Category Archives: reproducible research

A demo targets plan for reproducible pipelines for Neotoma data

In any analysis, there are a series of steps: data importing, cleaning, analysis, creating figures, and then putting it all together in an manuscript. Very often, some of these steps are time consuming, and you don’t want to rerun everything … Continue reading

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Reproducibility of high resolution reconstruction – one year on

It is about a year since my paper discussing the reproducibility of high resolution reconstructions was finally published, so I thought I should give a full account of what has happened since. Nothing. None of the authors of the papers … 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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Tools for a reproducible manuscript

It is all too easy to make a mistake putting a manuscript together: mistranscribe a number, forget to rerun some analyses after the data are revised, or simply bodge the round some numbers. Fortunately it is possible to avoid these … 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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