plot.haploAccum: Plotting haplotype accumulation curves

In spider: Species Identity and Evolution in R

Description

Plots the accumulation curves calculated by haploAccum.

Usage

## S3 method for class 'haploAccum'
plot(x, add = FALSE, ci = 2, ci.type = c("bar","line","polygon"), 
    col = par("fg"), ci.col = col, ci.lty = 1, xlab, ylab = "Haplotypes", ylim,  
    main = paste(x$method, "method of haplotype accumulation", sep=" "), ...)

Arguments

x	A ‘haploAccum’ object obtained from haploAccum.
add	Add graph to an existing graph.
ci	Multiplier for the calculation of confidence intervals from standard deviation. ci = 0 prevents the drawing of confidence intervals.
ci.type	Type of confidence intervals: "bar" for vertical bars, "line" for lines, and "polygon" for a shaded area.
col	Colour for curve line.
ci.col	Colour for lines or shaded area when "polygon".
ci.lty	Line type for confidence interval lines or border of the "polygon".
xlab	Label for the X-axis.
ylab	Label for the Y-axis.
ylim	Y-axis limits.
main	Title of the plot.
...	Other parameters to pass to plot.

Value

Plots a haplotype accumulation curve and confidence intervals depending on the options given to haploAccum.

Author(s)

Jagoba Malumbres-Olarte <[e-mail]>.

References

Gotellli, N.J. & Colwell, R.K. (2001). Quantifying biodiversity: procedures and pitfalls in measurement and comparison of species richness. _Ecology Letters_ *4* 379–391.

Examples

data(dolomedes)
#Generate multiple haplotypes
doloHaplo <- dolomedes[sample(37, size = 200, replace = TRUE), ] 
dolocurv <- haploAccum(doloHaplo, method = "random", permutations = 100)

plot(dolocurv)
plot(dolocurv, add = FALSE, ci = 2, ci.type = "polygon", col = "blue", ci.col = "red", 
    ci.lty = 1)

Example output

Registered S3 method overwritten by 'spdep':
  method   from
  plot.mst ape 
Registered S3 method overwritten by 'pegas':
  method      from
  print.amova ade4
There are missing or ambiguous data, which may cause an overestimation of the number of haplotypes

spider documentation built on May 2, 2019, 5:16 p.m.