NEWS

sads 0.6.0

New fitsadC-class for fitting abundance data pooled in abundance classe (e.g. coverage data for plants). Methods for fitting, ploting, etc adapted from fitsad-methods.
New coverpred-class for values predicted from models fitted to abundance classes with fitsadC
Function trueLL created to calculate likelihoods from datas in classes intervals.
New dataset with abundance classes addedd (grasslands)
Added a section in intro vignette about fitting sads to abundance classes models.
Small bug in rsads corrected
rpower now calls rpldis from poweRlaw package (way faster)

fixed bug that does not allow zero values in non-truncated poilog, geom, nbinom
fix: diagnostic octav plot Plot #1 returned by plot methods for fitsad and fitrad methods had a truncated bar for the first octave.
sads-package.Rd updated to be syncronized with package metadata
rsads now allows a numeric vector in argument 'sads', to define an arbitrary community to be sampled

new functions for density, distribution, quantile and random generators function for the Pueyo's powerbend distribution
several new functionalities for random sad generation (rsad)
now providing random generator functions for all distributions in the package (such as rls, rmzsm, rzipf, etc)
octav is now a S4 method, and octav plots have a new argument "mid=TRUE"
new function and class for likelregions; also changed the spline method for plotting in plotprofmle
better optimization and vectorization of several discrete quantile and distribution functions
fixed the support of Zipf, Zipf-Mandelbrot and geometric series to not include zero abundances or zero-th rank
added He & Tang's formula for initial parameter estimate of the geometric series
more robust checking for invalid data in the fitting functions
fixed bugs in octav, octavpred and dmzsm

octavpred now accepts a 'preston' argument (as does 'octav')
fixes a bug in fitvolkov under Windows
added a friendlier error message when the octavs provided in octavpred do not cover the data
deprecated the slot "distr" on fitsad/fitrad objects. Now users should use the 'distr' function (see ?distr)
fixed signature errors on several methods dealing with the 'trunc' parameter
now providing the coefficients, fitted, fitted.values, residuals methods on fitsad/fitrad methods
providing a summary method for fitsad/fitrad classes that allows for fixed parameters (such as produced by fitls, fitvolkov, etc)

fitgeom, fitpoilog and fitnbinom now can get argument trunc=NULL to avoid zero-truncation (the default)
fitgeom uses default optimization method from mle2 instead of Brent's method, to avoid some overflow errors for large datasets (e.g. moths)
dmzsm and dvolkov now returns zero for any abundance larger than the community size J. Accordingly, pzsm and pvolkov now return 1 for any q>J and lower.tail=TRUE and zero for lower.tail=FALSE.
fixes important bugs in AICc

Reworked the Volkov distribution for performance.
Reworked density, quantile and distribution functions for more consistent behaviour, error handling and large performance gains.
Added some missing functions for mzsm, poig and poix families.
New function *updatesad* to update a fitsad with better fit from profile.
*radpred* now uses exact solutions for extreme data points.
Reimplemented the *AIC* and *AICc* functions for better integration with fitsad and fitrad classes.
Removed trueLL method to an experimental branch
Improved grammar and clearer text in some manual pages and vignette.
Improved starting values for several distributions.
Replaced table(cut(x)) for hist for improved performance.
octav and rad classes now have validation functions and are more consistent.
More informative calls in *show* and *summary*.
Reduced code redundancy and improved readability.
Changed some "Depends" and "Imports" to make the package more light-weight, but still reliable
Fixed the Broken-Stick family to behave like a Discrete distribution.
Small but importante fixes in *octavpred*.
Workarounds for bugs and issues of the bbmle package.