R/AquaFlux_Server.R
In EwersLabUWyo/AquaFlux:
#####################################################################
#####################################################################
#####################################################################
# Server ##
#####################################################################
#####################################################################
#####################################################################
.AquaFlux.server <- function(input, output, session) {
v <- shiny::reactiveValues(
####### File name tags -- used to name AquaFlux's saves of data
tag.dT.raw = "All dT Data Unfiltered",
tag.dT.clean = "Sapflux dT cleaned- Current",
tag.flag = "All Sapflux Flags- Current",
tag.Tmax = "Tmax- Current",
tag.flux = "Sapflux- Current",
tag.log.deletion = "Deletion Log- Current",
tag.site.matadata = "Site MetaData.csv",
#### standard time format
standard.time.format = '%Y-%m-%d %H:%M', # Campbell default.
alternate.time.format = '%m/%d/%y %H:%M', # Excel default
third.time.format = '%d/%m/%Y %H:%M', # Excel default
R.time.format = "%Y-%m-%d %H:%M", # R default
######### doy
min.DOY = 0,
max.DOY = 367,
min.DOY.global = 0,
max.DOY.global = 367,
number.of.saves.to.keep = 10,
####################### opening blank values these are advance options
max.gap.length = 8,
min.number.of.columns.in.a.data.file = 2,
################ these are from your data
nonsapflux.columns = NA,
AquaFlux.work.dir = "<Copy & Paste file path>",
site.names = "MissingSiteName",
number.of.sites = 1,
n.met.data="<select>",
n.dT.data = "<select>",
importOption = "NoSite",
accepted.met.dir = F,
accepted.dt.dir = F,
################ for the "Set up" panel
setup.SiteType = "",
StartButton = "empty",
SetupStep = 1,
setup.done = F,
Setup1 = "no",
setup.load.message = " ",
setup.SiteType = " ",
################# import
import.status = "not.done",
sapflux.names = NA,
# plot
MinDT_brokensensor = 0,
VPD.thres = 0.2,
tree.number = 1,
b.range = NA,
tree.name = "none",
move.dir = "none",
pick.plot.options = "none",
LDate.local = c(0,400),
dT.local = c(0,1),
restore.options = "none",
i.need.for.Tmax.auto = NA,
autoQAQCmes = " ",
LastAutoFilter= "none",
export.done = F,
plotAutoQAQC = F,
BrokenSensors.mes.na = "<not ran yet>",
BrokenSensors.mes.sd = "<not ran yet>",
BrokenSensors.mes.low = "<not ran yet>",
#### QAQC
# qaqc.1orAll = "False",
######## export stuff
export.done = F,
export.mes.1=" ",
export.mes.2=" ",
export.mes.3=" ",
export.mes.4=" ",
export.mes.5=" ",
export.mes.6=" ",
export.mes.7=" ",
export.mes.8=" ",
export.mes.9=" ",
export.mes.10=" ",
time.last.save = Sys.time()
)
# ##############################################
# # GUI folder navigate ##
# ##############################################
# # GuiDir
shinyFiles::shinyDirChoose(input, 'GuiDirSave', roots = c(home = '~'))
shinyFiles::shinyDirChoose(input, 'GuiDirMet', roots = c(home = '~'))
shinyFiles::shinyDirChoose(input, 'GuiDirDT', roots = c(home = '~'))
output$GuiDir <- shiny::renderPrint(shiny::reactive(input$GuiDirSave))
output$GuiDir <- shiny::renderPrint(shiny::reactive(input$GuiDirMet))
output$GuiDir <- shiny::renderPrint(shiny::reactive(input$GuiDirDT))
# # path - I'm not sure what this does
# path <- shiny::reactive({
# home <- normalizePath("~")
# file.path(home, paste(unlist(dir()$path[-1]), collapse = .Platform$file.sep))
# print(file.path) #
# })
#### observe the paths
shiny::observe({ a = input$GuiDirSave; lab="GuiDirSave"; v = .test.GuiDir(a, lab); } )
shiny::observe({ a = input$GuiDirMet; lab="GuiDirMet"; v = .test.GuiDir(a, lab); } )
shiny::observe({ a = input$GuiDirDT; lab="GuiDirDT"; v = .test.GuiDir(a, lab); } )
##############################################
# Set up functions - step 0 ##
##############################################
shiny::observe({ v$AquaFlux.work.dir = input$AquaFlux.work.dir; })
shiny::observe({v$StartButton = input$StartButton})
output$start.up.questions <- renderUI({ if ( v$import.status == 'not.done') { .start.up.ui.questions } })
output$output.message <- renderText({ v$setup.SiteType })
output$start.up.warning <- renderUI({ if ( v$import.status == 'WARNING') {
shiny::fluidPage(
shiny::verbatimTextOutput("output.message"),
shiny::actionButton( "NotSure", "No! Don't delete my files!"),
shiny::actionButton( "IAmSure", "That's ok, I want to start fresh. Delete my files")
) } })
output$start.up.loading <- renderUI({ if ( v$import.status == 'Loading') {
shiny::fluidPage(
shiny::verbatimTextOutput("output.message")
) } })
shiny::observeEvent(input$NotSure,{ v$import.status <- "not.done"; v$setup.SiteType="Please enter your save directory" })
shiny::observeEvent(input$IAmSure,{ v = .IAmSureNewSite(v) })
shiny::observeEvent(input$launch.load,{
v$import.status <- "Loading";
v$setup.SiteType=paste("Loading your old and new data...")
