plot.sma: Draw an X-Y plot

In dfalster/smatr3: (Standardised) Major Axis Estimation and Testing Routines

Draw an X-Y plot

Description

Plot a (standardized) major axis fit, including the data and the fitted lines. There are many options for changing the appearance of the plot and generating high-quality publishable graphs.

Usage

## S3 method for class 'sma'
plot(
  x,
  which = c("default", "residual", "qq"),
  use.null = FALSE,
  add = FALSE,
  type = "o",
  xaxis = NULL,
  yaxis = NULL,
  xlab = NULL,
  ylab = NULL,
  pch = NULL,
  col = NULL,
  lty = NULL,
  from = NULL,
  to = NULL,
  log = x$log,
  frame.plot = TRUE,
  tck = par("tck"),
  p.lines.transparent = NA,
  axes = TRUE,
  ...
)

Arguments

x	Object of class 'sma'.
which	If 'residual', plots a residual plot; if 'qq', plots a qq plot; otherwise an x-y plot.
use.null	Logical. If FALSE, plots the fitted lines (the default), otherwise those corresponding to the null hypothesis.
add	Logical. If TRUE, adds lines or points to an existing plot.
type	As in 'lm.default' : 'p' plots points only, 'l' only lines, and 'o' or 'b' plot both.
xaxis, yaxis	Special axis objects. See Details and examples.
xlab, ylab	Labels for X and Y axes.
pch	Plotting symbols (see points).
col	Color of points and lines.
lty	Line type (see lines).
from, to	Min and max X values for the lines (defaults to values given by sma, which are the X values corresponding the maximum and minimum fitted values in the data.).
log	One of 'x','y' or 'xy', to denote which axes to log-scale.
frame.plot	a logical indicating whether a box should be drawn around the plot, by default = TRUE.
tck	The length of tick marks as a fraction of the smaller of the width or height of the plotting region. If tck >= 0.5 it is interpreted as a fraction of the relevant side, so if tck = 1 grid lines are drawn. By default set to current system defaults (tck = par("tck")).
p.lines.transparent	Adjusts transparency level of fitted lines according to p-value of correlation between X and Y, via formula opacity = 1-p/p.lines.transparent). Setting to a value 0.1 means the line for any group with p = 0.1 would be fully transparent, while line for a group with p =0.05 would be 50 perecent transparent. by default set to NA, which means lines are fully visible.
axes	If FALSE, suppress plotting of the axes (Default TRUE)
...	Further arguments passed to plot.default.

Details

The plot.sma function produces one of three different types of plot, depending on the which argument.

The default plot, which="default", produced a plot of y vs x, with separate symbols for each group if appropriate, and MA or SMA lines fitted through each group. The formula used in the sma object that is input to the plot function determines whether there is a group structure, whether fitted lines have common slope, etc.

A residual plot can be obtained via which="residual" - this is a plot of residuals against fitted values. This can be used to check assumptions - if assumptions are satisfied there should be no pattern.

A normal quantile plot can be obtained via which="qq" - this is a normal quantile plot of residuals. This can be used to check the normality assumption - if data are close to a straight line, normality is plausible. Note that non-normality is only important to the validity of the test in small samples. In larger samples, non-normality will not effect validity, but strong non-normality will reduce the power of tests.

If use.null=TRUE then the lines added to the plot use the coefficients estimated under the null hypothesis. For example, if the sma object x was produced using a common slopes test (via y~x*groups or similar) then use.null=TRUE will plot lines that apply the common slope to each group.

The arguments pch, col, lty, from & to, are used to modify characteristics of the plotted points and lines. If a vector of values for anyone of these arguments is passed to plot.sma, then successive values are applied to each group, provided group structure is included in x and the vector length is at least as long as the number of groups.

By default, plot.sma uses the default tick spacing given by plot.default. To customise axes, users can pass special axis objects to plot.sma, obtained using the defineAxis command as in the example below. This enables high quality publishable plots to be produced. See utils for more information.

Author(s)

D. Falster, R.A. Duursma, D.I. Warton

Examples

## Not run: 
# Load leaf lifetime dataset:
data(leaflife)

# Only consider low-nutrient sites:
leaf.low.soilp <- subset(leaflife, soilp == 'low')

# Fit SMA's separately at each of high and low 
# rainfall sites and test for common slope:
ft <- sma(longev~lma*rain, data=leaf.low.soilp, log="xy")

# Plot leaf longevity (longev) vs leaf mass per area (lma) 
# separately for each of high and low rainfall:
plot(ft)

# As before but add lines which have a common slope:
plot(ft, use.null=TRUE)

#As above, but adding the common slope lines to an existing plot
plot(ft, type='p', col="black")
plot(ft, use.null=TRUE, add=TRUE, type='l')

# Plot with equally spaced tick marks:
plot(ft, xaxis=defineAxis(major.ticks=c(40,80,160,320,640)), 
	yaxis=defineAxis(major.ticks=c(0.5,1,2,4,8)) )

# Produce a residual plot to check assumptions:
plot(ft,which="res")

# Produce a normal quantile plot:
plot(ft,which="qq")

## End(Not run)

dfalster/smatr3 documentation built on Aug. 30, 2022, 5:25 a.m.