-
Notifications
You must be signed in to change notification settings - Fork 1
/
README.Rmd
87 lines (60 loc) · 2.43 KB
/
README.Rmd
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# eHDPrep
<!-- badges: start -->
[![Downloads](https://cranlogs.r-pkg.org/badges/grand-total/eHDPrep)](https://cranlogs.r-pkg.org/badges/grand-total/eHDPrep)
[![CRAN status](https://www.r-pkg.org/badges/version/eHDPrep)](https://cran.r-project.org/package=eHDPrep)
[![R-CMD-check](https://github.com/overton-group/eHDPrep/actions/workflows/r.yml/badge.svg)](https://github.com/overton-group/eHDPrep/actions/workflows/r.yml/badge.svg)
<!-- badges: end -->
The goal of 'eHDPrep' is to provide robust quality control and semantic enrichment tools for preparation of health datasets. High-level and low-level functionality are included for general and specialist 'R' users, respectively. A detailed vignette can be accessed using: `vignette("Introduction_to_eHDPrep", package = "eHDPrep")`.
## Installation
You can install the released version of 'eHDPrep' from [CRAN](https://CRAN.R-project.org) with:
``` r
install.packages("eHDPrep")
```
Or from [GitHub](https://github.com) with:
``` r
install.packages("devtools")
devtools::install_github("overton-group/eHDPrep")
```
## Example
'eHDPrep' can prepare health data for analysis with several approaches. For example, standardising strings representing missing values to `NA`:
```{r example}
library(eHDPrep)
data("example_data")
# original values in t_stage variable
unique(example_data$t_stage)
# predefined value "equivocal" is removed
unique(eHDPrep::strings_to_NA(example_data, strings_to_replace = "equivocal")$t_stage)
```
## System Requirements
Some additional system dependencies are required for 'eHDPrep'. These are detailed below:
### Ubuntu
```{r ubuntu-req}
remotes::system_requirements(".", os = "ubuntu", os_release = "18.04")
remotes::system_requirements(".", os = "ubuntu", os_release = "20.04")
```
### Opensuse
```{r opensuse-req}
remotes::system_requirements(".", os = "opensuse", os_release = "42.3")
```
### CentOS
```{r centos-req}
remotes::system_requirements(".", os = "centos", os_release = "7")
remotes::system_requirements(".", os = "centos", os_release = "8")
```
### Red Hat
```{r redhat-req}
remotes::system_requirements(".", os = "redhat", os_release = "7")
remotes::system_requirements(".", os = "redhat", os_release = "8")
```