diff --git a/inst/ShinyApp/server.R b/inst/ShinyApp/server.R
index 9f2f3fabee3a2e8650e95a6b7c07684faa412bd8..d2dd7033044af21f860c07e113765906505d7beb 100644
--- a/inst/ShinyApp/server.R
+++ b/inst/ShinyApp/server.R
@@ -41,11 +41,11 @@ server <- function(input, output, session){
if(input$analysis_choice == "scenario"){
shinyjs::show("fatalities_input_type")
- if(input$fatalities_input_type == "Valeurs"){
+ if(input$fatalities_input_type == "val"){
shinyjs::show("fatalities_mean")
shinyjs::show("fatalities_se")
}
- if(input$fatalities_input_type == "Elicitation d'expert"){
+ if(input$fatalities_input_type == "eli_exp"){
shinyjs::show("fatalities_mat_expert")
shinyjs::show("fatalities_run_expert")
}
@@ -65,11 +65,11 @@ server <- function(input, output, session){
if(input$button_pop_size%%2 == 1){
shinyjs::show("pop_size_type")
shinyjs::show("pop_size_input_type")
- if(input$pop_size_input_type == "Valeurs"){
+ if(input$pop_size_input_type == "val"){
shinyjs::show("pop_size_mean")
shinyjs::show("pop_size_se")
}
- if(input$pop_size_input_type == "Elicitation d'expert"){
+ if(input$pop_size_input_type == "eli_exp"){
shinyjs::show("pop_size_mat_expert")
shinyjs::show("pop_size_run_expert")
}
@@ -79,10 +79,10 @@ server <- function(input, output, session){
if(input$button_carrying_cap%%2 == 1){
shinyjs::show("carrying_cap_input_type")
- if(input$carrying_cap_input_type == "Valeurs"){
+ if(input$carrying_cap_input_type == "val"){
shinyjs::show("carrying_capacity")
}
- if(input$carrying_cap_input_type == "Elicitation d'expert"){
+ if(input$carrying_cap_input_type == "eli_exp"){
shinyjs::show("carrying_cap_mat_expert")
shinyjs::show("carrying_cap_run_expert")
}
@@ -92,15 +92,15 @@ server <- function(input, output, session){
if(input$button_pop_trend%%2 == 1){
shinyjs::show("pop_growth_input_type")
- if(input$pop_growth_input_type == "Taux de croissance"){
+ if(input$pop_growth_input_type == "val"){
shinyjs::show("pop_growth_mean")
shinyjs::show("pop_growth_se")
}
- if(input$pop_growth_input_type == "Elicitation d'expert"){
+ if(input$pop_growth_input_type == "eli_exp"){
shinyjs::show("pop_growth_mat_expert")
shinyjs::show("pop_growth_run_expert")
}
- if(input$pop_growth_input_type == "Tendance locale ou régionale"){
+ if(input$pop_growth_input_type == "trend"){
shinyjs::show("pop_trend")
shinyjs::show("pop_trend_strength")
}
@@ -280,13 +280,11 @@ server <- function(input, output, session){
-
-
-
##--------------------------------------------
- ## Observe input and report values --
+ ## Select parameter values for simulations --
##--------------------------------------------
- ## Cumulated impacts or not ?
