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Merge pull request #35 from NIVANorge/dev
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option to show Chl 90pct
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@ciaran-dk
ciaran-dk authored Oct 17, 2024
2 parents 0fca1df + 7231a2f commit 8ba45e3
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Showing 9 changed files with 1,913 additions and 31 deletions.
246 changes: 246 additions & 0 deletions app/WB_results_OF_chl90.csv
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156 changes: 125 additions & 31 deletions app/app.R
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Original file line number Diff line number Diff line change
Expand Up @@ -13,12 +13,28 @@ names(r_colors) <- colors()


plottitle<-function(parameter){
params<-c("Ecological Status","Chl_summer","MSMDI","NQI1","H","Secchi","DO_bot","NH4_summer","NH4_winter",
params<-c("Ecological Status",
"Chl_summer",
"Chl",
"MSMDI",
"NQI1","H","Secchi","DO_bot",
"NH4_summer","NH4_winter",
"NO3_summer","NO3_winter","PO4_summer","PO4_winter",
"TN_summer","TN_winter","TP_summer","TP_winter")
titles<-c("Ecological status","Chl a [µg/l]","MSMDI [EQR]","NQI1 [EQR]","H [EQR]","Secchi [m]","DO bottom [ml/l]","NH4 summer [µg-N/l]","NH4 winter [µg-N/l]",
"NO3 summer [µg-N/l]","NO3 winter [µg-N/l]","PO4 summer [µg-P/l]","PO4 winter [µg-P/l]",
"TN summer [µg-N/l]","TN _winter [µg-N/l]","TP summer [µg-P/l]","TP winter [µg-P/l]")
titles<-c("Ecological status","Chl a [µg/l]","Chl a 90. pct [µg/l]",
"MSMDI [EQR]","NQI1 [EQR]",
"H [EQR]","Secchi [m]",
"DO bottom [ml/l]",
"NH4 summer [µg-N/l]",
"NH4 winter [µg-N/l]",
"NO3 summer [µg-N/l]",
"NO3 winter [µg-N/l]",
"PO4 summer [µg-P/l]",
"PO4 winter [µg-P/l]",
"TN summer [µg-N/l]",
"TN _winter [µg-N/l]",
"TP summer [µg-P/l]",
"TP winter [µg-P/l]")

title<-titles[params==parameter]
return(title)
Expand Down Expand Up @@ -88,25 +104,32 @@ ui <- dashboardPage(skin = "black",title="MARTINI Status Assessment",

# "NQI1","H" - currently no results for these parameters

column(2,selectInput("selParam",label="Display variable:",
c("Ecological Status"="Ecological Status",
"Chl a (summer)"="Chl_summer",
"MSMDI"="MSMDI",
"Secchi (summer)"="Secchi",
"DO (bottom)"="DO_bot",
"NH4 (summer)"="NH4_summer",
"NH4 (winter)"="NH4_winter",
"NO3 (summer)"="NO3_summer",
"NO3 (winter)"="NO3_winter",
"PO4 (summer)"="PO4_summer",
"PO4 (winter)"="PO4_winter"
#"TN_summer","TN_winter",
#"TP_summer","TP_winter"
))),
column(2,
# selectInput("selParam",label="Display variable:",
# c("Ecological Status"="Ecological Status",
# "Chl a (summer)"="Chl_summer",
# "Chl a (90pct.)"="Chl",
# "MSMDI"="MSMDI",
# "Secchi (summer)"="Secchi",
# "DO (bottom)"="DO_bot",
# "NH4 (summer)"="NH4_summer",
# "NH4 (winter)"="NH4_winter",
# "NO3 (summer)"="NO3_summer",
# "NO3 (winter)"="NO3_winter",
# "PO4 (summer)"="PO4_summer",
# "PO4 (winter)"="PO4_winter"
# #"TN_summer","TN_winter",
# #"TP_summer","TP_winter"
# ))
uiOutput("selectParam", inline=T)
),
column(2,
p(disabled(checkboxInput("scaleDiscrete","Discrete colours",value=F))),
p(checkboxInput("showStatus","Show status",value=TRUE))
),
column(2, offset = 2,
p(checkboxInput("useChl90","Use Chl a 90th percentile",value=F))
)
),
fluidRow(
column(5,
Expand Down Expand Up @@ -160,8 +183,10 @@ server <- function(input, output, session) {
quiet=T, check_ring_dir=T, promote_to_multi=F)

df_WB<-read.table(file="nve/WBlist.txt",header=T,stringsAsFactors=F,sep=";")
df_ind <- read.table(file="indicator_results_OF.csv",sep=";",header=T)
df_wb <- read.table(file="WB_results_OF.csv",sep=";",header=T)
df_ind1 <- read.table(file="indicator_results_OF.csv",sep=";",header=T)
df_wb1 <- read.table(file="WB_results_OF.csv",sep=";",header=T)
df_ind2 <- read.table(file="indicator_results_OF_chl90.csv",sep=";",header=T)
df_wb2 <- read.table(file="WB_results_OF_chl90.csv",sep=";",header=T)
df_wb_obs <- read.table(file="EQR_status.txt",sep=";",header=T)

param_lims <- read.table(file="param_limits.csv",sep=";",header=T)
Expand All @@ -170,10 +195,78 @@ server <- function(input, output, session) {
obs_stns <- read.table("obs_stations.csv", sep=";", header=T)

