Commit 1f494e80 authored by jfuser's avatar jfuser
Browse files

update for new CRAN submission

parent 44b20709
Pipeline #140 passed with stage
in 19 minutes and 21 seconds
......@@ -63,3 +63,18 @@ release-package:
only:
- tags
release-Mac:
tags:
- "Mac"
- "R"
script:
- "Rscript -e \"roxygen2::roxygenize('.', roclets=c('rd', 'collate', 'namespace'))\""
- "R CMD build . --resave-data"
- "R CMD INSTALL --binary $(ls -rt landsepi_*.tar.gz |tail -1)"
artifacts:
paths:
- "$(ls -rt landsepi_*.tgz | tail -1)"
only:
- tags
......@@ -2,8 +2,8 @@ Package: landsepi
Type: Package
Encoding: UTF-8
Title: Landscape Epidemiology and Evolution
Version: 0.0.4
Date: 2018-04-10
Version: 0.0.5
Date: 2018-04-25
Authors@R: c(person("Loup", "Rimbaud", role = "aut", email = "loup.rimbaud@csiro.au"),
person("Julien", "Papaix", role = "aut", email = "julien.papaix@inra.fr"),
person("Jean-Francois", "Rey", role = "cre", email = "jean-francois.rey@inra.fr"))
......@@ -17,7 +17,7 @@ Description: A spatio-temporal stochastic model to assess resistance deployment
pathogen, and a SEIR (Susceptible-Exposed-Infectious-Removed) architecture to simulate
plant response to disease.
Loup Rimbaud, Julien Papaïx, Jean-François Rey, Luke G Barrett,
Peter H Thrall (2018) <doi:10.1101/260836>.
Peter H Thrall (2018) <doi:10.1371/journal.pcbi.1006067>.
License: GPL (>= 2) | file LICENSE
LazyData: true
BuildVignettes: true
......
......@@ -55,6 +55,6 @@
#' @references Rimbaud L., Papaïx J., Rey J.-F., Barrett L. G. and Thrall P. H. (2018). Assessing the durability and efficiency of landscape-based strategies to deploy plant resistance to pathogens. \emph{PLoS Computational Biology} 14(4):e1006067.
#' @export
modelLandsEPI <- function(times, landscape, dispersal, inits, val_seed, hostP, epiP, evolP) {
invisible(.Call('landsepi_modelLandsEPI', PACKAGE = 'landsepi', times, landscape, dispersal, inits, val_seed, hostP, epiP, evolP))
invisible(.Call('_landsepi_modelLandsEPI', PACKAGE = 'landsepi', times, landscape, dispersal, inits, val_seed, hostP, epiP, evolP))
}
......@@ -36,8 +36,8 @@
#' @details \tabular{ll}{
#' Package: \tab lansepi\cr
#' Type: \tab Package\cr
#' Version: \tab 0.0.4\cr
#' Date: \tab 2018-04-10\cr
#' Version: \tab 0.0.5\cr
#' Date: \tab 2018-04-24\cr
#' License: \tab GPL (>=2)\cr
#' }
#'
......
......@@ -6,7 +6,7 @@ output:
# R package landsepi
Landscape Epidemiology and Evolution
<!--[![pipeline status](https://gitlab.paca.inra.fr/CSIRO-INRA/landsepi/badges/master/pipeline.svg)](https://gitlab.paca.inra.fr/CSIRO-INRA/landsepi/commits/master) -->
[![pipeline status](https://gitlab.paca.inra.fr/CSIRO-INRA/landsepi/badges/master/pipeline.svg)](https://gitlab.paca.inra.fr/CSIRO-INRA/landsepi/commits/master)
## Description
A spatio-temporal stochastic model to assess resistance deployment strategies against plant pathogens.
......@@ -65,8 +65,7 @@ R packages dependencies :
To install :
```r
install.packages(c("Rcpp","sp","rgdal","Matrix","MASS","rgeos","maptools"
,"fields","splancs","sf"))
install.packages(c("Rcpp","sp","rgdal","Matrix","MASS","rgeos","maptools","fields","splancs","sf"))
```
### Install landsepi
......@@ -87,7 +86,7 @@ Open R :
```r
library(Rcpp)
library(roxygen2)
Rcpp::compileAttribute(pkg=".")
Rcpp::compileAttributes(pkg=".")
roxygen2::roxygenize('.', roclets=c('rd', 'namespace'))
```
......
......@@ -22,8 +22,7 @@ bibentry(
year = 2018,
volume = 14,
issue = 4,
pages = e1006067,
doi = "10.1371/journal.pcbi.1006067",
journal = "PLoS Computational Biology")
journal = "PLOS Computational Biology")
)
......@@ -17,8 +17,8 @@ architecture to simulate plant response to disease.
\tabular{ll}{
Package: \tab lansepi\cr
Type: \tab Package\cr
Version: \tab 0.0.4\cr
Date: \tab 2018-04-10\cr
Version: \tab 0.0.5\cr
Date: \tab 2018-04-24\cr
License: \tab GPL (>=2)\cr
}
......
......@@ -7,7 +7,7 @@ using namespace Rcpp;
// modelLandsEPI
void modelLandsEPI(Rcpp::List times, Rcpp::List landscape, Rcpp::List dispersal, Rcpp::List inits, int val_seed, Rcpp::List hostP, Rcpp::List epiP, Rcpp::List evolP);
RcppExport SEXP landsepi_modelLandsEPI(SEXP timesSEXP, SEXP landscapeSEXP, SEXP dispersalSEXP, SEXP initsSEXP, SEXP val_seedSEXP, SEXP hostPSEXP, SEXP epiPSEXP, SEXP evolPSEXP) {
RcppExport SEXP _landsepi_modelLandsEPI(SEXP timesSEXP, SEXP landscapeSEXP, SEXP dispersalSEXP, SEXP initsSEXP, SEXP val_seedSEXP, SEXP hostPSEXP, SEXP epiPSEXP, SEXP evolPSEXP) {
BEGIN_RCPP
Rcpp::RNGScope rcpp_rngScope_gen;
Rcpp::traits::input_parameter< Rcpp::List >::type times(timesSEXP);
......@@ -22,3 +22,13 @@ BEGIN_RCPP
return R_NilValue;
END_RCPP
}
static const R_CallMethodDef CallEntries[] = {
{"_landsepi_modelLandsEPI", (DL_FUNC) &_landsepi_modelLandsEPI, 8},
{NULL, NULL, 0}
};
RcppExport void R_init_landsepi(DllInfo *dll) {
R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
R_useDynamicSymbols(dll, FALSE);
}
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