seasonality: Seasonality analysis

Description

Examine time series for seasonality of high (low) values

Usage

seasonality(
  dates,
  values,
  data,
  drange = NA,
  vrange = NA,
  shift = 0,
  janline = TRUE,
  hlines = FALSE,
  nmax = 0,
  maxargs = NULL,
  plot = 1,
  add = FALSE,
  nmin = 100,
  probs = c(0, 25, 50, 75, 95, 99.9)/100,
  width = 3,
  text = TRUE,
  texti = seq(200, 20, length.out = length(probs)),
  textargs = NULL,
  months = substr(month.abb, 1, 1),
  slab = "Month",
  tlab = "Year",
  vlab = NA,
  xlim = NA,
  ylim = NA,
  xaxs = NA,
  yaxs = NA,
  main = "Seasonality",
  adj = 0.2,
  mar = c(3, 3, 4, 1),
  mgp = c(1.7, 0.7, 0),
  keeppar = TRUE,
  legend = TRUE,
  legargs = NULL,
  returnall = FALSE,
  quiet = FALSE,
  ...
)

Value

The output is always invisible, don't forget to assign it. If returnall=FALSE: Data.frame with year, number of nonNA entries,

max value + doy of annual maxima. Please note that the column year does not match the calendrical year if shift!=0.

if returnall=TRUE: a list with annmax (df from above) as well as:

data: data.frame(doy, values, year) and optionally:

plot1, plot3, plot4, plot5: outputs from colPoints

plot2: output list from spiralDate

and other elements depending on plot type, like data3, data4, probs4, width4.

Arguments

dates: Dates in ascending order. Can be character strings or strptime results, as accepted (and coerced) by as.Date
values: Values to be mapped in color with colPoints
data: Optional: data.frame with the column names as given by dates and values
drange: Optional date range (analogous to xlim), can be a vector like dates. Can also be numerical years, in which case "-01-01" is appended. DEFAULT: NA (computed from dates internally)
vrange: Optional value range (analogous to ylim), can be a vector like values. DEFAULT: NA (computed from values internally)
shift: Number of days to move the year-break to. E.g. shift=61 for German hydrological year (Nov to Oct). DEFAULT: 0
janline: Logical: Should horizontal line be plotted at January 1st if shift!=0? DEFAULT: TRUE
hlines: Draw horizontal background lines in plot 1? Either FALSE (the default), TRUE to draw gray background lines at each month start, or a list of arguments passed to abline with owa. DEFAULT: FALSE
nmax: Number of annual maxima to be marked, plotted and returned. Currently, only 0 and 1 are implemented. DEFAULT: 0
maxargs: List of arguments passed to lines for annual maxima, e.g. maxargs=list(type="l", col="red", lty=3). DEFAULT: NULL (several internal defaults are used, but can be overridden)
plot: Integer specifying the type of plot. Can be a vector to produce several plots.
0: none, only return the data.frame with annual maxima.
1: color coded doy (day of the year) over year (the default).
2: Color coded spiral graph with spiralDate.
3: Spaghetti line plot with discharge over doy, one line per year.
4: probs quantileMean over doy, with optional aggregation window (width) around each doy.
5: Annmax over time for crude trend analysis.
DEFAULT: 1
add: Logical. Add to existing plot? DEFAULT: FALSE
nmin: Minimum number of values that must be present per (hydrological) year to be plotted in plot type 5. DEFAULT: 100
probs: Probabilities passed to quantileMean for plot=4. DEFAULT: c(0,25,50,75,95,99)/100
width: Numeric: window width for plot=4. Used as sd in gaussian weighting. Support (number of values around a DOY passed to quantile function at least once) is ca 4.9*width. The value at doy itself is used 10 times. Larger values of width require more computing time. DEFAULT: 3
text: Logical. Call textField if plot=4? DEFAULT: TRUE
texti: Numerical (vector): indices at which to label the lines. DEFAULT: seq(200,20,length.out=length(probs))
textargs: List of arguments passed to textField for plot=4. DEFAULT: NULL
months: Labels for the months. DEFAULT: J,F,M,A,M,J,J,A,S,O,N,D
slab, tlab, vlab: Labels for the season, time (year) and values used on the axes and title of colPointsLegend. DEFAULT: "Month", "Year", substitute(values)
xlim, ylim: Limits of x and y axis. DEFAULT: NA (specified internally per plot type)
xaxs, yaxs: x and y Axis style, see par. Use "r" for regular 4% expansion, "i" for in range only. DEFAULT: NA (specified internally per plot type)
main, adj: Graph title and offset to the left (adj passed to title). DEFAULT: "Seasonality", 0.2
mar, mgp: Parameters specifying plot margin size and labels placement. DEFAULT: c(3,3,4,1), c(1.7,0.7,0) (Changed for plot 3:5 if not given)
keeppar: Logical: Keep the margin parameters? If FALSE, they are reset to the previous values. DEFAULT: TRUE
legend: Logical. Should a legend be drawn? DEFAULT: TRUE
legargs: List of arguments passed as legargs to colPoints. DEFAULT: NULL (internally, plots 3 and 5 have density=F as default)
returnall: Logical: return all relevant output as a list instead of only annmax data.frame? DEFAULT: FALSE
quiet: Logical: suppress progress stuff and colPoints messages? DEFAULT: FALSE
...: Further arguments passed to colPoints like pch, main, xaxs, but not Range (use vrange). Passed to spiralDate if plot=2, like add, format, lines.

Author

Berry Boessenkool, berry-b@gmx.de, Jul-Oct 2016

Examples

Run this code

# browseURL("https://nrfa.ceh.ac.uk/data/station/meanflow/39072")
qfile <- system.file("extdata/discharge39072.csv", package="berryFunctions")
Q <- read.table(qfile, skip=19, header=TRUE, sep=",", fill=TRUE)[,1:2]
rm(qfile)
colnames(Q) <- c("date","discharge")
Q$date <- as.Date(Q$date)
Q$discharge[450:581] <- NA
plot(Q, type="l")
seas <- seasonality(date, discharge, data=Q, shift=100, main="NRFA: Thames\nRoyal Windsor Park")
head(seas)
# notice how n for nonmissing values is lower in the first hydrological year,
# which includes parts of two consecutive calendarical years.

# Be careful with your interpretation. This looks normal up to 2007, but then BAM!:
seasonality(date, discharge, data=Q[Q$date

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