{"id":23,"date":"2024-10-03T18:45:45","date_gmt":"2024-10-03T18:45:45","guid":{"rendered":"https:\/\/wordpress.clarku.edu\/pbergmann\/?page_id=23"},"modified":"2024-10-18T19:01:37","modified_gmt":"2024-10-18T19:01:37","slug":"resources","status":"publish","type":"page","link":"https:\/\/wordpress.clarku.edu\/pbergmann\/resources\/","title":{"rendered":"Resources"},"content":{"rendered":"<p>&nbsp;<\/p>\n<h1 style=\"text-align: left;\"><span style=\"color: #ffffff;\">Bergmann Lab Resources<\/span><\/h1>\n<hr>\n<p><strong>The Evolutionary Functional Morphology lab uses a variety of approaches and techniques. These include equipment and software for collecting data, code that we write in R to do analyses, and various statistical techniques. <\/strong><strong>Below are a series of standard operating procedures (SOPs) that we use to standardize how we do things and ensure data consistency and quality (please obtain in-person training prior to doing these techniques), R code along with <\/strong><strong>citations for analyses we have implemented, and Dr. Bergmann&#8217;s Advanced Biostatistics (Biol 206\/306) labs, covering more standard statistical techniques.<\/strong><\/p>\n<h3><span style=\"color: #ffffff;\"><u>Lab Standard Operating Procedures<\/u><\/span><\/h3>\n<ul>\n<li><strong><span style=\"color: #3810bf; font-size: 18px;\"><a style=\"color: #3810bf;\" href=\"https:\/\/wordpress.clarku.edu\/pbergmann\/wp-content\/uploads\/sites\/885\/2024\/10\/SOP-Animal-Video.pdf\" target=\"_blank\" rel=\"noopener\">Recording High-Speed Video of Animal Behavior<\/a><\/span><\/strong><\/li>\n<li><span style=\"color: #3810bf; font-size: 18px;\"><strong><a style=\"color: #3810bf;\" href=\"https:\/\/wordpress.clarku.edu\/pbergmann\/wp-content\/uploads\/sites\/885\/2024\/10\/SOP-Video-Data.pdf\" target=\"_blank\" rel=\"noopener\">Collecting Locomotor Data from High-Speed Video<\/a><\/strong><\/span><\/li>\n<li><span style=\"color: #3810bf; font-size: 18px;\"><strong><a style=\"color: #3810bf;\" href=\"https:\/\/wordpress.clarku.edu\/pbergmann\/wp-content\/uploads\/sites\/885\/2024\/10\/SOP-Video-Digitizing.pdf\" target=\"_blank\" rel=\"noopener\">Digitizing Points on a High-Speed Video<\/a><\/strong><\/span><\/li>\n<li><span style=\"color: #3810bf; font-size: 18px;\"><strong><a style=\"color: #3810bf;\" href=\"https:\/\/wordpress.clarku.edu\/pbergmann\/wp-content\/uploads\/sites\/885\/2024\/10\/SOP-Spline-Smoothing.pdf\" target=\"_blank\" rel=\"noopener\">Obtaining Instantaneous Velocity and Acceleration Data from a High-Speed Video<\/a><\/strong><\/span><\/li>\n<li><span style=\"color: #3810bf; font-size: 18px;\"><strong><a style=\"color: #3810bf;\" href=\"https:\/\/wordpress.clarku.edu\/pbergmann\/wp-content\/uploads\/sites\/885\/2024\/10\/SOP-Syncing-Cameras.pdf\" target=\"_blank\" rel=\"noopener\">Syncing a High-Speed Video Camera with Other Equipment<\/a><\/strong><\/span><\/li>\n<li><span style=\"color: #3810bf; font-size: 18px;\"><strong><a style=\"color: #3810bf;\" href=\"https:\/\/wordpress.clarku.edu\/pbergmann\/wp-content\/uploads\/sites\/885\/2024\/10\/SOP-Force-Plate.pdf\" target=\"_blank\" rel=\"noopener\">Using a Kistler Force Plate<\/a><\/strong><\/span><\/li>\n<li><span style=\"color: #3810bf; font-size: 18px;\"><strong><a style=\"color: #3810bf;\" href=\"https:\/\/wordpress.clarku.edu\/pbergmann\/wp-content\/uploads\/sites\/885\/2024\/10\/SOP-Force-Transducer.pdf\" target=\"_blank\" rel=\"noopener\">Using a Kistler Force Transducer<\/a><\/strong><\/span><\/li>\n<li><span