v= .launch.load(v) #
})
shiny::observeEvent(input$launch.new,{ v= .launch.new(v) })
output$setup.SiteType <- renderText({ v$setup.SiteType })
# ##############################################
# # Set up functions - step 1 ##
# ##############################################
.dir.declare.met.full = renderUI({
shiny::fluidPage(
if ( v$accepted.met.dir == F) { .dir.declare.met },
if ( v$accepted.met.dir == T) { shiny::helpText("Met directory accepted") }
)
})
.dir.declare.dt.full = renderUI({
shiny::fluidPage(
if ( v$accepted.dt.dir == F) { .dir.declare.dt },
if ( v$accepted.dt.dir == T) { shiny::helpText("Site directory accepted") }
)
})
output$ui.setup.1 = renderUI({ if ( v$import.status == 'ReadyForNew1') {
shiny::fluidPage(
.dir.declare.met.full,
shiny::helpText("Note: if your met and dT data are saved in the same files, paste that directory in both fields"),
shiny::selectInput("delim.sep", "Data Delimiter", .delim.options),
shiny::numericInput("number.of.before.headers", "How many lines before your data headers?", min=0,max=30, value=1),
shiny::numericInput("number.of.lines.before.data", "How many lines before your data proper?", min=1,max=30, value=4),
shiny::textAreaInput("site.names", "Site Names", "<Site name, 1 on each line>", width = "400px"),
.dir.declare.dt.full, #
shiny::actionButton( "Setup1", "Check my work (this will take a minute)"),
shiny::verbatimTextOutput(v$output.message)
) } })
# ##############################################
# # Set up functions - step 2 ##
# ##############################################
shiny::observe({ v$met.dir = input$met.dir})
shiny::observe({ v$delim.sep = input$delim.sep})
shiny::observe({ v$number.of.before.headers = input$number.of.before.headers })
shiny::observe({ v$number.of.lines.before.data = input$number.of.lines.before.data})
shiny::observe({ v$site.names = input$site.names})
shiny::observe({ v$dt.dir = input$dt.dir })
shiny::observeEvent(input$Setup1,{ v=.test.setup1(v) })
##############################################
# Set up functions - step 2 ##
##############################################
shiny::observe({ v$study.year = input$study.year})
shiny::observe({ v$selected.timestamp.format = input$selected.timestamp.format })
output$pick.dT.ts.name <- renderUI({
colnames = c("<select>", v$n.dT.data)
shiny::selectInput("dT.ts.name", "Timestamp Name in dT data",
choices = colnames,
selected = as.character(v$import.dT.ts.name) )
})
shiny::observe({ v$dT.ts.name = input$dT.ts.name})
output$pick.met.ts.name <- renderUI({
colnames = c("<select>", v$n.met.data)
shiny::selectInput("met.ts.name", "Timestamp Name in Met. data",
choices = colnames)
})
shiny::observe({ v$met.ts.name = input$met.ts.name})
shiny::observe({v$dT.units = input$dT.units })
output$pick_AirT_name <- renderUI({
colnames = c("<select>", "<No Air T data>", v$n.met.data)
shiny::selectInput("met.air.temp.label", "Air Temp = ?",
choices = colnames)
})
shiny::observe({ v$met.air.temp.label = input$met.air.temp.label})
shiny::observe({v$met.air.temp.units = input$met.air.temp.units })
output$pick_RH_name <- renderUI({
colnames = c("<select>", "<No RH data>", v$n.met.data)
shiny::selectInput("met.RH.label", "Relative Humidity = ?",
choices = colnames)
})
shiny::observe({ v$met.RH.label = input$met.RH.label})
shiny::observe({v$met.RH.units = input$met.RH.units })
output$choose_nonsapflux <- renderUI({
colnames <- v$n.dT.data
shiny::checkboxGroupInput("nonsapflux.columns", "Choose non-sap flux columns",
choices = colnames)
})
shiny::observe({ v$nonsapflux.columns = input$nonsapflux.columns})
shiny::observeEvent(input$finish.set.up,{
########### time
.save.site.metadata(v)
v = .finish.importing(v)
v$setup.load.message = "Loaded in your site and data. Continue on next panel."
v$setup.done = T
v$import.status = "done"
})
output$setup.load.message <- renderText({
v$setup.load.message
})
output$ui.setup.2 <- renderUI({ if ( v$import.status == 'ReadyForNew2') {
shiny::fluidPage(
shiny::helpText("Questions about your time format (see 'strptime' and manual for help)"),
shiny::textInput('study.year', "Study Year (can only do 1 year at a time)", value = "<Enter Study Year>"),
shiny::selectInput("selected.timestamp.format", "Common Timestamp Format", .timestamp.options),
shiny::uiOutput("pick.dT.ts.name"),
shiny::uiOutput("pick.met.ts.name"),
shiny::br(),
shiny::helpText("Questions about units"),
shiny::selectInput("dT.units", "What are the dT units?", .dT.units.options),
shiny::uiOutput("pick_AirT_name"),
shiny::selectInput("met.air.temp.units", "Air Temp. Units", .air.temp.units.options, selected="mV"),
shiny::uiOutput("pick_RH_name"),
shiny::selectInput("met.RH.units", "Relative Humidity Units", .RH.units.options),
uiOutput("choose_nonsapflux"),
conditionalPanel( "v$import.status = 'start.new'" , {
actionButton(inputId="finish.set.up", label="Finish Site Set Up (takes a minute)") }),
verbatimTextOutput("setup.load.message")
) } })
output$ui.setup.done <- renderUI({ if ( v$import.status == 'done') {
shiny::fluidPage(
shiny::helpText("Data Sucessfully Imported! Start processing.")
