Commit f5ad0829 authored by Jean-Francois Rey's avatar Jean-Francois Rey
Browse files

move from dev to prod

parent 90bafa17
Package: landsepiDev
Package: landsepi
Type: Package
Encoding: UTF-8
Title: Landscape Epidemiology and Evolution
Version: 1.0.0
Date: 2020-06-04
Date: 2020-07-01
Authors@R: c(person("Loup", "Rimbaud", role = "aut", email = "loup.rimbaud@inrae.fr"),
person("Julien", "Papaix", role = "aut", email = "julien.papaix@inrae.fr"),
person("Jean-Francois", "Rey", role = "cre", email = "jean-francois.rey@inrae.fr"),
......
......@@ -82,4 +82,4 @@ importFrom(splancs,polymap)
importFrom(utils,data)
importFrom(utils,installed.packages)
importFrom(utils,write.table)
useDynLib(landsepiDev, .registration = TRUE)
useDynLib(landsepi, .registration = TRUE)
......@@ -158,6 +158,6 @@
#'
#' @export
model_landsepi <- function(time_param, area_vector, rotation_matrix, croptypes_cultivars_prop, dispersal, inits, seed, cultivars_param, basic_patho_param, genes_param) {
invisible(.Call(`_landsepiDev_model_landsepi`, time_param, area_vector, rotation_matrix, croptypes_cultivars_prop, dispersal, inits, seed, cultivars_param, basic_patho_param, genes_param))
invisible(.Call(`_landsepi_model_landsepi`, time_param, area_vector, rotation_matrix, croptypes_cultivars_prop, dispersal, inits, seed, cultivars_param, basic_patho_param, genes_param))
}
......@@ -2,5 +2,5 @@
# 'tools::package_native_routine_registration_skeleton()' generates the required
# registration info for the 'run_testthat_tests' symbol.
(function() {
.Call("run_testthat_tests", PACKAGE = "landsepiDev")
.Call("run_testthat_tests", PACKAGE = "landsepi")
})
......@@ -38,7 +38,7 @@
#' Package: \tab landsepi\cr
#' Type: \tab Package\cr
#' Version: \tab 1.0.0\cr
#' Date: \tab 2020-06-04\cr
#' Date: \tab 2020-07-01\cr
#' License: \tab GPL (>=2)\cr
#' }
#'
......@@ -212,7 +212,7 @@
#' url: https://cran.r-project.org/package=landsepi.
#' @examples
#' \dontrun{
#' library("landsepiDev")
#' library("landsepi")
#'
#' ## Run demonstrations (in 20-year simulations) for different deployment strategies:
#' demo_landsepi(strat = "MO") ## for a mosaic of cultivars
......@@ -220,7 +220,7 @@
#' demo_landsepi(strat = "RO") ## for a rotation of cultivars
#' demo_landsepi(strat = "PY") ## for a pyramid of resistance genes
#' }
#' @useDynLib landsepiDev, .registration = TRUE
#' @useDynLib landsepi, .registration = TRUE
#' @import methods
#' @import graphics
#' @import stats
......
......@@ -5,7 +5,7 @@
#' @importFrom utils installed.packages
#' @export
runShinyApp <- function() {
appDir <- system.file("shiny-landsepi", "", package = "landsepiDev")
appDir <- system.file("shiny-landsepi", "", package = "landsepi")
if (appDir == "") {
stop("Could not find example directory. Try re-installing `landsepi`.", call. = FALSE)
}
......
#! /bin/sh
# Guess values for system-dependent variables and create Makefiles.
# Generated by GNU Autoconf 2.69 for landsepiDev 0.0.8.
# Generated by GNU Autoconf 2.69 for landsepi 1.0.0.
#
# Report bugs to <jean-francois.rey@inra.fr>.
#
......@@ -577,10 +577,10 @@ MFLAGS=
MAKEFLAGS=
# Identity of this package.
PACKAGE_NAME='landsepiDev'
PACKAGE_TARNAME='landsepidev'
PACKAGE_VERSION='0.0.8'
PACKAGE_STRING='landsepiDev 0.0.8'
PACKAGE_NAME='landsepi'
PACKAGE_TARNAME='landsepi'
PACKAGE_VERSION='1.0.0'
PACKAGE_STRING='landsepi 1.0.0'
PACKAGE_BUGREPORT='jean-francois.rey@inra.fr'
PACKAGE_URL=''
......@@ -1198,7 +1198,7 @@ if test "$ac_init_help" = "long"; then
# Omit some internal or obsolete options to make the list less imposing.
# This message is too long to be a string in the A/UX 3.1 sh.
cat <<_ACEOF
\`configure' configures landsepiDev 0.0.8 to adapt to many kinds of systems.
