diff --git a/inst/ShinyApp/server.R b/inst/ShinyApp/server.R
index 0a011550ea6f989bc3fda47cfaee9e971a2846e2..85c0e668b4232b48ef846fe3d5a5687c23ee2fa1 100644
--- a/inst/ShinyApp/server.R
+++ b/inst/ShinyApp/server.R
@@ -28,8 +28,6 @@ server <- function(input, output, session){
shinyjs::hide("pop_growth_run_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
@@ -109,15 +107,13 @@ server <- function(input, output, session){
# 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$fill_type_vr == "Manuelle"){
shinyjs::show("mat_fill_vr")
- }
}
- })
+
+ }) # en observe show/hide
+
+
+
# Elicitation experts part
@@ -300,14 +296,9 @@ server <- function(input, output, session){
# Survivals and fecundities
observeEvent({input$run}, {
- if(input$fill_type_vr == "Manuelle"){
param$survivals <- input$mat_fill_vr[,1]
param$fecundities <- input$mat_fill_vr[,2]
- } else {
- param$survivals <- survivals
- param$fecundities <- fecundities
- }
- })
+ }) # end observeEvent
# Survival and fecundity calibration
@@ -407,7 +398,15 @@ server <- function(input, output, session){
})
# End simulations
- # General informations output
+
+
+
+
+ ##--------------------------------------------
+ ## Display General information --
+ ##--------------------------------------------
+
+ #output$species_name <- renderText({ input$species_choice})
## Fatalities
@@ -532,17 +531,17 @@ server <- function(input, output, session){
paste0("Ecart-type de la croissance de la population : ", info)
})
+
## Vital rates
output$vital_rates_info <- renderTable({
- if(input$fill_type_vr == "Automatique"){
- input$mat_display_vr
- } else {
- input$mat_fill_vr
- }
- })
+ input$mat_fill_vr
+ }, rownames = TRUE)
+
# End genral informations output
+
+
## Update matrix cumulated impact
observeEvent({input$farm_number_cumulated}, {
@@ -566,20 +565,24 @@ server <- function(input, output, session){
# Survivals and Fecundities
- create.matrice <- function(species){
- tab_test <- data_sf %>%
+ create.matrice <- function(data_sf, species){
+ out_mat <- data_sf %>%
filter(species == data_sf$Nom_espece) %>%
select(classes_age, survie, fecondite)
- return(tab_test)
+ return(out_mat)
}
- observeEvent({input$species_list}, {
- if(input$species_list == "Espèce") {} else {
- tab_species <- create.matrice(input$species_list)
+
+## Update the vital rate matrix when changing species in the list
+ observeEvent({input$species_choice}, {
+
+ if(input$species_choice == "Espèce générique") {} else {
+
+ tab_species <- create.matrice(data_sf = data_sf, species = input$species_choice)
if(all(is.na(tab_species))) {
updateMatrixInput(session, inputId = "mat_fill_vr",
- value = matrix(data = "",
+ value = matrix(data = NA,
nrow = 4,
ncol = 2,
dimnames = list(c("Juv 1", "Juv 2", "Juv 3", "Adulte"), c("Survie", "Fécondité"))))
@@ -595,9 +598,12 @@ server <- function(input, output, session){
nrow = number_age_class,
ncol = 2,
dimnames = list(ages, c("Survie", "Fécondité"))))
- }
- }
- })
-}
-# End server
+ } # end if 2
+ } # end if 1
+
+ }) # end observeEvent species_list
+
+
+###################################################################################
+} # End server
diff --git a/inst/ShinyApp/species_list.csv b/inst/ShinyApp/species_list.csv
index 11b986995342fa1e1e23683668e2a2d6ab2e7749..62ef529e71a41efc86182b553885357a0e7c6631 100644
--- a/inst/ShinyApp/species_list.csv
+++ b/inst/ShinyApp/species_list.csv
@@ -1,57 +1,58 @@
-NomEspece,OrdreFamille
-Aigle de Bonelli,Accipitriformes
-Aigle royal,Accipitriformes
-Autour des palombes,Accipitriformes
-Balbuzard pêcheur,Accipitriformes
-Bondrée apivore,Accipitriformes
-Busard cendré,Accipitriformes
-Busard des roseaux,Accipitriformes
-Busard Saint-Martin,Accipitriformes
-Buse variable,Accipitriformes
-Elanion blanc,Accipitriformes
-Epervier d'Europe,Accipitriformes
-Faucon crécerelle,Accipitriformes
-Faucon crécerellette,Accipitriformes
