Adam H. Sparks

About

I am a bioeconomic modeller with botanical epidemiology and ecology training who specialises in agricultural simulation modelling and geographic information systems (GIS). I have expertise in R programming and have developed several tools to help gather weather and climate data and study pathogen populations using R and have also recently started using Julia too.

Along with Emerson Del Ponte, I co-founded Open Plant Pathology, a community of plant pathology, plant disease epidemiology, pathogen population biology, microbial ecology and genomics researchers that supports the several forms of open science practices in plant pathology.

Web

  0000-0002-0061-8359
  @adamshsparks@fosstodon.org
  @adamshsparks@aus.social
  adamhsparks
  adamhsparks

Pronouns

He/Him

CV

Adam H. Sparks’s CV

Education

Kansas State University, Manhattan, KS, USA

• 2009 - Ph.D. of Plant Pathology in Epidemiology and Ecology of Plant Pathogens studying with Dr Karen Garrett

• 2007 - Graduate Certificate in Geographic Information Systems and Remote Sensing

Purdue University, West Lafayette, IN, USA

• 2000 - B.S. of Agronomy in Soil and Crop Management

Employment

State of Western Australia Department of Primary Industries and Regional Development

• Senior Research Scientist, Bioeconomic Modeller from Jan 2021 to Current

University of Southern Queensland

• Associate Professor, Field Crops Pathology from Jan 2016 to Jan 2021

International Rice Research Institute

• Scientist I, Plant Disease Management Specialist from December 2012 to December 2015

• Post-doctoral Research Fellow, Botanical Modelling and GIS from January 2011 to November 2012

Kansas State University

• Post-Doctoral Research Associate, Modelling Wheat Fusarium Head Blight from January 2010 to January 2011

Service

rOpenSci

• Software Peer Review Associate Editor

• Statistical Software Peer Review Associate Editor

Open Plant Pathology

• Co-founder

Tropical Plant Pathology

• Reproducibility Editor, 03/2020 to present

• Associate Editor for Epidemiology, 2017 to 2020

Contact

Contact Adam H. Sparks

  e-mail Adam
  adamhsparks
  adamhsparks or a public chat using Keybase

Research

Highlighted research papers and project outputs

• Research compendium for “Timing of triazole-based spray schedules for controlling powdery mildew in Australia: a meta-analysis”

• Research compendium for “The role of conidia in the dispersal of Ascochyta rabiei”

• R Scripts and supporting data for creating metamodels, as published in Ecosphere, and using them to generate global estimates of potato late blight risk based on climate data as published in Global Change Biology.

• AfricaRice and IRRI MICCORDEA project for modelling effects of climate change on rice disease in Tanzania

• STRASA Biotic Stress Maps, maps of biotic stressors of rice in South Asia for the STRASA project, much of this work was published in Spatial and temporal patterns of rice production and productivity., here is the code for the book chapter.

Code

As a part of practising open science and reproducible research, some of my software’s code is available at my GitHub, @adamhsparks.

I have written and maintain several R packages available both on CRAN and GitHub.

Weather or Climate Data Clients for R

• bomrang - Australian Bureau of Meteorology (BOM) weather data API Client for R

• chirps - Climate Hazards Group InfraRed Precipitation with Station Data (CHIRPS) API data client for R

• getCRUCLdata - University of East Anglia Climate Research Unit (CRU) climate data API client for R

• GSODR - Global Surface Summary of the Day (GSOD) Weather Data API Client for R

• nasapower - NASA POWER Global Meteorology, Surface Solar Energy and Climatology Data API Client for R

Plant Pathology Packages for R

• ascotraceR - A mechanistic model to simulate the spread of Ascochyta blight in a chickpea field

• epicrop - Simulation modelling of crop diseases using a Susceptible-Exposed-Infectious-Removed (SEIR) model in R

• hagis - Analysis of plant pathogen pathotype complexities, distributions and diversity in R

Plant Pathology Package for Julia

• Epicrop.jl - Simulation modelling of crop diseases using a Healthy-Latent-Infectious-Postinfectious (HLIP) model in Julia