style=\"color: #3810bf; font-size: 18px;\"><strong><a style=\"color: #3810bf;\" href=\"https:\/\/wordpress.clarku.edu\/pbergmann\/wp-content\/uploads\/sites\/885\/2024\/10\/SOP-Specimen-Preservation.pdf\" target=\"_blank\" rel=\"noopener\">Fixing and Preserving Specimens<\/a><\/strong><\/span><\/li>\n<\/ul>\n<p>&nbsp;<\/p>\n<h3><span style=\"color: #ffffff;\"><u>R code<\/u><\/span><\/h3>\n<table border=\"0\" cellpadding=\"5\">\n<tbody>\n<tr>\n<td>&nbsp;<\/td>\n<td>\n<h4>Description<\/h4>\n<\/td>\n<td>\n<h4>Reference<\/h4>\n<\/td>\n<\/tr>\n<tr>\n<td>\n<ul>\n<li>\n<h4><strong><a style=\"color: #3810bf;\" href=\"https:\/\/wordpress.clarku.edu\/pbergmann\/wp-content\/uploads\/sites\/885\/2024\/10\/RMA_function.txt\" target=\"_blank\" rel=\"noopener\">RMA regression<\/a><\/strong><\/h4>\n<\/li>\n<\/ul>\n<\/td>\n<td><strong>Calculates a reduced major axis regression and its residuals in two ways, and calculates Kolmogorov-Smirnov and Shapiro-Wilks tests for normality on the residuals.<\/strong><\/td>\n<td><strong>Bergman, P.J., Berk, C.P. 2012. The evolution of positive allometry of weaponry in horned lizards (<i>Phrynosoma<\/i>). Evolutionary Biology 39: 311-323.<\/strong><\/td>\n<\/tr>\n<tr>\n<td>\n<ul>\n<li>\n<h4><strong><a style=\"color: #3810bf;\" href=\"https:\/\/wordpress.clarku.edu\/pbergmann\/wp-content\/uploads\/sites\/885\/2024\/10\/function_mantel.txt\" target=\"_blank\" rel=\"noopener\">Mantel test<\/a><\/strong><\/h4>\n<\/li>\n<\/ul>\n<\/td>\n<td><strong>Does a Mantel test to compare two matrices in different ways: You can compare just the lower triangle, the lower triangle and diagonal, or the whole matrix.<\/strong><\/td>\n<td><strong>Bergmann, P.J., McElroy, E.J. 2014. Many-to-many mapping of phenotype to performance: An extension of the F-matrix for studying functional complexity. Evolutionary Biology 41: 546-560.<\/strong><\/td>\n<\/tr>\n<tr>\n<td>\n<ul>\n<li>\n<h4><strong><a style=\"color: #3810bf;\" href=\"https:\/\/wordpress.clarku.edu\/pbergmann\/wp-content\/uploads\/sites\/885\/2024\/10\/function_fmat_MR.txt\" target=\"_blank\" rel=\"noopener\">F-matrix<\/a><\/strong><\/h4>\n<\/li>\n<\/ul>\n<\/td>\n<td><strong>Uses multiple regression to construct an F-matrix and associated statistics and metrics, including the FF<sup>T<\/sup> and F<sup>T<\/sup>F matrices for a data set of multiple phenotypic traits and multiple performance measures.<\/strong><\/td>\n<td><strong>Bergmann, P.J., McElroy, E.J. 2014. Many-to-many mapping of phenotype to performance: An extension of the F-matrix for studying functional complexity. Evolutionary Biology 41: 546-560.<\/strong><\/td>\n<\/tr>\n<tr>\n<td>\n<ul>\n<li>\n<h4><strong><a style=\"color: #3810bf;\" href=\"https:\/\/wordpress.clarku.edu\/pbergmann\/wp-content\/uploads\/sites\/885\/2024\/10\/function_farray_MR.txt\" target=\"_blank\" rel=\"noopener\">F-array<\/a><\/strong><\/h4>\n<\/li>\n<\/ul>\n<\/td>\n<td><strong>Creates an F-array and associated statistics for multiple phenotypic traits, multiple performance measures, and multiple species related by a phylogeny. Uses the Mantel and F-matrix functions.<\/strong><\/td>\n<td><strong>Bergmann, P.J., McElroy, E.J. 2014. Many-to-many mapping of phenotype to performance: An extension of the F-matrix for studying functional complexity. Evolutionary Biology 41: 546-560.