plot_TS: plot time series data

In RchivalTag: Analyzing and Interactive Visualization of Archival Tagging Data

plot time series data

Description

plotting functions for time series data (e.g. depth or temperature time series data from archival tags) with user specified xtick intervals.

Usage

plot_DepthTS(ts_df, y="Depth", xlim, ylim, xticks_interval,
             ylab=y, xlab, main, main.line=1, plot_info=TRUE, 
             ID, ID_label="Serial",
             plot_DayTimePeriods=FALSE, twilight.set="ast", 
             cex=1, cex.main=1.2*cex, cex.lab=1*cex, 
             cex.axis=.9*cex, cex.axis2=1*cex, 
             type="l", las=1, xaxs="i", yaxs="i", 
             plot_box=TRUE, bty="l", Return=FALSE, tz="UTC",...)
             
           
plot_TS(ts_df, y="Depth", xlim, ylim, xticks_interval,
        ylab=y, xlab, main, main.line=1, plot_info=TRUE, 
        ID, ID_label="Serial",
        plot_DayTimePeriods=FALSE, twilight.set="ast", 
        cex=1, cex.main=1.2*cex, cex.lab=1*cex, 
        cex.axis=.9*cex, cex.axis2=1*cex, 
        type="l", las=1, xaxs="i", yaxs="i", 
        plot_box=TRUE, bty="l", Return=FALSE, tz="UTC", ...)
       
empty.plot_TS(xlim, ylim, xticks_interval, ylab="", xlab, main="",
              cex=1, cex.main=1.2*cex, cex.lab=1*cex, 
              cex.axis=.9*cex, cex.axis2=1*cex,               
              las=1, xaxs="i", yaxs="i", do_xaxis=TRUE, do_yaxis = TRUE,
              plot_box=TRUE, bty="l", tz="UTC", ...)

Arguments

ts_df	data.frame holding the time series data to be plotted, including the x-vector 'datetime' (in POSIXct-format and UTC), and the numeric y-vector whose label is defined by y.
y	character label of time series vector to be plotted (by default 'Depth').
xlim	the x limits (x1, x2) of the plot (by default range(ts_df$datetime), but needs to be specified in empty.plot_TS).
ylim	the y limits of the plot (by default range(ts_df[[y]]), but needs to be specified in empty.plot_TS).
xticks_interval	time step of the x-axis ticklabels in (full) hours. By default 3 hours for xlim differences <= 1 day, and 6 hours for differences > 1 day.
ylab, xlab	the y- and x-axis labels. By default xlab="Time (UTC)" and ylab = "Depth (m)"
main, main.line	main title (by default "Tag ID") for the plot and its line (see mtext for reference).
plot_info	whether the plot title and axes labels should be shown (by default TRUE).
ID, ID_label	Tag ID and its label (column name; by default "Serial") to be selected (e.g. if input data frame holds tagging data from several tags).
type	what type of plot should be drawn. Possible types are: "p" for points, "l" for lines (default), "b" for both, "c" for the lines part alone of "b", "o" for both 'overlapped', "n" for nothing (similar to empty.plot_TS-function call)
las	numeric in {0,1,2,3}; the style of axis labels 0: always parallel to the axis [default], 1: always horizontal, 2: always perpendicular to the axis, 3: always vertical.
xaxs, yaxs	The style of axis interval calculation to be used for the x-and y-axes. Possible values are "r" and "i" (default). The styles are generally controlled by the range of data or xlim, if given. Style "r" (regular) first extends the data range by 4 percent at each end and then finds an axis with pretty labels that fits within the extended range. Style "i" (internal) just finds an axis with pretty labels that fits within the original data range.
cex,cex.main, cex.lab, cex.axis, cex.axis2	The standard font size of title, axis labels and tick labels.
plot_DayTimePeriods, twilight.set	whether day-time periods ('Night', 'Dawn', 'Day', 'Dusk') should be plotted as shaded areas. In case that plot_DayTimePeriods is set TRUE, the limits of each time period are required (columns sunrise, sunset, dawn.ast,/dawn.naut and dawn.ast/dawn.naut in POSIXct-format. In case of the twilight events, the additional argument twilight.set defines the suffix of the twlight-set to be selected ( "ast" for astronomical dawn and dusks vs "naut" for nautical twilight events). If any of the day-time columns, described above, is missing, it/they will be calculated based on geolocation estimates (required columns Lon and Lat) through an internal call of function get_DayTimeLimits.
do_xaxis,do_yaxis	Optional arguments in empty.plot_TS to define whether a x and and y-axis shall be plotted (by default TRUE).
plot_box, bty	whether a box of box-type bty should be plotted (by default TRUE. bty is one of "o" (the default), "l", "7", "c", "u", or "]" the resulting box resembles the corresponding upper case letter.
Return	whether edited time series data set should be returned (by default FALSE).
tz	The time zone in which the data should be illustrated (By default "UTC"). ATTENTION: The required date format of the input data is "UTC" (across all RchivalTag-functions). Run OlsonNames(tzdir = NULL) for valid time zone definitions.
...	additional arguments to be passed to plot.

