coenocliner 0.2-4

• Fixes due to deprecations in testthat

• Updated some of the package infrastructure to be more modern

coenocliner 0.2-3

• Fix an issue causing vignette compiling to fail due to an update to the LaTeX package hyperref. Reported by: Brian Ripley.

coenocliner 0.2-2

• NegBin() and ZINB() incorrectly specified the gamma part of the distribution. The shape argument to rgamma() should have been 1/alpha where alpha was used previously.

  Also clarified the parameterisation of the negative binomial used by NegBin() and ZINB as the NB2 version.

• NegBin() and ZINB() allow for vector alpha inputs. #25

coenocliner 0.2-1

• Minor package update to fix issues under R CMD check in the development version of R.

coenocliner 0.2-0

• Jari Oksanen is now listed as a contributor to the package having added several new stochastic distributions.

• The object returned by coenocline() now has S3 class "coenocline" and inherits from the "matrix" class.

• A print() method has been added for coenocline() which displays some summary information and the first n lines of the simulated counts. The print() method uses a new internal function modelled on the way dplyr prints data frames.

• A stack() method for coenocline() was added. This makes it much easier to reshape the simulated count data into a format suitable for use with ggplot or lattice graphics, or R’s modelling functions.

• An enhanced plot() method for coenocline() objects is provided, which can draw 1-d plots of single gradient simulations.

• A persp() method is now provided which can produced 3-d perspective plots of simulations with 2 gradients.

• Two new stochastic distributions were added by Jari Oksanen

  • Zero-inflated Binomial
  • Zero-inflated Beta-binomial

• A new extractor function is provided, locations(), which extracts the gradient locations at which counts were simulated.

Bug fixes

• Jari Oksanen noticed an annoying but important bug in the 2D Beta response function; the gamma parameter for the second gradient was being ignored, and the value of gamma for the first gradient was used instead.

coenocliner 0.1-0

• An R package for coenocline simulation; generating simulated species abundance or occurrence data along one or two gradients

• First public release of coenocliner on CRAN

• Species response can be parameterised using either the classic Gaussian response model or the generalise beta response model

• Random count or occurrence data can be simulated from species responses using random draws from a Poisson, Negative Binomial, Binomial, Beta-binomial, ZIP, ZINB, or Bernoulli distribution with the parameterised response curve taken as the mean or expectation of the distribution to draw from

• The main user-facing function is coenocline(). See ?coenocliner and ?coenocline for further details and examples of usage

• A basic overview and introductory tutorial for coenocliner is available. Run browseVignettes("coenocliner") in R to access the PDF, R code and sources.