<\/strong><\/td>\n<\/tr>\n<tr>\n<td>\n<ul>\n<li>\n<h4><strong><a style=\"color: #3810bf;\" href=\"https:\/\/wordpress.clarku.edu\/pbergmann\/wp-content\/uploads\/sites\/885\/2024\/10\/rand_anova.txt\" target=\"_blank\" rel=\"noopener\">Randomization ANOVA<\/a><\/strong><\/h4>\n<\/li>\n<\/ul>\n<\/td>\n<td><strong>Does a randomization ANOVA of any design that can be handled by the aov function in R with a user-specified number of data randomizations.<\/strong><\/td>\n<td><strong>Mitchell, A., Bergmann, P.J. 2016. Thermal and moisture habitat preferences do not maximize jumping performance in frogs. Functional Ecology 30: 733-742.<\/strong><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p>&nbsp;<\/p>\n<h3><span style=\"color: #ffffff;\"><u>Advanced Biostatistics Labs (Biol 206\/306, Fall 2016)<\/u><\/span><\/h3>\n<ul>\n<li><strong><a style=\"color: #3810bf;\" href=\"https:\/\/wordpress.clarku.edu\/pbergmann\/wp-content\/uploads\/sites\/885\/2024\/10\/Biol206-Lab01-Introduction-to-R.pdf\" target=\"_blank\" rel=\"noopener\">Lab 1<\/a> &#8211; Introduction to R<\/strong><\/li>\n<li><strong><a style=\"color: #3810bf;\" href=\"https:\/\/wordpress.clarku.edu\/pbergmann\/wp-content\/uploads\/sites\/885\/2024\/10\/Biol206-Lab02-Experimental-Design.pdf\" target=\"_blank\" rel=\"noopener\">Lab 2<\/a> &#8211; Experimental Design<\/strong><\/li>\n<li><strong><a style=\"color: #3810bf;\" href=\"https:\/\/wordpress.clarku.edu\/pbergmann\/wp-content\/uploads\/sites\/885\/2024\/10\/Biol206-Lab03-ANOVA.pdf\" target=\"_blank\" rel=\"noopener\">Lab 3<\/a> &#8211; ANOVA<\/strong><\/li>\n<li><strong><a style=\"color: #3810bf;\" href=\"https:\/\/wordpress.clarku.edu\/pbergmann\/wp-content\/uploads\/sites\/885\/2024\/10\/Biol206-Lab04-Bivariate-Regression.pdf\" target=\"_blank\" rel=\"noopener\">Lab 4<\/a> &#8211; OLS versus RMA Regression<\/strong><\/li>\n<li><strong><a style=\"color: #3810bf;\" href=\"https:\/\/wordpress.clarku.edu\/pbergmann\/wp-content\/uploads\/sites\/885\/2024\/10\/Biol206-Lab05-ANCOVA.pdf\" target=\"_blank\" rel=\"noopener\">Lab 5<\/a> &#8211; Multiple Regression and ANCOVA<\/strong><\/li>\n<li><strong><a style=\"color: #3810bf;\" href=\"https:\/\/wordpress.clarku.edu\/pbergmann\/wp-content\/uploads\/sites\/885\/2024\/10\/Biol206-Lab06-MANOVA.pdf\" target=\"_blank\" rel=\"noopener\">Lab 6<\/a> &#8211; MANOVA<\/strong><\/li>\n<li><strong><a style=\"color: #3810bf;\" href=\"https:\/\/wordpress.clarku.edu\/pbergmann\/wp-content\/uploads\/sites\/885\/2024\/10\/Biol206-Lab07-PCA.pdf\" target=\"_blank\" rel=\"noopener\">Lab 7<\/a> &#8211; PCA<\/strong><\/li>\n<li><strong><a style=\"color: #3810bf;\" href=\"https:\/\/wordpress.clarku.edu\/pbergmann\/wp-content\/uploads\/sites\/885\/2024\/10\/Biol206-Lab08-Randomization.pdf\" target=\"_blank\" rel=\"noopener\">Lab 8<\/a> &#8211; Randomization Tests<\/strong><\/li>\n<li><strong><a style=\"color: #3810bf;\" href=\"https:\/\/wordpress.clarku.edu\/pbergmann\/wp-content\/uploads\/sites\/885\/2024\/10\/Biol206-Lab09-Model-Selection.pdf\" target=\"_blank\" rel=\"noopener\">Lab 9<\/a> &#8211; Model Selection Using AIC<\/strong><\/li>\n<li><strong><a style=\"color: #3810bf;\" href=\"https:\/\/wordpress.clarku.edu\/pbergmann\/wp-content\/uploads\/sites\/885\/2024\/10\/Biol206-Lab10-Phylogenetic-Regression.pdf\" target=\"_blank\" rel=\"noopener\">Lab 10<\/a> &#8211; Phylogenetic Correlation and Regression<\/strong><\/li>\n<li><strong><a style=\"color: #3810bf;\" href=\"https:\/\/wordpress.clarku.edu\/pbergmann\/wp-content\/uploads\/sites\/885\/2024\/10\/Biol206-Lab11-Trait-Evolution-Models.pdf\" target=\"_blank\" rel=\"noopener\">Lab 11<\/a> &#8211; Models of Trait Evolution<\/strong><\/li>\n<li><strong><a style=\"color: #3810bf;\" href=\"https:\/\/wordpress.clarku.edu\/pbergmann\/wp-content\/uploads\/sites\/885\/2024\/10\/Biol206-Lab12-Bayesian-Inference.pdf\" target=\"_blank\" rel=\"noopener\">Lab 12<\/a> &#8211; Introduction to Bayesian Inference<\/strong><\/li>\n<\/ul>\n<p>&nbsp;<\/p>\n<p><img loading=\"lazy\" decoding=\"async\" class=\"size-full wp-image-69 alignleft\" src=\"https:\/\/wordpress.clarku.edu\/pbergmann\/wp-content\/uploads\/sites\/885\/2024\/10\/callisaurus-1.jpg\" alt=\"Callisaurus draconoides ready for video recording\" width=\"300\" height=\"200\"><\/p>\n<p><img loading=\"lazy\" decoding=\"async\" class=\"size-medium wp-image-48 alignnone\" src=\"https:\/\/wordpress.clarku.edu\/pbergmann\/wp-content\/uploads\/sites\/885\/2024\/10\/philip_austr-200x300.jpg\" alt=\"Dr. Bergmann using a racetrack\" width=\"200\" height=\"300\" srcset=\"https:\/\/wordpress.clarku.edu\/pbergmann\/wp-content\/uploads\/sites\/885\/2024\/10\/philip_austr-200x300.jpg 200w, https:\/\/wordpress.clarku.edu\/pbergmann\/wp-content\/uploads\/sites\/885\/2024\/10\/philip_austr.jpg 213w\" sizes=\"auto, (max-width: 200px) 100vw, 200px\" \/><img loading=\"lazy\" decoding=\"async\" class=\"size-medium wp-image-49 alignleft\" src=\"https:\/\/wordpress.clarku.edu\/pbergmann\/wp-content\/uploads\/sites\/885\/2024\/10\/xray_148-300x216.jpg\" alt=\"Lizard X-ray\" width=\"300\" height=\"216\" srcset=\"https:\/\/wordpress.clarku.edu\/pbergmann\/wp-content\/uploads\/sites\/885\/2024\/10\/xray_148-300x216.jpg 300w, https:\/\/wordpress.clarku.edu\/pbergmann\/wp-content\/uploads\/sites\/885\/2024\/10\/xray_148.jpg 319w\" sizes=\"auto, (max-width: 300px) 100vw, 300px\" \/><\/p>\n<p>&nbsp;<\/p>\n<h6>&nbsp;<\/h6>\n<h6>&nbsp;<\/h6>\n<h6>&nbsp;<\/h6>\n<h6>&nbsp;<\/h6>\n<h6>&nbsp;<\/h6>\n<h6>&nbsp;<\/h6>\n<h6>\u00a9 2005-2017 Philip J. Bergmann | Updated 1.26.2017<\/h6>\n<p>&nbsp;<\/p>\n<p>&nbsp;<\/p>\n","protected":false},"excerpt":{"rendered":"<p>&nbsp; Bergmann Lab Resources The Evolutionary Functional Morphology lab uses a variety of approaches and techniques. These include equipment and software for collecting data, code that we write in R&hellip;&nbsp;<a href=\"https:\/\/wordpress.clarku.edu\/pbergmann\/resources\/\" rel=\"bookmark\">Read More &raquo;<span class=\"screen-reader-text\">Resources<\/span><\/a><\/p>\n","protected":false},"author":1227,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"neve_meta_sidebar":"","neve_meta_container":"","neve_meta_enable_content_width":"off","neve_meta_content_width":100,"neve_meta_title_alignment":"","neve_meta_author_avatar":"","neve_post_elements_order":"","neve_meta_disable_header":"","neve_meta_disable_footer":"","neve_meta_disable_title":"","ngg_post_thumbnail":0,"footnotes":""},"class_list":["post-23","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/wordpress.clarku.edu\/pbergmann\/wp-json\/wp\/v2\/pages\/23","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/wordpress.clarku.edu\/pbergmann\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/wordpress.clarku.edu\/pbergmann\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/wordpress.clarku.edu\/pbergmann\/wp-json\/wp\/v2\/users\/1227"}],"replies":[{"embeddable":true,"href":"https:\/\/wordpress.clarku.edu\/pbergmann\/wp-json\/wp\/v2\/comments?post=23"}],"version-history":[{"count":0,"href":"https:\/\/wordpress.clarku.edu\/pbergmann\/wp-json\/wp\/v2\/pages\/23\/revisions"}],"wp:attachment":[{"href":"https:\/\/wordpress.clarku.edu\/pbergmann\/wp-json\/wp\/v2\/media?parent=23"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}