This function will plot the time series data. See the initial portion of the function for parts that you can alter.
PlotTimeSeries(
dframe = NA,
X = NA,
Y = NA,
Y2 = NULL,
Y.outlier = NULL,
threshold = NA,
threshold.loc = "below",
threshold.correct = FALSE,
sig.trend = NA,
sig.mean = NA,
stats.years = NA,
LWD = 1,
LWD.threshold = 1,
SE = NULL,
SEup = NA,
SElo = NA,
XLIM = NA,
YLIM = NA,
Xlab = NA,
Ylab = NULL,
Title = NULL,
Xangle = 0,
Xaxis.cex = 0.9,
Yaxis.cex = 0.9,
Ylab.cex = 0.9,
TitleCex = 0.9,
YATS = 3,
Y.lab.drop = FALSE,
Y.axis.labels = NA,
yminor = NA,
Label.cex = 0.9,
Pt.cex = 0.3,
TicsEvery = 10,
MinorTics = 1,
ALPHA = 200,
PERIOD = 5,
Arrow.cex = 2,
AltTxt.Period = "5-years",
AltTxt = NA,
AltTxt.file.name = NA,
Mar = c(0, 3.5, 0.7, 0),
Bmar = NA,
Lmar = NA,
Tmar = NA,
Rmar = NA,
Ylab_line = 2.5
)expected column names are: "year", "index", "timeseries", "metric","SEup", "SElo", "SE"
column name, typically "year", to plot on x axis
column name, typically "index", to plot on y axis
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threshold value
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significant trend
significant mean
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NOTE: if you call SEup separately (say to plot SD instead of SE), the first value cannot be an NA. Set it and SElo to the index data point for that value.
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The default plot is the standard IEA time series plot. If you include a "treshold" value, the plot will shift format to plotting versus a threshold. If so, threshold.loc, will swap the plotting of grey polygons to indicate periods where the timeseries is above or below the threshold.
There are special plots for Seabirds: For seabird plots you must include both Y2 and Y.outlier in the plot call. For seabird mortality, Y is all the data, Y2 is data with outliers removed, Y.outlier are just the outliers. Trends are evaluated with the outliers removed.