-Faucon pélerin,Accipitriformes
-Gypaète barbu,Accipitriformes
-Milan noir,Accipitriformes
-Milan royal ,Accipitriformes
-Pygarge à queue blanche,Accipitriformes
-Vautour fauve,Accipitriformes
-Vautour moine,Accipitriformes
-Vautour percnoptère,Accipitriformes
-Martinet noir,Caprimulgiformes
-Oedicnème criard,Charadriiformes
-Pluvier doré,Charadriiformes
-Sterne pierregarin,Charadriiformes
-Vanneau huppé,Charadriiformes
-Caille des blés,Galliformes
-Perdrix grise,Galliformes
-Perdrix rouge,Galliformes
-Grue cendrée,Gruiformes
-Goéland argenté,Laridés
-Mouette rieuse,Laridés
-Outarde canepetière,Otidiformes
-Alouette des champs,Passeriformes
-Alouette lulu,Passeriformes
-Bruant proyer,Passeriformes
-Bruant jaune,Passeriformes
-Chardonneret élégant,Passeriformes
-Etourneau sansonnet,Passeriformes
-Gobemouche noir,Passeriformes
-Grive musicienne,Passeriformes
-Hirondelle de fenetre,Passeriformes
-Linotte mélodieuse,Passeriformes
-Merle noir,Passeriformes
-Moineau domestique,Passeriformes
-Moineau friquet,Passeriformes
-Pies-grièches (4 espèces en PNA),Passeriformes
-Pouillot véloce,Passeriformes
-Roitelet huppé,Passeriformes
-Roitelet triple-bandeau,Passeriformes
-Rouge-gorge familier,Passeriformes
-Verdier d'Europe,Passeriformes
-Cigogne blanche,Pelecaniformes
-Cigogne noire,Pelecaniformes
-Grand Duc d'Europe,Strigiformes
-Hibou des marais,Strigiformes
+NomEspece,OrdreFamille
+Espèce générique,NA
+Aigle de Bonelli,Accipitriformes
+Aigle royal,Accipitriformes
+Autour des palombes,Accipitriformes
+Balbuzard pêcheur,Accipitriformes
+Bondrée apivore,Accipitriformes
+Busard cendré,Accipitriformes
+Busard des roseaux,Accipitriformes
+Busard Saint-Martin,Accipitriformes
+Buse variable,Accipitriformes
+Elanion blanc,Accipitriformes
+Epervier d'Europe,Accipitriformes
+Faucon crécerelle,Accipitriformes
+Faucon crécerellette,Accipitriformes
+Faucon pélerin,Accipitriformes
+Gypaète barbu,Accipitriformes
+Milan noir,Accipitriformes
+Milan royal ,Accipitriformes
+Pygarge à queue blanche,Accipitriformes
+Vautour fauve,Accipitriformes
+Vautour moine,Accipitriformes
+Vautour percnoptère,Accipitriformes
+Martinet noir,Caprimulgiformes
+Oedicnème criard,Charadriiformes
+Pluvier doré,Charadriiformes
+Sterne pierregarin,Charadriiformes
+Vanneau huppé,Charadriiformes
+Caille des blés,Galliformes
+Perdrix grise,Galliformes
+Perdrix rouge,Galliformes
+Grue cendrée,Gruiformes
+Goéland argenté,Laridés
+Mouette rieuse,Laridés
+Outarde canepetière,Otidiformes
+Alouette des champs,Passeriformes
+Alouette lulu,Passeriformes
+Bruant proyer,Passeriformes
+Bruant jaune,Passeriformes
+Chardonneret élégant,Passeriformes
+Etourneau sansonnet,Passeriformes
+Gobemouche noir,Passeriformes
+Grive musicienne,Passeriformes
+Hirondelle de fenetre,Passeriformes
+Linotte mélodieuse,Passeriformes
+Merle noir,Passeriformes
+Moineau domestique,Passeriformes
+Moineau friquet,Passeriformes
+Pies-grièches (4 espèces en PNA),Passeriformes
+Pouillot véloce,Passeriformes
+Roitelet huppé,Passeriformes
+Roitelet triple-bandeau,Passeriformes
+Rouge-gorge familier,Passeriformes
+Verdier d'Europe,Passeriformes
+Cigogne blanche,Pelecaniformes
+Cigogne noire,Pelecaniformes
+Grand Duc d'Europe,Strigiformes
+Hibou des marais,Strigiformes
diff --git a/inst/ShinyApp/ui.R b/inst/ShinyApp/ui.R
index c04acc457a8befe0d0edd3b9cbd6f9de852abfe6..0406d8a6dadab219613e5eaa16879e3cad5e4b02 100644
--- a/inst/ShinyApp/ui.R
+++ b/inst/ShinyApp/ui.R
@@ -11,7 +11,6 @@ library(eolpop)
## Load species list
species_data <- read.csv("./inst/ShinyApp/species_list.csv", sep = ",")
species_list <- unique(as.character(species_data$NomEspece))
-# species_list <- species_data$NomEspece
## Load survival and fecundities data
data_sf <- read.csv("./inst/ShinyApp/survivals_fecundities_species.csv", sep = ",")#, encoding = "UTF-8")
@@ -21,8 +20,8 @@ data_sf <- read.csv("./inst/ShinyApp/survivals_fecundities_species.csv", sep = "
