R: Percentile-percentile plots for species-abundance and...

ppsad and pprad methods {sads} | R Documentation

## Percentile-percentile plots for species-abundance and rank-abundance models

### Description

Plots empirical percentiles vs corresponding theoretical values expected by a model for species abundances (SAD) or a model for species abundance ranks (RAD).

### Usage

    ## S4 method for signature 'fitsad'
    ppsad(x, plot=TRUE, line=TRUE, ...)
    ## S4 method for signature 'numeric'
    ppsad(x, sad, coef, trunc=NA, plot=TRUE,
    line=TRUE, ...)
    ## S4 method for signature 'fitrad'
    pprad(x, plot=TRUE, line=TRUE, ...)
    ## S4 method for signature 'rad'
    pprad(x, rad, coef, trunc=NA, plot=TRUE, line=TRUE, ...)
    ## S4 method for signature 'numeric'
    pprad(x, rad, coef, trunc=NA, plot=TRUE, line=TRUE, ...)

### Arguments

`x` | a numeric vector of abundances of species or a fitted sad/rad model (object of `fitsad-class` or `fitrad-class`, respectively). For `pprad` this argument can be also a rank-abundance table of rad-class.
`sad, rad` | character; root name of sad or rad distribution to calculate expected percentiles. See `fitsad` and `fitrad` for available distributions.
`coef` | named list of numeric values; parameter values of the distribution given in `sad` or `rad`. Parameters should be named as in the corresponding density function, and in the same order
`trunc` | non-negative integer, trunc > min(x); truncation point to fit a truncated distribution.
`plot` | logical; if 'TRUE' a percentile-percentile plot is produced. If not, only a data frame with theoretical and empirical values for percentiles of the data is invisibly returned.
`line` | logical; if 'TRUE' and `plot` is 'TRUE', the equivalence line y=x with `abline(0,1)` is added to the plot. If not, no line is drawn.
`...` | further arguments to be passed to the `plot` function.

### Methods

ppsad

  `signature(x = "fitsad", sad = "missing", coef = "missing", trunc = "missing", plot="ANY", line="ANY")`: quantile-quantile plot for a fitted model of species abundances (a `fitsad-class` object). Only argument `x` should be provided.

ppsad

  `signature(x = "numeric", sad = "character", coef = "list", trunc = "ANY", plot="ANY", line="ANY")`: quantile-quantile plot of a numeric vector of abundances (`x`) vs a species abundance distributions defined by the following arguments.

pprad

  `signature(x = "fitrad", rad = "missing", coef = "missing", trunc = "missing", plot="ANY", line="ANY")`: quantile-quantile plot for a fitted model of species abundances ranks (a `fitrad-class` object). Only argument `x` should be provided.

pprad

  `signature(x = "rad", rad = "character", coef = "list", trunc = "ANY", plot="ANY", line="ANY")`: quantile-quantile plot of a table of abundance ranks (`x`) vs a species rank-abundance distribution defined by the following arguments.

pprad

  `signature(x = "numeric", rad = "character", coef = "list", trunc = "ANY", plot="ANY", line="ANY")`: quantile-quantile plot of a numeric vector of abundances (`x`) vs a species rank-abundance distribution defined by the following arguments.

### Author(s)

Paulo I Prado prado@ib.usp.br and Murilo Dantas Miranda.

### References

Thas, O. 2010. Comparing distributions. Springer.

### Examples

    ## An example with SADs
    data(moths)
    ## fits log-series distribution to abundance data
    moths.ls <- fitsad(moths, "ls")
    ## fits lognormal distribution truncated at 0.5
    moths.ln <- fitsad(moths,"lnorm", trunc=0.5)
    ## Plots with the model object and with abundance vector
    par(mfrow=c(2,2))
    ppsad(moths.ls)
    ppsad(moths, sad="ls", coef=as.list(coef(moths.ls)) )
    ppsad(moths.ln)
    ppsad(moths, sad="lnorm", coef=as.list(coef(moths.ln)), trunc=0.5)
    par(mfrow=c(1,1))

    ## An example with RADs
    data(okland)
    ## Fits broken-stick RAD model
    ok.bs <- fitrad(okland, "rbs")
    ## Fits geometric series RAD model
    ok.gs <- fitrad(okland, "gs")
    ## Plots with the model object and with the abundance vector
    par( mfrow=c(2, 2) )
    pprad(ok.bs)
    pprad(okland, rad="rbs", coef=as.list(coef(ok.bs)))
    pprad(ok.gs)
    pprad(okland, rad="gs", coef=as.list(coef(ok.gs)))
    par(mfrow=c(1,1))

[Package sads version 0.4.2 Index]