Category Archives: reproducible research

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

Posted in Data manipulation, R, reproducible research | Tagged | 1 Comment

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

Posted in reproducible research | Tagged | 2 Comments

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

Posted in R, reproducible research | Tagged | Leave a comment

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

Posted in R, reproducible research | Tagged | 2 Comments