I couldn't get this to work as the physarum() function is never defined.

From lines 61-63:

Make agents dance

envM <- physarum(envM, parF, decayT, FL, FR,
RA, SO, SS, depT, iters)

# Create a magnetic disc
for (i in 1:nrow(envM)){
  for (j in 1:ncol(envM)){
    if(sqrt((i-imageH/2)^2+(j-imageH/2)^2)>imageH/8 &
       sqrt((i-imageH/2)^2+(j-imageH/2)^2)<imageH/6) envM[i,j]=5
  }
}

if that is supposed to create a circle then it should use i-imageH and j-imageW something like

for (y in 1:nrow(envM)){
  for (x in 1:ncol(envM)){
    y2 = (y-imageH/2)
    x2 = (x-imageW/2)
    d = sqrt( x2*x2 + y2*y2 )
    if( d >imageH/8 & d <imageH/6) envM[i,j]=5
  }
}

I replaced this piece of code and get rid of this dependency

#Pick a top palette from colourlovers
url <- "http://www.colourlovers.com/api/palettes/top&format=json"
out <- rjson::fromJSON(readLines(url)[1], simplify = TRUE)
palette <- data.table::rbindlist(out)
colors <- palette %>% filter(id == sample(palette$id,1)) %>% select(colors) %>% pull %>% paste0("#", .)

#palette <- sample(clpalettes('top'), 1)[[1]]
#colors <- palette %>% swatch %>% .[[1]]