#' Plot PAM data with dygraphs
#'
#' @description This opens a java dygraph application which allows the user to zoom in and out. In Rstudio it will open in the viewer pane and in base R in an html readers. Note that this can be a bit slow
#'
#' @param dta PAM data to be plotted
#' @param from date that plotting starts
#' @param to date that plotting ends
#' @param toPLOT names of the variables to plot. For now this includes `light`, `pressure`, `acceleration` and `temperature`
#'
#' @return a plot of all the measurements
#'
#' @references Vanderkam, D., Allaire, J., Owen, J., Gromer, D., Shevtsov, P. and Thieurmel, B., dygraphs: Interface to Dygraphs Interactive Time Series Charting Library, 2015. URL http://CRAN. R-project. org/package= dygraphs. R package version 0.4, 5, p.7.
#'
#' @examples
#' ##load dummy data
#' #data(hoopoe)
#' #PAM_data=hoopoe
#'
#' ## This bit is for Rstudio users to prevent html from opening in Viewer pane and crashing
#' ## It opens in web browser instead
#' #backup_options <- options()
#' #options(viewer=NULL)
#'
#' ## Plot interactive graphics
#' #dygraphPAM(dta = PAM_data)
#'
#' ## restore Rstudio settings from before plot
#' #options(backup_options)
#'
#'
#' @importFrom dygraphs dygraph dyRangeSelector dyHighlight dyLegend dyOptions dyShading "%>%"
#' @importFrom htmltools browsable tagList
#' @importFrom xts xts
#' @export
dygraphPAM <- function(dta,
from = dta$light$date[1],
to = dta$light$date[length(dta$light$date)],
toPLOT = names(dta)) {
print("Error: This function is deprecated, use plot_interactive_timeseries, or install v.1.0 of PAMLr by running devtools::install_github('KiranLDA/PAMLr', ref = 'v.1.0')")
# # backup_options <- options()
# len = ifelse( ("id" %in% toPLOT) , length(names(dta))-1, length(names(dta)))
#
# dy_graph = list()
#
# if ("light" %in% toPLOT ){
# dy_graph$light = dygraph(xts(x = dta$light$obs, order.by = dta$light$date),
# xlab = "Time",
# ylab = "Light",
# group = dta$light$date, #This is useful for synchronosing multiple graphs
# main="Light as a function of time") %>%
# dyRangeSelector(dateWindow = c(from, to)) %>%
# dyHighlight(highlightSeriesOpts = list(strokeWidth = 2)) %>%
# dyLegend(hideOnMouseOut = TRUE, width = 600) %>%
# dyOptions(colors ="#66C2A5")
# }
# if ("temperature" %in% toPLOT ){
# dy_graph$temperature = dygraph(xts(x = dta$temperature$obs, order.by = dta$temperature$date),
# xlab = "Time",
# ylab = "Temperature (C)",
# group = dta$light$date,#dta$temperature$date, #This is useful for synchronosing multiple graphs
# main="Temperature as a function of time") %>%
# dyRangeSelector(dateWindow = c(from, to)) %>%
# dyHighlight(highlightSeriesOpts = list(strokeWidth = 2)) %>%
# dyLegend(hideOnMouseOut = TRUE, width = 600) %>%
# dyOptions(colors ="#A6D854")
# }
# if ("pressure" %in% toPLOT ){
# dy_graph$pressure = dygraph(xts(x = dta$pressure$obs, order.by = dta$pressure$date),
# xlab = "Time",
# ylab = "Pressure (hPa)",
# group = dta$light$date,#dta$pressure$date, #This is useful for synchronosing multiple graphs
# main="Pressure as a function of time") %>%
# dyRangeSelector(dateWindow = c(from, to)) %>%
# dyHighlight(highlightSeriesOpts = list(strokeWidth = 2)) %>%
# dyLegend(hideOnMouseOut = TRUE, width = 600) %>%
# dyOptions(colors ="#FC8D62")
# }
# if ("acceleration" %in% toPLOT ){
# dy_graph$activity = dygraph(xts(x = dta$acceleration$act, order.by = dta$acceleration$date),
# xlab = "Time",
# ylab = "Activity",
# group = dta$light$date,#dta$acceleration$date, #This is useful for synchronosing multiple graphs
# main="Activity as a function of time") %>%
# dyRangeSelector(dateWindow = c(from, to)) %>%
# dyHighlight(highlightSeriesOpts = list(strokeWidth = 2)) %>%
# dyLegend(hideOnMouseOut = TRUE, width = 600) %>%
# dyOptions(colors ="#8DA0CB")
# dy_graph$pitch = dygraph(xts(x = dta$acceleration$pit, order.by = dta$acceleration$date),
# xlab = "Time",
# ylab = "Pitch",
# group = dta$light$date,#dta$acceleration$date, #This is useful for synchronosing multiple graphs
# main="Pitch as a function of time") %>%
# dyRangeSelector(dateWindow = c(from, to)) %>%
# dyHighlight(highlightSeriesOpts = list(strokeWidth = 2)) %>%
# dyLegend(hideOnMouseOut = TRUE, width = 600) %>%
# dyOptions(colors ="#E78AC3")
# }
# if ("magnetic" %in% toPLOT ){
# dy_graph$magneticg = dygraph(xts(x = dta$magnetic[,c(2,3,4)], order.by = dta$magnetic$date),
# xlab = "Time",
# ylab = "Magnetic gX, gY,and gZ",
# group = dta$light$date,#dta$temperature$date, #This is useful for synchronosing multiple graphs
# main="Mgnetism g as a function of time") %>%
# dyRangeSelector(dateWindow = c(from, to)) %>%
# dyHighlight(highlightSeriesOpts = list(strokeWidth = 2)) %>%
# dyLegend(hideOnMouseOut = TRUE, width = 600) %>%
# dyOptions(colors = c("#8DA0CB","#A6D854","#FC8D62"))
# dy_graph$magneticm = dygraph(xts(x = dta$magnetic[,c(5,6,7)], order.by = dta$magnetic$date),
# xlab = "Time",
# ylab = "Magnetic mX, mY,and mZ",
# group = dta$light$date,#dta$temperature$date, #This is useful for synchronosing multiple graphs
# main="Magnetism m as a function of time") %>%
# dyRangeSelector(dateWindow = c(from, to)) %>%
# dyHighlight(highlightSeriesOpts = list(strokeWidth = 2)) %>%
# dyLegend(hideOnMouseOut = TRUE, width = 600) %>%
# dyOptions(colors = c("#8DA0CB","#A6D854","#FC8D62"))
# }
#
#
# # options(viewer=NULL)
# browsable(tagList(dy_graph))
# # options(backup_options)
}
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