) } })
##############################################
# Broken Sensors ##
##############################################
shiny::observeEvent(input$FindBrokenSensors,{ v$BrokenSensorReports = .BrokenSensors.detect(v) })
output$BrokenSensors.mes.na <- renderText({ v$BrokenSensors.mes.na })
output$BrokenSensors.mes.low <- renderText({ v$BrokenSensors.mes.low })
output$BrokenSensors.mes.sd <- renderText({ v$BrokenSensors.mes.sd })
##############################################
# Processing col 1: Generic Plot Data ##
##############################################
# pick a tree
output$tree.name <- renderUI({
colnames = c(v$sapflux.names)
# Create the checkboxes and select them all by default
shiny::selectInput("tree.name", "Pick a sensor",
choices = colnames)
})
observe({ v$tree.name = input$tree.name;
v = .get.local.data(v);
})
# doy range stuff
observe({ v$min.DOY = input$DOY.range[1] })
observe({ v$max.DOY = input$DOY.range[2] })
observe({ shiny::updateSliderInput(session, "DOY.range", value = c(v$min.DOY,v$max.DOY),
min = v$min.DOY.global , max = v$max.DOY.global )
})
# move doy
observeEvent(input$b.move.back, { v$move.dir= "back"; v=.move.window(v); })
observeEvent(input$save.data, { .save.AquaFlux(v); })
observeEvent(input$b.move.foward, { v$move.dir= "foward"; v=.move.window(v); })
##############################################
# Processing col 2: Pick processing options ##
##############################################
########### pick plot options
observe({ v$pick.plot.options = input$pick.plot.options})
observe({ shiny::updateCheckboxGroupInput(session, "pick.plot.options", selected = v$pick.plot.options) })
########### pick processing options
observe({ v$processOption = input$processOption;
if(v$processOption=="tmax"){ .Tmax.turn.on.plotting(v) } })
##############################################
# Processing col 3- QAQC auto ##
##############################################
# actually suggest
observeEvent(input$auto.clean, { v = .autoQAQC.suggest(v) })
# options
observe({ v$MinDT = as.numeric(as.character(input$MinDT)) })
observe({ v$MaxDT = as.numeric(as.character(input$MaxDT)) })
observe({ v$DT.despike.dev = as.numeric(as.character(input$DT.despike.dev)) })
# output message
output$autoQAQCmes <- renderText({ autoQAQCmes = v$autoQAQCmes })
# Accept / reject
observeEvent(input$b.AutoQAQC.keep, { v = .autoQAQC.keep(v) })
observeEvent(input$b.AutoQAQC.del, { v = .autoQAQC.del(v) })
##############################################
# Processing col 3- QAQC manual ##
##############################################
observeEvent(input$qaqc.manual, {
v$plotAutoQAQC = F;v$tmaxRadio="none";v$restore.option="none"; # clear other bottons
v$qaqc.manual <- input$qaqc.manual;
})
observe({ shiny::updateRadioButtons(session, "qaqc.manual", selected = v$qaqc.manual) })
# observe({ v$qaqc.1orAll = input$qaqc.1orAll})
##############################################
# Processing col 3- Calib ##
##############################################
observe({ v$alpha = as.numeric(as.character(input$alpha)) })
observe({ v$beta = as.numeric(as.character(input$beta)) })
##############################################
# Processing col 3- Tmax ##
##############################################
# generic bottons
observe({ v$VPD.thres = as.numeric(as.character(input$VPD.thres)); })
observe({ v$VPD.below.thres.for.x.hr = as.numeric(as.character(input$VPD.below.thres.for.x.hr)) })
# generic bottons
observe({ v$VPD.below.thres.for.x.hr = as.numeric(as.character(input$VPD.below.thres.for.x.hr)) })
observe({ v$auto.Tmax.window.size = as.numeric(as.character(input$auto.Tmax.window.size)) })
observeEvent(input$auto.Tmax, { v =.Tmax.autopick(v) })
observeEvent(input$tmaxRadio, {
v$tmaxRadio=input$tmaxRadio
if (v$tmaxRadio=="none"){} # no nothing
if (v$tmaxRadio=="manual" | v$tmaxRadio=="delete"){ v$qaqc.manual="none"; v$plotAutoQAQC = F; v$restore.option="none"; }# clear other bottons, then click on graph
} )
##############################################
# Processing col 3- Restore ##
##############################################
observeEvent(input$restore.option, {
v$restore.option <- input$restore.option; # save
if (v$restore.option!="none"){ # if not 'none', reset other bottons
v$plotAutoQAQC = F;v$qaqc.manual="none";v$tmaxRadio="none";
}
})
observe({ shiny::updateSelectInput(session, "restore.option", selected = v$restore.option) })
##############################################
# Plot Graphs ##
##############################################
output$plot.dT <- renderPlot({ ; v$pick.bottun = .plot.dT(v) })
output$plot.sapflux <- renderPlot({ ; .plot.sapflux(v) })
##############################################
# Click the dT graph ##
##############################################
observeEvent(input$dT_plot_click,
{
# auto qaqc - none
# manual qaqc -
if(v$qaqc.manual == "above"){ v=.delete.above(v,input$dT_plot_click$y); }
if(v$qaqc.manual == "below"){ v=.delete.below(v,input$dT_plot_click$y); }
if(v$qaqc.manual == "before"){ v=.delete.before(v,input$dT_plot_click$x); }
if(v$qaqc.manual == "after"){ v=.delete.after(v,input$dT_plot_click$x); }
if(v$qaqc.manual == "between"){v=.delete.between(v,input$dT_plot_click$x); }
if(v$qaqc.manual == "points"){ v=.delete.points(v,input$dT_plot_click); }
if(v$qaqc.manual == "all"){ v=.delete.all(v); }
if(v$qaqc.manual== "undo"){ v=.restore.undo(v); }
# Tmax
if(v$tmaxRadio=="delete"){ v = .Tmax.delete(v,input$dT_plot_click) }
if(v$tmaxRadio=="manual"){ v = .Tmax.pick.manual(v,input$dT_plot_click) }
# restore
if(v$restore.option=="undo"){ v=.restore.undo(v); }
if(v$restore.option=="between"){ v=.restore.between(v,input$dT_plot_click); }
if(v$restore.option=="all"){ v=.restore.all(v); }
}
)
##############################################
# Export ##
##############################################
observeEvent(input$b.export,{
.export.final.data(v)
v$export.mes.1 = paste("At",Sys.time(),"AquaFlux data was exported:")
v$export.mes.2 = paste("CSV data saved to:", v$final.dir)
v$export.mes.3 = paste( "PDF Graphs saved to:", v$graph.dir)
v$export.mes.4 = "Data was also exported to base R (global envir):"
v$export.mes.5 = " 'raw.dT.data' = your raw dT data, in C."
