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Heterogeneous disease progress of Black Leaf Streak Disease of banana at within-leaf scale

Summary

This repository contains scripts supporting a paper aiming to investigate the within-leaf progress of Black Leaf Streak Disease (BLSD) of banana plantain. Disease progress was measured over time in 192 leaf fragments of 3512 mm² taken from 9 banana leaves. Each fragment was monitored twice a week until fully covered by the disease. Functional principal component analysis was used to identify the main sources of variability in the disease progress over all individual fragments. Four groups of fragments with similar patterns of disease progress were clustered using k-means algorithm. The study revealed distinct temporal patterns that were significantly different from each other and linked to the predefined leaf compartments through a correspondence analysis.

Analyses step and corresponding scripts

Git_Repo_organisation

Packages required

All analyses were undertaken using R version 4.4.2 (http://www.r-project.org) with a two-sided p<0.05 considered statistically significant.

  • Exploratory and descriptives statistics were produced using the corrplot (version 0.95), arsenal (version 3.6.3), and multcomp (version 1.4-28) packages.
  • Functional analyses were performed using the refund package (version 0.1-37)
  • Clustering was performed using the stats package (version 4.4.2.). Clusters' visualizations were obtained using the cluster, FactoMineR (version 2.11), and factoextra (version 1.0.7) packages.
  • Generalized linear mixed models were fitted using the lme4 package (version 1.1-37) and the Estimated Marginal Means were computed using the emmeans package (version 1.11.1).
  • Correspondance analysis was performed using the FactoMineR package (version 2.11).

Authors

Marine Seidel ${1,4}$ *, Mathilde Chen ${2,4}$, Jacques Avelino ${2,4}$, Fabienne Ribeyre ${2,4}$, Clara Landry ${1,4}$, Catherine Abadie ${3,4}$

${1}$ CIRAD, UMR PHIM, F-97130 Capesterre-Belle-Eau, Guadeloupe, France.

${2}$ CIRAD, UMR PHIM, F-34398 Montpellier, France.

${3}$ CIRAD, UMR PHIM, 30501 Turrialba, Costa Rica.

${4}$ PHIM, CIRAD, INRAE, Institut Agro, IRD, Université de Montpellier, Montpellier, France.

*Corresponding author contact: marine.seidel@cirad.fr

Authors ORCID:

  • Marine Seidel : 0009-0002-3786-4673
  • Mathilde Chen : 0000-0002-5982-2143
  • Jacques Avelino : 0000-0003-1983-9431
  • Fabienne Ribeyre : 0000-0001-9721-1485
  • Catherine Abadie : 0000-0002-5075-6338

Key words

Pseudocercospora fijiensis, dynamics, spatial pattern, functional data analysis, Dominican Republic, plantain