README.md

In annakrystalli/metadatar: Tools for creating metadata files for reproducible research

metadatar

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:

#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 dataset

library(gapminder)
library(metadatar)
str(gapminder)
#> Classes 'tbl_df', 'tbl' and 'data.frame':    1704 obs. of  6 variables:
#>  $ country  : Factor w/ 142 levels "Afghanistan",..: 1 1 1 1 1 1 1 1 1 1 ...
#>  $ continent: Factor w/ 5 levels "Africa","Americas",..: 3 3 3 3 3 3 3 3 3 3 ...
#>  $ year     : int  1952 1957 1962 1967 1972 1977 1982 1987 1992 1997 ...
#>  $ lifeExp  : num  28.8 30.3 32 34 36.1 ...
#>  $ pop      : int  8425333 9240934 10267083 11537966 13079460 14880372 12881816 13867957 16317921 22227415 ...
#>  $ gdpPercap: num  779 821 853 836 740 ...

meta_shell <- mt_create_meta_shell(gapminder)
knitr::kable(meta_shell)

| attributeName | attributeDefinition | columnClasses | numberType | unit | minimum | maximum | formatString | definition | code | levels | | :------------ | :------------------ | :------------ | :--------- | :--- | :------ | :------ | :----------- | :--------- | :--- | :----- | | country | NA | factor | NA | NA | NA | NA | NA | NA | NA | NA | | continent | NA | factor | NA | NA | NA | NA | NA | NA | NA | NA | | year | NA | numeric | NA | NA | NA | NA | NA | NA | NA | NA | | lifeExp | NA | numeric | NA | NA | NA | NA | NA | NA | NA | NA | | pop | NA | numeric | NA | NA | NA | NA | NA | NA | NA | NA | | gdpPercap | NA | numeric | NA | NA | NA | NA | NA | NA | NA | NA |

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 and working with units)
• 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

meta_df <- readr::read_csv(system.file("extdata", "gapminder_meta.csv", package="metadatar"))

knitr::kable(meta_df)

