• PPBstats website
  • Preface
    • Contact
    • Authors and contributors of PPBstats and the book
    • Copyright, Licence, citation
  • 1 Philosophy of PPBstats
    • 1.1 What is Participatory Plant Bredding ?
      • 1.1.1 Decentralize the selection
      • 1.1.2 Involve all actors in the breeding decision process
    • 1.2 Objectives of PPBstats
    • 1.3 Contribute
    • 1.4 Design and statistical methods according to the objectives
    • 1.5 Let’s go: install PPBstats and the data used in the book!
  • 2 Analysis of network seed circulation (M8)
    • 2.1 Introduction
      • 2.1.1 Workflow and function relations in PPBstats regarding network analysis
    • 2.2 Unipart network for seed lots analysis
      • 2.2.1 Steps with PPBstats
      • 2.2.2 Format the data
      • 2.2.3 Describe the data
    • 2.3 Unipart network for location analysis
      • 2.3.1 Steps with PPBstats
      • 2.3.2 Format the data
      • 2.3.3 Format and describe the data for each germplasm
      • 2.3.4 Format and describe the data for each year
    • 2.4 Bipart network analysis
      • 2.4.1 Steps with PPBstats
      • 2.4.2 Format the data
      • 2.4.3 Describe the data
  • 3 Analysis of agronomic traits
    • 3.1 Introduction
      • 3.1.1 Analysis according to the objectives
      • 3.1.2 Family of analyses
      • 3.1.3 Experimental design
      • 3.1.4 Decision tree
      • 3.1.5 Workflow and function relations in PPBstats regarding agronomic analysis
      • 3.1.6 Data format
    • 3.2 Design the experiment
      • 3.2.1 Fully-replicated (D1)
      • 3.2.2 Incomplete Block Design (D2)
      • 3.2.3 Row-column (D3)
      • 3.2.4 Regional and satellite farms (D4)
    • 3.3 Sow, note, harvest, measure …
    • 3.4 Describe the data
      • 3.4.1 Format the data
      • 3.4.2 presence abscence matrix
      • 3.4.3 histogramm
      • 3.4.4 barplot
      • 3.4.5 boxplot
      • 3.4.6 interaction
      • 3.4.7 biplot
      • 3.4.8 radar
      • 3.4.9 raster
      • 3.4.10 map
    • 3.5 Family 1 of analysis : Compare different varieties evaluated for selection in different locations.
      • 3.5.1 Decision tree
      • 3.5.2 Workflow and function relations in PPBstats regarding family 1 of analysis
      • 3.5.3 Classic ANOVA (M4a)
      • 3.5.4 Spatial analysis (M4b)
      • 3.5.5 Mixted model for incomplete block design (M5)
      • 3.5.6 Hierarchical Bayesian intra-location model to perform mean comparisons with each farm (M7a)
    • 3.6 Family 2 of analysis : Study the response of varieties under selection over several environments
      • 3.6.1 Decision tree
      • 3.6.2 Workflow and function relations in PPBstats regarding family 2 of analysis
      • 3.6.3 AMMI (M6a)
      • 3.6.4 GGE (M6b)
      • 3.6.5 Hierarchical Bayesian \(G \times E\) model to analyse \(G \times E\) interaction in the network of farms (M7b)
    • 3.7 Family 3 of analysis : effects from family 1 and 2 in a network of farms
      • 3.7.1 model 3
    • 3.8 Family 4 of analysis : specific research questions on one farm or more
      • 3.8.1 Study reponse to selection
      • 3.8.2 Study local adaptation
      • 3.8.3 Study variance within germplasm
    • 3.9 Family 5 of analysis : multivariate analysis
      • 3.9.1 Decision tree
      • 3.9.2 Workflow and function relations in PPBstats regarding family 2 of analysis
      • 3.9.3 Steps with PPBstats
      • 3.9.4 Format the data
      • 3.9.5 Look at correlation
      • 3.9.6 Run the analysis
      • 3.9.7 Check outputs and results
  • 4 Sensory analysis
    • 4.1 Introduction
      • 4.1.1 Analysis according to the objectives
      • 4.1.2 Decision tree
      • 4.1.3 Workflow and function relations in PPBstats regarding organoleptic analysis
      • 4.1.4 Data format
    • 4.2 Taste and measure …
    • 4.3 Hedonic analysis (M9b)
      • 4.3.1 Method description
      • 4.3.2 Steps with PPBstats
      • 4.3.3 Format the data
      • 4.3.4 Describe the data
      • 4.3.5 Run the model
      • 4.3.6 Check and visualize model outputs
      • 4.3.7 Get and visualize mean comparisons on note
      • 4.3.8 Get and visualize biplot regarding samples (CA) and juges (HCPC)
    • 4.4 Napping analysis (M9a)
      • 4.4.1 Method description
      • 4.4.2 Steps with PPBstats
      • 4.4.3 Format the data
      • 4.4.4 Describe the data
      • 4.4.5 Run the model
      • 4.4.6 Check and visualize model outputs
      • 4.4.7 Get and visualize biplot
    • 4.5 Rank analysis (M9c)
      • 4.5.1 Method description
      • 4.5.2 Steps with PPBstats
      • 4.5.3 Format the data
      • 4.5.4 Run the model
  • 5 Molecular analysis (M3)
  • 6 Communicate results to farmers
    • 6.1 Technical aspects
      • 6.1.1 Run the analysis
      • 6.1.2 Create a .Rmd template
      • 6.1.3 Generate a report for each location
    • 6.2 Organisational aspects on collective work
  • Acknowledgement
  • References
  • PPBstats website

PPBstats : An R package for Participatory Plant Breeding statisticial analyses

Copyright, Licence, citation

Copyright Réseau Semences Paysannes and Institut National de la Recherche Agronomique

The R code is under licence GPL-3.

The book is under licence creative commons BY-NC-SA 4.0

To cite the package :

citation("PPBstats")
## 
## To cite the PPBstats package in publications use:
## 
##   Pierre Riviere and al, 2019, PPBstats: An R package to perform
##   analysis found within PPB programmes.  Version 0.25, URL:
##   https://github.com/priviere/PPBstats_web_site
## 
## A BibTeX entry for LaTeX users is
## 
##   @Manual{,
##     title = {PPBstats: An R package to perform analysis found within PPB programmes
##   regarding network of seeds circulation, agronomic trials, organoleptic tests and
##   molecular experiments. Version 0.25},
##     author = {{Pierre Riviere and Gaelle {Van Franck} and Olivier David and Facundo Muñoz and Baptiste Rouger and Camille Vindras and Mathieu Thomas and Isabelle Goldringer}},
##     organisation = {{Reseau Semences Paysannes}, {INRA}, {CIRAD}, {ITAB}},
##     year = {2019},
##     url = {https://github.com/priviere/PPBstats_web_site},
##     note = {R code is under licence GPL-3. 
##           Vignette is under licence creative commons BY-NC-SA 4.0.},
##   }

To cite the book :

bibtex entry

@book{ppbstats_book_2018,
  title = "{PPBstats : An R package for Participatory Plant Breeding statisticial analyses.}",
    author = "{Pierre Riviere and Gaelle {Van Franck} and Olivier David and Baptiste Rouger and Camille Vindras and Mathieu Thomas and Isabelle Goldringer}",
    year = "2019",
    version = "0.25",
    licence = "CC BY NC SA",
    url = "https://priviere.github.io/PPBstats_book/"
}