Package 'yamlet' reference manual

Title:	Versatile Curation of Table Metadata
Description:	A YAML-based mechanism for working with table metadata. Supports compact syntax for creating, modifying, viewing, exporting, importing, displaying, and plotting metadata coded as column attributes. The 'yamlet' dialect is valid 'YAML' with defaults and conventions chosen to improve readability. See ?yamlet, ?decorate, ?modify, ?io_csv, and ?ggplot.decorated.
Authors:	Tim Bergsma [aut, cre]
Maintainer:	Tim Bergsma <[email protected]>
License:	GPL-3
Version:	1.1.4
Built:	2024-10-22 07:29:14 UTC
Source:	CRAN

Coerce Units to Decorated Vector

Description

Coerces units to dvec.

Usage

## S3 method for class 'units'
as_dvec(x, ...)
## S3 method for class 'units'
as_dvec(x, ...)

Arguments

`x`	units
`...`	passed arguments

Examples

library(magrittr)
library(dplyr)
a <- data.frame(id = 1:4, wt = c(70, 80, 70, 80), sex = c(0,1,0,1))
a %<>% decorate('wt: [ body weight, kg ]')
a %<>% decorate('sex: [ sex, [ female: 0, male: 1]]')
a %<>% decorate('id: identifier')
a %<>% resolve
a %<>% mutate(wt = as_units(wt))
a %<>% mutate(wt = as_dvec(wt))
str(a$wt)
library(magrittr)
library(dplyr)
a <- data.frame(id = 1:4, wt = c(70, 80, 70, 80), sex = c(0,1,0,1))
a %<>% decorate('wt: [ body weight, kg ]')
a %<>% decorate('sex: [ sex, [ female: 0, male: 1]]')
a %<>% decorate('id: identifier')
a %<>% resolve
a %<>% mutate(wt = as_units(wt))
a %<>% mutate(wt = as_dvec(wt))
str(a$wt)

Coerce Decorated Vector to Units

Description

Coerces dvec to units. If x has a units attribute, it is used to create class 'units'. It is an error if x has no units attribute.

Usage

## S3 method for class 'dvec'
as_units(x, ..., preserve = getOption("yamlet_as_units_preserve", "label"))
## S3 method for class 'dvec'
as_units(x, ..., preserve = getOption("yamlet_as_units_preserve", "label"))

Arguments

`x`	dvec
`...`	ignored
`preserve`	attributes to preserve; just label by default (class and units are handled implicitly)

Examples

library(magrittr)
a <- data.frame(id = 1:4, wt = c(70, 80, 70, 80), sex = c(0,1,0,1))
a %<>% decorate('wt: [ body weight, kg ]')
a %<>% decorate('sex: [ sex, [ female: 0, male: 1]]')
a %<>% decorate('id: identifier')
a %<>% resolve
a$wt %>% as_units
library(magrittr)
a <- data.frame(id = 1:4, wt = c(70, 80, 70, 80), sex = c(0,1,0,1))
a %<>% decorate('wt: [ body weight, kg ]')
a %<>% decorate('sex: [ sex, [ female: 0, male: 1]]')
a %<>% decorate('id: identifier')
a %<>% resolve
a$wt %>% as_units

Coerce Classified to Integer

Description

Coerces classified to integer. Result is like as.integer(as.numeric(x)) + offset but has a guide attribute: a list of integers whose names are the original levels of x. If you need a simple integer, consider coercing first to numeric.

Usage

## S3 method for class 'classified'
as.integer(
  x,
  offset = 0L,
  ...,
  persistence = getOption("yamlet_persistence", TRUE)
)
## S3 method for class 'classified'
as.integer(
  x,
  offset = 0L,
  ...,
  persistence = getOption("yamlet_persistence", TRUE)
)

Arguments

`x`	classified, see `classified`
`offset`	an integer value to add to intermediate result
`...`	passed to `desolve`
`persistence`	whether to return 'dvec' (is.integer(): TRUE) or just integer.