| attributeName | attributeDefinition | columnClasses | numberType | unit | minimum | maximum | formatString | definition | code | levels | | :------------ | :-------------------------------- | :------------ | :--------- | :-------------------- | ------: | ------: | :----------- | :--------- | :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | | country | Country | factor | NA | NA | NA | NA | NA | NA | Afghanistan;Albania;Algeria;Angola;Argentina;Australia;Austria;Bahrain;Bangladesh;Belgium;Benin;Bolivia;Bosnia and Herzegovina;Botswana;Brazil;Bulgaria;Burkina Faso;Burundi;Cambodia;Cameroon;Canada;Central African Republic;Chad;Chile;China;Colombia;Comoros;Congo, Dem. Rep.;Congo, Rep.;Costa Rica;Cote d’Ivoire;Croatia;Cuba;Czech Republic;Denmark;Djibouti;Dominican Republic;Ecuador;Egypt;El Salvador;Equatorial Guinea;Eritrea;Ethiopia;Finland;France;Gabon;Gambia;Germany;Ghana;Greece;Guatemala;Guinea;Guinea-Bissau;Haiti;Honduras;Hong Kong, China;Hungary;Iceland;India;Indonesia;Iran;Iraq;Ireland;Israel;Italy;Jamaica;Japan;Jordan;Kenya;Korea, Dem. Rep.;Korea, Rep.;Kuwait;Lebanon;Lesotho;Liberia;Libya;Madagascar;Malawi;Malaysia;Mali;Mauritania;Mauritius;Mexico;Mongolia;Montenegro;Morocco;Mozambique;Myanmar;Namibia;Nepal;Netherlands;New Zealand;Nicaragua;Niger;Nigeria;Norway;Oman;Pakistan;Panama;Paraguay;Peru;Philippines;Poland;Portugal;Puerto Rico;Reunion;Romania;Rwanda;Sao Tome and Principe;Saudi Arabia;Senegal;Serbia;Sierra Leone;Singapore;Slovak Republic;Slovenia;Somalia;South Africa;Spain;Sri Lanka;Sudan;Swaziland;Sweden;Switzerland;Syria;Taiwan;Tanzania;Thailand;Togo;Trinidad and Tobago;Tunisia;Turkey;Uganda;United Kingdom;United States;Uruguay;Venezuela;Vietnam;West Bank and Gaza;Yemen, Rep.;Zambia;Zimbabwe | Afghanistan;Albania;Algeria;Angola;Argentina;Australia;Austria;Bahrain;Bangladesh;Belgium;Benin;Bolivia;Bosnia and Herzegovina;Botswana;Brazil;Bulgaria;Burkina Faso;Burundi;Cambodia;Cameroon;Canada;Central African Republic;Chad;Chile;China;Colombia;Comoros;Congo, Dem. Rep.;Congo, Rep.;Costa Rica;Cote d’Ivoire;Croatia;Cuba;Czech Republic;Denmark;Djibouti;Dominican Republic;Ecuador;Egypt;El Salvador;Equatorial Guinea;Eritrea;Ethiopia;Finland;France;Gabon;Gambia;Germany;Ghana;Greece;Guatemala;Guinea;Guinea-Bissau;Haiti;Honduras;Hong Kong, China;Hungary;Iceland;India;Indonesia;Iran;Iraq;Ireland;Israel;Italy;Jamaica;Japan;Jordan;Kenya;Korea, Dem. Rep.;Korea, Rep.;Kuwait;Lebanon;Lesotho;Liberia;Libya;Madagascar;Malawi;Malaysia;Mali;Mauritania;Mauritius;Mexico;Mongolia;Montenegro;Morocco;Mozambique;Myanmar;Namibia;Nepal;Netherlands;New Zealand;Nicaragua;Niger;Nigeria;Norway;Oman;Pakistan;Panama;Paraguay;Peru;Philippines;Poland;Portugal;Puerto Rico;Reunion;Romania;Rwanda;Sao Tome and Principe;Saudi Arabia;Senegal;Serbia;Sierra Leone;Singapore;Slovak Republic;Slovenia;Somalia;South Africa;Spain;Sri Lanka;Sudan;Swaziland;Sweden;Switzerland;Syria;Taiwan;Tanzania;Thailand;Togo;Trinidad and Tobago;Tunisia;Turkey;Uganda;United Kingdom;United States;Uruguay;Venezuela;Vietnam;West Bank and Gaza;Yemen, Rep.;Zambia;Zimbabwe | | continent | Continent | factor | NA | NA | NA | NA | NA | NA | Africa;Americas;Asia;Europe;Oceania | Africa;Americas;Asia;Europe;Oceania | | year | Year | numeric | interval | NA | 1952 | 2007 | NA | NA | NA | NA | | lifeExp | Life Expectancy | numeric | ratio | NA | 0 | NA | NA | NA | NA | NA | | pop | Population | numeric | ratio | NA | 0 | NA | NA | NA | NA | NA | | gdpPercap | Per capita Gross Domestic Product | numeric | ratio | International Dollars | NA | NA | NA | NA | NA | NA |

Extracting factors

mt_extract_factors_tbl(meta_df)
#> # A tibble: 147 x 3
#>    attributeName code        definition 
#>    <fct>         <fct>       <fct>      
#>  1 country       Afghanistan Afghanistan
#>  2 country       Albania     Albania    
#>  3 country       Algeria     Algeria    
#>  4 country       Angola      Angola     
#>  5 country       Argentina   Argentina  
#>  6 country       Australia   Australia  
#>  7 country       Austria     Austria    
#>  8 country       Bahrain     Bahrain    
#>  9 country       Bangladesh  Bangladesh 
#> 10 country       Belgium     Belgium    
#> # … with 137 more rows

Data visualisation utilities

Create more descriptive variable labels for plot axes/titles or tables

mt_label(meta_df, var = "gdpPercap")
#> [1] "Per capita Gross Domestic Product (International Dollars)"

Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.

annakrystalli/metadatar documentation built on May 14, 2019, 6:09 a.m.