+
+ ## Cumulated impacts or not ? ###~~~~~~~~~~~~~~~~~~~~~~~~~~###
observeEvent({
input$run
}, {
@@ -298,19 +296,7 @@ server <- function(input, output, session){
}) # end observeEvent
-
-
-
- ### Plot distribution
-
-
-
-
-
-
- ##--------------------------------------------
- ## Select parameter values for simulations --
- ##--------------------------------------------
+ ###~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~###
## Fatalities ###~~~~~~~~~~~~~~~~~~~~~~~~~~###
observeEvent({
input$run
@@ -319,7 +305,7 @@ server <- function(input, output, session){
if(input$analysis_choice == "scenario"){
# Case 1.1 : Values from expert elicitation (if2)
- if(input$fatalities_input_type == "Elicitation d'expert"){
+ if(input$fatalities_input_type == "eli_exp"){
param$fatalities_mean <- c(0, round(param$fatalities_eli_result$mean))
param$onset_time <- NULL
param$fatalities_se <- c(0, round(param$fatalities_eli_result$SE))
@@ -341,18 +327,24 @@ server <- function(input, output, session){
} # end (if1)
}) # end observeEvent
+ ###~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~###
+ ###~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~###
+ ## Population size ###~~~~~~~~~~~~~~~~~~~~~~~~~~###
+ observeEvent({
+ input$run
+ },{
- # Observe pop size value
- ## Mean, se and type
- observeEvent({input$run},{
- if(input$pop_size_input_type == "Elicitation d'expert"){
+ # Case 1 : Values from expert elicitation
+ if(input$pop_size_input_type == "eli_exp"){
if(!(is.null(param$pop_size_eli_result))){
param$pop_size_mean <- round(param$pop_size_eli_result$mean)
param$pop_size_se <- round(param$pop_size_eli_result$SE)
} else {
- print("#intégrer un message d'erreur")
+ print("Erreur: Vous n'avez pas lancer l'analyse 'valeurs experts'")
}
+
+ # Case 2 : Values directly provided (i.e., not from expert elicitation)
} else {
param$pop_size_mean <- input$pop_size_mean
param$pop_size_se <- input$pop_size_se
@@ -360,16 +352,25 @@ server <- function(input, output, session){
param$pop_size_type <- input$pop_size_type
})
- # Observe pop growth value
- observeEvent({input$run}, {
- if(input$pop_growth_input_type == "Elicitation d'expert"){
+
+ ###~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~##
+ ## Population growth ###~~~~~~~~~~~~~~~~~~~~~~~~~~###
+ observeEvent({
+ input$run
+ }, {
+
+ # Case 1 : Values from expert elicitation
+ if(input$pop_growth_input_type == "eli_exp"){
if(!(is.null(param$pop_growth_eli_result))){
param$pop_growth_mean <- round(min(1 + param$rMAX_species, round(param$pop_growth_eli_result$mean, 2)), 2)
param$pop_growth_se <- round(param$pop_growth_eli_result$SE, 2)
} else {
- print("#intégrer un message d'erreur")
+ print("Erreur: Vous n'avez pas lancer l'analyse 'valeurs experts'")
}
- } else if(input$pop_growth_input_type == "Tendance locale ou régionale"){
+
+ # Case 2 : Trend information
+ } else if(input$pop_growth_input_type == "trend"){
+
if(input$pop_trend == "Croissance") {
if(input$pop_trend_strength == "Faible") {
param$pop_growth_mean <- 1.01
@@ -390,8 +391,9 @@ server <- function(input, output, session){
param$pop_growth_mean <- 1
}
param$pop_growth_se <- 0.03
- }
- else {
+
+ # Case 3 : Values directly provided (i.e., not from expert elicitation)
+ } else {
param$pop_growth_mean <- round(min(1 + param$rMAX_species, input$pop_growth_mean), 2)
param$pop_growth_se <- input$pop_growth_se
}
@@ -420,7 +422,7 @@ server <- function(input, output, session){
