Supplement 1. Matlab code for phylogenetic linear mixed models (PLMMs).

2016-08-10T03:18:11Z (GMT) by Nicole E. Rafferty Anthony R. Ives
<h2>File List</h2><div> <p><a href="bipartitePLMM.m">bipartitePLMM.m</a> (MD5: 1faa3ddc7f0b798584516c24a25f0910)</p> <p><a href="LMM_ML_funct.m">LMM_ML_funct.m</a> (MD5: b349b7e49bad43c44c712d6f95b25223)</p> <p><a href="LMM_REML_funct.m">LMM_REML_funct.m</a> (MD5: 50543ce9f7389cfaf48de292576add19)</p> <p><a href="Example_bipartitePLMM_11Apr13.m">Example_bipartitePLMM_11Apr13.m</a> (MD5: efb0763a133c4320794b326724d16f94)</p> <p><a href="anneal.m">anneal.m</a> (MD5: 70672ad1d98fcf004cea433bbcbc214d)</p> <p><a href="insectVforMatlab_7Apr11.txt">insectVforMatlab_7Apr11.txt</a> (MD5: 79c98da8147d38241d9405d17605b8da)</p> <p><a href="plantVforMatlab_14Apr11.txt">plantVforMatlab_14Apr11.txt</a> (MD5: 70aad149b8a565dc21753a5d23ef97fb)</p> </div><h2>Description</h2><div> <p>bipartitePLMM.m – This function is the general workhorse for bipartite PLMMs. It can be configured to perform the analyses of both equations 2 and 3 in the main text.</p> <p>LMM_ML_funct.m – This is a dependency program for bipartitePLMM.m that computes the likelihood function.</p> <p>LMM_REML_funct.m –  This is a dependency program for bipartitePLMM.m that computes the restricted likelihood function.</p> <p>Example_bipartitePLMM_11Apr13.m – This function runs bipartitePLMM.m for the simulations used to produce figures 2 and 3 in the main text.</p> <p>anneal.m – This is a dependency program for bipartitePLMM.m that performs simulated annealing. It was written by Joachim Vandekerckhove and is publicly available at http://www.mathworks.com/matlabcentral/fileexchange/authors/23107.</p> <p>insectVforMatlab_7Apr11.txt – File giving the phylogenetic covariance matrix for insects used in the analyses.</p> <p>plantVforMatlab_14Apr11.txt – File giving the phylogenetic covariance matrix for plants used in the analyses.</p> </div>