knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) knitr::opts_chunk$set(package.startup.message = FALSE)
R datasets of modest size are routinely stored as flat files and retrieved as data frames. Unfortunately, the classic storage formats (comma delimited, tab delimited) do not have obvious mechanisms for storing data about the data: i.e., metadata such as column labels, units, and meanings of categorical codes. In many cases we hold such information in our heads and hard-code it in our scripts as axis labels, figure legends, or table enhancements. That's probably fine for simple cases but does not scale well in production settings where the same metadata is re-used extensively. Is there a better way to store, retrieve, and bind table metadata for consistent reuse?
yamlet is a storage format for table metadata,
implemented as an R package.
It was designed to be:
Although intended mainly to document (or pre-specify!) data column
labels and units, there are few restrictions
on the types of metadata that can be stored.
In fact, the only real restriction is that
the stored form must be valid yaml.
Below, we use yamlet to indicate the
paradigm or package, and yamlet
to indicate
stored instances.
Actually, yamlet
(think: "just a little yaml")
is a special case of yaml
that stores column attributes in one record
per column. For instance, to store the fact
that data for an imaginary drug trial
has a column called 'ID',
pop open a text file and write
ID:
This in itself is valid yaml
!
But if you know a label to go with ID, you can add it:
ID: subject identifier
If you have (or expect) a second column with units, you can add it below.
ID: subject identifier CONC: concentration, ng/mL
A couple of notes here.
To get a sequence, just add square brackets. For instance, above we have said that 'CONC' has the label 'concentration, ng/mL' but what we really intend is that it has label 'concentration' and unit 'ng/mL' so we rewrite it as
ID: subject identifier CONC: [ concentration, ng/mL ]
Now label and units are two different things. Notice we have not explicitly named them. Unless we say otherwise, the yamlet package will treat the first two un-named items as 'label' (a short description) and 'guide' (a hint about how to interpret the values). 'guide' might be units for continuous variables, levels (and possibly labels) for categorical values, format strings for dates and times, or perhaps something else.
The yamlet package
gives you five ways of controlling how
data items are identified (see details for ?as_yamlet.character
).
The most direct way is to supply explicit yaml
keys:
ID: [ label: subject identifier ] CONC: [ label: concentration, guide: ng/mL ]
We see that rather complex data can be expressed
using only colons, commas, and square brackets.
yaml
itself also uses curly braces to express
"maps", but for purposes here they are unnecessary.
Note above that we had to add square brackets for 'ID' when introducing the second colon (can't really have two colons at the same level, so to speak). Note also that sequences can be nested arbitrarily deep. We take advantage of this principle to transform 'guide' into a set of categorical levels.
ID: [ label: subject identifier ] CONC: [ label: concentration, guide: ng/mL ] RACE: [ label: race, guide: [ 0, 1, 2 ]]
or more simply (taking advantage of default keys)
ID: subject identifier CONC: [ concentration, ng/mL ] RACE: [ race, [ 0, 1, 2 ]]
So now we have 'codes' (levels) for our dataset that represent races. What do these codes mean? We supply 'decodes' (labels) as keys.
ID: subject identifier CONC: [ concentration, ng/mL ] RACE: [ race, [ white: 0, black: 1, asian: 2 ]]
Elegantly, yaml
(and therefore yamlet) gives
us a way to represent a code even if we don't
know the decode, and a way to represent a
decode even though we don't know the code.
Imagine a dataset is under collaborative
development, and we already know that there
are some 'RACE' values of 0 but we're not sure what
they mean. We also know that there will be
some 'asian' race values, but we haven't
assigned a code yet. We can write:
ID: subject identifier CONC: [ concentration, ng/mL ] RACE: [ race, [ 0, black: 1, ? asian ]]
The whole point of this exercise (and I'm getting a little ahead of myself) is to have some stored metadata that we can read into R and apply to a data frame as column attributes. If typing square brackets isn't your thing, you can actually do this backwards by supplying column attributes to a data frame and writing them out!
suppressMessages(library(dplyr)) library(magrittr) library(yamlet) x <- data.frame( ID = 1, CONC = 1, RACE = 1 ) x$ID %<>% structure(label = 'subject identifier') x$CONC %<>% structure(label = 'concentration', guide = 'ng/mL') x$RACE %<>% structure(label = 'race', guide = list(white = 0, black = 1, asian = 2)) x %>% as_yamlet %>% as.character %>% writeLines # or x %>% as_yamlet %>% as.character %>% writeLines(file.path(tempdir(), 'drug.yaml'))
Let's take advantage of that last example to show how we can read yamlet into R.
