simcoms/PrepareSimModels.Rmd at master · ljpollock/simcoms · GitHub

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#' ---
#' title: "Community Assembly Simulations"
#' author: "LJ Pollock"
#' date: "`r Sys.Date()`"
#' output: pdf_document
#'
#' ---

#+ setup, message=FALSE


Input parameters and run functions from 'RunSimModels.Rmd'


```{r, eval=FALSE}

setwd("~/Dropbox/JSDMCommunities/SimulateCommunities/ExampleFiles")


lapply(list.files(path = "."),load,.GlobalEnv)


test.coms <- simulate_community()


sim_data <- mapply(
  simulate_community,
  niche_optima = 2,
  type         = "original",
  comp_inter   = NA,
  fac_inter    = NA,
  beta_comp    = 5,
  beta_fac     = 0,
  K            = 40,
  competition  = "facilitation",
  intra_sp_com = 0,
  SIMPLIFY = FALSE
)


sim_data =
  list(
    niche_optima = unlist(replicate(7, lapply(c(5, 10, 20), function(x) seq(2, 98, length.out = x)), FALSE), FALSE),
    type         = list("original", "manual")[c(rep(1, 3), rep(2, 18))],
    comp_inter   = comp_inter,
    fac_inter    = fac_inter,
    beta_comp    = rep(list(0, 10, 4), each = 7),
    beta_fac     = rep(list(0, 3, 3, 0, 0, 1, 2), each = 3),
    K            = rep(list(10, 20, 40), 7),
    competition  = list("symmetric", "both")[c(rep(1, 3), rep(2, 18))],
    intra_sp_com = rep(list(1), 21)
  )
  %>%
  pmap(sim_com) %>%
  #map(abund2occur) %>%
  set_names(sim_names)


```