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server <- function(input, output){
# Hide all inputs excepted actionButtons
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shinyjs::hide("fatal_constant")
shinyjs::hide("fatalities_input_type")
shinyjs::hide("fatalities_mean")
shinyjs::hide("fatalities_se")
shinyjs::hide("fatalities_mat_expert")
shinyjs::hide("farm_number_cumulated")
shinyjs::hide("fatalities_mat_cumulated")
shinyjs::hide("pop_size_type")
shinyjs::hide("pop_size_input_type")
shinyjs::hide("pop_size_mean")
shinyjs::hide("pop_size_se")
shinyjs::hide("pop_size_mat_expert")
shinyjs::hide("carrying_cap_input_type")
shinyjs::hide("carrying_cap_mean")
shinyjs::hide("carrying_cap_se")
shinyjs::hide("carrying_cap_mat_expert")
shinyjs::hide("lambda_input_type")
shinyjs::hide("pop_growth_mean")
shinyjs::hide("pop_growth_se")
shinyjs::hide("pop_growth_mat_expert")
shinyjs::hide("pop_trend")
shinyjs::hide("pop_trend_strength")
shinyjs::hide("fill_type_vr")
shinyjs::hide("mat_display_vr")
shinyjs::hide("mat_fill_vr")
# Show fatalities part
if(input$button_fatalities%%2 == 1){
shinyjs::show("fatal_constant")
# Show inputs for none cumulated impacts scenario
if(input$analysis_choice == "scenario"){
shinyjs::show("fatalities_input_type")
if(input$fatalities_input_type == "Valeurs"){
shinyjs::show("fatalities_mean")
shinyjs::show("fatalities_se")
}
if(input$fatalities_input_type == "Elicitation d'expert"){
shinyjs::show("fatalities_mat_expert")
}
}
# Show inputs for cumulated scenario
if(input$analysis_choice == "cumulated"){
shinyjs::show("farm_number_cumulated")
shinyjs::show("fatalities_mat_cumulated")
# Show inputs for population size part
if(input$button_pop_size%%2 == 1){
shinyjs::show("pop_size_type")
shinyjs::show("pop_size_input_type")
if(input$pop_size_input_type == "Valeurs"){
shinyjs::show("pop_size_mean")
shinyjs::show("pop_size_se")
}
if(input$pop_size_input_type == "Elicitation d'expert"){
shinyjs::show("pop_size_mat_expert")
}
}
# Show inputs for carrying capacity part
if(input$button_carrying_cap%%2 == 1){
shinyjs::show("carrying_cap_input_type")
if(input$carrying_cap_input_type == "Valeurs"){
shinyjs::show("carrying_cap_mean")
shinyjs::show("carrying_cap_se")
}
if(input$carrying_cap_input_type == "Elicitation d'expert"){
shinyjs::show("carrying_cap_mat_expert")
}
# Show inputs for population trend part
if(input$button_pop_trend%%2 == 1){
shinyjs::show("lambda_input_type")
if(input$lambda_input_type == "Taux de croissance"){
shinyjs::show("pop_growth_mean")
shinyjs::show("pop_growth_se")
}
if(input$lambda_input_type == "Elicitation d'expert"){
shinyjs::show("pop_growth_mat_expert")
}
if(input$lambda_input_type == "Tendance locale ou régionale"){
shinyjs::show("pop_trend")
shinyjs::show("pop_trend_strength")
}
# Show inputs vital rates part
if(input$button_vital_rates%%2 == 1){
shinyjs::show("fill_type_vr")
if(input$fill_type_vr == "Automatique"){
shinyjs::show("mat_display_vr")
}
if(input$fill_type_vr == "Manuelle"){
shinyjs::show("mat_fill_vr")
}
}
## Output
out <- reactiveValues(N1 = NULL, fatalities_mean = NULL, fecundities = NULL, survivals = NULL,
cumulated_impacts = NULL, onset_time = NULL, onset_year = NULL,
DD_params = NULL)
# Reactive values (cumulated impacts, fatalities mean, fatalities se, onset_time, survivals mean, fecundities mean)
observeEvent({input$run}, {
if(input$analysis_choice == "scenario"){
out$cumulated_impacts = FALSE
} else {
out$cumulated_impacts = TRUE
}
})
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observeEvent({input$run}, {
if(input$analysis_choice == "scenario"){
out$fatalities_mean <- c(0, input$fatalities_mean)
out$onset_time = NULL
} else {
out$fatalities_mean <- c(0, input$fatalities_mat_cumulated[,1])
out$onset_year <- c(min(input$fatalities_mat_cumulated[,3]), input$fatalities_mat_cumulated[,3])
out$onset_time <- out$onset_year - min(out$onset_year) + 1
}
})
# fatalities se
observeEvent({input$run}, {
if(input$analysis_choice == "scenario"){
out$fatalities_se <- input$fatalities_se
} else {
out$fatalities_se <- c(min(input$fatalities_mat_cumulated[,2]), input$fatalities_mat_cumulated[,2])
}
})
# Survivals and fecundities means
observeEvent({input$run}, {
if(input$fill_type_vr == "Manuelle"){
