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All analyses were conducted in R 3.1.0 (R Core Team 2014) using the survey package (Lumley 2012).
Survey adjusted population frequencies and histograms were calculated using the survey package [ 26, 27].
A crude and weighted stratified analysis of HPV prevalence by sex was conducted using the survey package in R, with schools nested within EAs.
We analyzed the data using regression models, with adjustments for the complex survey design involving clustering and stratification; the analyses were performed using the survey package in R (version 2.9.0; The R Foundation for Statisitical Computing, Vienna, Austria).
All statistical analyses were performed using the survey package in the R statistical language to account for the complex sampling design and weights in NHANES 1999 2004 and to obtain appropriate standard errors for all estimates (Lumley 2007).
Statistical analyses were performed using the survey package (Lumley 2004) in R software (version 2.12.1; R Development Core Team 2011) to account for the complex sampling design and weights in NHANES 1988 2008 and to obtain appropriate standard errors for all estimates.
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To account for the complex, stratified, and multistage cluster sampling design, analyses were conducted using the survey packages of Stata (v.12; StataCorp) and R (v.2.11.1; R Foundation) to obtain appropriate estimates and standard errors.
To perform all the statistical analyses we used the survey package (Lumley 2004) in R software (version 2.12.1; R Development Core Team 2011) to account for the complex sampling design and weights of the NHANES and to obtain appropriate standard errors.
Analyses were performed using the survey and mitools packages in R [ 30, 36], and all analyses account for the sample weights, sample design and multiple imputations.
Clustering of piglets within sows was defined using the survey set command of the statistical package (STATA 12), with sows being defined as random effects both in the univariable and multivariable models.
The statistical significance of the observed differences (e.g., are levels of HDL cholesterol more strongly correlated with PBFDXA than with adjusted BMI?) were based on jackknife replicate weights which were calculated using the 'withReplicates' function of the survey package [ 36].
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