plot_brc: Plot BRC

In ngwalton/iec: Index of Ecological Condition (IEC)

Description

plot_brc plots biotic response curves generated by est_brc along with the observations used to generate them.

Usage

plot_brc(sp, brc, ref_grad, env_bad = NULL, env_good = NULL,
  ylab = "Response", sub_xlab = NULL, sub_main = NULL)

Arguments

sp	community data frame (sites as rows, taxa as columns, observations as values).
brc	BRC data frame generated by est_brc.
ref_grad	numeric vector of reference gradient scores (0-10), one for each site.
env_bad	numeric scalar worst condition of original environmental gradient (optional).
env_good	numeric scalar best condition of original environmental gradient (optional).
ylab	a title for the y axis (optional; defaults to "Response").
sub_xlab	name of environmental gradient (optional); sub title to x-axis.
sub_main	a sub title for the plots (optional); printed below main title (taxon name).

Details

BRC plots are generated for each taxa in data frames sp and brc. sp and brc must contain the same taxa in the same order. Generally, sp and ref_grad will be the same variables used to generate brc with est_brc. Because many plots will be generated by this function, it may be best to send it to a file plotting device (e.g., pdf).

The optional arguments, env_bad and env_good, provide a way to label each end of the x-axis with the worst and best observed values of the original environmental gradient. This can be helpful while exploring the data to see if a gradient has been scaled correctly (inverted or not). sub_xlab can be used to add the original name of the gradient to the x-axis below the x-axis label. sub_main provides an optional sub title printed below the main title (name of taxon extracted from input sp). This can be a good place to print additional information about the plot such at the project or input dataset.

See Also

est_brc, scale10, Devices

ngwalton/iec documentation built on May 23, 2019, 4:43 p.m.