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Plot Species Sensitivity Data and Distributions

Source: R/ssd-plot.R
ssd_plot.Rd

Plots species sensitivity data and distributions.

Usage

ssd_plot(
  data,
  pred,
  left = "Conc",
  right = left,
  ...,
  label = NULL,
  shape = NULL,
  color = NULL,
  size,
  linetype = NULL,
  linecolor = NULL,
  xlab = "Concentration",
  ylab = "Species Affected",
  ci = TRUE,
  ribbon = TRUE,
  hc = 0.05,
  shift_x = 3,
  add_x = 0,
  bounds = c(left = 1, right = 1),
  big.mark = ",",
  suffix = "%",
  trans = "log10",
  xbreaks = waiver(),
  xlimits = NULL,
  text_size = 11,
  label_size = 2.5,
  theme_classic = FALSE
)

Arguments

data

A data frame.

pred

A data frame of the predictions.

left

A string of the column in data with the concentrations.

right

A string of the column in data with the right concentration values.

...

Unused.

label

A string of the column in data with the labels.

shape

A string of the column in data for the shape aesthetic.

color

A string of the column in data for the color aesthetic.

size

A number for the size of the labels. Deprecated for label_size. #' [Deprecated]

linetype

A string of the column in pred to use for the linetype.

linecolor

A string of the column in pred to use for the line color.

xlab

A string of the x-axis label.

ylab

A string of the x-axis label.

ci

A flag specifying whether to estimate confidence intervals (by bootstrapping).

ribbon

A flag indicating whether to plot the confidence interval as a grey ribbon as opposed to green solid lines.

hc

A value between 0 and 1 indicating the proportion hazard concentration (or NULL).

shift_x

The value to multiply the label x values by (after adding add_x).

add_x

The value to add to the label x values (before multiplying by shift_x).

bounds

A named non-negative numeric vector of the left and right bounds for uncensored missing (0 and Inf) data in terms of the orders of magnitude relative to the extremes for non-missing values.

big.mark

A string specifying used between every 3 digits to separate thousands on the x-axis.

suffix

Additional text to display after the number on the y-axis.

trans

A string of which transformation to use. Accepted values include "log10", "log", and "identity" ("log10" by default).

xbreaks

The x-axis breaks as one of:

  • NULL for no breaks

  • waiver() for the default breaks

  • A numeric vector of positions

xlimits

The x-axis limits as one of:

  • NULL to use the default scale range

  • A numeric vector of length two providing the limits. Use NA to refer to the existing minimum or maximum limits.

text_size

A number for the text size.

label_size

A number for the size of the labels.

theme_classic

A flag specifying whether to use the classic theme or the default.

See also

ssd_plot_cdf() and geom_ssdpoint()

Examples

ssd_plot(ssddata::ccme_boron, boron_pred, label = "Species", shape = "Group")