graph.abundmodel: Output histograms of little.r across species, observed and...
In forestgeo/ctfs: Tools for the Analysis of Forest Dynamics

Description Usage Arguments Arguments details Warning See Also

Output histograms of little.r across species, observed and fitted, using the result of model.littleR.Gibbs(). The histogram of black points is all species, blue points only those starting with N >= minabund.

graph.abundmodel(fit, datafile = NULL, div = 0.01, tinydiv = 0.001,
  modeltype = "asympower", xrange = NULL, yrange = NULL,
  minabund = 50, conf = 25, returnextreme = TRUE,
  xname = "Rate of population change", yname = "Frequency",
  ltype = "solid", lwidth = 2, modelclr = "green", bartype = FALSE,
  addpts = TRUE, makeleg = TRUE, add = FALSE, newgraph = FALSE,
  ax = TRUE, mortcorr = FALSE, debug = FALSE)

`fit`	result of model.littleR.Gibbs
`datafile`	optional name of file where the fitted result is saved
`div`	width of bins for histogram of observed rate of population change
`tinydiv`	width of bins used to draw the fitted distribution
`modeltype`	Functional forms to fit to the distribution; it can be: Gaussian `modeltype = "norm"`, with the quotes Asymmetric Gaussian (a different standard deviation on left and right of the mode) `modeltype = "asymnorm"`, with the quotes Laplace (exponential distribution, with mirror image for negative values) `modeltype = "symexp"`, with the quotes Asymmetric Laplace (different rate constant for left and right of the center) `modeltype = "asymexp"`, with the quotes Asymmetric power distribution (different rate constant for left and right of the center) 'modeltype = "asympower", with the quotes.
`xrange, yrange`	Range of graph's x-axis (or y-axis).
`minabund`	minimum abundance of species to be used in histogram of observed rates of population change
`conf`	number of alternate fits to graph, as indication of confidence; if conf = NULL, no confidence lines are added
`returnextreme`	whether to print a list of the fastest increases and decreases in abundance to the screen
`xname, yname`	axis names
`ltype`	Line type; see `ltype` in ?`graphics::par()`.
`lwidth`	Line width; see `width` in ?`graphics::par()`.
`modelclr`	Line color; see ?`graphics::par()`.
`bartype`	if TRUE, histogram is bar graph
`addpts`	if TRUE, histogram is a point graph
`makeleg`	whether to add legend
`add`	Logical. Whether to add elements such as points or line to an existing graph. if TRUE, there must be an appropriate existing graph, otherwise, a new graph is drawn.
`newgraph`	if FALSE, just graph to the screen and export is ignored; use TRUE to create a new plot window or export to a file.
`ax`	if FALSE, the axes are not added
`mortcorr`	whether to graph the correlation between mortality and population change across species
`debug`	Logical. If TRUE, call browser to debug.
`graphit`	xxxdocparam in graph.abundmodel() is truncated: "if set to false," What follows?

mortcorr If the argument mortcorr = TRUE, a graph of mortality rate vs. population change for every species is also produced. Otherwise, a table of the species with biggest increases and biggest decreases in abundance is printed to the screen.

If you use the argument datafile, beware that it uses attach(). After use you should remove the attached object from the serach path. See Good practice in ?attach(). This argument may be deprecated in future versions.

?graphics::plot(), ?graphics::par().

forestgeo/ctfs documentation built on May 3, 2019, 6:44 p.m.