting research, I came across a meta-analysis that sounded interesting. With the provocative title of ‘A Meta-Analysis of the Impacts of Genetically Modified Crops’ (1)Klumper and Qaim, A Meta-Analysis of the Impacts of Genetically Modified Crops. PLoS ONE 9(11): e111629. (2014) doi: 10.1371/journal.pone.0111629 who wouldn’t read it? (more…) Notes   [ + ] 1. ↑ Klumper and Qaim, A Meta-Analysis of the Impacts of Genetically Modified Crops. PLoS ONE 9(11): e111629. (2014) doi: 10.1371/journal.pone.0111629

JetDrive for Macs

With a recent incident involving me and my external hard drive, I’ve realized that I really need to improve my data backup system. Luckily I was able to save the drive and all the data on it, but there is no guarantee that I’ll be so fortunate next time. I’m one of those guys with a Macbook pro and a Solid State Drive (SSD) with a measly 128 GB of storage capacity. Hence the need for an external drive, which is awesome except that it doesn’t allow for hardly any redundancy. Since my laptop can’t hold much more than my...

Information Theory

Imagine you are standing, waiting for the T. Off the side of the tunnel you see that glimmer of not the T’s headlight, but rather the glimmer of the reflection of the T’s headlight as it snakes its way through the labyrinth on underground tunnels. The T dashes into view, and it would be surprising if only the sound wasn’t defening. A few seconds later the train comes to a screechy halt and the doors open. You and your neighbors quickly, yet respectfully, shuffle aboard to take a seat or, if your luck so dictates, a spot to stand either...