In ToonVanDaele/metapop:

knitr::opts_chunk$set(echo = TRUE)

IBM assumptions and input parameters

female only model

Stages

• Juvenile (J)
• Adult (A)

survival

survival (probability):
Sj: mean = 0.3, sd = 0.05 (min= 0, max= 0.9)
Sa: 0.7

(for the moment independent of patches area)

Fecundity

reproduction probability = 0.5

nestsize: poisson, lambda = 3

(for the moment independent of the patch area)

Carrying capacity

Ceiling model density dependence

maximum number of reproducing individuals per ha = 5

landscape patches

Table columns:

• ID: (integer)
• Area: (num) (m²)
• x: (num) (m)
• y: (num) (m)

library(MetaLandSim)
library(dplyr)

set.seed(420)
patches.tmp <- rland.graph(mapsize = 1000, dist_m = 200, 
                  areaM = 2.5, areaSD = 0.8, Npatch = 6, 
                  disp = 500, plotG = TRUE)

patches <- patches.tmp$nodes.characteristics %>%
  select(ID, areas, x, y)
patches$K <- round(patches$areas * 5, 0)
write.csv2(patches, "patches.txt",  eol = ",\n")
saveRDS(patches, "pachtes.RDS")

Migration

migratie tussen patches in functie van de euclidische afstand: 1/Dist^2

distM <- dist(patches[,c("x","y")], diag = TRUE, upper = TRUE)
probM <- as.matrix(distM)
diag(probM) <- 100  # hoe groter hoe sneller een individu uit de huidige patch migreert
probM <- 1 / (probM + 1) ^ 2
sumprob <- rowSums(probM, na.rm = TRUE)
probM <- probM %*% diag(1/sumprob)
write.csv2(probM, "markov_transition.txt",  eol = ",\n")

(Eventueel later te verbeteren, diffusion approximation, (Cornell, 2003), toegepast in Ovaskainen & Hanski (2004)

Initial population (time = 1)

Equal distribution of individuals over the patches. Adults only

init <- data.frame(patch = rep(seq(1:max(patches$ID)), times = 5), timestep = 1)
init$ID <- rownames(init)
write.csv2(init, "init_pop.txt",  eol = ",\n")
init

IBM output example

Table columns:

• ID: patch ID birth : individual ID
• time: (integer) (year)
• stage: (factor) (mag een level of een integer zijn 1 = "juv"", 2 = "ad"")
• patch: (integer)

example:

ID | time | stage | patch ------|-------|-------|------ 3:1 | 1 | juv | 3 4:1 | 1 | juv | 4 3:2 | 1 | ad | 3 4:2 | 1 | ad | 4 3:1 | 2 | ad | 3 3:3 | 2 | ad | 3 3:4 | 2 | ad | 3 4:3 | 2 | juv | 4 3:5 | 2 | juv | 3 5:1 | 3 | juv | 5 3:3 | 3 | ad | 3 3:5 | 3 | juv | 3

ToonVanDaele/metapop documentation built on May 9, 2019, 5:11 p.m.