daijiang/Plant_Co-occurrence_Patterns — pull request #1 by davharris (2014-11-20 22:51:45+00:00)
Title: add data-generating parameters

The attached file includes the "true" parameters used to generate the data set.

The conditional occurrence probability for species `i` is

`y[,i] = b[i] + x %*% w[,i] + y %*% l[,i]`

where

* `b` is a vector of intercept terms
* `x` is the environmental data matrix
* `w` is the matrix of species responses to the environment
* `y` is the presence-absence matrix
* `l` is a matrix of species' direct pairwise interaction strengths.

As I mentioned on Twitter, all the `l` coefficients are negative, i.e. there is no mutualism or facilitation in this data set.