brc_pdf: Save BRC plots to PDF file.

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

Description

brc_pdf saves the output from plot_lof and plot_brc to a PDF.

Usage

brc_pdf(out_pdf, sp, brc, ref_grad, min_lof = 1, env_bad = NULL,
  env_good = NULL, ylab = "Response", sub_xlab = NULL, sub_main = NULL)

Arguments

out_pdf	name of output PDF file.
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.
min_lof	numeric value indicating minimum LOF to label.
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_pdf checks for if the output file already exists and returns an error is it does. Otherwise, brc_pdf opens a PDF device to print to (out_pdf) and then saves the output from plot_lof and plot_brc to the PDF file. This is done within tryCatch such that dev.off is safely called even if the printing fails.

See Also

est_brc, scale10, Devices

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