From 55c7dae61456f53fcd7d627b4612a2af01608451 Mon Sep 17 00:00:00 2001
From: thierrychambert <thierry.chambert@gmail.com>
Date: Fri, 13 Aug 2021 16:43:21 +0200
Subject: [PATCH] Fixed some issue
Added observe(param) in server to make sure param used in simulations keep up to date !
---
inst/ShinyApp/runApp.R | 1 +
inst/ShinyApp/server.R | 23 +++++++++++++----------
inst/ShinyApp/ui.R | 7 ++++---
run_analysis.R | 1 +
4 files changed, 19 insertions(+), 13 deletions(-)
diff --git a/inst/ShinyApp/runApp.R b/inst/ShinyApp/runApp.R
index 266fa21..01caab2 100644
--- a/inst/ShinyApp/runApp.R
+++ b/inst/ShinyApp/runApp.R
@@ -1,3 +1,4 @@
+library(eolpop)
source("./inst/ShinyApp/ui.R")
source("./inst/ShinyApp/server.R")
diff --git a/inst/ShinyApp/server.R b/inst/ShinyApp/server.R
index d2dd703..981b865 100644
--- a/inst/ShinyApp/server.R
+++ b/inst/ShinyApp/server.R
@@ -157,6 +157,7 @@ server <- function(input, output, session){
carrying_cap_eli_result = NULL)
###~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~###
+ observe(param)
##--------------------------------------------
## Display parameter distribution --
@@ -192,7 +193,6 @@ server <- function(input, output, session){
## Run expert elicitation --
##--------------------------------------------
plot_expert <- function(out, show_se = TRUE, ...){
- #plot_elicitation(out, ylab = "Densité de probabilité", xlab = "Valeur du paramètre", cex.lab = 1.2)
plot_elicitation(out, ylab = "", xlab = "Valeur du paramètre", cex.lab = 1.2, yaxt = "n")
mtext(text = "Densité de probabilité", side = 2, line = 2, cex = 1.2)
@@ -353,6 +353,17 @@ server <- function(input, output, session){
})
+ ###~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~##
+ ## Survivals, fecundities and rMAX_species ###~~~~~~~~~~~~~~~~~~~~~~~~~~###
+ observeEvent({input$run}, {
+ param$survivals <- input$mat_fill_vr[,1]
+ param$fecundities <- input$mat_fill_vr[,2]
+ param$rMAX_species <- rMAX_spp(surv = tail(param$survivals,1), afr = min(which(param$fecundities != 0)))
+ }) # end observeEvent
+
+
+
+
###~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~##
## Population growth ###~~~~~~~~~~~~~~~~~~~~~~~~~~###
observeEvent({
@@ -399,14 +410,6 @@ server <- function(input, output, session){
}
})
- # Survivals and fecundities
- observeEvent({input$run}, {
- param$survivals <- input$mat_fill_vr[,1]
- param$fecundities <- input$mat_fill_vr[,2]
- param$rMAX_species <- rMAX_spp(surv = tail(param$survivals,1), afr = min(which(param$fecundities != 0)))
- }) # end observeEvent
-
-
# Survival and fecundity calibration
observeEvent({
input$run
@@ -466,7 +469,7 @@ server <- function(input, output, session){
fecundities = param$f_calibrated,
carrying_capacity = param$carrying_capacity,
- theta = param$theta,
+ theta = theta,
rMAX_species = param$rMAX_species,
model_demo = NULL,
diff --git a/inst/ShinyApp/ui.R b/inst/ShinyApp/ui.R
index d0da8bc..6d38db5 100644
--- a/inst/ShinyApp/ui.R
+++ b/inst/ShinyApp/ui.R
@@ -219,7 +219,8 @@ ui <- fluidPage(
radioButtons(inputId = "pop_size_type",
label = h4("Unité"),
- choices = c("Nombre de couple" = "Npair", "Effectif total" = "Ntotal")),
+ choices = c("Nombre de couple" = "Npair", "Effectif total" = "Ntotal"),
+ selected = "Ntotal"),
radioButtons(inputId = "pop_size_input_type",
label = h4("Type de saisie"),
@@ -265,7 +266,7 @@ ui <- fluidPage(
numericInput(inputId = "pop_growth_mean",
label = "Moyenne de la croissance de la population",
- value = 1,
+ value = 1.1,
min = 0, max = Inf, step = 0.01),
numericInput(inputId = "pop_growth_se",
@@ -311,7 +312,7 @@ ui <- fluidPage(
numericInput(inputId = "carrying_capacity",
label = "Capacité de charge",
- value = 1000,
+ value = 500,
min = 0, max = Inf, step = 100),
matrixInput(inputId = "carrying_cap_mat_expert",
diff --git a/run_analysis.R b/run_analysis.R
index 1b4a70e..affe7bd 100644
--- a/run_analysis.R
+++ b/run_analysis.R
@@ -69,6 +69,7 @@ lambda( build_Leslie(s = s_calibrated, f = f_calibrated) )
#fatal_constant = "M"
#cumulated_impacts = FALSE
+pop_growth_mean = 1.1
pop_size_type = "Ntotal"
carrying_capacity = 500
--
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