10.6084/m9.figshare.3557655.v1 Nicole E. Rafferty Nicole E. Rafferty Anthony R. Ives Anthony R. Ives Supplement 1. Matlab code for phylogenetic linear mixed models (PLMMs). Wiley 2016 climate change plant–pollinator interactions phenology interaction network linear mixed models phylogenetic signal Environmental Science Ecology 2016-08-10 03:18:11 Dataset https://wiley.figshare.com/articles/dataset/Supplement_1_Matlab_code_for_phylogenetic_linear_mixed_models_PLMMs_/3557655 <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>