Category Archives: R

Bergen: a year with some sunshine

May was glorious.  December less so. The data are from the Geofysisk Institutt in Bergen. Here is the code I used Advertisements

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Statigraphic diagrams with ggplot

rioja::strat.plot is a great tool for plotting stratigraphic plots in R, but sometimes it is not obvious how to do something I want, perhaps a summary panel showing the percent trees/shrubs/herbs. Of course, I could extend strat.plot, but I do … Continue reading

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How to calculate percent from counts in R

Micropaleontologists and others often want to calculate percent from count data. From looking at archived data, I realise that what should be an easy process goes wrong far more often that it should (which is of course never). Yesterday, I … Continue reading

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Package version control

One aspect of writing a manuscript that I find tedious is checking the versions of the R packages I used. So I wrote a small function to do this automatically. (I don’t use ​= as an assignment operator in my … Continue reading

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Please archive assemblage data as counts not percent

A large fraction of the microfossil assemblage that has been archived on-line by palaeoecologists is percent data, often without the count sums, rather than the raw count data. This is unfortunate as some analyses need count data. Calculating percent from … Continue reading

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The European Pollen Database meets SQLite

The European Pollen Database is a fantastic resource for palaeoecologists, storing pollen stratigraphies from across the continent. Getting the data into R for analysis is facilitated by the EPDr package. However, first you need to set up the database and … Continue reading

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OxCal and R

OxCal is perhaps the most powerful of the three main Bayesian age-depth modelling procedures, with many many options and the potential for building far more complicated than your typical palaeolimnologist needs to use. Unlike Bchron and Bacon, OxCal is not … Continue reading

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