Author(s)

Robert K. Bauer

See Also

ggboxplot_DepthTS_by_hour, dy_DepthTS, plot_DepthTempTS

Examples

### load sample depth and temperature time series data from miniPAT:
ts_file <- system.file("example_files/104659-Series.csv",package="RchivalTag")
ts_df <- read_TS(ts_file)
ts_df$Serial <- ts_df$DeployID
head(ts_df)

## load same data in LOTEK format
ts_file <- system.file("example_files/104659_PSAT_Dive_Log.csv",package="RchivalTag")
ts_df <- read_TS(ts_file,date_format="%m/%d/%Y %H:%M:%S")
head(ts_df) ## attention no identifier (Ptt, Serial, DeployID) included!
ts_df$DeployID <- ts_df$Ptt <- "104659"
ts_df$Serial <- "Tag1"

### select subsets (dates to plot)
# plot_DepthTS(ts_df, plot_DayTimePeriods = FALSE, xlim = unique(ts_df$date)[2:3])
# xlim <- c("2016-08-10 6:10:00", "2016-08-11 17:40:00")
# plot_DepthTS(ts_df, plot_DayTimePeriods = FALSE, xlim = xlim)

### check xtick time step:
# plot_DepthTS(ts_df, plot_DayTimePeriods = FALSE, xlim = "2016-08-10")
# plot_DepthTS(ts_df, plot_DayTimePeriods = FALSE, xlim = "2016-08-10", xticks_interval = 2)


### add daytime periods during plot-function call and return extended data set
# ts_df$Lon <- 5; ts_df$Lat <- 43
# plot_DepthTS(ts_df, plot_DayTimePeriods = TRUE, xlim = unique(ts_df$date)[2:3])
# ts_df2 <- plot_DepthTS(ts_df, plot_DayTimePeriods = TRUE, Return = TRUE) 
# names(ts_df)
# names(ts_df2)

### add daytime periods before function call
# ts_df_extended <- get_DayTimeLimits(ts_df)
# plot_DepthTS(ts_df_extended, plot_DayTimePeriods = TRUE)
# plot_DepthTS(ts_df_extended, plot_DayTimePeriods = TRUE, twilight.set = "naut")

### introduce data transmission gaps that are then filled internally
### as well as daytime periods based on interpolated Lon & Lat positions
# ts_df_cutted <- ts_df[-c(200:400, 1800:2200), ]
# plot_DepthTS(ts_df_cutted, plot_DayTimePeriods = FALSE)
# plot_DepthTS(ts_df_cutted, plot_DayTimePeriods = TRUE) 

### example for empty.plotTS and adding time series data as line:
# empty.plot_TS(xlim="2016-08-10",ylim=c(100,0))
# lines(ts_df$datetime, ts_df$Depth)

### alternative:
# plot_DepthTS(ts_df, xlim=c("2016-08-10","2016-08-12"), plot_DayTimePeriods = TRUE, type='n') 
# lines(ts_df$datetime, ts_df$Depth)

RchivalTag documentation built on Nov. 10, 2023, 5:06 p.m.