Value

integer (possibly of class dvec)

Examples

library(magrittr)

# create factor with codelist attribute
classified(c('knife','fork','spoon'))

# give back a simple numeric
classified(c('knife','fork','spoon')) %>% as.numeric

# intentionally preserve levels as 'guide' attribute
classified(c('knife','fork','spoon')) %>% as.integer

# implement offset
classified(c('knife','fork','spoon')) %>% as.integer(-1)

# globally defeat the 'persistence' paradigm
options(yamlet_persistence = FALSE)
c('knife','fork','spoon') %>% 
  classified %>%
  as.integer %>% 
  class # integer
  
# remove option to restore default persistence paradigm
options(yamlet_persistence = NULL)
c('knife','fork','spoon') %>% 
  classified %>%
  as.integer %>% 
  class # dvec
  
# locally defeat persistence paradigm
c('knife','fork','spoon') %>% 
  classified %>%
  as.integer(persistence = FALSE) %>% 
  class # integer
  

library(magrittr)

# create factor with codelist attribute
classified(c('knife','fork','spoon'))

# give back a simple numeric
classified(c('knife','fork','spoon')) %>% as.numeric

# intentionally preserve levels as 'guide' attribute
classified(c('knife','fork','spoon')) %>% as.integer

# implement offset
classified(c('knife','fork','spoon')) %>% as.integer(-1)

# globally defeat the 'persistence' paradigm
options(yamlet_persistence = FALSE)
c('knife','fork','spoon') %>% 
  classified %>%
  as.integer %>% 
  class # integer
  
# remove option to restore default persistence paradigm
options(yamlet_persistence = NULL)
c('knife','fork','spoon') %>% 
  classified %>%
  as.integer %>% 
  class # dvec
  
# locally defeat persistence paradigm
c('knife','fork','spoon') %>% 
  classified %>%
  as.integer(persistence = FALSE) %>% 
  class # integer

Sort Decorations

Description

Enforces canonical attribute order for class 'decorated'. Set of default_keys will be augmented with all observed attribute names and will be expanded or reduced as necessary for each data item.

Usage

## S3 method for class 'decorated'
canonical(
  x,
  default_keys = getOption("yamlet_default_keys", list("label", "guide")),
  ...
)
## S3 method for class 'decorated'
canonical(
  x,
  default_keys = getOption("yamlet_default_keys", list("label", "guide")),
  ...
)

Arguments

`x`	decorated
`default_keys`	attribute names in preferred order
`...`	ignored

Value

decorated

Examples

# make some decorated data
library(magrittr)
x <- data.frame(x = 1, y = 1, z = factor('a'))
x %<>% decorate('
x: [ guide: mm, desc: this, label: foo ]
"y": [ guide: bar, desc: other ]
')

# retrieve decorations: label not first!
decorations(x)

# sort label first by default
decorations(canonical(x))

# equivalent invocation
canonical(decorations(x))

# make some decorated data
library(magrittr)
x <- data.frame(x = 1, y = 1, z = factor('a'))
x %<>% decorate('
x: [ guide: mm, desc: this, label: foo ]
"y": [ guide: bar, desc: other ]
')

# retrieve decorations: label not first!
decorations(x)

# sort label first by default
decorations(canonical(x))

# equivalent invocation
canonical(decorations(x))

Create Classified by Default

Description

Creates a factor of subclass 'classified', for which there are attribute-preserving methods. In particular, classified has a codelist attribute indicating the origin of its levels: it is constructed from the codelist attribute of x if available, or from 'levels' and 'labels' by default. Unlike the case for factor, length of labels cannot be one (i.e., different from length of levels).