v$export.mes.6 = " 'dT.data' = your post-QAQC dT data, in C."
v$export.mes.7 = " 'Tmax.data.points' = the Tmax points you picked."
v$export.mes.8 = " 'Tmax.data.line' = the Tmax line (interpolated from Tmax.data.points)"
v$export.mes.9 = " 'sapflux.data' = your sap flux dT data, in g s-1 m-2.sapwood"
v$export.mes.10 = " 'met.data' = your met data, including VPD."
}) #
output$export.mes.1 <- renderText({ v$export.mes.1 })
output$export.mes.2 <- renderText({ v$export.mes.2 })
output$export.mes.3 <- renderText({ v$export.mes.3 })
output$export.mes.4 <- renderText({ v$export.mes.4 })
output$export.mes.5 <- renderText({ v$export.mes.5 })
output$export.mes.6 <- renderText({ v$export.mes.6 })
output$export.mes.7 <- renderText({ v$export.mes.7 })
output$export.mes.8 <- renderText({ v$export.mes.8 })
output$export.mes.9 <- renderText({ v$export.mes.9 })
output$export.mes.10 <- renderText({ v$export.mes.10 })
########################################
# v$processOption == 'autoqaqc
output$Aqaqc_pro_minDT <- renderUI({ if ( v$processOption == 'autoqaqc'){ shiny::textInput('MinDT', "Min accepted dT", value = "10") } } )
output$Aqaqc_pro_maxDT <- renderUI({ if ( v$processOption == 'autoqaqc'){ shiny::textInput('MaxDT', "Max accepted dT", value = "30") } })
output$Aqaqc_dt_spike <- renderUI({ if ( v$processOption == 'autoqaqc') { shiny::textInput('DT.despike.dev', "Max Deviance (for despike)", value = "12")}})
output$Aqaqc_auto.clean<- renderUI({ if ( v$processOption == 'autoqaqc') { shiny::actionButton(inputId="auto.clean", label="Suggest new QAQC")}})
output$Aqaqc_autoQAQCmes<- renderUI({ if ( v$processOption == 'autoqaqc') { shiny::verbatimTextOutput("autoQAQCmes") }})
output$Aqaqc_Delete <- renderUI({ if ( v$processOption == 'autoqaqc') { shiny::actionButton(inputId="b.AutoQAQC.del", label="Delete") }})
# v$processOption == 'manqaqc
output$Mqaqc_1orAll <- renderUI({ if ( v$processOption == 'manqaqc') { shiny::checkboxGroupInput("qaqc.1orAll", label=" ", choices = c("Apply to *ALL* trees-- can NOT 'undo delete' " = "all")) }})
output$Mqaqc_manual <- renderUI({ if ( v$processOption == 'manqaqc') { shiny::radioButtons( "qaqc.manual", "Manual QAQC Options:", .qaqc.button.vector,selected = "none",inline=F) }})
# v$processOption == 'tmax
output$tmax_VPDthres <- renderUI({ if ( v$processOption == 'tmax') { shiny::textInput('VPD.thres', "VPD Threshold (kPa)", value = 0.2) }})
output$tmax_VPDhr <- renderUI({ if ( v$processOption == 'tmax') { shiny::textInput('VPD.below.thres.for.x.hr', "VPD must be below thres for X hrs", value = "2") }})
output$tmax_Tmaxsize <- renderUI({ if ( v$processOption == 'tmax') { shiny::textInput('auto.Tmax.window.size', "Window size (days)", value = "7") }})
output$tmax_AutoTmax <- renderUI({ if ( v$processOption == 'tmax') { shiny::actionButton(inputId="auto.Tmax", label="Auto Pick Tmax") }})
output$tmax_radio <- renderUI({ if ( v$processOption == 'tmax') { .tmaxRadio }})
# v$processOption == 'restore
output$restore_picker <- renderUI({ if ( v$processOption == 'restore') { .restore.picker }})
# v$processOption == 'calib
output$calib_alpha <- renderUI({ if ( v$processOption == 'calib') { shiny::textInput('alpha', "alpha", value = 118.99 * 10^(-6) ) }})
output$calib_beta <- renderUI({ if ( v$processOption == 'calib') { shiny::textInput('beta', "beta", value = 1.231) }})
}
EwersLabUWyo/AquaFlux documentation built on July 6, 2019, 5:16 a.m.
