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 […]

Environment Canada HYDAT data in R

by on July 21, 2017

The HYDAT database contains over 1 GB of hydrological observation data collected by Environment Canada. The database is freely available from the Environment Canada website, however extracting data can be difficult. Recently a student in our lab was working with this data, so I adapted some previously shotty code that cleaned up the somewhat difficult […]

10,000 Years of Metal Dynamics in the Tantramar Marshes

by on May 26, 2017

Almost six years ago, my honours thesis (Using paleolimnological methods to track late holocene environmental change at Long Lake, New Brunswick – Nova Scotia border region, Canada) and my friend Hilary’s master’s thesis were completed, but it was only this year that we finally got around to submitting the combined manuscript to FACETS, a new […]

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”, […]

The Mineralogical Paragram

by on March 19, 2017

Matt Hall from Agile Geoscience recently wrote a post on the problem of finding the shortest possible pangram (sentence containing all letters in the alphabet) using only mineral names. The post goes into the details on the set cover problem, of which assembling a pangram from a list of minerals is one example. Matt’s best […]

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