\`configure' configures landsepi 1.0.0 to adapt to many kinds of systems.
Usage: $0 [OPTION]... [VAR=VALUE]...
......@@ -1247,7 +1247,7 @@ Fine tuning of the installation directories:
--infodir=DIR info documentation [DATAROOTDIR/info]
--localedir=DIR locale-dependent data [DATAROOTDIR/locale]
--mandir=DIR man documentation [DATAROOTDIR/man]
--docdir=DIR documentation root [DATAROOTDIR/doc/landsepidev]
--docdir=DIR documentation root [DATAROOTDIR/doc/landsepi]
--htmldir=DIR html documentation [DOCDIR]
--dvidir=DIR dvi documentation [DOCDIR]
--pdfdir=DIR pdf documentation [DOCDIR]
......@@ -1260,7 +1260,7 @@ fi
if test -n "$ac_init_help"; then
case $ac_init_help in
short | recursive ) echo "Configuration of landsepiDev 0.0.8:";;
short | recursive ) echo "Configuration of landsepi 1.0.0:";;
esac
cat <<\_ACEOF
......@@ -1345,7 +1345,7 @@ fi
test -n "$ac_init_help" && exit $ac_status
if $ac_init_version; then
cat <<\_ACEOF
landsepiDev configure 0.0.8
landsepi configure 1.0.0
generated by GNU Autoconf 2.69
Copyright (C) 2012 Free Software Foundation, Inc.
......@@ -1446,7 +1446,7 @@ cat >config.log <<_ACEOF
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.
It was created by landsepiDev $as_me 0.0.8, which was
It was created by landsepi $as_me 1.0.0, which was
generated by GNU Autoconf 2.69. Invocation command line was
$ $0 $@
......@@ -3053,7 +3053,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
# report actual input values of CONFIG_FILES etc. instead of their
# values after options handling.
ac_log="
This file was extended by landsepiDev $as_me 0.0.8, which was
This file was extended by landsepi $as_me 1.0.0, which was
generated by GNU Autoconf 2.69. Invocation command line was
CONFIG_FILES = $CONFIG_FILES
......@@ -3106,7 +3106,7 @@ _ACEOF
cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
ac_cs_version="\\
landsepiDev config.status 0.0.8
landsepi config.status 1.0.0
configured by $0, generated by GNU Autoconf 2.69,
with options \\"\$ac_cs_config\\"
......
......@@ -10,8 +10,8 @@ dnl #################################################################
dnl -----------------------------------------------
dnl Package name and version number (user defined)
dnl -----------------------------------------------
define([THE_PACKAGE_NAME], [landsepiDev])
define([THE_PACKAGE_VERSION], [0.0.8])
define([THE_PACKAGE_NAME], [landsepi])
define([THE_PACKAGE_VERSION], [1.0.0])
define([THE_PACKAGE_MAINTAINER], [jean-francois.rey@inra.fr])
dnl --------------------------------
......
......@@ -70,7 +70,7 @@ RUN echo '#!/bin/sh\n\
COPY . /landsepi/
RUN R CMD build --no-build-vignettes /landsepi \
&& R CMD INSTALL --no-docs landsepiDev_*.tar.gz \
&& R CMD INSTALL --no-docs landsepi_*.tar.gz \
&& rm -r /landsepi
RUN apt-get update && apt-get remove --purge -y \
......
......@@ -2,8 +2,8 @@ library(shiny)
library(DT)
library(shinyjs)
#library(shinycssloaders)
library(landsepiDev)
data(package = "landsepiDev")
library(landsepi)
data(package = "landsepi")
source("server.R")
source("ui.R")
......
......@@ -11,8 +11,8 @@ library(promises)
library(tools)
library("landsepiDev")
data(package = "landsepiDev")
library("landsepi")
data(package = "landsepi")
## del all file and directory of a path
cleanDir <- function(path) {
......
