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Commit 7551911b authored by thierrychambert's avatar thierrychambert
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More cleaning 

Check run issue with run analysis (works again...)
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inst/ShinyApp/server.R
+ 68
− 54
View file @ 7551911b
......@@ -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$pop_growth_input_type == "Tendance locale ou rgionale"){
if(input$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$SE)
} else {
print("#intgrer un message d'erreur")
print("Erreur: Vous n'avez pas lancer l'analyse 'valeurs experts'")
}
# Case 2 : Values directly provided (i.e., not from expert elicitation)
} else {
param$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$SE, 2)
} else {
print("#intgrer un message d'erreur")
print("Erreur: Vous n'avez pas lancer l'analyse 'valeurs experts'")
}
} else if(input$pop_growth_input_type == "Tendance locale ou rgionale"){
# 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 rgionale"){
} 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 rgionale") {
} else if (input$pop_growth_input_type == "trend") {
info <- 0.03
}
else {
......
inst/ShinyApp/ui.R
+ 6
− 4
View file @ 7551911b
......@@ -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 rgionale")),
choices = c("Taux de croissance" = "val",
"Elicitation d'expert" = "eli_exp",
"Tendance locale ou rgionale" = "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 = "Capacit de charge",
......
run_analysis.R
+ 31
− 11
View file @ 7551911b
......@@ -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)
......
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Documentation | Mentions légales | CGU | Accessibilité : non conforme