R. Ives, Anthony R. Helmus, Matthew Supplement 1. Matlab computer code for PGLMM estimation and data simulation. <h2>File List</h2><blockquote> <p><a href="PGLMM_funct.m">PGLMM_funct.m</a><br><br> <a href="PGLMM_REML_funct.m">PGLMM_REML_funct.m</a><br><br> <a href="PGLMM_REML_tozero_funct.m">PGLMM_REML_tozero_funct.m</a><br><br> <a href="PGLMM_nosparse_funct.m">PGLMM_nosparse_funct.m</a><br><br> <a href="PGLMM_REML_nosparse_funct.m">PGLMM_REML_nosparse_funct.m</a><br><br> <a href="PGLMM_REML_tozero_nosparse_funct.m">PGLMM_REML_tozero_nosparse_funct.m</a><br><br> <a href="fminsearchNoMsg.m">fminsearchNoMsg.m</a><br><br> <a href="PGLMM_model_simulations.m">PGLMM_model_simulations.m</a></p> </blockquote> <p>All files at once</p> <blockquote> <p><a href="PGLMM.zip">PGLMM.zip</a></p> </blockquote><h2>Description</h2><blockquote> <p>The matlab function PGLMM_funct.m performs our implementation of PGLMM estimation.  This function calls PGLMM_REML_funct.m and PGLMM_REML_tozero_funct.m.  All three of these programs have versions in which sparse matrices are not used (PGLMM_nosparse_funct.m, PGLMM_REML_nosparse_funct.m, and PGLMM_REML_tozero_nosparse_funct.m); these versions run faster when matrices have few zeros, as in the case of model II in the article.   The program fminsearchNoMsg.m is a version of fminsearch.m that does not print warning messages.  The program PGLMM_model_simulations.m simulates data sets used for models I-V in the text and estimates parameters from the corresponding PGLMMs with a call to PGLMM_funct.m.</p> </blockquote> generalized linear models, GLMM;phylogenetic diversity;trait-based community assembly;environmental gradient;ecophylogenetics;trait variation;phylogenetic community structure;null model;phylogenetic signal;Environmental Science;Ecology 2016-08-10
    https://wiley.figshare.com/articles/dataset/Supplement_1_Matlab_computer_code_for_PGLMM_estimation_and_data_simulation_/3567789
10.6084/m9.figshare.3567789.v1