From 82cec786244ff554c4f9229b98675649fe946e57 Mon Sep 17 00:00:00 2001
From: Daniel Angst <daniel.angst@env.ethz.ch>
Date: Tue, 10 Jan 2017 09:58:03 +0100
Subject: [PATCH] timezone fix

---
 R/data_functions.R        |  10 ++++++++--
 R/interactive_functions.R |  32 +++++++++++++++++++-------------
 R/plot_functions.R        |  25 ++++++++++---------------
 data/timeZones.rda        | Bin 0 -> 4776 bytes
 man/periodPlot.Rd         |   4 ++--
 man/readBatscopeXLSX.Rd   |   6 ++++--
 man/shiny_batPlots.Rd     |   6 ++++--
 7 files changed, 47 insertions(+), 36 deletions(-)
 create mode 100644 data/timeZones.rda

diff --git a/R/data_functions.R b/R/data_functions.R
index f2441ae..8afe812 100644
--- a/R/data_functions.R
+++ b/R/data_functions.R
@@ -10,6 +10,7 @@
 #'  relevant quality scores
 #' @param quality_threshold sequences with species assignment quality below this
 #'  threshold will be discarded.
+#' @param time_zone time zone of timestamps
 #' @param shiny_progress display more progress info for shiny
 #' @param shiny_progress_n fraction of progres bar for multiple files
 #' @family data functions
@@ -17,8 +18,8 @@
 readBatscopeXLSX <- function(path = file.choose(),
   species_col_name = "AutoClass1",
   quality_col_name = "AutoClass1Qual",
-  time_zone = Sys.timezone(),
   quality_threshold = 0.8,
+  time_zone = "UTC",
   shiny_progress = FALSE,
   shiny_progress_n = 1
   ){
@@ -58,6 +59,11 @@ readBatscopeXLSX <- function(path = file.choose(),
 
   data_r$temperature <- as.numeric(data_r$temperature)
 
+  data_r$ImportDate  <- force_tz(data_r$ImportDate, tzone = time_zone)
+  data_r$SurveyDate  <- force_tz(data_r$SurveyDate, tzone = time_zone)
+  data_r$recDate  <- force_tz(data_r$recDate, tzone = time_zone)
+  data_r$recTime  <- force_tz(data_r$recTime, tzone = time_zone)
+
   return(data_r)
 }
 
@@ -141,7 +147,7 @@ sumBatscopeData <- function(
 
   data_binned <- rbind(data_binned_bySpecies, data_binned_allSpecies)
 
-  data_binned$bins <- as.POSIXct(data_binned$bins_factor)
+  data_binned$bins <- as.POSIXct(data_binned$bins_factor, tz = tz(unique(data_r$SurveyDate)[1]))
 
   # GPS Koordinaten
 
diff --git a/R/interactive_functions.R b/R/interactive_functions.R
index f0cbdc8..3d67f21 100644
--- a/R/interactive_functions.R
+++ b/R/interactive_functions.R
@@ -7,11 +7,16 @@
 #' @family interactive functions
 #' @export
 shiny_batPlots <- function(
+  lat_default = 47.4,
+  long_default = 8.52,
+  customCoord_default = FALSE,
+  time_zone_default = "UTC+1",
   option.list = list(
     shiny.launch.browser = TRUE,
     shiny.maxRequestSize = 100 * 1024 ^ 2,
     encoding = "UTF-8")
   ){
+  tz_def_n <- which(names(timeZones)=="UTC+1")
   shinyApp(
     onStart = function(options = option.list){
       options(options)
@@ -48,9 +53,10 @@ shiny_batPlots <- function(
             multiple = TRUE,
             accept = c(".xlsx", ".xls")
           ),
-          selectizeInput(
+          selectInput(
             "time_zone", "Zeitzone",
-            choices = OlsonNames(), selected = "UTC",multiple = FALSE
+            choices = as.list(timeZones),
+            selected = timeZones[tz_def_n], multiple = FALSE, selectize = FALSE
           ),
           selectizeInput(
             "project", "Standorte",
@@ -199,11 +205,11 @@ shiny_batPlots <- function(
                       tags$h4("GPS-Daten Optionen"),
                       checkboxInput("customCoord",
                         label = "eigene Koordinaten (in  Dezimalgrad)",
-                        value = FALSE),
+                        value = customCoord_default),
                       numericInput("lat", label = "Breite",
-                        value =  47.4, step = 0.1),
+                        value =  lat_default, step = 0.1),
                       numericInput("long", label = "Länge",
-                        value =  8.52, step = 0.1)
+                        value =  long_default, step = 0.1)
                     ),
                     column(4,
                       tags$h4("Generelle Plotoptionen"),
@@ -287,16 +293,17 @@ shiny_batPlots <- function(
         )
 
