README.md

In jknowles/metaframe: Metadata for Dataframes

An R package to extend the functionality of data.frame and data.frame-like objects with metadata and codebook annotations.

Introduction

Metadata is not easily accessed and used in R and this is a big challenge to the efforts to make data analysis more automated and more reproducible. This package seeks to create a simple object-type for easily storing, updating, and outputting metadata during the course of an analysis project. This way the codebook can be baked right into the code.

Overview

metaframe is organized around a meta.data object. This is an S4 object that stores lists of attributes for a data set. The package will also contain a small set of basic functions to package a data.frame and a meta.data object together, while retaining the functionality of a data.frame with some additional enhancements.

Storing Metadata in R

metaframe organizes your meta.data into a few categories -- some of which it can helpfully auto-complete for you.

Example

Consider that we wish to document the airquality dataset built into R. After loading the dataset, you can call the document function to create a new object that contains the data, along with an attached meta.data attribute.

library(metaframe)
#> Loading required package: rmarkdown
#> Loading required package: knitr
doco <- document(airquality)
class(doco)
#> [1] "metaframe"  "data.frame"

The new documented object still behaves the way a dataframe would be expected to behave in R but with some additional information provided.

summary(doco)
#>      Ozone           Solar.R           Wind             Temp      
#>  Min.   :  1.00   Min.   :  7.0   Min.   : 1.700   Min.   :56.00  
#>  1st Qu.: 18.00   1st Qu.:115.8   1st Qu.: 7.400   1st Qu.:72.00  
#>  Median : 31.50   Median :205.0   Median : 9.700   Median :79.00  
#>  Mean   : 42.13   Mean   :185.9   Mean   : 9.958   Mean   :77.88  
#>  3rd Qu.: 63.25   3rd Qu.:258.8   3rd Qu.:11.500   3rd Qu.:85.00  
#>  Max.   :168.00   Max.   :334.0   Max.   :20.700   Max.   :97.00  
#>  NA's   :37       NA's   :7                                       
#>      Month            Day      
#>  Min.   :5.000   Min.   : 1.0  
#>  1st Qu.:6.000   1st Qu.: 8.0  
#>  Median :7.000   Median :16.0  
#>  Mean   :6.993   Mean   :15.8  
#>  3rd Qu.:8.000   3rd Qu.:23.0  
#>  Max.   :9.000   Max.   :31.0  
#>                                
#> ** Completeness of meta.data for object ** 
#> ----------------------------------------
#> Percentage of meta.data complete: 
#>     units    labels   sources     notes revisions 
#>         0         0         0       100       100 
#> ----- 
#> Complete elements by column: 
#>         units labels sources notes revisions
#> Ozone       0      0       0     1         1
#> Solar.R     0      0       0     1         1
#> Wind        0      0       0     1         1
#> Temp        0      0       0     1         1
#> Month       0      0       0     1         1
#> Day         0      0       0     1         1
print(doco)
#> Showing metadata for object:  airquality
#>  ------------------------------------------------------------- 
#> Showing metadata for following variables in object: 
#>  OVERALL :  
#>  Ozone :  
#>  Solar.R :  
#>  Wind :  
#>  Temp :  
#>  Month :  
#>  Day :  
#>  
#> ---------------------------------------------------------------- 
#> Data from following sources: 
#>  OVERALL :  
#>  Ozone :  
#>  Solar.R :  
#>  Wind :  
#>  Temp :  
#>  Month :  
#>  Day :  
#>  
#> ---------------------------------------------------------------- 
#> Data expressed in the following units: 
#>  Ozone :  
#>  Solar.R :  
#>  Wind :  
#>  Temp :  
#>  Month :  
#>  Day :  
#>  
#> ---------------------------------------------------------------- 
#> Additional notes on the data: 
#>   : No notes listed. 
#>  
#> ---------------------------------------------------------------- 
#> Revision history for data elements: 
#>   : No revisions listed. 
#>  
#> ---------------------------------------------------------------- 
#> Output truncated to first 10 rows 
#> 
#>    Ozone Solar.R Wind Temp Month Day
#> 1     41     190  7.4   67     5   1
#> 2     36     118  8.0   72     5   2
#> 3     12     149 12.6   74     5   3
#> 4     18     313 11.5   62     5   4
#> 5     NA      NA 14.3   56     5   5
#> 6     28      NA 14.9   66     5   6
#> 7     23     299  8.6   65     5   7
#> 8     19      99 13.8   59     5   8
#> 9      8      19 20.1   61     5   9
#> 10    NA     194  8.6   69     5  10

print(attr(doco, "meta.data"))
#> Showing metadata for object:  airquality
#>  ------------------------------------------------------------- 
#> Showing metadata for following variables in object: 
#>  OVERALL :  
#>  Ozone :  
#>  Solar.R :  
#>  Wind :  
#>  Temp :  
#>  Month :  
#>  Day :  
#>  
#> ---------------------------------------------------------------- 
#> Data from following sources: 
#>  OVERALL :  
#>  Ozone :  
#>  Solar.R :  
#>  Wind :  
#>  Temp :  
#>  Month :  
#>  Day :  
#>  
#> ---------------------------------------------------------------- 
#> Data expressed in the following units: 
#>  Ozone :  
#>  Solar.R :  
#>  Wind :  
#>  Temp :  
#>  Month :  
#>  Day :  
#>  
#> ---------------------------------------------------------------- 
#> Additional notes on the data: 
#>   : No notes listed. 
#>  
#> ---------------------------------------------------------------- 
#> Revision history for data elements: 
#>   : No revisions listed. 
#>  
#> ----------------------------------------------------------------

Adding Metadata

The basic metadata is not very helpful, just some basic numeric summaries re-organized. The power of metaframe comes from the ability to add metadata directly to the data object and to render that metadata out.

To do this, you can use a named list with names referring to the columns in the metaframe object.

# Column labels

my_data_labels <- list("Ozone" = "numeric Ozone (ppb)")

doco <- add_label(doco, label = my_data_labels)

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.

confusion when rendering HTML documents, mimic the formatting of data.frame, and to make searching for this specific implementation of metadata in R easier.

jknowles/metaframe documentation built on May 19, 2019, 11:43 a.m.