### R code from vignette source '/Users/hedvig/Documents/Demoniche/model/demoniche_manual.Rnw' ### Encoding: UTF-8 options(width=72) library(demoniche) data(Hmontana) str(Hmontana) Hmontana$env_stochas_type noCC_nodispersal <- demoniche_model(modelname = "Hmontana", Niche = FALSE, Dispersal = FALSE, repetitions = 2, foldername = "noCC_nodispersal") CC_nodispersal <- demoniche_model(modelname = "Hmontana", Niche = TRUE, Dispersal = FALSE, repetitions = 2, foldername = "CC_nodispersal") dim(noCC_nodispersal) dimnames(noCC_nodispersal) noCC_nodispersal[,"Meanpop","Matrix_1"] barplot(cbind(noCC_nodispersal[40,2,], CC_nodispersal[40,2,]), beside = TRUE, legend.text = Hmontana$list_names_matrices, names.arg = c("no Niche values","with Niche values")) barplot(cbind(noCC_nodispersal[40,2,], CC_nodispersal[40,2,]), beside = TRUE, legend.text = Hmontana$list_names_matrices, names.arg = c("no Niche values","with Niche values")) list.files(path = "noCC_nodispersal") load('noCC_nodispersal/eigen_results.rda') str(eigen_results) image2(eigen_results$Reference_matrix$sensitivities) title("Sensitivity, Reference Matrix") image2(eigen_results$Reference_matrix$sensitivities) title("Sensitivity, Reference Matrix") args(demoniche_setup) Populations_mine <- read.table(file = "Hudsonia_Populations_grids.csv", sep = ";", header = TRUE) head(Populations_mine) Nichemap_mine <- read.table(file = "Hudsonia_SDMmodelling.csv", sep = ";", header = TRUE) tail(Nichemap_mine) niche_formulas <- as.formula(paste(paste(colnames(Nichemap_mine)[-c(1:3)], collapse="+"),"X+Y",sep="~")) print(levelplot(niche_formulas, Nichemap_mine, col.regions=rev(heat.colors(100)), main = "Niche Values")) print(levelplot(niche_formulas, Nichemap_mine, col.regions=rev(heat.colors(100)), main = "Niche Values")) no_yrs_mine <- 10 library(popbio) data(hudvrs) data(hudsonia) matrices_mine <- cbind(meanmatrix = as.vector(hudmxdef(hudvrs$mean)), sapply(hudsonia, unlist)) head(matrices_mine) colnames(matrices_mine) <- c("Reference_matrix", "Matrix_1", "Matrix_2", "Matrix_3", "Matrix_4") matrix(matrices_mine[,"Reference_matrix"], ncol = 6, byrow = FALSE) stages_mine <- colnames(hudsonia$A85) sumweight_mine <- c(0,1,1,1,1,1) transition_affected_niche_mine <- c(1,3) matrices_mine[transition_affected_niche_mine,1] transition_affected_env_mine <- "all" transition_affected_demogr_mine <- "all" env_stochas_type_mine <- "normal" matrices_var_mine <- matrix(0.01, ncol = 1, nrow = nrow(matrices_mine), dimnames = list(NULL, "sd")) proportion_initial_mine <- c(0.9818098089, 0.0006907668, 0.0069076675, 0.0036840893, 0.0057563896, 0.0011512779) density_individuals_mine <- 20000 K_mine <- 10000 Kweight_mine <- c(0,1.5,1,1,1,1) prob_scenario_mine <- c(0.5, 0.5) noise_mine <- 0.1 fraction_SDD_mine <- 0.05 fraction_LDD_mine <- 0.05 dispersal_constants_mine <- c(0.7, 0.7, 0.1, 3) rm(CC_nodispersal, eigen_results, Hmontana, hudsonia,hudvrs, niche_formulas, noCC_nodispersal) ls() demoniche_setup(modelname = "Hmontana", Populations = Populations_mine, Nichemap = Nichemap_mine, matrices = matrices_mine, matrices_var = matrices_var_mine, noise = noise_mine, prob_scenario = prob_scenario_mine, stages = stages_mine, proportion_initial = proportion_initial_mine, density_individuals = density_individuals_mine, fraction_LDD = 0.05, fraction_SDD = fraction_SDD_mine, dispersal_constants = dispersal_constants_mine, transition_affected_niche = transition_affected_niche_mine, transition_affected_demogr = transition_affected_demogr_mine, transition_affected_env = transition_affected_env_mine, env_stochas_type = env_stochas_type_mine, no_yrs = no_yrs_mine, K = K_mine, Kweight = Kweight_mine, sumweight = sumweight_mine) demoniche_setup(modelname = "Hmontana_minimal", Populations = Populations_mine, matrices_var = matrices_var_mine, matrices = matrices_mine, stages = stages_mine, proportion_initial = proportion_initial_mine, density_individuals = density_individuals_mine, no_yrs = no_yrs_mine) example_minimal <- demoniche_model(modelname = "Hmontana_minimal", Niche = FALSE, Dispersal = FALSE, repetitions = 1, foldername = "Hmontana_minimal") Hmontana$neigh_index