Commit 64f1f7e8 authored by Jean-Francois Rey's avatar Jean-Francois Rey
Browse files

change dkpdown config

parent 6cc7106e
......@@ -24,3 +24,4 @@
^doc$
^Meta$
^_pkgdown.yml$
^index.md$
......@@ -2,7 +2,7 @@ Package: landsepiDev
Type: Package
Encoding: UTF-8
Title: Landscape Epidemiology and Evolution
Version: 1.0.2
Version: 1.0.2.9999
Date: 2020-07-02
Authors@R:
c(person(given = "Loup",
......@@ -32,8 +32,9 @@ Description: A stochastic, spatially-explicit, demo-genetic model simulating the
respect to their epidemiological, evolutionary and economic outcomes.
Loup Rimbaud, Julien Papaïx, Jean-François Rey, Luke G Barrett,
Peter H Thrall (2018) <doi:10.1371/journal.pcbi.1006067>.
URL: https://gitlab.paca.inra.fr/CSIRO-INRA/landsepi
BugReports: https://gitlab.paca.inra.fr/CSIRO-INRA/landsepi/issues
URL: https://csiro-inra.pages.biosp.inrae.fr/landsepi/,
https://gitlab.paca.inra.fr/CSIRO-INRA/landsepi
BugReports: https://gitlab.paca.inrae.fr/CSIRO-INRA/landsepi/-/issues
License: GPL (>= 2) | file LICENSE
LazyData: true
BuildVignettes: true
......
......@@ -142,7 +142,7 @@ You can try the [online Landsepi R Shiny App](https://shiny.biosp.inrae.fr/app/l
or run it into R. To run the shiny interface into R you will need the following packages:
```r
Install packages : install.packages(c("shiny","DT", "shinyjs", "gridExtra", "png", "grid"
, "future", "promises", "tools"))
, "future", "promises", "tools", "shinyalert"))
```
The app can be launched with:
......
......@@ -2,9 +2,13 @@ repo:
url:
home: https://gitlab.paca.inrae.fr/CSIRO-INRA/landsepi
authors:
Jean-François Rey:
href: "https://jeff.biosp.org"
navbar:
structure:
left: [home, intro, reference, articles, tutorials, news]
left: [home, intro, reference, articles, tutorials, news, shinyapp]
right: [gitlab]
components:
gitlab:
......@@ -13,3 +17,10 @@ navbar:
github:
icon: fab fa-gitlab fa-lg
href: https://gitlab.paca.inrae.fr/CSIRO-INRA/landsepi
intro:
text: Get Started
href: articles/O1-run_simple_simul.html
shinyapp:
text: -> Shiny app <-
href: https://shiny.biosp.inrae.fr/app_direct/landsepi
# landsepi : Landscape Epidemiology and Evolution
<!-- badges: start -->
[![pipeline status](https://gitlab.paca.inra.fr/CSIRO-INRA/landsepi/badges/master/pipeline.svg)](https://gitlab.paca.inra.fr/CSIRO-INRA/landsepi/commits/master)
[![CRAN status](https://www.r-pkg.org/badges/version/landsepi)](https://cran.r-project.org/package=landsepi)
<!-- badges: end -->
## Description
A stochastic, spatially-explicit, demo-genetic model simulating the spread and evolution of a plant pathogen in a heterogeneous landscape to assess resistance deployment strategies.
It is based on a spatial geometry for describing the landscape and allocation of different cultivars, a dispersal kernel for the dissemination of the pathogen, and a SEIR ('Susceptible-Exposed-Infectious-Removed’) structure with a discrete time step.
It provides a useful tool to assess the performance of a wide range of deployment options with respect to their epidemiological, evolutionary and economic outcomes.
## Installation
### Configuration and dependencies
Read file "DESCRIPTION" for details on configuration requirements (with linux and R).
The package for compiling needs g++, gsl dev library and ffmpeg (for videos).
Under Linux OS:
```bash
sudo apt-get install g++ libgsl2 libgsl-dev ffmpeg
```
Under Windows use the zip.
> You can install Rtools and get g++, gsl and ffmpeg binaries under Windows (using pacman).
R packages dependencies :
* Rcpp
* sp
* Matrix
* mvtnorm
* maptools
* fields
* splancs
* sf
* DBI
* RSQLite
* foreach
* parallel
* doParallel
To install :
```r
install.packages(c("Rcpp","sp","Matrix","mvtnorm","maptools","fields","splancs","sf","DBI","RSQLite","foreach","parallel","doParallel"))
```
### Shiny interface
You can try the [online Landsepi R Shiny App](https://shiny.biosp.inrae.fr/app/landsepi)
or run it into R. To run the shiny interface into R you will need the following packages:
```r
Install packages : install.packages(c("shiny","DT", "shinyjs", "gridExtra", "png", "grid"
, "future", "promises", "tools", "shinyalert"))
```
The app can be launched with:
```r
library(landsepi)
runShinyApp()
```
## Usage
### Demonstrations
Run demonstrations (in 20-year simulations) for different deployment strategies:
```r
demo_landsepi(strat = "MO") ## for a mosaic of cultivars
demo_landsepi(strat = "MI") ## for a mixture of cultivars
demo_landsepi(strat = "RO") ## for a rotation of cultivars
demo_landsepi(strat = "PY") ## for a pyramid of resistance genes
```
### Get started
To get started see the [first article](articles/O1-run_simple_simul.html)
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