......@@ -52,7 +52,7 @@ server <- function(input, output, session) {
# Modal Dialog
observeEvent(input$About, {
showModal(modalDialog(
title = paste0("About : Landsepi V", packageVersion("landsepiDev")),
title = paste0("About : Landsepi V", packageVersion("landsepi")),
easyClose = TRUE,
size = "l",
footer = NULL,
......@@ -378,7 +378,7 @@ server <- function(input, output, session) {
#print(simul_params)
future_process <<- future({
res <- landsepiDev::runSimul(simul_params,
res <- landsepi::runSimul(simul_params,
graphic = FALSE, videoMP4 = TRUE)
})
......
/* CULTIVAR */
INSERT INTO Cultivar VALUES(0, "wheat1", 0.10, 2.0, 0.10, 0.0, 0.0, 0.0000083, 0.0, 0.0, 0.0, 0.001, 0.2),
(1, "wheat2", 0.10, 2.0, 0.10, 0.0, 0.0, 0.0000083, 0.0, 0.0, 0.0, 0.001, 0.2),
(2, "wheat3", 0.10, 2.0, 0.10, 0.0, 0.0, 0.0000083, 0.0, 0.0, 0.0, 0.001, 0.2),
(3, "wheat4", 0.10, 2.0, 0.10, 0.0, 0.0, 0.0000083, 0.0, 0.0, 0.0, 0.001, 0.2),
(4, "wheat5", 0.10, 2.0, 0.10, 0.0, 0.0, 0.0000083, 0.0, 0.0, 0.0, 0.001, 0.2),
(5, "wheat6", 0.10, 2.0, 0.10, 0.0, 0.0, 0.0000083, 0.0, 0.0, 0.0, 0.001, 0.2);
/* CULTIVARLIST */
INSERT INTO CultivarList VALUES(0, 0, 0, 1.0),
(1, 1, 1, 0.5),
(2, 1, 2, 0.5),
(3, 2, 3, 0.5),
(4, 2, 4, 0.5),
(5, 3, 5, 1.0);
/* GENE */
INSERT INTO Gene VALUES(0, "gene1", 1.0, 0.0, 0.0, 0.0001, 2, 0.75, 1.0, "IR"),
(1, "gene2", 1.0, 0.0, 0.0, 0.0001, 2, 0.75, 1.0, "IR"),
(2, "gene3", 1.0, 0.0, 0.0, 0.0001, 2, 0.75, 1.0, "IR"),
(3, "gene4", 1.0, 0.0, 0.0, 0.0001, 2, 0.75, 1.0, "IR"),
(4, "QTL1", 0.5, 0.0, 0.0, 0.0001, 10, 0.75, 1.0, "IR"),
(5, "QTL2", 0.5, 0.0, 0.0, 0.0001, 10, 0.75, 1.0, "LAT"),
(6, "QTL3", 0.5, 30.0, 30.0, 0.0001, 10, 0.75, 1.0, "IP"),
(7, "QTL4", 0.5, 30.0, 30.0, 0.0001, 10, 0.75, 1.0, "PR");
/* GENELIST */
INSERT INTO GeneList VALUES(0,1,0),
(1,2,1),
(2,3,0),
(3,3,1),
(4,5,7);
/************************* CULTIVAR *************************/
INSERT INTO Cultivar VALUES(0, "Susceptible", 0.1, 2.0, 0.1, 0.0, 0.0, 0.0000083, 0.0, 0.0, 0.0, 0.001, 0.2),
(1, "Resistant1", 0.1, 2.0, 0.1, 0.0, 0.0, 0.0000083, 0.0, 0.0, 0.0, 0.001, 0.2),
(2, "Resistant2", 0.1, 2.0, 0.1, 0.0, 0.0, 0.0000083, 0.0, 0.0, 0.0, 0.001, 0.2);
/************************* CULTIVARLIST *************************/
INSERT INTO CultivarList VALUES(0, 0, 0, 1.0),
(1, 1, 1, 0.5),
(2, 1, 2, 0.5);
/************************* GENE *************************/
INSERT INTO Gene VALUES(0, "MG1", 1.0, 0.0, 0.0, 0.0000001, 2, 0.5, 1.0, "IR"),
(1, "MG2", 1.0, 0.0, 0.0, 0.0000001, 2, 0.5, 1.0, "IR"),
(2, "MG3", 1.0, 0.0, 0.0, 0.0000001, 2, 0.5, 1.0, "IR"),
(3, "MG4", 1.0, 0.0, 0.0, 0.0000001, 2, 0.5, 1.0, "IR"),
