What is Open Plant Pathology?

We are a community of plant pathologists, mostly computationally-oriented, that supports the several forms of Open Science practices. We support efforts from individuals or groups to develop and deliver next-generation databases and tools for plant pathology-related subjects and applications using open source software, data and repositories.

Know our Vision and Mission and request to join

Recent Posts

Updates on our recent work, projects, tutorials and viewpoints

More Posts

So You Want to Write an R Package? So you want to write your first R package, but you don’t know where to start? We can help with that! Writing an R package is not difficult per se, but it can be intimidating for a first timer. Why would you want to write an R package? Well, as @PhytophthoraLab says, if you have more than two functions, you have a package, plus it means you can get citations!


We talked with Prof. Sophien Kamoun, a biology scientist with the Sainsbury Laboratory, Norwich, UK. Dr. Kamoun is known for his prolific Tweeting and advocacy for Open Science but, also importantly, for his work with oomycetes (#notafungus), effectors and evolution and, more recently, wheat blast.


Get to know one of our leaders, Dr. Niklaus J. Grünwald, a plant pathologist with USDA ARS, Corvallis, OR, USA. Nik has made significant scientific contributions to the understanding of the population biology and evolution of Phytophthora infestans worldwide and developed R packages to advance and facilitate the analysis of genetic and genome sequence data with applications in taxonomy and evolution.


OPP Notes

Teaching notes peer-reviewed by community members.

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This teaching note recreates the fit of linear and quadratic models using R for the population response of Pratylenchus thornei in Queensland, Australia wheat to temperature as described in the original paper.

Workshops & Talks

Get access to presentations and instructional materials produced by OPP members

More Talks

This Workshop will prepare participants to interpret network analyses, and will provide participants with experience in network analysis for several representative data sets. The workshop will use the R programming environment, and will provide a brief introduction to R.

This Workshop will combine lectures on concepts with practical computer exercises to allow participants to learn to calculate key information quantities that are important in understanding how DSS’s and diagnostics work, fundamentally, by capturing information from the world and making it available for use in decision-making

This Workshop cover analyses of plan pathological data from tools such as whole-genome variant calling and genotyping-by-sequencing or RADseq once variant call data are in hand. This workshop will not cover genome assembly, read mapping to reference genomes or the calling of variants.

This Workshop aims to introduce new users to several different and useful multivariate analysis methods available in the R statistical computing language. It is focus will be on application rather than background theory.

A Growing Global Community!

Check detailed information about the members, institutions, knowledge domains and the global map of Open Plant Pathology

Knowledge domains

General Plant Pathology, Epidemiology, Geophytopathology, Modeling, Population Biology, Genomics, Microbial Ecology, Programming, Embedded Systems.



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Adam Sparks

Founder. Plant pathologist and epidemiologist. University of Southern Queensland, Australia

Emerson Del Ponte

Founder. Plant disease epidemiologist. Universidade Federal de Viçosa, Brazil

Neil McRoberts

Plant disease epidemiologist and modeller. University of California - Davis, USA

Nik Cunniffe

Mathematical modeller. University of Cambridge, UK

Nik Grunwald

Plant pathologist. USDA, Oregon, USA

Paul Esker

Plant disease epidemiologist and modeller. Pennsylvania State University, USA

Sydney Everhart

Plant disease epidemiologist and population biologist. University of Nebraska, USA

Kaique dos S. Alves

MSc student. Universidade Federal de Viçosa. Disease modeling and risk assessment.

Lisa Ann Rothmann

Lecturer and Phd Student. Free State University. Risk modeling and management of vegetables and cereal crop diseases

Mladen Čučak

Phd student Maynooth University, Ireland. Disease modeling and forecasting.

René Heim

Post-Doctoral Fellow. University of Florida, USA. Remote sensing and spectroscopy