Category Archives: R

Resampling Assemblage Counts

Imagine that one diatom assemblage has 20 species and another has 25, but the more species rich assemblage also has more diatoms counted.A fair comparison of the richness of each assemblage can only be made when the number of individuals … Continue reading

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Making a pollen diagram from Neotoma

Last week I gave a course on R for palaeoecologists covering data handling using tidyverse, reproducibility and some some ordinations and transfer functions. One of the exercises was to download some pollen data from Neotoma and make a pollen diagram. … Continue reading

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Funky ordination plots with ggvegan

Yesterday, I tweeted a photo of a ordination I plotted with ggvegan, and thought I should show how I made it. ggvegan and ggplot make it easy to make complex ordination plots — Richard Telford (@richardjtelford) April 10, 2019 … Continue reading

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Introducing ggpalaeo

I’ve put some code I used for plotting figures for my soon-to-be-resubmitted manuscript into a package because I thought it might be useful to others. The main use of ggpalaeo is to make ggplot2 plots of transfer function diagnostics from … Continue reading

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The elevation of Lake Tilo

For my PhD, I studied the palaeolimnology of two lakes in the Ethiopian rift valley, using diatoms to reconstruct changes in the water chemistry of Lake Awassa, an oligosaline caldera lake which retains its low salinity despite having no effluent … Continue reading

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Insist() on the text and numbers agree in Rmarkdown

The manuscript I submitted a long time ago contains multiple sentences where I describe the result with both text and numbers. For example: With a three-year moving average, the correlation is weak (r = 0.21) and not statistically significant (p … Continue reading

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Citing R and packages automatically

Almost every manuscript I write has a paragraph that looks something like this: All analyses were done in R version 3.4.4 (R Core Team 2017). Ordinations were fitted with vegan version 2.4-6 (Oksanen et al. 2017) with square-root transformed assemblage … Continue reading

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Merging taxa in assemblage data

One possible reason for the impossible percent values I’ve found in assemblages data is that taxa have been merged in Excel after percent were calculated. Doing anything in Excel is to invite disaster, if nothing else, it is very difficult … Continue reading

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Extracting data from a PDF image

Some scientists archive their data. Some scientists email their data on request. Some editors cajole authors into releasing data to interested parties. And sometimes none of these approaches yields data. What then? One option is to request data via the … Continue reading

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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

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