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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 library("tidyverse") library("lubridate") florida =...
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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...
View ArticleMerging 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,...
View ArticleCiting 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...
View ArticleInsist() 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...
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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...
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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...
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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 pic.twitter.com/zmEal7W4Q8...
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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...
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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...
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