# Observe carrying capacity
observeEvent({input$run}, {
- if(input$carrying_cap_input_type == "Elicitation d'expert"){
+ if(input$carrying_cap_input_type == "eli_exp"){
if(!(is.null(param$carrying_cap_eli_result))){
param$carrying_capacity <- round(param$carrying_cap_eli_result$mean)
} else {
@@ -505,12 +507,13 @@ server <- function(input, output, session){
## Fatalities
-
output$fatalities_mean_info <- renderText({
- if(input$fatalities_input_type == "Elicitation d'expert"){
+ if(input$fatalities_input_type == "eli_exp"){
if(!(is.null(param$fatalities_eli_result))){
info <- round(param$fatalities_eli_result$mean, 2)
- } else {info <- NA}
+ } else {
+ info <- NA
+ }
}
else {
info <- input$fatalities_mean
@@ -519,10 +522,12 @@ server <- function(input, output, session){
})
output$fatalities_se_info <- renderText({
- if(input$fatalities_input_type == "Elicitation d'expert"){
+ if(input$fatalities_input_type == "eli_exp"){
if(!(is.null(param$fatalities_eli_result))){
- info <- round(param$fatalities_eli_result$SE)
- } else {info <- NA}
+ info <- round(param$fatalities_eli_result$SE, 2)
+ } else {
+ info <- NA
+ }
}
else {
info <- input$fatalities_se
@@ -530,6 +535,15 @@ server <- function(input, output, session){
paste0("Erreur-type : ", info)
})
+
+
+
+
+
+
+
+
+
## Poplutation size
output$pop_size_type_info <- renderText({
@@ -541,7 +555,7 @@ server <- function(input, output, session){
})
output$pop_size_mean_info <- renderText({
- if(input$pop_size_input_type == "Elicitation d'expert"){
+ if(input$pop_size_input_type == "eli_exp"){
if(!(is.null(param$pop_size_eli_result))){
info <- round(param$pop_size_eli_result$mean)
} else {info <- NA}
@@ -553,7 +567,7 @@ server <- function(input, output, session){
})
output$pop_size_se_info <- renderText({
- if(input$pop_size_input_type == "Elicitation d'expert"){
+ if(input$pop_size_input_type == "eli_exp"){
if(!(is.null(param$pop_size_eli_result))){
info <- round(param$pop_size_eli_result$SE)
} else {info <- NA}
@@ -567,7 +581,7 @@ server <- function(input, output, session){
## Carrying capacity
output$carrying_capacity_info <- renderText({
- if(input$carrying_cap_input_type == "Elicitation d'expert"){
+ if(input$carrying_cap_input_type == "eli_exp"){
if(!(is.null(param$carrying_cap_eli_result))){
info <- round(param$carrying_cap_eli_result$mean)
} else {info <- NA}
@@ -583,11 +597,11 @@ server <- function(input, output, session){
output$pop_trend_type_info <- renderText({paste0("Type de Tendance de pop : ", input$pop_growth_input_type)})
output$pop_growth_mean_info <- renderText({
- if(input$pop_growth_input_type == "Elicitation d'expert"){
+ if(input$pop_growth_input_type == "eli_exp"){
if(!(is.null(param$pop_growth_eli_result))){
info <- round(param$pop_growth_eli_result$mean, 2)
} else {info <- NA}
- } else if(input$pop_growth_input_type == "Tendance locale ou régionale"){
+ } else if(input$pop_growth_input_type == "trend"){
if(input$pop_trend == "Croissance") {
if(input$pop_trend_strength == "Faible") {
info <- 1.01
@@ -614,11 +628,11 @@ server <- function(input, output, session){
})
output$pop_growth_se_info <- renderText({
- if(input$pop_growth_input_type == "Elicitation d'expert"){
+ if(input$pop_growth_input_type == "eli_exp"){
if(!(is.null(param$pop_growth_eli_result))){
info <- round(param$pop_growth_eli_result$SE, 2)
} else {info <- NA}
- } else if (input$pop_growth_input_type == "Tendance locale ou régionale") {
