index.Rmd

% About

Here I present the results of the field trial, set up to evaluate the opportunities for the IPM of potato late blight under Irish conditions.  
[Link to publication](https://apsjournals.apsnet.org/doi/abs/10.1094/PHYTO-01-20-0011-R)  

### Content  

We looked into potential for using the environmental disease risk prediction, varietal resistance and information on the pathogen population for the reduction of the pesticide usage.  
The presentation is split into following sections:  
- Disease: The analysis of the foliar disease control.  
- Treatment: Number of treatments and proportion of the total dose used in fungicide trials.  
- Yield: The effects of the fungicide programme, varietal resistance on marketable yield over the evaluated period.  
- Population data: Presentation of the sampling and a descriptive analysis of the samples collected.   
- Pop(ulation) Bruvo: Bruvo charts for population data.  
- Pop(ulation) DAPC: Discriminant analysis of principal components (DAPC) analysis of the population data.

 The funding for this project comes from [DAFM (Department of Agriculture, Food and Marine)](https://www.agriculture.gov.ie).  
   
The repository is built on the example research compendium provided by Emerson Del Ponte [here](https://github.com/emdelponte/research-compendium-website). 
  
### Previous work
**The open-access publication of the manuscript where we have presented the preceding work on the evaluation of the Irish Rules, potato late blight risk model used in Ireland, can be found** [here](https://www.mdpi.com/2073-4395/9/9/515).  
The accompanying compendium with open access to the code is [here.](https://mladencucak.github.io/AnalysisPLBIreland/)

### The location

```{r map, echo=FALSE, message=FALSE, warning=FALSE}
library("leaflet")
greenLeafIcon <- makeIcon(
  iconUrl = "http://leafletjs.com/examples/custom-icons/leaf-green.png",
  iconWidth = 38, iconHeight = 95,
  iconAnchorX = 22, iconAnchorY = 94,
  shadowUrl = "http://leafletjs.com/examples/custom-icons/leaf-shadow.png",
  shadowWidth = 50, shadowHeight = 64,
  shadowAnchorX = 4, shadowAnchorY = 62
)

leaflet() %>%
  addTiles(group = "OSM (default)") %>%
    setView(-8, 53.5, 6) %>%
  addMarkers(
    lng = -6.9121167,
    lat = 52.8560667,
    label = "Oak Park",
    icon = greenLeafIcon
  )

```

### Notes 

This project contains a snapshot of packages used in the project. For the full reproducibility just download the whole R project. 
Some code chunks are folded and they can be accessed by clicking on the arrow (The code).  
Try not to have other R sessions running because it could produce problems installing libraries.  
If there are any problems reproducing the analysis, please raise an issue on GitHub.  

### Project team

Maynooth University:
- [Rowan Fealy](https://www.maynoothuniversity.ie/people/rowan-fealy)

Teagasc:
- [Stephen Kildea](https://www.teagasc.ie/contact/staff-directory/k/steven-kildea/)

Met Eirean:
- [Keith Lambkin](https://www.researchgate.net/profile/Keith_Lambkin)

### Citation

Please cite this research compendium as:


>Cucak, M., Moral, R.D.A., Fealy, R., Lambkin, K. and Kildea, S., Opportunities for an improved potato late blight management in the Republic of Ireland: Field evaluation of the modified Irish Rules crop disease risk prediction model. *Phytopathology*.

### Licences

Data: [CC-0](https://creativecommons.org/publicdomain/zero/1.0/) attribution requested in reuse
Manuscript: [CC-BY-4.0](https://creativecommons.org/licenses/by/4.0/)  
Code: [MIT](https://opensource.org/licenses/MIT) year: 2019, copyright holder: Mladen Cucak

### Contributions

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