Usage

## Default S3 method:
classified(
  x = character(),
  levels,
  labels,
  exclude = NA,
  ordered = is.ordered(x),
  nmax = NA,
  token = character(0),
  ...
)
## Default S3 method:
classified(
  x = character(),
  levels,
  labels,
  exclude = NA,
  ordered = is.ordered(x),
  nmax = NA,
  token = character(0),
  ...
)

Arguments

`x`	see `factor`
`levels`	see `factor`
`labels`	see `factor`, must have same length as levels
`exclude`	see `factor`
`ordered`	see `factor`
`nmax`	see `factor`
`token`	informative label for messages
`...`	ignored

Value

'classified' 'factor'

Examples


# classified creates a factor with a corresponding codelist attribute
classified(c('a','b','c'))

# codelist 'remembers' the origins of levels
classified(c('a','b','c'), labels = c('A','B','C'))

# classified is 'reversible'
library(magrittr)
c('a','b','c') %>%
  classified(labels = c('A','B','C')) %>%
  unclassified
# classified creates a factor with a corresponding codelist attribute
classified(c('a','b','c'))

# codelist 'remembers' the origins of levels
classified(c('a','b','c'), labels = c('A','B','C'))

# classified is 'reversible'
library(magrittr)
c('a','b','c') %>%
  classified(labels = c('A','B','C')) %>%
  unclassified

Create Classified from Factor

Description

Creates classified from factor. Uses classified.default, but supplies existing levels by default.

Usage

## S3 method for class 'factor'
classified(
  x = character(),
  levels,
  labels,
  exclude = NA,
  ordered = is.ordered(x),
  nmax = NA,
  token = character(0),
  ...
)
## S3 method for class 'factor'
classified(
  x = character(),
  levels,
  labels,
  exclude = NA,
  ordered = is.ordered(x),
  nmax = NA,
  token = character(0),
  ...
)

Arguments

`x`	see `factor`
`levels`	passed to `classified.default`; defaults to `levels(x)`
`labels`	passed to `classified.default`; must be same length as levels(after removing values in `exclude`) and must not contain duplicates
`exclude`	see `factor`
`ordered`	see `factor`
`nmax`	see `factor`
`token`	informative label for messages
`...`	ignored

Value

'classified' 'factor'

Examples

a <- factor(c('c','b','a'))
levels(classified(a))
attr(classified(a), 'codelist')
a <- factor(c('c','b','a'))
levels(classified(a))
attr(classified(a), 'codelist')

Capture Groups as Decorations for Data Frame

Description

Captures groups as decorations for class 'data.frame'. Creates a sequentially-valued integer attribute with name 'groups' for each corresponding column (after clearing all such existing designations). It is an error if not all such columns are present. Defaults to groups(x). If no columns are specified and x has no groups, x is returned with any existing column-level 'groups' attributes removed.

Usage

## S3 method for class 'data.frame'
decorate_groups(x, ...)
## S3 method for class 'data.frame'
decorate_groups(x, ...)

Arguments

`x`	data.frame
`...`	unquoted names of columns to assign as groups; defaults to `groups(x)`

Value

same class as x

Examples

library(magrittr)
library(dplyr)
Theoph %>% decorate_groups(Subject, Time) %>% groups # nothing!
Theoph %>% decorate_groups(Subject, Time) %>% decorations # note well
Theoph %>% group_by(Subject, Time) %>% decorate_groups %>% decorations # same

library(magrittr)
library(dplyr)
Theoph %>% decorate_groups(Subject, Time) %>% groups # nothing!
Theoph %>% decorate_groups(Subject, Time) %>% decorations # note well
Theoph %>% group_by(Subject, Time) %>% decorate_groups %>% decorations # same

Decorate Character

Description

Treats x as a file path. By default, metadata is sought from a file with the same base but the 'yaml' extension.

Usage

## S3 method for class 'character'
decorate(
  x,
  meta = NULL,
  ...,
  read = getOption("yamlet_import", as.csv),
  ext = getOption("yamlet_extension", ".yaml")
)
## S3 method for class 'character'
decorate(
  x,
  meta = NULL,
  ...,
  read = getOption("yamlet_import", as.csv),
  ext = getOption("yamlet_extension", ".yaml")
)

Arguments

`x`	file path for table data
`meta`	file path for corresponding yamlet metadata, or a yamlet object
`...`	passed to `read` (if accepted) and to `as_yamlet.character`
`read`	function or function name for reading x
`ext`	file extension for metadata file, if relevant

Value

class 'decorated' 'data.frame'

