https://github.com/annakrystalli/metadatar
Tools for creating metadata files for reproducible research.
https://github.com/annakrystalli/metadatar
Last synced: 4 days ago
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Tools for creating metadata files for reproducible research.
- Host: GitHub
- URL: https://github.com/annakrystalli/metadatar
- Owner: annakrystalli
- License: other
- Created: 2018-04-27T10:16:18.000Z (almost 7 years ago)
- Default Branch: master
- Last Pushed: 2019-03-26T14:43:41.000Z (about 6 years ago)
- Last Synced: 2025-04-11T00:55:19.190Z (4 days ago)
- Language: R
- Size: 33.2 KB
- Stars: 8
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.Rmd
- Contributing: .github/CONTRIBUTING.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
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README
---
output: github_document
---
```{r setup, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# metadatar
[](https://travis-ci.org/annakrystalli/metadatar) [](https://www.tidyverse.org/lifecycle/#experimental)
The goal of metadatar is to help produce minimum metadata files to document datasets in simple formats that can form building blocks of more complex metadata formats (eg. EML, rdf).
## Installation
You can install the developent version of metadatar from GitHub with:
``` r
#install.packages("devtools")
devtools::install_github("annakrystalli/metadatar")
```
## Example
This is a basic example which shows you how to create a metadata table for the [**gapminder**](https://github.com/jennybc/gapminder) dataset
```{r example}
library(gapminder)
library(metadatar)
str(gapminder)
```
```{r}
meta_shell <- mt_create_meta_shell(gapminder)
knitr::kable(meta_shell)
```
I've focused on recognized column headers to make it easier to create an EML object down the line and on the core columns required but additional ones can be added.
### Attributes associated with all variables:
- attributeName (required, free text field)
- attributeDefinition (required, free text field)
- columnClasses (required, `"numeric"`, `"character"`, `"factor"`, `"ordered"`,
or `"Date"`, case sensitive)
### `columnClasses` dependant attributes
- For `numeric` (ratio or interval) data:
- unit (required, see [eml-unitTypeDefinitions](https://knb.ecoinformatics.org/#external//emlparser/docs/eml-2.1.1/./eml-unitTypeDefinitions.html) and [working with units](https://github.com/ropensci/EML/blob/master/vignettes/working-with-units.Rmd))
- For `character` (textDomain) data:
- definition (required)
- For `dateTime` data:
- formatString (required)
e.g for date `11-03-2001` formatString would be `"DD-MM-YYYY"`
- I use the columns `code` and `levels` to store information on factors. I use `";"` to separate code and level descriptions. These can be extracted by `metadatar` function `mt_extract_attr_factors()` later on.
## Complete metadata table
```{r, message=FALSE, warning=FALSE}
meta_df <- readr::read_csv(system.file("extdata", "gapminder_meta.csv", package="metadatar"))
```
```{r}
knitr::kable(meta_df)
```
## Extracting factors
```{r}
mt_extract_factors_tbl(meta_df)
```
## Data visualisation utilities
Create more descriptive variable labels for plot axes/titles or tables
```{r}
mt_label(meta_df, var = "gdpPercap")
```
***
Please note that this project is released with a [Contributor Code of Conduct](CODE_OF_CONDUCT.md).
By participating in this project you agree to abide by its terms.