nsim = 10
coeff_var_environ = 0.10
time_horzion = 30
-survivals <- c(0.5, 0.7, 0.8, 0.95)
-fecundities <- c(0, 0, 0.05, 0.55)
+init_survivals <- c(0.5, 0.5, 0.5)
+init_fecundities <- c(0, 0.8, 1.2)
#####################
### Pre-fill data ###
@@ -64,13 +63,13 @@ init_cumul_add <- c(3, 0.05, 2020)
# vital rates
-data_vr = c(survivals, fecundities)
+init_vr = c(init_survivals, init_fecundities)
# DD parameters
theta = 1
# Define theoretical rMAX for the species
-rMAX_species <- rMAX_spp(surv = tail(survivals,1), afr = min(which(fecundities != 0)))
+rMAX_species <- rMAX_spp(surv = tail(init_survivals,1), afr = min(which(init_fecundities != 0)))
rMAX_species
@@ -81,15 +80,18 @@ ui <- fluidPage(
useShinyjs(),
titlePanel("eolpop : Impact demographique des éoliennes"),
- # Creation of the first page (select species, analysis type choice)
+ # Creation of the first page (select species, analysis type choice)
wellPanel(
- selectInput(inputId = "species_list",
+
+ selectInput(inputId = "species_choice", selected = 1,
h4(strong("Sélection d'une espèce ou groupe d'espèces")),
choices = species_list),
+
radioButtons(inputId = "analysis_choice",
h4(strong("Sélectionner un type d'analyse")),
choices = c("Impacts non cumulés" = "scenario", "Impacts cumulés" = "cumulated"))
+
), # End wellPanel
@@ -98,32 +100,44 @@ ui <- fluidPage(
##--------------------------------------------
wellPanel(
+ h2("Valeurs sélectionnées"),
+
fluidRow(
+ textOutput(outputId = "species_name"),
+
column(width = 4,
- textOutput(outputId = "specie_name"),
+
+ br(),
h4("Mortalités"),
textOutput(outputId = "fatalities_mean_info"),
textOutput(outputId = "fatalities_se_info"),
+
+ br(),
h4("Taille de la population"),
textOutput(outputId = "pop_size_type_info"),
textOutput(outputId = "pop_size_mean_info"),
textOutput(outputId = "pop_size_se_info")),
- fluidRow(
+
column(width = 4,
+
+ br(),
h4("Capacité de charge"),
textOutput(outputId = "carrying_capacity_info"),
+
+ br(),
h4("Tendance de la population"),
textOutput(outputId = "pop_trend_type_info"),
textOutput(outputId = "pop_growth_mean_info"),
textOutput(outputId = "pop_growth_se_info")),
- fluidRow(
+
column(width = 4,
+
+ br(),
h4("Paramètres démographiques"),
tableOutput(outputId = "vital_rates_info"))
- )
- )
- )
- ), # End wellPanel
+
+ ) # # End wellPanel
+ ), # End fluidRow
# Paramter Inputs (fatalities, pop size, carrying capacity, pop trend and vital rates).
@@ -262,7 +276,7 @@ ui <- fluidPage(
label = "Tendance de la population"),
radioButtons(inputId = "lambda_input_type",
- label = h4("Type de tendance"),
+ label = h4("Type de saisie"),
choices = c("Taux de croissance", "Elicitation d'expert", "Tendance locale ou régionale")),
numericInput(inputId = "pop_growth_mean",
@@ -286,8 +300,6 @@ ui <- fluidPage(
actionButton(inputId = "pop_growth_run_expert", label = "Analyse"),
- h4("Tendance de la population"),
-
radioButtons(inputId = "pop_trend",
label = NULL,
choices = c("Croissance", "Stable", "Déclin")),
@@ -307,20 +319,9 @@ ui <- fluidPage(
actionButton(inputId = "button_vital_rates",
label = "Paramètres démographiques"),
- radioButtons(inputId = "fill_type_vr",
- label = "Type de saisie",
- choices = c("Automatique", "Manuelle")),
-
- # tableOutput(outputId = "mat_display_vr"),
-
- matrixInput(inputId = "mat_display_vr",
- value = matrix("", 4, 2, dimnames = list(c("Juv 1", "Juv 2", "Juv 3", "Adulte"), c("Survie", "Fécondité"))),
- class = "numeric",
- rows = list(names = TRUE),
- cols = list(names = TRUE)),
-
matrixInput(inputId = "mat_fill_vr",
- value = matrix(data = data_vr, 4, 2, dimnames = list(c("Juv 1", "Juv 2", "Juv 3", "Adulte"), c("Survie", "Fécondité"))),
+ value = matrix(data = init_vr, 3, 2,
+ dimnames = list(c("Juv 1", "Juv 2", "Adulte"), c("Survie", "Fécondité"))),
class = "numeric",
rows = list(names = TRUE),
cols = list(names = TRUE))