phonto

PHONTO - PHenome ONTOlogy for NHANES

This package is designed to work with the Docker container available from https://github.com/ccb-hms/NHANES That container can be obtained by running the code below. Once installed and started users can log in via a web browser to analyze NHANES data using any tools they would like. The data live in a SQL database and can be accessed by a variety of tools. We provide an interface via RStudio and this package works together with the nhanesA package to support a wide variety of analyses. phonto provides a few vignettes and users can familiarize themselves with the Quick Start vignette in order to find out how to interact with the DB. More docs can be found Phonto page

Start Docker

1. Start Docker

Start Docker on Mac or Linux

docker \
    run \
        --rm \
        --platform=linux/amd64 \
        --name nhanes-workbench \
        -v <YOUR LOCAL PATH>:/mnt/ \
        -d \
        -p 8787:8787 \
        -p 2200:22 \
        -p 1433:1433 \
        -e 'CONTAINER_USER_USERNAME=USER' \
        -e 'CONTAINER_USER_PASSWORD=PASSWORD' \
        -e 'ACCEPT_EULA=Y' \
        -e 'SA_PASSWORD=yourStrong(!)Password' \
         hmsccb/nhanes-workbench:version-0.2.0

Start Docker on Windows

docker ^
    run ^
        --rm ^
        --platform=linux/amd64 ^
        --name nhanes-workbench ^
  -v <YOUR LOCAL PATH>:/mnt/ ^
  -p 8787:8787 -p 2200:22 -p 1433:1433 ^
  -e "CONTAINER_USER_USERNAME=USER" ^
  -e "CONTAINER_USER_PASSWORD=PASSWORD" ^
  -e "ACCEPT_EULA=Y" -e "SA_PASSWORD=yourStrong(!)Password" ^
  hmsccb/nhanes-workbench:version-0.2.0

2. Log into Rstudio

Log into RStudio via: http://localhost:8787 and using the username set in the command above. In the above command, the username and password are set as USER and PASSWORD, respectively, but you can modify them if you prefer.

More details about the NHANES Docker.

Installation

You can install the development version of phonto from GitHub with:

# install.packages("devtools")

devtools::install_github("ccb-hms/phonto")

Examples

This is a basic example which shows you how to solve a common problem: Testing to see if I can push to this directory (Teresa)