Reconstructing a coagulant optimization model using R and Shiny

by on January 30, 2019

Inspired by Lindsay Anderson’s suggestion that “somebody code up that Edwards 1997 model”, I successfully avoided proofreading my Ph.D. thesis proposal for much of a day doing just that. The paper is a classic paper, and one of many that attempt to predict dissolved organic carbon removal using easily measurable water quality parameters (in this case, […]

Stratigraphic diagrams with tidypaleo & ggplot2

by on August 14, 2018

This post covers creating stratigraphic diagrams using ggplot2, highlighting the helpers contained within the tidypaleo package, which I’ve been using for the past few months to create diagrams. I chose the ggplot2 framework because it is quite flexible and can be used to create almost any time-stratigraphic diagram except ones that involve multiple axes (we […]

The Circumpolar Diatom Database using R, the tidyverse, and mudata2

by on April 8, 2018

It is an exciting time for the integration of limnological and paleolimnological datasets. The National (US) Water Quality Monitoring Council Water Quality Portal has just made decades of state and federal water quality measurements available, the Pages2k project has collected hundreds of temperature proxy records for the last 2000 (ish) years, and the Neotoma database […]

Comparing approaches to age-depth modelling in R

by on March 15, 2018

Working with radiocarbon dating in R has long been possible, especially since the Intcal dataset itself contains R code in the supplement. Other tools like Bacon (Blauuw and Christen 2011), the slightly simpler Clam (Blaauw 2010), and BChron (Haslett and Parnell 2008) have helped users calibrate radiocarbon dates and produce reproducible age models. A comprehensive […]

Modifying facet scales in ggplot2

by on February 27, 2018

There is a very old issue in ggplot2 about the ability to modify particular scales when using facet_wrap() or facet_grid(). I often have this problem when using lots of facets, as sometimes the labels overlap with eachother on some of the scales. Without a way to set the breaks on one particular scale, it’s hard […]

Verbifying nouns and using the pipe in ggplot2

by on February 27, 2018

There is a lot of talk about the ggplot2 package and the pipe. Should it be used? Some approaches, like the ggpipe package, replace many ggplot2 functions, adding the plot as the first argument so they can be used with the pipe. This ignores the fact that ggplot2 functions construct objects that can (and should) […]

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