smooth PRC diagram — plotsmoothPRC • PRC

Creates a smooth PRC diagram with treatment curves and a vertical species-loading plot.

plotsmoothPRC(
  object,
  axis = 1,
  mod_prc = NULL,
  with_classical_lines = TRUE,
  with_unconstrained_scores = TRUE,
  flip = FALSE,
  widths = c(4, 1),
  title = NULL,
  left = "Treatment curves",
  right = "taxon scores",
  threshold = 14,
  y_lab_interval = 0.5,
  speciesname = NULL,
  selectname = "Fratio",
  sample_times_only = FALSE,
  verbose = TRUE
)

Arguments

object: a result of smoothPRC.
axis: the number of the axis to plot
mod_prc: a results of doPRC, i.e. a classical PRC with the same data and design. Default NULL, in which the classical PRC is computed using doPRC and the data in object.
with_classical_lines: logical to add or suppress classical PRC lines. Default TRUE, i.e. with classical PRC lines.
with_unconstrained_scores: logical to add or suppress the unconstrained scores in the smooth PRC showing the scatter of the individual samples (cosms). Default TRUE, i.e. with individual points.
flip: logical. Should the axis be reversed? Default FALSE. Can be numeric with -1 meaning: reverse, and 1 meaning do not reverse.
widths: relative width of treatment PRC plot and the loading plot (see grid.arrange).
title: overall title.
left: left axis text (see arrangeGrob).
right: right axis text (see arrangeGrob).
threshold: species with criterion (specified by selectname) higher than the threshold are displayed. Default: 7 (which is the threshold F-ratio for testing a single regression coefficient at p = 0.01 with 60 df for the error in a multiple regression of each single species onto the condition and the ordination axis). If selectname is not in species_scores, the threshold is divided by 14, so that the default is 0.5.
y_lab_interval: interval of the y-axis ticks. A tick at no effect (0) is always included; default: 0.5.
speciesname: name of the variable containing the species names (default NULL uses row names).
selectname: name of the column or variable containing the criterion for the selection of species to be displayed. Default: "Fratio1"; if selectname is not found in species_scores, set to scoresname.
sample_times_only: logical to PRClines based on the sampled times only, i.e. without interpolation. Default FALSE.
verbose: logical for printing the number of species with names out of the total number (default: TRUE).

Details

sample_times_only = TRUE can be useful for comparison with classical PRC. It avoids interpolation and may work when the default fails to produce a plot.