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I am working with several large databases (e.g. PISA and NAEP) that use a complex survey design with replicate weights and multiple plausible values. I can address the former using the survey package. However, does there exist an R package/function to analyze the latter?
For reference, I have found this article to provide a good overview of the issue: http://www.ierinstitute.org/fileadmin/Documents/IERI_Monograph/IERI_Monograph_Volume_02_Chapter_01.pdf
I’m not sure how the general idea of ‘plausible values’ differs from using multiple imputation to generate several sets of imputed values (such as the the Amelia package does). But Thomas Lumley’s mitools package can be used to combine the various sets of imputed values, and it might be the case that it can be used to combine your sets of plausible values to obtain the ‘correct’ standard errors of the estimates.