HistMapR: 12 Months from Coffee Break Musings to a Debut R Package

Post provided by Alistair Auffret

I was really happy to hear that our paper, ‘HistMapR: Rapid digitization of historical land‐use maps in R’ was shortlisted for the 2017 Robert May Prize, and to be asked to write a blog to mark the occasion. The paper was already recommended in an earlier blog post by Sarah Goslee (the Associate Editor who took care of our submission), and described by me in an instructional video, so I thought that I would write the story of our first foray into making an R package, and submitting a paper to a journal that I never thought I would ever get published in.

Background: Changing Land-Use and Digitizing Maps

Land-use change in Europe is often typified by land-drainage to create arable fields.

Land-use change in Europe is often typified by land-drainage to create arable fields.

Land-use change is largely accepted to be one of the major threats to biodiversity worldwide at the moment. At the same time, a warming climate means that species’ ranges need to move poleward – something that can be hampered by changing land use. Quantifying how land use has changed in the past can help us to understand how species diversity and distributions respond to environmental change.

Unfortunately, quantifying this change by digitizing historical maps is a pretty tedious business. It involves a lot of clicking around various landscape features in a desktop GIS program. So, in many cases, historical land use is only analyzed in a relatively small number of selected landscapes for each particular study. In our group at Stockholm University, we thought that it would be useful to digitize maps over much larger areas, making it possible to assess change in all types of landscape and assess biodiversity responses to land-use change at macroecological scales. The question was, how could we do this? Continue reading

Digitizing Historical Land-use Maps with HistMapR

Habitat destruction and degradation represent serious threats to biodiversity, and quantification of land-use change over time is important for understanding the consequences of these changes to organisms and ecosystem service provision.

Historical land-use maps are important for documenting how habitat cover has changed over time, but digitizing these maps is a time consuming process. HistMapR is an R package designed to speed up the digitization process, and in this video we take an example map to show you how the method works.

Digitization is fast, and agreement with manually digitized maps of around 80–90% meets common targets for image classification. We hope that the ability to quickly classify large areas of historical land use will promote the inclusion of land-use change into analyses of biodiversity, species distributions and ecosystem services.

This video is based on the Applications article ‘HistMapR: Rapid digitization of historical land-use maps in R‘ by Auffret et al. This article is freely available to anyone (no subscription required).

The package is hosted on GitHub and example scripts can be downloaded from Figshare.

Topography of Teeth: Tools to Track Animal and Ecosystem Responses to Environmental Changes

Below is a press release about the Methods paper ‘Inferring diet from dental morphology in terrestrial mammals‘ taken from the Smithsonian Institution.

By charting the slopes and crags on animals’ teeth as if they were mountain ranges, scientists at the Smithsonian’s National Museum of Natural History have created a powerful new way to learn about the diets of extinct animals from the fossil record.

Understanding the diets of animals that lived long ago can tell researchers about the environments they lived in and help them piece together a picture of how the planet has changed over deep time. The new quantitative approach to analysing dentition, reported on 21 November in the journal Methods in Ecology and Evolution, will also give researchers a clearer picture of how animals evolve in response to changes in their environment.


A 3D reconstruction of the teeth of a western gorilla (Gorilla gorilla).

Continue reading

NLMpy: a python software package for the creation of neutral landscape models

In this video Thomas Etherington shows how to use the NLMpy Python package to create neutral landscape models.  The video demonstrates how the paper’s Supporting Information documentation, Python scripts, and GIS data can be used to create a the example neutral landscape models that are shown in the paper.

Recognising that some ecologists may not be very familiar with Python, the authors have also created a video that provides some advice about choosing a suitable scientific distribution of Python, and demonstrates how to install the NLMpy package itself.

Issue 2 is now online

Issue 2 of Methods in Ecology and Evolution is now online, the table of contents is here.  In this issue there are 14 new papers on:

  • Statistical methods
  • Monitoring & modelling plant populations
  • Telemetry
  • Entomology
  • Modelling wildlife disease
  • Building databases of life-history traits
  • GIS methods

One innovation is that we now have a correspondence site:


From here you can send in correspondence about papers, as well as view other correspondence. We think that this is a really useful feature for a journal devoted to methods: corresp0ndence between authors and readers will be a useful resource, allowing discussion of techniques, refinement of methods, ironing out of problems as well as further suggestions for developments.  We encourage readers and authors to use this to discuss papers. The site is fully moderated so all material appearing should be constructive and useful to all.

The methods digest for the last month will be appearing soon:- delayed largely as a consequence of volcano ash.

Finally do check out the latest podcasts and videos, they are being updated all the time. The very latest video is an interview with Aaron Ellison from his field site!