Examples


# find data file
file <- system.file(package = 'yamlet', 'extdata','quinidine.csv')
file

# find metadata file
meta <- system.file(package = 'yamlet', 'extdata','quinidine.yaml')
meta

# decorate with explicit metadata reference
a <- decorate(file, meta)

# rely on default metadata path
b <- decorate(file)

# in this case: same
stopifnot(identical(a, b))
# find data file
file <- system.file(package = 'yamlet', 'extdata','quinidine.csv')
file

# find metadata file
meta <- system.file(package = 'yamlet', 'extdata','quinidine.yaml')
meta

# decorate with explicit metadata reference
a <- decorate(file, meta)

# rely on default metadata path
b <- decorate(file)

# in this case: same
stopifnot(identical(a, b))

Decorate Data Frame

Description

Decorates a data.frame. Expects metadata in yamlet format, and loads it onto columns as attributes.

Usage

## S3 method for class 'data.frame'
decorate(
  x,
  meta = NULL,
  ...,
  persistence = getOption("yamlet_persistence", TRUE)
)
## S3 method for class 'data.frame'
decorate(
  x,
  meta = NULL,
  ...,
  persistence = getOption("yamlet_persistence", TRUE)
)

Arguments

`x`	data.frame
`meta`	file path for corresponding yaml metadata, or a yamlet; an attempt will be made to guess the file path if x has a 'source' attribute
`...`	passed to `decorate.list`
`persistence`	whether to coerce decorated columns to 'dvec' where suitable method exists

Details

As of v0.8.8, the data.frame method for decorate() coerces affected columns using as_dvec if persistence is true and a suitable method exists. 'vctrs' methods are implemented for class dvec to help attributes persist during tidyverse operations. Details are described in c.dvec. Disable this functionality with options(yamlet_persistence = FALSE).

Value

class 'decorated' 'data.frame'

Examples


# find data path
library(csv)
file <- system.file(package = 'yamlet', 'extdata','quinidine.csv')
file
dat <- as.csv(file) # dat now has 'source' attribute

# use source attribute to find metadata 
a <- decorate(as.csv(file))

# supply metadata path (or something close) explicitly
b <- decorate(dat, meta = file)

# these are equivalent
stopifnot(identical(a, b))
# find data path
library(csv)
file <- system.file(package = 'yamlet', 'extdata','quinidine.csv')
file
dat <- as.csv(file) # dat now has 'source' attribute

# use source attribute to find metadata 
a <- decorate(as.csv(file))

# supply metadata path (or something close) explicitly
b <- decorate(dat, meta = file)

# these are equivalent
stopifnot(identical(a, b))

Recover Groups Decorations for Data Frame

Description

Recovers groups decorations for class 'data.frame'. Seeks a sequentially-valued integer attribute with name 'groups' for each column, sorts these, and returns a character vector like group_vars(x).

Usage

## S3 method for class 'data.frame'
decorations_groups(x, ...)
## S3 method for class 'data.frame'
decorations_groups(x, ...)

Arguments

`x`	data.frame
`...`	ignored

Value

character: names of groups columns

Examples

library(magrittr)
library(dplyr)
Theoph %<>% group_by(Subject, Time)
Theoph %>% group_vars
Theoph %>% decorations_groups # nothing!
Theoph %<>% decorate_groups
Theoph %>% decorations_groups # something!
Theoph %<>% ungroup
Theoph %>% group_vars # gone!
Theoph %<>% group_by(across(all_of(decorations_groups(.))))
Theoph %>% group_vars # recovered!
Theoph %<>% group_by_decorations
Theoph %>% group_vars # same
rm(Theoph)

library(magrittr)
library(dplyr)
Theoph %<>% group_by(Subject, Time)
Theoph %>% group_vars
Theoph %>% decorations_groups # nothing!
Theoph %<>% decorate_groups
Theoph %>% decorations_groups # something!
Theoph %<>% ungroup
Theoph %>% group_vars # gone!
Theoph %<>% group_by(across(all_of(decorations_groups(.))))
Theoph %>% group_vars # recovered!
Theoph %<>% group_by_decorations
Theoph %>% group_vars # same
rm(Theoph)

Retrieve Decorations for Data Frame

Description

Retrieve the decorations of a data.frame; i.e., the metadata used to decorate it. Returns a list with same names as the data.frame. By default, 'class' and 'level' attributes are excluded from the result, as you likely don't want to manipulate these independently.