         #update DateRange
+        date_range <- force_tz(range(dataInput()$SurveyDate), tzone = "UTC")
         if (input$tabs == "NightPlot"){
           updateDateRangeInput(session, "dates",
-            start = format(min(dataInput()$SurveyDate), "%Y-%m-%d"),
-            end = format(min(dataInput()$SurveyDate), "%Y-%m-%d")
+            start = date_range[1],
+            end = date_range[1]
           )
         }
         if (input$tabs == "PeriodPlot"){
           updateDateRangeInput(session, "dates",
-            start = format(min(dataInput()$SurveyDate), "%Y-%m-%d"),
-            end = format(max(dataInput()$SurveyDate), "%Y-%m-%d")
+            start = date_range[1],
+            end = date_range[2]
           )
         }
         #update yAxis Input
@@ -416,7 +423,7 @@ shiny_batPlots <- function(
             collapse = ":")
           xlim <- as.POSIXct(
             c(paste(as.character(input$dates[1]), hhmm1),
-            paste(as.character(input$dates[2] + 1), hhmm2)))
+            paste(as.character(input$dates[2] + 1), hhmm2)), tz = input$time_zone)
         } else {
           xlim <- NULL
         }
@@ -426,10 +433,10 @@ shiny_batPlots <- function(
         } else {
           ylim <- NULL
         }
-
         plotData <- subset(data_r(), ProjectName %in% input$project)
+
         nightPlot(plotData,
-          day = input$dates,
+          day = with_tz(input$dates, tzone = input$time_zone),
           sel_species = input$species,
           x_limits = xlim,
           y_limits = ylim,
@@ -475,7 +482,6 @@ shiny_batPlots <- function(
           x_break_distance = x_breaks,
           y_break_distance = "2 hour",
           x_break_label = x_breaks_label,
-          time_zone = input$time_zone,
           text_size = input$text_size)
       }) #shiny_periodPlot
 
diff --git a/R/plot_functions.R b/R/plot_functions.R
index 04c32ab..9b13e93 100644
--- a/R/plot_functions.R
+++ b/R/plot_functions.R
@@ -25,18 +25,13 @@ nightPlot <- function(plotData,
   plot_T_color = "black",
   n_ybreaks = 5,
   text_size = 16){
-
-  if (is.POSIXct(day) == FALSE){
-    day <- as.POSIXct(day, format = "%Y-%m-%d")
-  }
-
+  time_zone <- tz(unique(plotData$SurveyDate)[1])
   if (sel_species[1] == "every"){
-    plotData_sub <- subset(plotData, SurveyDate %in% day & species != "all")
+    plotData_sub <- dplyr::filter(plotData, SurveyDate == day & species != "all")
   } else {
-    plotData_sub <- subset(plotData, SurveyDate %in% day &
+    plotData_sub <- dplyr::filter(plotData, SurveyDate == day &
       species %in% sel_species)
   }
-
   if (is.null(x_limits)){
     x_limits <- c(min(plotData_sub$sunset) - 0.5 * 3600,
       max(plotData_sub$sunrise) + 0.5 * 3600)
@@ -50,7 +45,6 @@ nightPlot <- function(plotData,
     str_c(format(day, format = "%d.%m.%Y"), collapse = " - "))
 
   bin_width <- plotData$bin_length[1] * 60
-
   plotData_sub$t <- "Temperatur [°C]"
 
   nightPlot <- ggplot(plotData_sub,
@@ -66,7 +60,7 @@ nightPlot <- function(plotData,
     scale_x_datetime(
       limits = x_limits, breaks = date_breaks("2 hour"),
       minor_breaks = date_breaks("1 hour"),
-      labels = date_format("%H:%M")) +
+      labels = date_format("%H:%M", tz = time_zone)) +
     scale_fill_brewer(name = "Spezies", palette = "Set1") +
     scale_y_continuous(limits = y_limits,
       breaks = trans_breaks("identity", function(x) x, n = n_ybreaks)) +
@@ -117,11 +111,12 @@ periodPlot <- function(plotData,
   x_limits = NULL,
   y_limits = NULL,
   x_break_distance = "1 month",
-  y_break_distance = "2 hour",
+  y_break_distance = "1 hour",
   x_break_label = "%b",
-  time_zone = Sys.timezone(),
   text_size = 16){
 
