Data from: Joined at the hip: linked characters and the problem of missing data in studies of disparity

Paleontological investigations into morphological diversity, or disparity, are often confronted with large amounts of missing data. We illustrate how missing discrete data effects disparity using a novel simulation for removing data based on parameters from published datasets that contain both extinct and extant taxa. We develop an algorithm that assesses the distribution of missing characters in extinct taxa, and simulates data loss by applying that distribution to extant taxa. We term this technique 'linkage'. We compare differences in disparity metrics and ordination spaces produced by linkage and random character removal. When we incorporated linkage among characters, disparity metrics declined and ordination spaces shrank at a slower rate with increasing missing data, indicating that correlations among characters govern the sensitivity of disparity analysis. We also present and test a new disparity method that uses the linkage algorithm to correct for the bias caused by missing data. We equalized proportions of missing data among time bins before calculating disparity, and found that estimates of disparity changed when missing data were taken into account. By removing the bias of missing data, we can gain new insights into the morphological evolution of organisms and highlight the detrimental effects of missing data on disparity analysis.AnalyzeDataContains the functions to run the correction factor and data removal scripts.CorrectionFunctions.SourceThe source file read by AnalyzeData that contains all the functions for calculating the correction factor.Ordination-Disparity.SourceThe source file read by AnalyzeData that contains all the functions for calculating the ordination spaces and disparity analysis following data removal.Luo2007ExampleAn example data file to use with the correction factor script. Data from Luo et al. 2007.PCOMatrixExampleAn example PCO data file that the correction factor outputs. To be used with the t-test function.LuoMatrixExtantExample extant dataset used in the data removal component of the study.LuoMatrixExtinctExample extinct dataset used in the linkage data removal component of the study.LuoMatrixExtinctRandomExample extinct dataset used in the random data removal component of the study.PCO_AllDifferences between original and 'data removed' ordination spaces for all taxa datasets.Linkage_AllDisparity metric outputs following linkage data removal for all taxa datasets.Random_AllDisparity metric outputs following random data removal for all taxa datasets.Disparity_TTestT-test results for mammals and pterosaurs for all disparity metrics. The test examines disparity differences between adjacent time bins.FunctionDocumentationInstructions on how to use the R scripts. Contains detailed information on each function used by correction factor