Usage

## S3 method for class 'data.frame'
decorations(
  x,
  ...,
  exclude_attr = getOption("yamlet_exclude_attr", c("class", "levels"))
)
## S3 method for class 'data.frame'
decorations(
  x,
  ...,
  exclude_attr = getOption("yamlet_exclude_attr", c("class", "levels"))
)

Arguments

`x`	data.frame
`...`	optional unquoted column names to limit output (passed to `select`)
`exclude_attr`	attributes to remove from the result

Value

named list of class 'yamlet'

Examples

# prepare a decorated data.frame
file <- system.file(package = 'yamlet', 'extdata','quinidine.csv')
x <- decorate(file)

# retrieve the decorations
decorations(x, Subject, time, conc)
# prepare a decorated data.frame
file <- system.file(package = 'yamlet', 'extdata','quinidine.csv')
x <- decorate(file)

# retrieve the decorations
decorations(x, Subject, time, conc)

Desolve Guide for Classified

Description

Un-resolves explicit usage of default key 'guide' to implicit usage for class 'classified'. Calls drop_title (a non-action by default), unclassified, followed by implicit_guide.

Usage

## S3 method for class 'classified'
desolve(x, ...)
## S3 method for class 'classified'
desolve(x, ...)

Arguments

`x`	classified
`...`	passed to `drop_title`, `unclassified`, and `unclassified`

Value

dvec

Examples

library(magrittr)
x <- as_dvec(
  4:6, 
  guide = list(a = 4L, b = 5L, c = 6L)
)

# untouched
x %>% str

# resolved
x %>% resolve %>% str

# resolved and desolved
x %>% resolve %>% desolve %>% str
library(magrittr)
x <- as_dvec(
  4:6, 
  guide = list(a = 4L, b = 5L, c = 6L)
)

# untouched
x %>% str

# resolved
x %>% resolve %>% str

# resolved and desolved
x %>% resolve %>% desolve %>% str

Desolve Guide for Decorated

Description

Un-resolves explicit usage of default key 'guide' to implicit usage for 'decorated' class. Simply calls drop_title, unclassified, and implicit_guide.

Usage

## S3 method for class 'decorated'
desolve(x, ...)
## S3 method for class 'decorated'
desolve(x, ...)

Arguments

`x`	decorated
`...`	passed to `drop_title`, `unclassified`, and `implicit_guide`

Value

decorated

Examples

library(magrittr)
file <- system.file(package = 'yamlet', 'extdata','quinidine.csv')
x <- decorate(file)

# this is how Age, glyco, Race look when resolved
x %>% resolve %>% decorations(Age, glyco, Race)

# we can resolve two of them and then 'unresolve' all of them
x %>% resolve(glyco, Race) %>% desolve %>% decorations(Age, glyco, Race)
library(magrittr)
file <- system.file(package = 'yamlet', 'extdata','quinidine.csv')
x <- decorate(file)

# this is how Age, glyco, Race look when resolved
x %>% resolve %>% decorations(Age, glyco, Race)

# we can resolve two of them and then 'unresolve' all of them
x %>% resolve(glyco, Race) %>% desolve %>% decorations(Age, glyco, Race)

Create a New ggplot for a Decorated Data Frame

Description

Creates a new ggplot object for a decorated data.frame. This is the ggplot() method for class 'decorated'. It creates a ggplot object using the default method, but reclassifies it as 'decorated_ggplot' so that a custom print method is invoked; see print.decorated_ggplot.

Usage

## S3 method for class 'decorated'
ggplot(data, ...)
## S3 method for class 'decorated'
ggplot(data, ...)

Arguments

`data`	decorated, see `decorate`
`...`	passed to `ggplot`

Details

This approach is similar to but more flexible than the method for ggready. For fine control, you can switch between 'data.frame' and 'decorated' using as_decorated (supplies null decorations) and as.data.frame (preserves decorations).

