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### 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
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