+  time_zone <- tz(unique(plotData$SurveyDate)[1])
+
   if (is.POSIXct(start_date) == FALSE){
     start_date <- as.POSIXct(start_date, format = "%Y-%m-%d", tz = time_zone)
   }
@@ -190,12 +185,12 @@ periodPlot <- function(plotData,
     facet_wrap(~ProjectName, ncol = 2) +
     scale_x_datetime(limits = x_limits,
       breaks = date_breaks(x_break_distance),
-      labels = date_format(x_break_label)) +
+      labels = date_format(x_break_label, tz = time_zone)) +
     scale_y_datetime(limits = y_limits,
       breaks = date_breaks(y_break_distance),
       minor_breaks = date_breaks("1 hour"),
-      labels = date_format("%H:%M")) +
-    labs(x = "Datum", y = "Uhrzeit [UTC]", title = plottitle) +
+      labels = date_format("%H:%M", tz = time_zone)) +
+    labs(x = "Datum", y = str_c("Uhrzeit (", time_zone,")"), title = plottitle) +
     theme(text = element_text(size = text_size))
 
   if (sel_species[1] != "every" & length(sel_species) == 1){
diff --git a/data/timeZones.rda b/data/timeZones.rda
new file mode 100644
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diff --git a/man/periodPlot.Rd b/man/periodPlot.Rd
index 5d74150..e0dd375 100644
--- a/man/periodPlot.Rd
+++ b/man/periodPlot.Rd
@@ -7,8 +7,8 @@
 periodPlot(plotData, start_date = floor_date(min(plotData$SurveyDate),
   "year"), end_date = ceiling_date(max(plotData$SurveyDate), "year"),
   sel_species = "every", x_limits = NULL, y_limits = NULL,
-  x_break_distance = "1 month", y_break_distance = "2 hour",
-  x_break_label = "\%b", time_zone = Sys.timezone(), text_size = 16)
+  x_break_distance = "1 month", y_break_distance = "1 hour",
+  x_break_label = "\%b", text_size = 16)
 }
 \arguments{
 \item{plotData}{data generated by \code{\link{sumBatscopeData}}}
diff --git a/man/readBatscopeXLSX.Rd b/man/readBatscopeXLSX.Rd
index aa4662c..7678614 100644
--- a/man/readBatscopeXLSX.Rd
+++ b/man/readBatscopeXLSX.Rd
@@ -5,8 +5,8 @@
 \title{read Batscope export}
 \usage{
 readBatscopeXLSX(path = file.choose(), species_col_name = "AutoClass1",
-  quality_col_name = "AutoClass1Qual", time_zone = Sys.timezone(),
-  quality_threshold = 0.8, shiny_progress = FALSE, shiny_progress_n = 1)
+  quality_col_name = "AutoClass1Qual", quality_threshold = 0.8,
+  time_zone = "UTC", shiny_progress = FALSE, shiny_progress_n = 1)
 }
 \arguments{
 \item{path}{filename}
@@ -20,6 +20,8 @@ relevant quality scores}
 \item{quality_threshold}{sequences with species assignment quality below this
 threshold will be discarded.}
 
+\item{time_zone}{time zone of timestamps}
+
 \item{shiny_progress}{display more progress info for shiny}
 
 \item{shiny_progress_n}{fraction of progres bar for multiple files}
diff --git a/man/shiny_batPlots.Rd b/man/shiny_batPlots.Rd
index afcdfba..b089cc4 100644
--- a/man/shiny_batPlots.Rd
+++ b/man/shiny_batPlots.Rd
@@ -4,8 +4,10 @@
 \alias{shiny_batPlots}
 \title{batPlotR}
 \usage{
-shiny_batPlots(option.list = list(shiny.launch.browser = TRUE,
-  shiny.maxRequestSize = 100 * 1024^2, encoding = "UTF-8"))
+shiny_batPlots(lat_default = 47.4, long_default = 8.52,
+  customCoord_default = FALSE, time_zone_default = "UTC+1",
+  option.list = list(shiny.launch.browser = TRUE, shiny.maxRequestSize = 100 *
+  1024^2, encoding = "UTF-8"))
 }
 \arguments{
 \item{option.list}{a list of global shiny options}