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#####################################################################
#####################################################################
#####################################################################
# Server ##
#####################################################################
#####################################################################
#####################################################################
.AquaFlux.server <- function(input, output, session) {
v <- shiny::reactiveValues(
####### File name tags -- used to name AquaFlux's saves of data
tag.dT.raw = "All dT Data Unfiltered",
tag.dT.clean = "Sapflux dT cleaned- Current",
tag.flag = "All Sapflux Flags- Current",
tag.Tmax = "Tmax- Current",
tag.flux = "Sapflux- Current",
tag.log.deletion = "Deletion Log- Current",
tag.site.matadata = "Site MetaData.csv",
#### standard time format
standard.time.format = '%Y-%m-%d %H:%M', # Campbell default.
alternate.time.format = '%m/%d/%y %H:%M', # Excel default
third.time.format = '%d/%m/%Y %H:%M', # Excel default
R.time.format = "%Y-%m-%d %H:%M", # R default
######### doy
min.DOY = 0,
max.DOY = 367,
min.DOY.global = 0,
max.DOY.global = 367,
number.of.saves.to.keep = 10,
####################### opening blank values these are advance options
max.gap.length = 8,
min.number.of.columns.in.a.data.file = 2,
################ these are from your data
nonsapflux.columns = NA,
AquaFlux.work.dir = "<Copy & Paste file path>",
site.names = "MissingSiteName",
number.of.sites = 1,
n.met.data="<select>",
n.dT.data = "<select>",
importOption = "NoSite",
accepted.met.dir = F,
accepted.dt.dir = F,
################ for the "Set up" panel
setup.SiteType = "",
StartButton = "empty",
SetupStep = 1,
setup.done = F,
Setup1 = "no",
setup.load.message = " ",
setup.SiteType = " ",
################# import
import.status = "not.done",
sapflux.names = NA,
# plot
MinDT_brokensensor = 0,
VPD.thres = 0.2,
tree.number = 1,
b.range = NA,
tree.name = "none",
move.dir = "none",
pick.plot.options = "none",
LDate.local = c(0,400),
dT.local = c(0,1),
restore.options = "none",
i.need.for.Tmax.auto = NA,
autoQAQCmes = " ",
LastAutoFilter= "none",
export.done = F,
plotAutoQAQC = F,
BrokenSensors.mes.na = "<not ran yet>",
BrokenSensors.mes.sd = "<not ran yet>",
BrokenSensors.mes.low = "<not ran yet>",
#### QAQC
# qaqc.1orAll = "False",
######## export stuff
export.done = F,
export.mes.1=" ",
export.mes.2=" ",
export.mes.3=" ",
export.mes.4=" ",
export.mes.5=" ",
export.mes.6=" ",
export.mes.7=" ",
export.mes.8=" ",
export.mes.9=" ",
export.mes.10=" ",
time.last.save = Sys.time()
)
# ##############################################
# # GUI folder navigate ##
# ##############################################
# # GuiDir
shinyFiles::shinyDirChoose(input, 'GuiDirSave', roots = c(home = '~'))
shinyFiles::shinyDirChoose(input, 'GuiDirMet', roots = c(home = '~'))
shinyFiles::shinyDirChoose(input, 'GuiDirDT', roots = c(home = '~'))
output$GuiDir <- shiny::renderPrint(shiny::reactive(input$GuiDirSave))
output$GuiDir <- shiny::renderPrint(shiny::reactive(input$GuiDirMet))
output$GuiDir <- shiny::renderPrint(shiny::reactive(input$GuiDirDT))
# # path - I'm not sure what this does
# path <- shiny::reactive({
# home <- normalizePath("~")
# file.path(home, paste(unlist(dir()$path[-1]), collapse = .Platform$file.sep))
# print(file.path) #
# })
#### observe the paths
shiny::observe({ a = input$GuiDirSave; lab="GuiDirSave"; v = .test.GuiDir(a, lab); } )
shiny::observe({ a = input$GuiDirMet; lab="GuiDirMet"; v = .test.GuiDir(a, lab); } )
shiny::observe({ a = input$GuiDirDT; lab="GuiDirDT"; v = .test.GuiDir(a, lab); } )
##############################################
# Set up functions - step 0 ##
##############################################
shiny::observe({ v$AquaFlux.work.dir = input$AquaFlux.work.dir; })
shiny::observe({v$StartButton = input$StartButton})
output$start.up.questions <- renderUI({ if ( v$import.status == 'not.done') { .start.up.ui.questions } })
output$output.message <- renderText({ v$setup.SiteType })
output$start.up.warning <- renderUI({ if ( v$import.status == 'WARNING') {
shiny::fluidPage(
shiny::verbatimTextOutput("output.message"),
shiny::actionButton( "NotSure", "No! Don't delete my files!"),
shiny::actionButton( "IAmSure", "That's ok, I want to start fresh. Delete my files")
) } })
output$start.up.loading <- renderUI({ if ( v$import.status == 'Loading') {
shiny::fluidPage(
shiny::verbatimTextOutput("output.message")
) } })
shiny::observeEvent(input$NotSure,{ v$import.status <- "not.done"; v$setup.SiteType="Please enter your save directory" })
shiny::observeEvent(input$IAmSure,{ v = .IAmSureNewSite(v) })
shiny::observeEvent(input$launch.load,{
v$import.status <- "Loading";
v$setup.SiteType=paste("Loading your old and new data...")
