update output bug/hack

try to include pdf parameters into pkgdown et reduce size

DESCRIPTION

@@ -22,7 +22,7 @@ Authors@R:
              family = "Gaussen",
              role = "ctb",
              email = "jean-loup-thomas.gaussen@inrae.fr"))
-Maintainer: Jean-Francois Rey <jean-francois.rey@inrae.fr>
+Maintainer: Jean-François Rey <jean-francois.rey@inrae.fr>
 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, 

R/output.R

@@ -846,7 +846,8 @@ evol_output <- function(types = "all", time_param, Npoly, cultivars_param, genes
   return(res[match(types, valid_outputs)])
 }
 
-
+## Hack foreach dopar y variable
+utils::globalVariables(c("y"))
 #' @title Generation of a video
 #' @name video
 #' @description Generates a video showing the epidemic dynamics on a map representing the cropping landscape.
@@ -1015,6 +1016,7 @@ video <- function(audpc, time_param, Npatho, landscape, area, rotation, croptype
   # legend_prev <- sprintf("%.3f", intvls)
   legend_prev <- paste(intvls * 100, "%", sep = "")
 
+
   registerDoParallel(parallel::detectCores())
   foreach(y = 1:Nyears) %dopar% {
     print(paste("Year", y, "/", Nyears))

man/landsepi-package.Rd

@@ -211,7 +211,7 @@ url: https://cran.r-project.org/package=landsepi.
 Useful links:
 \itemize{
   \item \url{https://csiro-inra.pages.biosp.inrae.fr/landsepi/}
-  \item \url{https://gitlab.paca.inra.fr/CSIRO-INRA/landsepi}
+  \item \url{https://gitlab.paca.inrae.fr/CSIRO-INRA/landsepi}
   \item Report bugs at \url{https://gitlab.paca.inrae.fr/CSIRO-INRA/landsepi/-/issues}
 }
 

vignettes/O1-run_simple_simul.Rmd

@@ -8,6 +8,8 @@ vignette: >
   %\VignetteEngine{knitr::rmarkdown}
 editor_options: 
   chunk_output_type: console
+resource_files:
+  - inst/doc/list_of_parameters.pdf
 ---
 
 ```{r, include = FALSE}