R data structures for Chemical Modeling

by on August 25, 2017

In the past few months I’ve done some work on PHREEQC modeling in R, as well as a whole lot of XRF data work that required converting what seemed like an ungodly number of molecular concentrations (e.g. Al2O3) into elemental concentrations (Al). Both of these highlighted a need for chemical data structures in R such […]

Using the tidyverse to wrangle core data

by on August 24, 2017

The paleolimnological data I work with most days is voluminous and difficult to wrangle. There are a lot of cores, a lot of variables, and a lot of parameters thanks to the multi-element analysis of the X-Ray Fluorescence spectrometer we’ve used recently on our sediment samples. However, since the advent of the tidyverse, this job […]

Dynamic Forms & Formsets in Django

by on August 6, 2017

In working on a Django web app recently, I ran across the problem of creating programatically-created forms. Creating regular forms in Django is a piece of cake: from django import forms class NameForm(forms.Form): your_name = forms.CharField(label=’Your name’, max_length=100) Creating many forms is equally easy, once the initial form class has been defined: from django.forms import […]

An Alternative R Wrapper for PHREEQC Geochemical Modelling

by on May 1, 2017

Recently I was introduced to PHREEQC, which is a program that models chemical interactions between rocks and water (among many, many other things). It is an open-source project by the USGS, and has a number of powerful features, including modeling equilibrium concentrations of elements according to various input parameters (e.g. temperature, pH). My task for […]

Major ggspatial updates

by on March 28, 2017

I took the day to update ggspatial an old R project that was never published to CRAN. The idea is to create ggplot layer() calls from sp Spatial* objects using a consistent interface. Last year I wrote a blog post about how that might work, and while the usage hasn’t changed much, the implementation is […]

Line-by-line, row-by-row…

by on March 27, 2017

The NatChem database from Environment Canada contains the best long-term atmospheric monitoring data that exists for Canada, similar to the National Atmospheric Deposition Program (NADP) in the US. Unlike the NADP, the distribution format associated with NatChem data is a hideous export format that looks like it was used by SAS at one point. readLines(“natchem_sample.CSV”, […]

Processing sub-bottom profiling data in Python

by on November 17, 2016

In addition to processing bathymetric data, my research on lakes requires sub-bottom profiling, or the collection of low-energy seismic data collected similarly to bathymetric data. The system we use is the SyQwest HydroBox, which, due to many hardware and software limitations, has been particularly frustrating. Still, when it does work properly, the HydroBox data has […]

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