v= .launch.load(v) #
})
shiny::observeEvent(input$launch.new,{ v= .launch.new(v) })
output$setup.SiteType <- renderText({ v$setup.SiteType })
# ##############################################
# # Set up functions - step 1 ##
# ##############################################
.dir.declare.met.full = renderUI({
shiny::fluidPage(
if ( v$accepted.met.dir == F) { .dir.declare.met },
if ( v$accepted.met.dir == T) { shiny::helpText("Met directory accepted") }
)
})
.dir.declare.dt.full = renderUI({
shiny::fluidPage(
if ( v$accepted.dt.dir == F) { .dir.declare.dt },
if ( v$accepted.dt.dir == T) { shiny::helpText("Site directory accepted") }
)
})
output$ui.setup.1 = renderUI({ if ( v$import.status == 'ReadyForNew1') {
shiny::fluidPage(
.dir.declare.met.full,
shiny::helpText("Note: if your met and dT data are saved in the same files, paste that directory in both fields"),
shiny::selectInput("delim.sep", "Data Delimiter", .delim.options),
shiny::numericInput("number.of.before.headers", "How many lines before your data headers?", min=0,max=30, value=1),
shiny::numericInput("number.of.lines.before.data", "How many lines before your data proper?", min=1,max=30, value=4),
shiny::textAreaInput("site.names", "Site Names", "<Site name, 1 on each line>", width = "400px"),
.dir.declare.dt.full, #
shiny::actionButton( "Setup1", "Check my work (this will take a minute)"),
shiny::verbatimTextOutput(v$output.message)
) } })
# ##############################################
# # Set up functions - step 2 ##
# ##############################################
shiny::observe({ v$met.dir = input$met.dir})
shiny::observe({ v$delim.sep = input$delim.sep})
shiny::observe({ v$number.of.before.headers = input$number.of.before.headers })
shiny::observe({ v$number.of.lines.before.data = input$number.of.lines.before.data})
shiny::observe({ v$site.names = input$site.names})
shiny::observe({ v$dt.dir = input$dt.dir })
shiny::observeEvent(input$Setup1,{ v=.test.setup1(v) })
##############################################
# Set up functions - step 2 ##
##############################################
shiny::observe({ v$study.year = input$study.year})
shiny::observe({ v$selected.timestamp.format = input$selected.timestamp.format })
output$pick.dT.ts.name <- renderUI({
colnames = c("<select>", v$n.dT.data)
shiny::selectInput("dT.ts.name", "Timestamp Name in dT data",
choices = colnames,
selected = as.character(v$import.dT.ts.name) )
})
shiny::observe({ v$dT.ts.name = input$dT.ts.name})
output$pick.met.ts.name <- renderUI({
colnames = c("<select>", v$n.met.data)
shiny::selectInput("met.ts.name", "Timestamp Name in Met. data",
choices = colnames)
})
shiny::observe({ v$met.ts.name = input$met.ts.name})
shiny::observe({v$dT.units = input$dT.units })
output$pick_AirT_name <- renderUI({
colnames = c("<select>", "<No Air T data>", v$n.met.data)
shiny::selectInput("met.air.temp.label", "Air Temp = ?",
choices = colnames)
})
shiny::observe({ v$met.air.temp.label = input$met.air.temp.label})
shiny::observe({v$met.air.temp.units = input$met.air.temp.units })
output$pick_RH_name <- renderUI({
colnames = c("<select>", "<No RH data>", v$n.met.data)
shiny::selectInput("met.RH.label", "Relative Humidity = ?",
choices = colnames)
})
shiny::observe({ v$met.RH.label = input$met.RH.label})
shiny::observe({v$met.RH.units = input$met.RH.units })
output$choose_nonsapflux <- renderUI({
colnames <- v$n.dT.data
shiny::checkboxGroupInput("nonsapflux.columns", "Choose non-sap flux columns",
choices = colnames)
})
shiny::observe({ v$nonsapflux.columns = input$nonsapflux.columns})
shiny::observeEvent(input$finish.set.up,{
########### time
.save.site.metadata(v)
v = .finish.importing(v)
v$setup.load.message = "Loaded in your site and data. Continue on next panel."
v$setup.done = T
v$import.status = "done"
})
output$setup.load.message <- renderText({
v$setup.load.message
})
output$ui.setup.2 <- renderUI({ if ( v$import.status == 'ReadyForNew2') {
shiny::fluidPage(
shiny::helpText("Questions about your time format (see 'strptime' and manual for help)"),
shiny::textInput('study.year', "Study Year (can only do 1 year at a time)", value = "<Enter Study Year>"),
shiny::selectInput("selected.timestamp.format", "Common Timestamp Format", .timestamp.options),
shiny::uiOutput("pick.dT.ts.name"),
shiny::uiOutput("pick.met.ts.name"),
shiny::br(),
shiny::helpText("Questions about units"),
shiny::selectInput("dT.units", "What are the dT units?", .dT.units.options),
shiny::uiOutput("pick_AirT_name"),
shiny::selectInput("met.air.temp.units", "Air Temp. Units", .air.temp.units.options, selected="mV"),
shiny::uiOutput("pick_RH_name"),
shiny::selectInput("met.RH.units", "Relative Humidity Units", .RH.units.options),
uiOutput("choose_nonsapflux"),
conditionalPanel( "v$import.status = 'start.new'" , {
actionButton(inputId="finish.set.up", label="Finish Site Set Up (takes a minute)") }),
verbatimTextOutput("setup.load.message")
) } })
output$ui.setup.done <- renderUI({ if ( v$import.status == 'done') {
shiny::fluidPage(
shiny::helpText("Data Sucessfully Imported! Start processing.")
