abund {pastecs} | R Documentation |
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.
abund(x, f=0.2) ## S3 method for class 'abund': summary(abd) ## S3 method for class 'abund': plot(abd, n=abd$n, lvert=TRUE, lvars=TRUE, lcol=2, llty=2, all=TRUE, dlab=c("cumsum", "% log(ind.)", "% non-zero"), dcol=c(1, 2, 4), dlty, dpos=c(1.5, 20), ...) ## S3 method for class 'abund': lines(abd, n=abd$n, lvert=TRUE, lvars=TRUE, ...) ## S3 method for class 'abund': identify(abd, label.pts=FALSE, lvert=TRUE, lvars=TRUE, ...) ## S3 method for class 'abund': extract(abd, n=abd$n, left=TRUE)
x |
A data frame containing the variables to sort according to their abundance in columns |
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 |
abd |
An 'abund' object returned by abund |
n |
The number of variables selected at left |
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 |
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 |
... |
additional graph 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 |
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.
An object of type 'abund' is returned. It has methods print()
, summary()
, plot()
, lines()
, identify()
, extract()
.
Philippe Grosjean (phgrosjean@sciviews.org), Frédéric Ibanez (ibanez@obs-vlfr.fr)
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.
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)