eHDPrep
Quality Control and Semantic Enrichment of Datasets
A tool for the preparation and enrichment of health datasets for analysis (Toner et al. (2023)
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"