Description
Quality Control and Semantic Enrichment of Datasets.
Description
A tool for the preparation and enrichment of health datasets for analysis (Toner et al. (2023) <doi:10.1093/gigascience/giad030>). Provides functionality for assessing data quality and for improving the reliability and machine interpretability of a dataset. 'eHDPrep' also enables semantic enrichment of a dataset where metavariables are discovered from the relationships between input variables determined from user-provided ontologies.
README.md
eHDPrep
The goal of ‘eHDPrep’ is to provide robust quality control and semantic enrichment tools for preparation of health datasets. High-level and low-level functionality are included for general and specialist R users, respectively. A detailed vignette can be accessed using: vignette("Introduction_to_eHDPrep", package = "eHDPrep").
Installation
You can install the released version of ‘eHDPrep’ from CRAN with:
install.packages("eHDPrep")
Or from GitHub with:
install.packages("devtools")
devtools::install_github("overton-group/eHDPrep")
Example
‘eHDPrep’ can prepare health data for analysis with several approaches. For example, standardising strings representing missing values to NA:
library(eHDPrep)
data("example_data")
# original values in t_stage variable
unique(example_data$t_stage)
#> [1] "T3a" "T3b" "T1" "T4" "T2" "equivocal"
# predefined value "equivocal" is removed
unique(eHDPrep::strings_to_NA(example_data, strings_to_replace = "equivocal")$t_stage)
#> [1] "T3a" "T3b" "T1" "T4" "T2" NA
System Requirements
Some additional system dependencies are required for ‘eHDPrep’. These are detailed below:
Ubuntu
remotes::system_requirements(".", os = "ubuntu", os_release = "18.04")
#> [1] "apt-get install -y libicu-dev"
#> [2] "apt-get install -y pandoc"
#> [3] "apt-get install -y make"
#> [4] "apt-get install -y libcurl4-openssl-dev"
#> [5] "apt-get install -y libssl-dev"
#> [6] "apt-get install -y libxml2-dev"
#> [7] "apt-get install -y libfontconfig1-dev"
#> [8] "apt-get install -y libfreetype6-dev"
#> [9] "apt-get install -y libpng-dev"
#> [10] "apt-get install -y imagemagick"
#> [11] "apt-get install -y libmagick++-dev"
#> [12] "apt-get install -y gsfonts"
#> [13] "apt-get install -y libglpk-dev"
#> [14] "apt-get install -y libgmp3-dev"
remotes::system_requirements(".", os = "ubuntu", os_release = "20.04")
#> [1] "apt-get install -y libicu-dev"
#> [2] "apt-get install -y pandoc"
#> [3] "apt-get install -y make"
#> [4] "apt-get install -y libcurl4-openssl-dev"
#> [5] "apt-get install -y libssl-dev"
#> [6] "apt-get install -y libxml2-dev"
#> [7] "apt-get install -y libfontconfig1-dev"
#> [8] "apt-get install -y libfreetype6-dev"
#> [9] "apt-get install -y libpng-dev"
#> [10] "apt-get install -y imagemagick"
#> [11] "apt-get install -y libmagick++-dev"
#> [12] "apt-get install -y gsfonts"
#> [13] "apt-get install -y libglpk-dev"
#> [14] "apt-get install -y libgmp3-dev"
Opensuse
remotes::system_requirements(".", os = "opensuse", os_release = "42.3")
#> [1] "zypper install -y libicu-devel"
#> [2] "zypper install -y pandoc"
#> [3] "zypper install -y make"
#> [4] "zypper install -y libcurl-devel"
#> [5] "zypper install -y libopenssl-devel"
#> [6] "zypper install -y libxml2-devel"
#> [7] "zypper install -y fontconfig-devel"
#> [8] "zypper install -y freetype2-devel"
#> [9] "zypper install -y libpng16-compat-devel"
#> [10] "zypper install -y ImageMagick"
#> [11] "zypper install -y ImageMagick-devel"
#> [12] "zypper install -y libMagick++-devel"
#> [13] "zypper install -y gmp-devel"
CentOS
remotes::system_requirements(".", os = "centos", os_release = "7")
#> [1] "yum install -y epel-release"
#> [2] "yum install -y libicu-devel"
#> [3] "yum install -y pandoc"
#> [4] "yum install -y make"
#> [5] "yum install -y libcurl-devel"
#> [6] "yum install -y openssl-devel"
#> [7] "yum install -y libxml2-devel"
#> [8] "yum install -y fontconfig-devel"
#> [9] "yum install -y freetype-devel"
#> [10] "yum install -y libpng-devel"
#> [11] "yum install -y ImageMagick"
#> [12] "yum install -y ImageMagick-c++-devel"
#> [13] "yum install -y glpk-devel"
#> [14] "yum install -y gmp-devel"
remotes::system_requirements(".", os = "centos", os_release = "8")
#> [1] "dnf install -y dnf-plugins-core"
#> [2] "dnf config-manager --set-enabled powertools"
#> [3] "dnf install -y epel-release"
#> [4] "dnf install -y libicu-devel"
#> [5] "dnf install -y pandoc"
#> [6] "dnf install -y make"
#> [7] "dnf install -y libcurl-devel"
#> [8] "dnf install -y openssl-devel"
#> [9] "dnf install -y libxml2-devel"
#> [10] "dnf install -y fontconfig-devel"
#> [11] "dnf install -y freetype-devel"
#> [12] "dnf install -y libpng-devel"
#> [13] "dnf install -y ImageMagick"
#> [14] "dnf install -y ImageMagick-c++-devel"
#> [15] "dnf install -y glpk-devel"
#> [16] "dnf install -y gmp-devel"
Red Hat
remotes::system_requirements(".", os = "redhat", os_release = "7")
#> [1] "rpm -q epel-release || yum install -y https://dl.fedoraproject.org/pub/epel/epel-release-latest-7.noarch.rpm"
#> [2] "yum install -y libicu-devel"
#> [3] "yum install -y pandoc"
#> [4] "yum install -y make"
#> [5] "yum install -y libcurl-devel"
#> [6] "yum install -y openssl-devel"
#> [7] "yum install -y libxml2-devel"
#> [8] "yum install -y fontconfig-devel"
#> [9] "yum install -y freetype-devel"
#> [10] "yum install -y libpng-devel"
#> [11] "yum install -y ImageMagick"
#> [12] "yum install -y ImageMagick-c++"
#> [13] "yum install -y glpk-devel"
#> [14] "yum install -y gmp-devel"
remotes::system_requirements(".", os = "redhat", os_release = "8")
#> [1] "dnf install -y https://dl.fedoraproject.org/pub/epel/epel-release-latest-8.noarch.rpm"
#> [2] "dnf install -y libicu-devel"
#> [3] "dnf install -y make"
#> [4] "dnf install -y libcurl-devel"
#> [5] "dnf install -y openssl-devel"
#> [6] "dnf install -y libxml2-devel"
#> [7] "dnf install -y fontconfig-devel"
#> [8] "dnf install -y freetype-devel"
#> [9] "dnf install -y libpng-devel"
#> [10] "dnf install -y ImageMagick"
#> [11] "dnf install -y ImageMagick-c++"
#> [12] "dnf install -y glpk-devel"
#> [13] "dnf install -y gmp-devel"