meta <- read_yamlet(file.path(tempdir(), 'drug.yaml')) meta
meta
is just a named list of column attributes.
decorate()
loads them onto columns of a data frame.
x <- data.frame(ID = 1, CONC = 1, RACE = 1) x <- decorate(x, meta = meta) decorations(x)
If you like, you can skip the external file and
decorate directly with yamlet
(instead of, say, structure() like
we did above).
x <- data.frame(ID = 1, CONC = 1, RACE = 1) x <- decorate(x,' ID: subject identifier CONC: [ concentration, ng/mL ] RACE: [ race, [white: 0, black: 1, asian: 2 ]] ') decorations(x)
We saw earlier that as_yamlet()
can
pull "decorations" off a data frame and
present them as yamlet.
this is the default behavior of decorations()
.
decorations(x)
write_yamlet()
calls as_yamlet()
on its
primary argument, and sends the result to a
connection of our choice.
file <- file.path(tempdir(), 'out.yaml') write_yamlet(x, con = file ) file %>% readLines %>% writeLines
A useful convention is to store metadata in a file
next to the file it describes, with the same name
but the 'yaml' extension. decorate()
expects
this, and if given a file path to a CSV
file, it will look for a '*.yaml' file nearby.
To "decorate" a CSV path means to read it,
read its yamlet
(if any) and apply the yamlet
as attributes on the resulting data frame.
library(csv) # see ?Quinidine in package nlme file <- system.file(package = 'yamlet', 'extdata','quinidine.csv') a <- decorate(file) as_yamlet(a)[1:3]
Another way to achieve the same thing is with io_csv()
.
It is a toggle function that returns a path if
given a file to store, and returns a decorated data frame
if given a path to read (same for io_table()
, which
has all the formatting options of read.table()
and write.table()
).
The path is just the path
to the primary data, but the path to the metadata is implied
as well.
options(csv_source = FALSE) # see ?as.csv file <- system.file(package = 'yamlet', 'extdata','quinidine.csv') x <- decorate(file) out <- file.path(tempdir(), 'out.csv') io_csv(x, out) y <- io_csv(out) identical(x, y) # lossless 'round-trip' file.exists(out) meta <- sub('csv','yaml', out) file.exists(meta) meta %>% readLines %>% head %>% writeLines options(csv_source = TRUE) # restore
Metadata can be used prospectively or retrospectively. Early in the data life cycle, it can be used prospectively to guide table development in a collaborative setting (i.e. as a data specification). Later in the life cycle, metadata can be used retrospectively to consistently inform report elements such as figures and tables.
For example, The yamlet package provides an experimental wrapper for ggplot that uses column attributes to automatically generate informative axis labels and legends.
suppressWarnings(library(ggplot2)) library(dplyr) library(magrittr) file <- system.file(package = 'yamlet', 'extdata','quinidine.csv') file %>% decorate %>% filter(!is.na(conc)) %>% resolve %>% ggplot(aes(x = time, y = conc, color = Heart)) + geom_point()
The table1 package uses labels and units stored
as attributes to enrich table output. In the example
below, we use resolve()
to re-implement guides
as units and factor levels, which is what table1()
needs.
suppressMessages(library(table1)) file %>% decorate %>% resolve %>% group_by(Subject) %>% slice(1) %>% table1(~ Age + Weight + Race | Heart, .)
It is a well-known problem that many table manipulations in R cause column attributes to be dropped. Binding of metadata is best done at a point in a workflow where few or no such manipulations remain. Else, precautions should be taken to preserve or restore attributes as necessary.
Remember to quote a literal value of yes, no, y, n, true false, on, off, or any of these capitalized, or any of these as all-caps. Otherwise they will be converted to TRUE or FALSE per the usual rules for yaml.
The yamlet package implements a metadata storage syntax that is easy to write, read, and bind to data frame columns. Systematic curation of metadata enriches and simplifies efforts to create and describe tables stored in flat files. Conforming tools can take advantage of internal and external yamlet representations to enhance data development and reporting.
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.