animate_model2.R

In javimarlop/spdynmod: Spatio-Dynamic Wetland Plant Communities Model

#' Make an animation of the model output containing all state variables.
#' 
#' It requires ImageMagick installed in the system to work.
#'
#' @return a GIF animated file
#'
#' @keywords animation
#'
#' @export
#' 
#' @examples
#' ## Not run animate_model()

animate_model2<-function(){
#require(raster)
out<-get('out')
nr<-get('nr')
nc<-get('nc')
NN<-get('NN')

#brks <- seq(0, 30, by=1) 
#nb <- length(brks)-1 
out[out<0]<-0
out[out>25]<-25
#require(animation)

animation::saveGIF({
for (i in seq(1, dim(out)[1], by = 1)){
 #i2<-seq(1984.25,2008,0.25)
 #par(mfrow=c(3,2))
 #par(mar=c(2,1,2,0.8))
 a<-raster::raster(matrix(nrow = nr, ncol = nc, out[i, (3*NN+2):(4*NN+1)]))
 b<-raster::raster(matrix(nrow = nr, ncol = nc, out[i, (NN+2):(2*NN+1)]))
 c<-raster::raster(matrix(nrow = nr, ncol = nc, out[i, 2:(NN+1)]))
 d<-raster::raster(matrix(nrow = nr, ncol = nc, out[i, (2*NN+2):(3*NN+1)]))

own2<-c('#fed976','#feb24c','#addd8e','#78c679','#41ab5d','#238443','#006837','#004529')# '#d9f0a3'
map0<-stack(a,b,c,d)
names(map0)<-c('Bare soil','Salt steppe','Salt marsh','Reed beds')
#map<-spplot(map0,col.regions = terrain.colors(25))
map<-spplot(map0,zlim=c(0,25),col.regions = colorRampPalette(own2)(25))
#map2<-map+layer(barplot(i2[i],col="black",horiz=T,xlim=c(1984,2008),axes=F,cex.sub=1.4, main="Time",cex.main=1.5))
print(map)

 #par(mar=c(13,1,3,1.5))
 #print(barplot(i2[i],col="black",horiz=T,xlim=c(1984,2008),axes=F,cex.sub=1.4, main="Time",cex.main=1.5))
 #par(las=2)
 #axis(1,at=c(1984,1992,1995,1997,2001,2008))
 }},movie.name='movie2.gif')

}

### PLOT GOOGLEVIS CHART

## Data preparation
#out2<-as.data.frame(out)
#b<-1:96
#DatosApilados <- stack(out2[, c('Salt marsh','Salt steppe','Reed beds','Bare soil')])
#tiempo<-rep(b,4)
#DatosApilados2<-DatosApilados
#DatosApilados2[,1]<-DatosApilados$ind
#DatosApilados2[,2]<-tiempo
#DatosApilados2[,3]<-DatosApilados$values
#names(DatosApilados2) <- c("factor", "tiempo","valor")

## Plot
#require(googleVis)
#Motion=gvisMotionChart(DatosApilados2, idvar="factor", timevar="tiempo", options=list(height=350, width=400))
## Display chart
#plot(Motion) 
## Create Google Gadget
##cat(createGoogleGadget(Motion), file="motionchart.xml")

###