+ } else if (input$pop_growth_input_type == "trend") {
info <- 0.03
}
else {
diff --git a/inst/ShinyApp/ui.R b/inst/ShinyApp/ui.R
index 185512e855ee97f94d7148bb0a75597f4e59a63b..d0da8bc82f8ab63c277d4a4f5e68831236d42341 100644
--- a/inst/ShinyApp/ui.R
+++ b/inst/ShinyApp/ui.R
@@ -166,7 +166,7 @@ ui <- fluidPage(
# Input type
radioButtons(inputId = "fatalities_input_type",
label = h4("Type de saisie"),
- choices = c("Valeurs", "Elicitation d'expert")),
+ choices = c("Valeurs" = "val", "Elicitation d'expert" = "eli_exp")),
# Values
numericInput(inputId = "fatalities_mean",
@@ -223,7 +223,7 @@ ui <- fluidPage(
radioButtons(inputId = "pop_size_input_type",
label = h4("Type de saisie"),
- choices = c("Valeurs", "Elicitation d'expert")),
+ choices = c("Valeurs" = "val", "Elicitation d'expert" = "eli_exp")),
numericInput(inputId = "pop_size_mean",
label = "Moyenne de la taille de la population",
@@ -259,7 +259,9 @@ ui <- fluidPage(
radioButtons(inputId = "pop_growth_input_type",
label = h4("Type de saisie"),
- choices = c("Taux de croissance", "Elicitation d'expert", "Tendance locale ou régionale")),
+ choices = c("Taux de croissance" = "val",
+ "Elicitation d'expert" = "eli_exp",
+ "Tendance locale ou régionale" = "trend")),
numericInput(inputId = "pop_growth_mean",
label = "Moyenne de la croissance de la population",
@@ -305,7 +307,7 @@ ui <- fluidPage(
radioButtons(inputId = "carrying_cap_input_type",
label = h4("Type de saisie"),
- choices = c("Valeurs", "Elicitation d'expert")),
+ choices = c("Valeurs" = "val", "Elicitation d'expert" = "eli_exp")),
numericInput(inputId = "carrying_capacity",
label = "Capacité de charge",
diff --git a/run_analysis.R b/run_analysis.R
index 9a581d00f6340cb022834c74bfef28302c3ab3ba..1b4a70edb71e46aa401f53b0e9d6306f2ff18450 100644
--- a/run_analysis.R
+++ b/run_analysis.R
@@ -64,9 +64,11 @@ lambda( build_Leslie(s = s_calibrated, f = f_calibrated) )
-pop_size_mean = 200
-pop_growth_mean = 1.1
-fatal_constant = "M"
+#pop_size_mean = 200
+#pop_growth_mean = 1.1
+#fatal_constant = "M"
+#cumulated_impacts = FALSE
+
pop_size_type = "Ntotal"
carrying_capacity = 500
@@ -74,16 +76,34 @@ carrying_capacity = 500
##==============================================================================
## Analyses (simulations) ==
##==============================================================================
-run0 <- run_simul(nsim, cumulated_impacts,
- fatalities_mean, fatalities_se, onset_time,
- pop_size_mean, pop_size_se, pop_size_type,
- pop_growth_mean, pop_growth_se,
- survivals = s_calibrated, fecundities = f_calibrated,
- carrying_capacity = carrying_capacity, theta = theta,
- rMAX_species = rMAX_species,
- model_demo, time_horzion, coeff_var_environ, fatal_constant)
+run0 <- run_simul(nsim = nsim,
+ cumulated_impacts = cumulated_impacts,
+
+ fatalities_mean = fatalities_mean,
+ fatalities_se = fatalities_se,
+ onset_time = onset_time,
+
+ pop_size_mean = pop_size_mean,
+ pop_size_se = pop_size_se,
+ pop_size_type = pop_size_type,
+
+ pop_growth_mean = pop_growth_mean,
+ pop_growth_se = pop_growth_se,
+
+ survivals = s_calibrated,
+ fecundities = f_calibrated,
+
+ carrying_capacity = carrying_capacity,
+ theta = theta,
+ rMAX_species = rMAX_species,
+
+ model_demo = NULL,
+ time_horzion = time_horzion,
+ coeff_var_environ = coeff_var_environ,
+ fatal_constant = fatal_constant)
+#####################################################
names(run0)