pastecs: abund – R documentation

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abund

Sort variables by abundance

Description

Sort variables (usually species in a species x stations matrix) in function of their abundance, either in number of non-null values, or in number of individuals (in log). The f coefficient allows adjusting weight given to each of these two criteria.

Usage

abund(x, f = 0.2)

## S3 method for class 'abund'
extract(e, n, left = TRUE, ...)
## S3 method for class 'abund'
identify(x, label.pts = FALSE, lvert = TRUE, lvars = TRUE, col = 2, lty = 2, ...)
## S3 method for class 'abund'
lines(x, n = x$n, lvert = TRUE, lvars = TRUE, col = 2, lty = 2, ...)
## S3 method for class 'abund'
plot(x, n = x$n, lvert = TRUE, lvars = TRUE, lcol = 2, llty = 2, all = TRUE,
    dlab = c("cumsum", "% log(ind.)", "% non-zero"), dcol = c(1,2,4),
    dlty = c(par("lty"), par("lty"), par("lty")), dpos = c(1.5, 20), type = "l",
    xlab = "variables", ylab = "abundance",
    main = paste("Abundance sorting for:",x$data, "with f =", round(x$f, 4)), ...)
## S3 method for class 'abund'
print(x, ...)
## S3 method for class 'summary.abund'
print(x, ...)
## S3 method for class 'abund'
summary(object, ...)

Arguments

`x`	A data frame containing the variables to sort according to their abundance in columns for `abund`, or an 'abund' object for the methods
`f`	Weight given to the number of individuals criterium (strictly included between 0 and 1; weight for the non-null values is `1-f`. The default value, `f=0.2`, gives enough weight to the number of non-null values to get abundant species according to this criterium first, but allowing to get at the other extreme rare, but locally abundant species
`object`	An 'abund' object returned by `abund`
`e`	An 'abund' object returned by `abund`
`n`	The number of variables selected at left
`type`	the type of graph to plot. By default, lines with 'l'
`lvert`	If `TRUE` then a vertical line separate the n variables at left from the others
`lvars`	If `TRUE` then the x-axis labels of the n left variables are printed in a different color to emphasize them
`lcol`	The color to use to draw the vertical line (`lvert=TRUE`) and the variables labels (`lvars=TRUE`) at left af the nth variable. By default, color 2 is used
`llty`	The style used to draw the vertical line (`lvert=TRUE`). By default, a dashed line is used
`xlab`	the label of the x-axis
`ylab`	the label of the y-axis
`main`	the main title of the graph
`all`	If `TRUE` then all lines are drawn (cumsum, %log(ind.) and %non-null). If `FALSE`, only the cumsum line is drawn
`dlab`	The legend labels
`dcol`	Colors to use for drawing the various curves on the graph
`dlty`	The line style to use for drawing the various curves on the graph
`dpos`	The position of the legend box on the graph (coordinates of its top-left corner). A legend box is drawn only if `all=TRUE`
`col`	The color to use to draw lines
`lty`	The style used to draw lines
`...`	additional parameters
`label.pts`	Do we have to label points on the graph or to chose an extraction level with the `identify()` method?
`left`	If `TRUE`, the n variables at left are extracted. Otherwise, the total-n variables at right are extracted

Details

Successive sorts can be applied. For instance, a first sort with f = 0.2, followed by an extraction of rare species and another sort with f = 1 allows to collect only rare but locally abundant species.

Value

An object of type 'abund' is returned. It has methods print(), summary(), plot(), lines(), identify(), extract().

Author(s)

Philippe Grosjean (phgrosjean@sciviews.org), Frédéric Ibanez (ibanez@obs-vlfr.fr)

References

Ibanez, F., J.-C. Dauvin & M. Etienne, 1993. Comparaison des évolutions à long terme (1977-1990) de deux peuplements macrobenthiques de la baie de Morlaix (Manche occidentale): relations avec les facteurs hydroclimatiques. J. Exp. Mar. Biol. Ecol., 169:181-214.

Examples

data(bnr)
bnr.abd <- abund(bnr)
summary(bnr.abd)
plot(bnr.abd, dpos=c(105, 100))
bnr.abd$n <- 26
# To identify a point on the graph, use: bnr.abd$n <- identify(bnr.abd)
lines(bnr.abd)
bnr2 <- extract(bnr.abd)
names(bnr2)

pastecs

Package for Analysis of Space-Time Ecological Series

v1.3.21

GPL-2

Authors

Philippe Grosjean [aut, cre], Frederic Ibanez [aut], Michele Etienne [ctb]

Initial release