# "NQI1","H" - currently no results for these parameters
params<-c("Ecological Status","Chl_summer","MSMDI","Secchi","DO_bot","NH4_summer","NH4_winter",
params<-c("Ecological Status","Chl_summer","Chl","MSMDI",
"Secchi","DO_bot","NH4_summer","NH4_winter",
"NO3_summer","NO3_winter","PO4_summer","PO4_winter",
"TN_summer","TN_winter","TP_summer","TP_winter")

df_ind <- reactive({
if(input$useChl90){
return(df_ind2)
}else{
return(df_ind1)
}
})

df_wb <- reactive({
if(input$useChl90){
return(df_wb2)
}else{
return(df_wb1)
}
})


param_select_list <- reactive({
if(input$useChl90){
list_param_sel <- c("Ecological Status"="Ecological Status",
"Chl a (90pct.)"="Chl",
"MSMDI"="MSMDI",
"Secchi (summer)"="Secchi",
"DO (bottom)"="DO_bot",
"NH4 (summer)"="NH4_summer",
"NH4 (winter)"="NH4_winter",
"NO3 (summer)"="NO3_summer",
"NO3 (winter)"="NO3_winter",
"PO4 (summer)"="PO4_summer",
"PO4 (winter)"="PO4_winter"
#"TN_summer","TN_winter",
#"TP_summer","TP_winter"
)
}else{
list_param_sel <- c("Ecological Status"="Ecological Status",
"Chl a (summer)"="Chl_summer",
"MSMDI"="MSMDI",
"Secchi (summer)"="Secchi",
"DO (bottom)"="DO_bot",
"NH4 (summer)"="NH4_summer",
"NH4 (winter)"="NH4_winter",
"NO3 (summer)"="NO3_summer",
"NO3 (winter)"="NO3_winter",
"PO4 (summer)"="PO4_summer",
"PO4 (winter)"="PO4_winter"
#"TN_summer","TN_winter",
#"TP_summer","TP_winter"
)
}
return(list_param_sel)
})


output$selectParam <- renderUI({
list_param_sel <- param_select_list()

tagList(selectInput(
"selParam",
"Display variable:",
choices = list_param_sel,
selected = list_param_sel[1],
multiple = FALSE,
#width="200px",
selectize = T
))
})

round_sig <- function(x, n, max_dec=3){
base <- ifelse(x==0, -2, ceiling(log10(abs(x))))
ndig <- n - base
Expand Down Expand Up @@ -218,10 +311,11 @@ server <- function(input, output, session) {
#load("indicators.Rda")

WB_name<-df_WB[df_WB$VANNFOREKOMSTID==values$wbselected,"VANNFOREKOMSTNAVN"]
df_ind <- df_ind %>% dplyr::filter(WB==values$wbselected)
type<-df_ind$type[1]
Salinity<-df_ind$Salinity[1]
CoastType<-df_ind$Type[1]
df_ind_wb <- df_ind() %>%
dplyr::filter(WB==values$wbselected)
type<-df_ind_wb$type[1]
Salinity<-df_ind_wb$Salinity[1]
CoastType<-df_ind_wb$Type[1]
cat(file=stderr(),values$wbselected," ",WB_name,", ",type," ",CoastType,", ",Salinity,"\n")
WB_name<-df_WB[df_WB$VANNFOREKOMSTID==values$wbselected,"VANNFOREKOMSTNAVN"]

Expand Down Expand Up @@ -299,14 +393,14 @@ server <- function(input, output, session) {
dplyr::select(WB=Vannforeko, Status=Class)

}else{
df<-df_wb %>%
df<-df_wb() %>%
dplyr::filter(Period==values$period) %>%
dplyr::filter(scenario==scenario_sel()) %>%
dplyr::select(WB,Status)
}
}else{

df<-df_ind %>%
df<-df_ind() %>%
dplyr::filter(Indicator==values$parameter) %>%
dplyr::filter(Period==values$period) %>%
dplyr::filter(scenario==scenario_sel()) %>%
Expand Down Expand Up @@ -570,7 +664,7 @@ server <- function(input, output, session) {

shiny::req(values$wbselected)

df<-df_ind %>%
df<-df_ind() %>%
dplyr::select(WB,Indicator,Indikator, IndikatorDesc, Period,scenario,Kvalitetselement,Value,EQR,
Ref,HG,GM,MP,PB,Worst,Status)
if(values$wbselected==""){
Expand Down Expand Up @@ -738,7 +832,7 @@ server <- function(input, output, session) {
# browser()
shiny::req(values$wbselected)
ClassList<-c("Bad","Poor","Mod","Good","High")
df<-df_wb %>%
df<-df_wb() %>%
dplyr::select(WB,Period,scenario,Worst_Biological,Biological,Worst_Supporting,Supporting,EQR,Status)
show_base <- ifelse(scenario_sel()==scenario_comparison, F, T)

Expand Down Expand Up @@ -812,7 +906,7 @@ server <- function(input, output, session) {
# browser()
shiny::req(values$wbselected)
ClassList<-c("Bad","Poor","Mod","Good","High")
df<-df_wb %>%
df<-df_wb() %>%
dplyr::select(WB,Period,scenario,Worst_Biological,Biological,Worst_Supporting,Supporting,EQR,Status)
show_base <- ifelse(scenario_sel()==scenario_comparison, F, T)

Expand Down
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