Jari Oksanen
Jari Oksanen
This PR provides autoplot and fortify methods for vegan::permustats results. These will eventually replace lattice methods densityplot and qqmath, and provide an alternative ggplot2 graphics for boxplot.
Should it be useful to switch to `shuffleSet(..., control = how(complete = TRUE))` when `nperm` is a high proportion of all permutations or in general when the number of all...
Next **vegan** release after 2.6-6 is scheduled to have changes that can break CRAN packages (discussion #645). This issue monitors breakage and the goal is to fix all these before...
I am planning a new CRAN release of **vegan** in the latter half of August. There are quite a few changes, although nothing very dramatic. For most users the main...
We have had reference output for vegan examples for a decade. In principle, it is useful as it can spot unwanted changes and regression in the results of functions. However,...
All that needs to be said was said in https://github.com/vegandevs/vegan3d/issues/7. Just be aware.
`permatswap` and `permatfull` provided the first quantitative null models in **vegan** and they were used in simulation in `adipart` and `multipart`. Later, the quantitative null models were transfrerred to `make.commsim`...
Function `designdist` is currently faster than `vegdist`. With `"binary"` and `"quadratic"` terms it is much faster than `vegdist`. With `"minimum"` terms (used by most dissimilarity functions in `vegdist`) it used...
`qqmath` function accepts argument `distribution` to find the expected quantiles in the Q-Q plot. The default is to plot permutations against Gaussian distribution (`qnorm`). However, this is a bad choice...
If _x_ or _y_ is zero, the expression for information distance simplifies to 0 * log(0) which is NaN, and if there is any NaN, the sum is NaN. Therefore...