out$survivals <- input$mat_fill_vr[,1]
out$fecundities <- input$mat_fill_vr[,2]
out$survivals <- c(0.5, 0.7, 0.8, 0.95)
out$fecundities <- c(0, 0, 0.05, 0.55)
})
# observe({
# DD_params$K <- input$carrying_cap_mean
# })
# End of reactive
# Simulations
observeEvent({
input$run
}, {
out$N1 <- run_simul(nsim = 10, cumuated_impacts = out$cumulated_impacts, onset_time = out$onset_time, fatalities_mean = out$fatalities_mean,
fatalities_se = input$fatalities_se*out$fatalities_mean, DD_params = DD_params,
pop_size_type = input$pop_size_type, pop_size_mean = input$pop_size_mean, pop_size_se = input$pop_size_se,
pop_growth_mean = input$pop_growth_mean, pop_growth_se = input$pop_growth_se, survivals = out$survivals,
fecundities = out$fecundities, model_demo = NULL, time_horzion = 30, coeff_var_environ = 0.1,
fatal_constant = input$fatal_constant)
})
plot_out_impact <- function(){
if(is.null(out$N1)) {} else {plot_impact(N = out$N1$N, xlab = "year", ylab = "pop size")}
}
output$graph_impact <- renderPlot({
plot_out_impact()
})
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plot_out_traj <- function(){
if(is.null(out$N1)) {} else {plot_traj(N = out$N1$N, xlab = "year", ylab = "pop size")}
}
output$graph_traj <- renderPlot({
plot_out_traj()
})
# End simulations
# Elicitation experts part
func_eli <- function(mat_expert){
t_mat_expert <- t(mat_expert)
vals = t_mat_expert[3:5,]
Cp = t_mat_expert[6,]
weights = t_mat_expert[2,]
out <- elicitation(vals, Cp, weights)
return(list(out = out, mean = out$mean_smooth, SE = sqrt(out$var_smooth)))
}
func_eli_plot <- function(out){
plot_elicitation(out)
}
observeEvent({input$run_expert}, {
if(all(is.na(input$fatalities_mat_expert))) {} else {
fatalities_result_eli <- func_eli(input$fatalities_mat_expert)
output$fatalities_expert_mean <- renderText({paste0("Moyenne : ", fatalities_result_eli$mean)})
output$fatalities_expert_sqrt_var <- renderText({paste0("Ecart-type : ", fatalities_result_eli$SE)})
output$fatalities_expert_plot <- renderPlot({func_eli_plot(fatalities_result_eli$out)})
}
if(all(is.na(input$pop_size_mat_expert))) {} else {
pop_size_result_eli <- func_eli(input$pop_size_mat_expert)
output$pop_size_expert_mean <- renderText({paste0("Moyenne : ", pop_size_result_eli$mean)})
output$pop_size_expert_sqrt_var <- renderText({paste0("Ecart-type : ", pop_size_result_eli$SE)})
output$pop_size_expert_plot <- renderPlot({func_eli_plot(pop_size_result_eli$out)})
}
if(all(is.na(input$carrying_cap_mat_expert))) {} else {
carrying_cap_result_eli <- func_eli(input$carrying_cap_mat_expert)
output$carrying_cap_expert_mean <- renderText({paste0("Moyenne : ", carrying_cap_result_eli$mean)})
output$carrying_cap_expert_sqrt_var <- renderText({paste0("Ecart-type : ", carrying_cap_result_eli$SE)})
output$carrying_cap_expert_plot <- renderPlot({func_eli_plot(carrying_cap_result_eli$out)})
}
if(all(is.na(input$pop_growth_mat_expert))) {} else {
pop_growth_result_eli <- func_eli(input$pop_growth_mat_expert)
output$pop_growth_expert_mean <- renderText({paste0("Moyenne : ", pop_growth_result_eli$mean)})
output$pop_growth_expert_sqrt_var <- renderText({paste0("Ecart-type : ", pop_growth_result_eli$SE)})
output$pop_growth_expert_plot <- renderPlot({func_eli_plot(pop_growth_result_eli$out)})
}
# End of elicitation part
# Info outputs
output$fatalities_mean_info <- renderText({paste0("Moyenne des mortalités : ", input$fatalities_mean)})
output$fatalities_se_info <- renderText({paste0("Ecart-type des mortalités : ", input$fatalities_se)})
output$pop_size_mean_info <- renderText({paste0("Moyenne Taille de pop : ", input$pop_size_mean)})
output$pop_size_se_info <- renderText({paste0("Ecart-type Taille de pop : ", input$pop_size_se)})
output$carrying_cap_mean_info <- renderText({paste0("Moyenne Capacité de charge : ", input$carrying_cap_mean)})
output$carrying_cap_se_info <- renderText({paste0("Ecart-type Capacité de charge : ", input$carrying_cap_se)})
output$pop_trend_type_info <- renderText({paste0("Type de Tendance de pop : ", input$lambda_input_type)})
output$pop_trend_mean_info <- renderText({paste0("Moyenne Tendance de pop : ", input$pop_growth_mean)})
output$pop_trend_se_info <- renderText({paste0("Ecart-type Tendance de pop : ", input$pop_growth_se)})
}
# End server