) } })
##############################################
# Broken Sensors ##
##############################################
shiny::observeEvent(input$FindBrokenSensors,{ v$BrokenSensorReports = .BrokenSensors.detect(v) })
output$BrokenSensors.mes.na <- renderText({ v$BrokenSensors.mes.na })
output$BrokenSensors.mes.low <- renderText({ v$BrokenSensors.mes.low })
output$BrokenSensors.mes.sd <- renderText({ v$BrokenSensors.mes.sd })
##############################################
# Processing col 1: Generic Plot Data ##
##############################################
# pick a tree
output$tree.name <- renderUI({
colnames = c(v$sapflux.names)
# Create the checkboxes and select them all by default
shiny::selectInput("tree.name", "Pick a sensor",
choices = colnames)
})
observe({ v$tree.name = input$tree.name;
v = .get.local.data(v);
})
# doy range stuff
observe({ v$min.DOY = input$DOY.range[1] })
observe({ v$max.DOY = input$DOY.range[2] })
observe({ shiny::updateSliderInput(session, "DOY.range", value = c(v$min.DOY,v$max.DOY),
min = v$min.DOY.global , max = v$max.DOY.global )
})
# move doy
observeEvent(input$b.move.back, { v$move.dir= "back"; v=.move.window(v); })
observeEvent(input$save.data, { .save.AquaFlux(v); })
observeEvent(input$b.move.foward, { v$move.dir= "foward"; v=.move.window(v); })
##############################################
# Processing col 2: Pick processing options ##
##############################################
########### pick plot options
observe({ v$pick.plot.options = input$pick.plot.options})
observe({ shiny::updateCheckboxGroupInput(session, "pick.plot.options", selected = v$pick.plot.options) })
########### pick processing options
observe({ v$processOption = input$processOption;
if(v$processOption=="tmax"){ .Tmax.turn.on.plotting(v) } })
##############################################
# Processing col 3- QAQC auto ##
##############################################
# actually suggest
observeEvent(input$auto.clean, { v = .autoQAQC.suggest(v) })
# options
observe({ v$MinDT = as.numeric(as.character(input$MinDT)) })
observe({ v$MaxDT = as.numeric(as.character(input$MaxDT)) })
observe({ v$DT.despike.dev = as.numeric(as.character(input$DT.despike.dev)) })
# output message
output$autoQAQCmes <- renderText({ autoQAQCmes = v$autoQAQCmes })
# Accept / reject
observeEvent(input$b.AutoQAQC.keep, { v = .autoQAQC.keep(v) })
observeEvent(input$b.AutoQAQC.del, { v = .autoQAQC.del(v) })
##############################################
# Processing col 3- QAQC manual ##
##############################################
observeEvent(input$qaqc.manual, {
v$plotAutoQAQC = F;v$tmaxRadio="none";v$restore.option="none"; # clear other bottons
v$qaqc.manual <- input$qaqc.manual;
})
observe({ shiny::updateRadioButtons(session, "qaqc.manual", selected = v$qaqc.manual) })
# observe({ v$qaqc.1orAll = input$qaqc.1orAll})
##############################################
# Processing col 3- Calib ##
##############################################
observe({ v$alpha = as.numeric(as.character(input$alpha)) })
observe({ v$beta = as.numeric(as.character(input$beta)) })
##############################################
# Processing col 3- Tmax ##
##############################################
# generic bottons
observe({ v$VPD.thres = as.numeric(as.character(input$VPD.thres)); })
observe({ v$VPD.below.thres.for.x.hr = as.numeric(as.character(input$VPD.below.thres.for.x.hr)) })
# generic bottons
observe({ v$VPD.below.thres.for.x.hr = as.numeric(as.character(input$VPD.below.thres.for.x.hr)) })
observe({ v$auto.Tmax.window.size = as.numeric(as.character(input$auto.Tmax.window.size)) })
observeEvent(input$auto.Tmax, { v =.Tmax.autopick(v) })
observeEvent(input$tmaxRadio, {
v$tmaxRadio=input$tmaxRadio
if (v$tmaxRadio=="none"){} # no nothing
if (v$tmaxRadio=="manual" | v$tmaxRadio=="delete"){ v$qaqc.manual="none"; v$plotAutoQAQC = F; v$restore.option="none"; }# clear other bottons, then click on graph
} )
##############################################
# Processing col 3- Restore ##
##############################################
observeEvent(input$restore.option, {
v$restore.option <- input$restore.option; # save
if (v$restore.option!="none"){ # if not 'none', reset other bottons
v$plotAutoQAQC = F;v$qaqc.manual="none";v$tmaxRadio="none";
}
})
observe({ shiny::updateSelectInput(session, "restore.option", selected = v$restore.option) })
##############################################
# Plot Graphs ##
##############################################
output$plot.dT <- renderPlot({ ; v$pick.bottun = .plot.dT(v) })
output$plot.sapflux <- renderPlot({ ; .plot.sapflux(v) })
##############################################
# Click the dT graph ##
##############################################
observeEvent(input$dT_plot_click,
{
# auto qaqc - none
# manual qaqc -
if(v$qaqc.manual == "above"){ v=.delete.above(v,input$dT_plot_click$y); }
if(v$qaqc.manual == "below"){ v=.delete.below(v,input$dT_plot_click$y); }
if(v$qaqc.manual == "before"){ v=.delete.before(v,input$dT_plot_click$x); }
if(v$qaqc.manual == "after"){ v=.delete.after(v,input$dT_plot_click$x); }
if(v$qaqc.manual == "between"){v=.delete.between(v,input$dT_plot_click$x); }
if(v$qaqc.manual == "points"){ v=.delete.points(v,input$dT_plot_click); }
if(v$qaqc.manual == "all"){ v=.delete.all(v); }
if(v$qaqc.manual== "undo"){ v=.restore.undo(v); }
# Tmax
if(v$tmaxRadio=="delete"){ v = .Tmax.delete(v,input$dT_plot_click) }
if(v$tmaxRadio=="manual"){ v = .Tmax.pick.manual(v,input$dT_plot_click) }
# restore
if(v$restore.option=="undo"){ v=.restore.undo(v); }
if(v$restore.option=="between"){ v=.restore.between(v,input$dT_plot_click); }
if(v$restore.option=="all"){ v=.restore.all(v); }
}
)
##############################################
# Export ##
##############################################
observeEvent(input$b.export,{
.export.final.data(v)
v$export.mes.1 = paste("At",Sys.time(),"AquaFlux data was exported:")
v$export.mes.2 = paste("CSV data saved to:", v$final.dir)
v$export.mes.3 = paste( "PDF Graphs saved to:", v$graph.dir)
v$export.mes.4 = "Data was also exported to base R (global envir):"
v$export.mes.5 = " 'raw.dT.data' = your raw dT data, in C."
