chickpeaascodispersal

Chickpea _Ascochyta rabiei_ Spore Dispersal Modelling

https://github.com/adamhsparks/chickpeaascodispersal

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Chickpea _Ascochyta rabiei_ Spore Dispersal Modelling

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Host: GitHub
Owner: adamhsparks
Language: R
Default Branch: master
Homepage: https://adamhsparks.github.io/ChickpeaAscoDispersal/
Size: 101 MB

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Stars: 3
Watchers: 3
Forks: 1
Open Issues: 0
Releases: 6

Created about 6 years ago · Last pushed almost 2 years ago

Metadata Files

Readme Codemeta

README.md

The role of conidia in the dispersal of Ascochyta rabiei

The goal of this research is to examine the role of Ascochyta rabiei conidia dispersal of chickpea ascochyta blight in Australia.

A user-friendly website of this research compendium is available here, https://adamhsparks.github.io/ChickpeaAscoDispersal/. Interested parties may wish to view the data analysis and visualisation pipeline as well as model fitting, these are available under the "Articles" menu item of the web page.

A preprint of this paper is available from BioRxiv: https://doi.org/10.1101/2020.05.12.091827 and is included in "analysis/paper/".

The published paper is available from the European Journal of Plant Pathology: https://doi.org/10.1007/s10658-020-02126-2.

Reproducibility

This analysis is packaged a fully complete Docker instance. To get started, install Docker for your respective OS, https://docs.docker.com/get-docker/, and run the following commands.

docker pull adamhsparks/chickpea_asco_dispersal docker run -p 8787:8787 -d adamhsparks/chickpea_asco_dispersal

Once the image is running, open a browser window and go to localhost:8787, log in with rstudio and password rstudio.

From there, the files are available in the "ChickpeaAscoDispersal" folder shown in the lower right-hand window pane. The paper is located in "analysis/paper". The vignettes, located in "vignettes" detail the data processing, weather data validation and and modelling work. These files can be opened and run interactively or knit using the "knit" button in RStudio to recreate the full analysis.

Data availability

All data from this work are included in this repository and R package in the "inst/extdata" folder but also archived and documented with Zenodo, 10.5281/zenodo.3842293, for reuse.

Project team

Dr Ihsanul Khaliq, University of Southern Queensland, Centre for Crop Health, Toowoomba, Queensland 4350, Australia
Dr Joshua Fanning, Agriculture Victoria, Horsham, Victoria, 3401, Australia
Dr Paul Melloy, University of Southern Queensland, Centre for Crop Health, Toowoomba, Queensland 4350, Australia
Ms Jean Galloway, Department of Primary Industries and Regional Development (DPIRD), Northam, WA, 6401, Australia
Dr Kevin Moore, New South Wales Department of Primary Industries, 4 Marsden Park Rd, Tamworth, NSW, 2340, Australia
Mr Daniel Burrell, University of Southern Queensland, Centre for Crop Health, Toowoomba, Queensland 4350, Australia

Project PI:

Associate Professor Adam H. Sparks, University of Southern Queensland, Centre for Crop Health, Toowoomba, Queensland 4350, Australia

Abstract

Ascochyta rabiei asexual spores (conidia) were assumed to spread over short distances (~10 m) in combination of rain and strong wind. We investigated the potential distance of conidial spread in three rainfall and three sprinkler irrigation events. Chickpea trap plants were distributed at the distances of 0, 10, 25, 50 and 75 m from infested chickpea plots before scheduled irrigation and forecast rainfall events. Trap plants were transferred to a controlled temperature room (20 °C) for 48 h (100% humidity) after being exposed in the field for 2–6 days for rainfall events, and for one day for irrigation events. After 48 h incubation period, trap plants were transferred to a glasshouse (20 °C) to allow lesion development. Lesions on all plant parts were counted after two weeks, which gave an estimate of the number of conidia released and the distance travelled. Trap plants at all distances were infected in all sprinkler irrigation and rainfall events. The highest number of lesions on trap plants were recorded closest to the infested plots – the numbers decreased as the distance from the infested plots increased. There was a positive relationship between the amount of rainfall and the number of lesions recorded on trap plants. A generalised additive model was developed that efficiently described spatial patterns of conidial spread. With further development, the model can be used to predict the spread of A. rabiei. This is the first systematic study to show that conidia distribute A. rabiei over longer distances than previously reported.

Citation

Please cite this research compendium as:

Ihsanul Khaliq, Joshua Fanning, Paul Melloy, Jean Galloway, Kevin Moore, Daniel Burrell and Adam H. Sparks. ChickpeaAscoDispersal: A research compendium to accompany 'The role of conidia in the dispersal of Ascochyta rabiei'. Online at https://doi.org/10.5281/zenodo.3810826.

Licences

Data: CC-BY-4.0 International attribution requested in reuse
Manuscript: CC-BY-4.0
Code: GPL (>= 3) Year: 2020, copyright holder: University of Southern Queensland (USQ) and Grains Research and Development Corporation (GRDC)

Contributions

We welcome contributions from everyone. Before you get started, please see our contributor guidelines. Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.

Owner

Name: Adam H. Sparks
Login: adamhsparks
Kind: user
Location: Perth, Western Australia, Australia
Company: CCDM-CBADA

Website: https://adamhsparks.netlify.app/
Repositories: 19
Profile: https://github.com/adamhsparks

Professor of Biometry and Agricultural Data Analytics. Co-founder of @OpenPlantPathology. Editor at @ropensci

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GitHub Events

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Watch event: 1

Last Year

Watch event: 1

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Last synced: 8 months ago

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Total Commits: 427
Total Committers: 4
Avg Commits per committer: 106.75
Development Distribution Score (DDS): 0.124

Past Year

Commits: 0
Committers: 0
Avg Commits per committer: 0.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
Adam H. Sparks	a**s@g**m	374
PaulMelloy	p**l@m**u	51
Lars Gohr	l**s@g**l	1
IhsanKhaliq	5****q	1

Committer Domains (Top 20 + Academic)

gohr.digital: 1 melloy.com.au: 1

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Last synced: 8 months ago

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Total issues: 6
Total pull requests: 1
Average time to close issues: 2 days
Average time to close pull requests: about 10 hours
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Average comments per issue: 2.5
Average comments per pull request: 0.0
Merged pull requests: 1
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Bot pull requests: 0

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Issue authors: 0
Pull request authors: 0
Average comments per issue: 0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

chickpeaascodispersal

Science Score: 49.0%

Repository

Basic Info

Statistics

Metadata Files

README.md

The role of conidia in the dispersal of Ascochyta rabiei

Reproducibility

Data availability

Project team

Abstract

Citation

Licences

Contributions

Owner

CodeMeta (codemeta.json)

GitHub Events

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