Commit 64580ce4 authored by jfuser's avatar jfuser
Browse files

update readme

update data use and info (cran check now will fail)
parent 91a1d67d
Pipeline #71 passed with stage
in 6 minutes and 40 seconds
......@@ -54,6 +54,6 @@
#' Each file indicates for every time-step the number of individuals in each field, and when appropriate for each cultivar and pathotype)
#' @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))
}
......@@ -44,8 +44,8 @@ demo_landsepi <- function(seed=12345){
Cmax0 <- 2
Cmax1 <- 2
# hack for cran check
landscapeTEST1 <- NULL
data(landscapeTEST1, envir=environment())
#landscapeTEST1 <- NULL
#data("landscapeTEST1", envir=environment())
landscape <- AgriLand(landscapeTEST1,filename="landscapeTEST1",propSR,isolSR,propRR,isolRR,strat,Nhote,nYears,Cmax0,Cmax1,seed,graphOn)
#time parameters
......@@ -55,10 +55,10 @@ demo_landsepi <- function(seed=12345){
#dispersal
# Hack for cran check
dispP_1 <- NULL
dispH <- NULL
data(dispP_1,envir=environment())
data(dispH, envir=environment())
#dispP_1 <- NULL
#dispH <- NULL
#data(dispP_1,envir=environment())
#data(dispH, envir=environment())
#host parameters
croisH0 <- 0.10
......
......@@ -168,44 +168,44 @@ test_landsepi <- function(seed=12345, idLan=1, propSR=2/3, isolSR=3, propRR=1/2,
paramT <- list(nYears=nYears,nTSpY=nTSpY)
## Landscape and dispersal
dispH <- NULL # Hack for cran check
data(dispH, envir=environment())
#dispH <- NULL # Hack for cran check
#data(dispH, envir=environment())
landscape <- NULL
dispP <- NULL
if (idLan==1){
landscapeTEST1 <- NULL
data(landscapeTEST1, envir=environment())
dispP_1 <- NULL # Hack for cran check
data(dispP_1,envir=environment())
#landscapeTEST1 <- NULL
#data(landscapeTEST1, envir=environment())
#dispP_1 <- NULL # Hack for cran check
#data(dispP_1,envir=environment())
landscape <- landscapeTEST1
dispP <- dispP_1
}else if (idLan==2){
landscapeTEST2 <- NULL
data(landscapeTEST2, envir=environment())
dispP_2 <- NULL
data(dispP_2,envir=environment())
#landscapeTEST2 <- NULL
#data(landscapeTEST2, envir=environment())
# dispP_2 <- NULL
#data(dispP_2,envir=environment())
landscape <- landscapeTEST1
dispP <- dispP_2
}else if (idLan==3){
landscapeTEST3 <- NULL
data(landscapeTEST3, envir=environment())
dispP_3 <- NULL
data(dispP_3,envir=environment())
#landscapeTEST3 <- NULL
#data(landscapeTEST3, envir=environment())
#dispP_3 <- NULL
#data(dispP_3,envir=environment())
landscape <- landscapeTEST3
dispP <- dispP_3
}else if (idLan==4){
landscapeTEST4 <- NULL
data(landscapeTEST4, envir=environment())
dispP_4 <- NULL
data(dispP_4,envir=environment())
#landscapeTEST4 <- NULL
#data(landscapeTEST4, envir=environment())
#dispP_4 <- NULL
#data(dispP_4,envir=environment())
landscape <- landscapeTEST4
dispP <- dispP_4
}else if (idLan==5){
landscapeTEST5 <- NULL
data(landscapeTEST5, envir=environment())
dispP_5 <- NULL
data(dispP_5,envir=environment())
#landscapeTEST5 <- NULL
#data(landscapeTEST5, envir=environment())
#dispP_5 <- NULL
#data(dispP_5,envir=environment())
landscape <- landscapeTEST5
dispP <- dispP_5 }
......
---
output:
pdf_document: default
html_document: default
---
# R package landsepi
Landscape Epidemiology and Evolution
......
......@@ -7,7 +7,7 @@
\description{
A landscape SpatialPolygons for testing, composed of 155 fields.
}
\usage{data("landscapeTEST1")}
\usage{landscapeTEST1}
\format{
The format is:
Formal class 'SpatialPolygons' [package "sp"] with 4 slots
......
......@@ -7,7 +7,7 @@
\description{
A landscape SpatialPolygons for testing, composed of 154 fields.
}
\usage{data("landscapeTEST2")}
\usage{landscapeTEST2}
\format{
The format is:
Formal class 'SpatialPolygons' [package "sp"] with 4 slots
......
......@@ -7,7 +7,7 @@
\description{
A landscape SpatialPolygons for testing, composed of 152 fields.
}
\usage{data("landscapeTEST3")}
\usage{landscapeTEST3}
\format{
The format is:
Formal class 'SpatialPolygons' [package "sp"] with 4 slots
......
......@@ -7,7 +7,7 @@
\description{
A landscape SpatialPolygons for testing, composed of 153 fields.
}
\usage{data("landscapeTEST4")}
\usage{landscapeTEST4}
\format{
The format is:
Formal class 'SpatialPolygons' [package "sp"] with 4 slots
......
......@@ -7,7 +7,7 @@
\description{
A landscape SpatialPolygons for testing, composed of 156 fields.
}
\usage{data("landscapeTEST5")}
\usage{landscapeTEST5}
\format{
The format is:
Formal class 'SpatialPolygons' [package "sp"] with 4 slots
......
......@@ -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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