## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.width=7,
  tidy=T,
  fig.align='center',
  tidy.opts = list(width.cutoff=80)
)

## ----eval=FALSE---------------------------------------------------------------
# Ncol<-31
# Nrow<-31
# Ntimesteps<-140

## ----eval=FALSE---------------------------------------------------------------
# #Create the temperature array and matrix:
# temp_array<-array(NA,dim=c(Nrow,Ncol,Ntimesteps))
# temp_dataframe<-matrix(NA,nrow=Nrow*Ncol, ncol=length(c(Ncol,Nrow))+Ntimesteps)
# 
# #Create the precipitation array and matrix:
# prec_array<-array(NA,dim=c(Nrow,Ncol,Ntimesteps))
# prec_dataframe<-matrix(NA,nrow=Nrow*Ncol, ncol=length(c(Ncol,Nrow))+Ntimesteps)
# 
# #Creating a vector for the names to be used to name input files (one per time step)
# stringtimestepsnames<-vector(mode="character",length=Ntimesteps)

## ----tidy=T, out.width='100%', echo=F, fig.cap='A1: Animation of the conceptual island that we will create as an input landscape for gen3sis.', fig.margin=T----
knitr::include_graphics("../inst/extdata/CaseStudy1/landscape/case_study_landscape.gif")

## ----eval=FALSE---------------------------------------------------------------
# for (timestep in 1:Ntimesteps){ # temporal loop
#   counting<-1
#   stringtimestepsnames[timestep]<-paste("X",timestep,"", sep="")
#   for (y in 1:Nrow){ #loop over the first spatial dimension
#     for (x in 1:Ncol){ #loop over the second spatial dimension
#       if((timestep<=10)||(timestep>120 && timestep<=140)){#time steps with only four (2x2) suitable sites
#         if((y>=15 && y<=16)&&(x>=15 && x<=16)) {  #suitable sites
#           temp_array[x,y,timestep] <- rnorm(1,20,0.5) #temperature
#           prec_array[x,y,timestep] <- rnorm(1,500,50) #precipitation
#         }
#       }
#       if((timestep>10 && timestep<=20)||(timestep>100 && timestep<=120)){#time steps with nine (3x3) suitable sites
#         if((y>=15 && y<=17)&&(x>=15 && x<=17)) {
#           temp_array[x,y,timestep] <- rnorm(1,20,0.5)
#           prec_array[x,y,timestep] <- rnorm(1,500,50)
#         }
#       }
#       if((timestep>20 && timestep<=30)||(timestep>80 && timestep<=100)){#time steps with 25 (5x5) suitable sites
#         if((y>=14 && y<=18)&&(x>=14 && x<=18)) {
#           temp_array[x,y,timestep] <- rnorm(1,20,0.5)
#           prec_array[x,y,timestep] <- rnorm(1,500,50)
#         }
#       }
#       if((timestep>30 && timestep<=40)||(timestep>60 && timestep<=80)){#time steps with 49 (7x7) suitable sites
#         if((y>=13 && y<=19)&&(x>=13 && x<=19)) {
#           temp_array[x,y,timestep] <- rnorm(1,20,0.5)
#           prec_array[x,y,timestep] <- rnorm(1,500,50)
#         }
#       }
#       if(timestep>40 && timestep<=60){#time steps with 81 (9x9) suitable sites
#         if((y>=12 && y<=20)&&(x>=12 && x<=20)) {
#           temp_array[x,y,timestep] <- rnorm(1,20,0.5)
#           prec_array[x,y,timestep] <- rnorm(1,500,50)
#         }
#       }
#       #Saving the environmental variables in a dataframe format for distance matrices
#       if(timestep==1){
#         temp_dataframe[counting,1]<-x
#         temp_dataframe[counting,2]<-y
#         prec_dataframe[counting,1]<-x
#         prec_dataframe[counting,2]<-y
#       }
#       temp_dataframe[counting,2+timestep]<-temp_dataframe[x,y,timestep]
#       prec_dataframe[counting,2+timestep]<-prec_dataframe[x,y,timestep]
#       counting<-counting+1
#     }
#   }
# }

## ----eval=FALSE---------------------------------------------------------------
# library(raster)
# landscapes_list <- list()
# for (timestep in 1:Ntimesteps){
#   temp_raster <- rasterFromXYZ(temp_dataframe[, c(1,2, timestep+2)])
#   prec_raster <- rasterFromXYZ(prec_dataframe[, c(1,2, timestep+2)])
# 
#   landscapes_list$temp <- c(landscapes_list$temp, temp_raster)
#   landscapes_list$prec <- c(landscapes_list$prec, prec_raster)
# }
# 
# ##saving the list of rasters into .rds format to be used as input
# saveRDS(landscapes_list, "inputfolder/my_experiment/landscapes.rds")