foldpkg: fold: A Self-Describing Dataset Format and Interface

In bergsmat/origami: A Self-Describing Dataset Format and Interface

Description

The fold package defines a compact, table-based, tool-neutral data format designed to accommodate embedded metadata. Not surprisingly, it also implements an interface for this format in R.

Details

The goal is to store metadata along with data. We do this by transforming tabular data into a folded format – still a table, but with a META column that associates attributes (metadata) with the data items they describe.

This all works much better when the data is clean: that is, there are a set of grouping columns, the interaction of which makes each record unique. The fold package can guess a lot of things, but you need to specify the groups – most general first.

Here we supply a quick-start micro-vignette. See also fold.data.frame.

Examples

library(magrittr)
library(wrangle)
library(dplyr)

data(events)
x <- events

# Step 0.  Rename columns to remove semantic (non-syntactic) underscores.

# Step 1.  De-interlace the data.  Limit to a subset so that each column means only one thing. 

x %<>% filter(CMT == 2) %>% select(-EVID,-CMT,-AMT)

# Step 2.  Describe the groups (unique key).  Order is important. (Start with most general.)

x %<>% group_by(USUBJID, TIME)
x %>% status

# Step 3.  Supply metadata as values or factors. Hardcode or merge from source.

x %<>% mutate(
  ID_LABEL      = 'subject identifier',
  C_LABEL       = 'comment flag',
  USUBJID_LABEL = 'universal subject identifier',
  TIME_LABEL    = 'time',
  DV_LABEL      = 'parent drug',
  BLQ_LABEL     = 'below limit of quantitation',
  LLOQ_LABEL    = 'lower limit of quantitation',
  TAD_LABEL     = 'time since most recent dose',
  SEX_LABEL     = 'sex',
  WT_LABEL      = 'weight',
  PRED_LABEL    = 'population prediction'
)

x %<>% mutate(
  C_GUIDE       = factor(paste(C), exclude = NULL,
   levels       = c('NA','C'),
   labels       = c('not commented','commented')),
  TIME_GUIDE    = 'h',
  DV_GUIDE      = 'ng/mL',
  BLQ_GUIDE     = factor(BLQ,
   levels       = 0:1,
   labels       = c('not quantifiable','quantifiable')),
  LLOQ_GUIDE    = 'ng/mL',
  TAD_GUIDE     = 'h',
  SEX_GUIDE     = factor(SEX,
   levels       = 0:1,
   labels       = c('female','male')),
  WT_GUIDE      = 'kg',
  PRED_GUIDE    = 'ng/mL'
)

# Step 4. Fold and unfold your data.

x %>% fold
x %>% fold %>% unfold
x %>% fold %>% unfold %>% fold
x %>% fold %>% unfold(PRED,TIME,WT)

data(eventsf)
stopifnot(identical(x %>% fold, eventsf) )

bergsmat/origami documentation built on May 12, 2019, 3:08 p.m.