v$export.mes.6 = " 'dT.data' = your post-QAQC dT data, in C."
v$export.mes.7 = " 'Tmax.data.points' = the Tmax points you picked."
v$export.mes.8 = " 'Tmax.data.line' = the Tmax line (interpolated from Tmax.data.points)"
v$export.mes.9 = " 'sapflux.data' = your sap flux dT data, in g s-1 m-2.sapwood"
v$export.mes.10 = " 'met.data' = your met data, including VPD."
}) #
output$export.mes.1 <- renderText({ v$export.mes.1 })
output$export.mes.2 <- renderText({ v$export.mes.2 })
output$export.mes.3 <- renderText({ v$export.mes.3 })
output$export.mes.4 <- renderText({ v$export.mes.4 })
output$export.mes.5 <- renderText({ v$export.mes.5 })
output$export.mes.6 <- renderText({ v$export.mes.6 })
output$export.mes.7 <- renderText({ v$export.mes.7 })
output$export.mes.8 <- renderText({ v$export.mes.8 })
output$export.mes.9 <- renderText({ v$export.mes.9 })
output$export.mes.10 <- renderText({ v$export.mes.10 })
########################################
# v$processOption == 'autoqaqc
output$Aqaqc_pro_minDT <- renderUI({ if ( v$processOption == 'autoqaqc'){ shiny::textInput('MinDT', "Min accepted dT", value = "10") } } )
output$Aqaqc_pro_maxDT <- renderUI({ if ( v$processOption == 'autoqaqc'){ shiny::textInput('MaxDT', "Max accepted dT", value = "30") } })
output$Aqaqc_dt_spike <- renderUI({ if ( v$processOption == 'autoqaqc') { shiny::textInput('DT.despike.dev', "Max Deviance (for despike)", value = "12")}})
output$Aqaqc_auto.clean<- renderUI({ if ( v$processOption == 'autoqaqc') { shiny::actionButton(inputId="auto.clean", label="Suggest new QAQC")}})
output$Aqaqc_autoQAQCmes<- renderUI({ if ( v$processOption == 'autoqaqc') { shiny::verbatimTextOutput("autoQAQCmes") }})
output$Aqaqc_Delete <- renderUI({ if ( v$processOption == 'autoqaqc') { shiny::actionButton(inputId="b.AutoQAQC.del", label="Delete") }})
# v$processOption == 'manqaqc
output$Mqaqc_1orAll <- renderUI({ if ( v$processOption == 'manqaqc') { shiny::checkboxGroupInput("qaqc.1orAll", label=" ", choices = c("Apply to *ALL* trees-- can NOT 'undo delete' " = "all")) }})
output$Mqaqc_manual <- renderUI({ if ( v$processOption == 'manqaqc') { shiny::radioButtons( "qaqc.manual", "Manual QAQC Options:", .qaqc.button.vector,selected = "none",inline=F) }})
# v$processOption == 'tmax
output$tmax_VPDthres <- renderUI({ if ( v$processOption == 'tmax') { shiny::textInput('VPD.thres', "VPD Threshold (kPa)", value = 0.2) }})
output$tmax_VPDhr <- renderUI({ if ( v$processOption == 'tmax') { shiny::textInput('VPD.below.thres.for.x.hr', "VPD must be below thres for X hrs", value = "2") }})
output$tmax_Tmaxsize <- renderUI({ if ( v$processOption == 'tmax') { shiny::textInput('auto.Tmax.window.size', "Window size (days)", value = "7") }})
output$tmax_AutoTmax <- renderUI({ if ( v$processOption == 'tmax') { shiny::actionButton(inputId="auto.Tmax", label="Auto Pick Tmax") }})
output$tmax_radio <- renderUI({ if ( v$processOption == 'tmax') { .tmaxRadio }})
# v$processOption == 'restore
output$restore_picker <- renderUI({ if ( v$processOption == 'restore') { .restore.picker }})
# v$processOption == 'calib
output$calib_alpha <- renderUI({ if ( v$processOption == 'calib') { shiny::textInput('alpha', "alpha", value = 118.99 * 10^(-6) ) }})
output$calib_beta <- renderUI({ if ( v$processOption == 'calib') { shiny::textInput('beta', "beta", value = 1.231) }})
}
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