plot_ts: Plot time series
In marinebon/ecoidx: Marine ecological indicators R package for CA Current IEA

Description Usage Arguments Details Value Examples

Plot time series in the style of the California Current IEA. Dashed lines are used in between missing data and points colored by color_pts. Include a ribbon around y if low (y_lo) and high (y_hi) values are provided. Include long-term average if add_avg = TRUE with average as a black dashed line and solid lines indicating the standard deviation in the color of color_avg. Include rectangle in the color of color_avg between the standard deviation of the long-term average since x_recent if provided. Include icons in the right-hand margin for recent trend (→, ↗, ↘) and recent average (o, +, -) if stable, increasing, or decreasing (respectively) relative to the long-term standard deviation.

plot_ts(
  d,
  x = year,
  y = index,
  y_lo = SElo,
  y_hi = SEup,
  x_recent = 5,
  units_recent = "years",
  add_avg = TRUE,
  add_icons = TRUE,
  font_size = 24,
  icon_size = font_size/2,
  color_pts = rgb(225, 118, 44, max = 255),
  color_avg = rgb(63, 173, 213, max = 255),
  color_hilo = "lightgrey",
  alpha_avg = 0.8,
  alpha_hilo = 0.8,
  theme_plot = theme_iea
)

`d`	Default dataset to use for plotting with `ggplot2::ggplot()`. Typically includes columns: `year`, `index`, `SElo` and `SEup`.
`x`	column for x axis from `d`, unquoted. Defaults to `year`.
`y`	column for y axis from `d`, unquoted. Defaults to `index`.
`y_lo`	unquoted column for low value to apply to gray ribbon, typically `y - sd(y)`. Defaults to `SElo` if present.
`y_hi`	unquoted column for highy value to apply to gray ribbon, typically `y + sd(y)`. Defaults to `SEhi` if present.
`x_recent`	duration of `x`, typically an integer, for which to consider as recent period to derive rectangle and icons. Defaults to `5`, as in years.
`units_recent`	units to describe `x`, used in caption.
`add_avg`	whether to add average as a black dashed line and solid lines indicating the standard deviation in the color of `color_avg`. Defaults to `TRUE`.
`add_icons`	whether to include icons in the right-hand margin for recent trend (→, ↗, ↘) and recent average (o, +, -) if stable, increasing, or decreasing (respectively) relative to the long-term standard deviation. Defaults to `TRUE`.
`font_size`	font size. Defaults to 24.
`icon_size`	size of icon font. Defaults to half the `font_size`, 12.
`color_pts`	color for points, as named color (see `colors()`) or hexadecimal value as provided by red green blue `rgb()` specification. Defaults to dusty orange.
`color_avg`	color for standard deviation lines around long-term average and rectangle between since `x_recent`.
`color_hilo`	color for ribbon around `y` between values `y_lo` and `y_hi`.
`alpha_avg`	transparency (0 to 1) for colored elements of long-term average: standard deviation and recent rectangle.
`alpha_hilo`	transparency (0 to 1) for ribbon around `y` between values `y_lo` and `y_hi`.
`theme_plot`	theme function to apply to the ggplot. Defaults to `theme_iea`.

The attribute caption includes a textual summary.

This function returns a ggplot object with attributes for: caption, recent_trend and recent_avg.

# example time series dataset with some NAs to show dashed line between non-NA values
ts1

# defaults to include all options data frame contains x, y, SElo, SEhi
g <- plot_ts(ts1)
g

# show the caption attributed to the returned ggplot object
cat(attr(g, "caption"))

# without SElo or SEhi columns, just year and index
g <- plot_ts(ts1[,c("year","index")])
g

# same caption as previously, since defaults to x_recent=5 and add_avg=T
cat(attr(g, "caption"))

# without default x_recent, add_avg, or add_icons
g <- plot_ts(ts1, x_recent=NA, add_icons=F, add_avg=F)
g
# no caption, since missing x_recent and add_avg
cat(attr(g, "caption")) # empty caption without x_recent