(4, "QTL1", 0.5, 0.0, 0.0, 0.0000001, 10, 0.5, 1.0, "IR"),
(5, "QTL2", 0.5, 0.0, 0.0, 0.0000001, 10, 0.5, 1.0, "LAT"),
(6, "QTL3", 0.5, 30.0, 30.0, 0.0000001, 10, 0.5, 1.0, "IP"),
(7, "QTL4", 0.5, 30.0, 30.0, 0.0000001, 10, 0.5, 1.0, "PR");
/************************* GENELIST *************************/
INSERT INTO GeneList VALUES(0,1,0),
(1,2,1);
/************************* CULTIVAR *************************/
INSERT INTO Cultivar VALUES(0, "Susceptible", 0.1, 2.0, 0.1, 0.0, 0.0, 0.0000083, 0.0, 0.0, 0.0, 0.001, 0.2),
(1, "Resistant1", 0.1, 2.0, 0.1, 0.0, 0.0, 0.0000083, 0.0, 0.0, 0.0, 0.001, 0.2),
(2, "Resistant2", 0.1, 2.0, 0.1, 0.0, 0.0, 0.0000083, 0.0, 0.0, 0.0, 0.001, 0.2);
/************************* CULTIVARLIST *************************/
INSERT INTO CultivarList VALUES(0, 0, 0, 1.0),
(1, 1, 1, 1.0),
(2, 2, 2, 1.0);
/************************* GENE *************************/
INSERT INTO Gene VALUES(0, "MG1", 1.0, 0.0, 0.0, 0.0000001, 2, 0.5, 1.0, "IR"),
(1, "MG2", 1.0, 0.0, 0.0, 0.0000001, 2, 0.5, 1.0, "IR"),
(2, "MG3", 1.0, 0.0, 0.0, 0.0000001, 2, 0.5, 1.0, "IR"),
(3, "MG4", 1.0, 0.0, 0.0, 0.0000001, 2, 0.5, 1.0, "IR"),
(4, "QTL1", 0.5, 0.0, 0.0, 0.0000001, 10, 0.5, 1.0, "IR"),
(5, "QTL2", 0.5, 0.0, 0.0, 0.0000001, 10, 0.5, 1.0, "LAT"),
(6, "QTL3", 0.5, 30.0, 30.0, 0.0000001, 10, 0.5, 1.0, "IP"),
(7, "QTL4", 0.5, 30.0, 30.0, 0.0000001, 10, 0.5, 1.0, "PR");
/************************* GENELIST *************************/
INSERT INTO GeneList VALUES(0,1,0),
(1,2,1);
/************************* CULTIVAR *************************/
INSERT INTO Cultivar VALUES(0, "Susceptible", 0.1, 2.0, 0.1, 0.0, 0.0, 0.0000083, 0.0, 0.0, 0.0, 0.001, 0.2),
(1, "Resistant", 0.1, 2.0, 0.1, 0.0, 0.0, 0.0000083, 0.0, 0.0, 0.0, 0.001, 0.2);
/************************* CULTIVARLIST *************************/
INSERT INTO CultivarList VALUES(0, 0, 0, 1.0),
(1, 1, 1, 1.0);
/************************* GENE *************************/
INSERT INTO Gene VALUES(0, "MG1", 1.0, 0.0, 0.0, 0.0001, 2, 0.5, 1.0, "IR"),
(1, "MG2", 1.0, 0.0, 0.0, 0.0001, 2, 0.5, 1.0, "IR"),
(2, "MG3", 1.0, 0.0, 0.0, 0.0001, 2, 0.5, 1.0, "IR"),
(3, "MG4", 1.0, 0.0, 0.0, 0.0001, 2, 0.5, 1.0, "IR"),
(4, "QTL1", 0.5, 0.0, 0.0, 0.0001, 10, 0.5, 1.0, "IR"),
(5, "QTL2", 0.5, 0.0, 0.0, 0.0001, 10, 0.5, 1.0, "LAT"),
(6, "QTL3", 0.5, 30.0, 30.0, 0.0001, 10, 0.5, 1.0, "IP"),
(7, "QTL4", 0.5, 30.0, 30.0, 0.0001, 10, 0.5, 1.0, "PR");
/************************* GENELIST *************************/
INSERT INTO GeneList VALUES(0,1,0),
(1,1,1);
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