vegan-internal: Internal vegan functions
In pattakosn/Rworkshop: Community Ecology Package

Internal vegan functions that are not intended to be called directly, but only within other functions.

ordiGetData(call, env)
ordiParseFormula(formula, data, xlev = NULL, envdepth = 2, 
   na.action = na.fail, subset = NULL)
ordiTerminfo(d, data)
ordiNAexclude(x, excluded)
ordiNApredict(omit, x)
ordiArrowMul(x, at = c(0,0), fill = 0.75)
ordiArrowTextXY(vect, labels, ...)
ordiArgAbsorber(..., shrink, origin, scaling, triangular,
                display, choices, const, FUN)
centroids.cca(x, mf, wt)
permuted.index(n, strata)
pasteCall(call, prefix = "Call:")
veganCovEllipse(cov, center = c(0, 0), scale = 1, npoints = 100)
hierParseFormula(formula, data)

The description here is only intended for vegan developers: these functions are not intended for users, but they only should be used within functions. In general, these functions are not exported to the namespace, but you must use get or ::: to directly call these functions.

ordiGetData finds the model frame of constraints and conditions in constrained ordination in the defined environment. ordiParseFormula returns a list of three matrices (dependent variables, and model.matrix of constraints and conditions, possibly NULL) needed in constrained ordination. Argument xlev is passed to model.frame and argument envdepth specifies the depth at which the community data (dependent data) are evaluated; default envdepth = 2 evaluates that in the environment of the parent of the calling function, and envdepth = 1 within the calling function (see eval.parent). ordiTermInfo finds the term information for constrained ordination as described in cca.object. ordiNAexclude implements na.action = na.exclude for constrained ordination finding WA scores of CCA components and site scores of unconstrained component from excluded rows of observations. Function ordiNApredict puts pads the result object with these or with WA scores similarly as napredict.

ordiArrowMul finds a multiplier to scale a bunch of arrows to fill an ordination plot, and ordiArrowTextXY finds the coordinates for labels of these arrows. See envfit for an application.

ordiArgAbsorber absorbs arguments of scores function of vegan so that these do not cause superfluous warnings in graphical function FUN. If you implement scores functions with new arguments, you should update ordiArgAbsorber.

centroids.cca finds the weighted centroids of variables.

permuted.index creates permuted index of length n possibly stratified within strata. This is the basic vegan permutation function that should be replaced with more powerful shuffle in the future releases of vegan, and all new functions should use shuffle.

pasteCall prints the function call so that it is nicely wrapped in Sweave output.

veganCovEllipse finds the coordinates for drawing a covariance ellipse.

hierParseFormula returns a list of one matrix (left hand side) and a model frame with factors representing hierarchy levels (right hand side) to be used in adipart, multipart and hiersimu.

pattakosn/Rworkshop documentation built on May 24, 2019, 8:22 p.m.