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RNHANES

R package for accessing and analyzing CDC NHANES data

https://github.com/silentspringinstitute/rnhanes

Science Score: 23.0%

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Keywords

cran nhanes publichealth rstats
Last synced: 11 months ago · JSON representation

Repository

R package for accessing and analyzing CDC NHANES data

Basic Info
  • Host: GitHub
  • Owner: SilentSpringInstitute
  • License: apache-2.0
  • Language: R
  • Default Branch: master
  • Size: 281 KB
Statistics
  • Stars: 87
  • Watchers: 5
  • Forks: 13
  • Open Issues: 1
  • Releases: 2
Topics
cran nhanes publichealth rstats
Created over 10 years ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog License

README.md

RNHANES

RNHANES is an R package for accessing and analyzing CDC NHANES (National Health and Nutrition Examination Survey) data that was developed by Silent Spring Institute.

CRAN Version Build Status codecov.io downloads per month grand total downloads

Demo of RNHANES

Features

  • Download and search NHANES variable and data file lists
  • Download and cache NHANES data files
  • Compute survey-weighted detection frequencies, quantiles, and geometric means
  • Plot weighted histograms

Install

You can install the latest stable version from github:

```R library(devtools)

install_github("silentspringinstitute/RNHANES") ```

The version through CRAN is older and will pull errors when working with more recent NHANES cycles: R install.packages("RNHANES")

Documentation

You can browse the package's documentation on the RNHANES website: http://silentspringinstitute.github.io/RNHANES/.

Examples

```R

library(RNHANES)

Download environmental phenols & parabens data from the 2011-2012 survey cycle

dat <- nhanesloaddata("EPH", "2011-2012")

Download the same data, but this time include demographics data (which includes sample weights)

dat <- nhanesloaddata("EPH", "2011-2012", demographics = TRUE)

Find the sample size for urinary triclosan

nhanessamplesize(dat, column = "URXTRS", commentcolumn = "URDTRSLC", weightscolumn = "WTSA2YR")

Compute the detection frequency of urinary triclosan

nhanesdetectionfrequency(dat, column = "URXTRS", commentcolumn = "URDTRSLC", weightscolumn = "WTSA2YR")

Compute 95th and 99th quantiles for urinary triclosan

nhanesquantile(dat, column = "URXTRS", commentcolumn = "URDTRSLC", weights_column = "WTSA2YR", quantiles = c(0.95, 0.99))

Compute geometric mean of urinary triclosan

nhanesgeometricmean(dat, column = "URXTRS", weights_column = "WTSA2YR")

Plot a histogram of the urinary triclosan distribution

nhaneshist(dat, column = "URXTRS", commentcolumn = "URDTRSLC", weights_column = "WTSA2YR")

Build a survey design object for use with survey package

design <- nhanessurveydesign(dat, weights_column = "WTSA2YR")

```

Geometric mean

An easy way to calculate geometric means is now built into RNHANES via the nhanes_geometric_mean function, but the version in CRAN hasn't been updated yet. If you are using the CRAN version, however, you can compute them by taking the arithmetic mean of a log-transformed variable and exponentiating. Here's an example: ```R library(survey) library(RNHANES) library(tidyverse)

dat <- nhanesloaddata("EPHPP_H", "2013-2014", demographics = TRUE) %>% filter(!is.na(URXBPH))

des <- nhanessurveydesign(dat, "WTSB2YR")

logmean <- svymean(~log(URXBPH), des, na.rm = TRUE)

Geometric mean lower 95% confidence interval

exp(logmean[1] - 1.96 * sqrt(attr(logmean, "var")))

Geometric mean

exp(logmean)[1]

Geometric mean upper 95% confidence interval

exp(logmean[1] + 1.96 * sqrt(attr(logmean, "var"))) ```

Correlations

I recommend using the svycor function from the jtools package to compute survey-weighted Pearson correlations between NHANES variables:

```R library(RNHANES) library(tidyverse) library(jtools)

Download PAH dataset

nhanesdat <- nhanesloaddata("PAHH", "2013-2014", demographics = TRUE)

Build the survey design object

des <- nhanessurveydesign(nhanes_dat)

svycor(~log(URXP01) + log(URXP04) + log(URXP06) + log(URXP10), design = des, na.rm = TRUE)

```

Acknowledgements

Thanks to the following people for contributing pull requests: - Xiaosong Zhang xiaosongz - John McGuigan jrm5100

Owner

  • Name: Silent Spring Institute
  • Login: SilentSpringInstitute
  • Kind: organization
  • Email: info@silentspring.org
  • Location: Newton, MA

Silent Spring Institute researches the environment and women’s health, with a focus on breast cancer prevention.

GitHub Events

Total
  • Issues event: 3
  • Watch event: 22
  • Delete event: 2
  • Issue comment event: 1
  • Push event: 8
  • Fork event: 3
  • Create event: 1
Last Year
  • Issues event: 3
  • Watch event: 22
  • Delete event: 2
  • Issue comment event: 1
  • Push event: 8
  • Fork event: 3
  • Create event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 220
  • Total Committers: 4
  • Avg Commits per committer: 55.0
  • Development Distribution Score (DDS): 0.032
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Herb Susmann h****0@g****m 213
John McGuigan j****0@p****u 4
Xiaosong Zhang z****i@g****m 2
Herb Susmann h****b@H****l 1
Committer Domains (Top 20 + Academic)
psu.edu: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 14
  • Total pull requests: 5
  • Average time to close issues: about 2 years
  • Average time to close pull requests: 6 days
  • Total issue authors: 12
  • Total pull request authors: 3
  • Average comments per issue: 2.43
  • Average comments per pull request: 1.6
  • Merged pull requests: 5
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 2
  • Pull requests: 0
  • Average time to close issues: about 2 months
  • Average time to close pull requests: N/A
  • Issue authors: 2
  • Pull request authors: 0
  • Average comments per issue: 1.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
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Top Authors
Issue Authors
  • jenineharris (2)
  • herbps10 (2)
  • ThomasKraft (1)
  • earlytm (1)
  • yknot (1)
  • royarkaprava (1)
  • Thomas-Richardson (1)
  • rwbaer (1)
  • gerdaya (1)
  • jrm5100 (1)
  • carlyechaney (1)
  • gadeelashashi (1)
Pull Request Authors
  • jrm5100 (2)
  • xiaosongz (2)
  • herbps10 (1)
Top Labels
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Packages

  • Total packages: 1
  • Total downloads:
    • cran 376 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 2
  • Total maintainers: 1
cran.r-project.org: RNHANES

Facilitates Analysis of CDC NHANES Data

  • Versions: 2
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 376 Last month
Rankings
Stargazers count: 6.5%
Forks count: 7.9%
Average: 18.0%
Downloads: 22.9%
Dependent repos count: 23.9%
Dependent packages count: 28.7%
Maintainers (1)
susmann@silentspring.org
Last synced: 12 months ago

Dependencies

DESCRIPTION cran
  • R >= 2.10 depends
  • dplyr * imports
  • foreign * imports
  • methods * imports
  • rvest * imports
  • survey * imports
  • xml2 * imports
  • knitr * suggests
  • rmarkdown * suggests
  • testthat * suggests