Value

return value like ggplot but inheriting 'decorated_ggplot'

Examples

file <- system.file(package = 'yamlet', 'extdata','quinidine.csv')
library(ggplot2)
library(dplyr)
library(magrittr)
# par(ask = FALSE)

x <- decorate(file)
x %<>% filter(!is.na(conc))

# Manipulate class to switch among ggplot methods.
class(x)
class(data.frame(x))
class(as_decorated(data.frame(x)))

# The bare data.frame gives boring labels and un-ordered groups.
map <- aes(x = time, y = conc, color = Heart)
data.frame(x) %>% ggplot(map) + geom_point()

# Decorated data.frame uses supplied labels.
# Notice CHF levels are still not ordered. (Moderate first.)
x %>% ggplot(map) + geom_point()

# If we resolve Heart, CHF levels are ordered.
x %<>% resolve(Heart)
x %>% ggplot(map) + geom_point()

# We can map aesthetics as decorations.
x %<>% decorate('Heart: [ color: [gold, purple, green]]')
x %>% ggplot(map) + geom_point()

# Colors are matched to particular levels. Purple drops out here:
x %>% filter(Heart != 'Moderate') %>% ggplot(map) + geom_point()

# We can resolve other columns for a chance to enrich the output with units.
x %<>% resolve
suppressWarnings( # because this complains for columns with no units
  x <- modify(x, title = paste0(label, '\n(', units, ')'))
)
x %>% ggplot(map) + geom_point()

# Or something fancier.
x %<>% modify(conc, title = 'conc_serum. (mg*L^-1.)')
x %>% ggplot(map) + geom_point()

# The y-axis title is deliberately given in spork syntax for elegant coercion:
library(spork)
x %<>% modify(conc, expression = as.expression(as_plotmath(as_spork(title))))
x %>% ggplot(map) + geom_point()
# Add a fancier label for Heart, and facet by a factor:
x %<>% modify(Heart, expression = as.expression(as_plotmath(as_spork('CHF^\\*'))))
x %>% ggplot(map) + geom_point() + facet_wrap(~Creatinine)

# ggready handles the units and plotmath implicitly for a 'standard' display:
x %>% ggready %>% ggplot(map) + geom_point() + facet_wrap(~Creatinine)

# Notice that instead of over-writing the label
# attribute, we are creating a stack of label
# substitutes (title, expression) so that
# label is still available as an argument
# if we want to try something else.  The
# print method by default looks for all of these.
# Precedence is expression, title, label, column name.
# Precedence can be controlled using
# options(decorated_ggplot_search = c(a, b, ...) ).

# Here we try a dataset with conditional labels and units.

file <- system.file(package = 'yamlet', 'extdata','phenobarb.csv')
x <- file %>% decorate %>% resolve
# Note that value has two elements for label and guide.
x %>% decorations(value)

# The print method defaults to the first, with warning.
map <- aes(x = time, y = value, color = event)

x %>% ggplot(map) + geom_point()


# If we subset appropriately, the relevant value is substituted.
x %>% filter(event == 'conc') %>% ggplot(map) + geom_point()

x %>% filter(event == 'conc') %>%
ggplot(aes(x = time, y = value, color = ApgarInd)) + geom_point()

x %>% filter(event == 'dose') %>%
ggplot(aes(x = time, y = value, color = Wt)) +
geom_point() +
scale_y_log10() +
scale_color_gradientn(colours = rainbow(4))

# print.decorated_ggplot will attempt to honor coordinated aesthetics.
x <- data.frame(x = c(1:6, 3:8), y = c(1:6,1:6), z = letters[c(1:6,1:6)])
x %<>% decorate('z: [color: ["red", "blue", "green", "gold", "black", "magenta"]]')
x %<>% decorate('z: [fill: ["red", "blue", "green", "gold", "black", "magenta"]]')
x %<>% decorate('z: [shape: [20, 21, 22, 23, 24, 25]]')
x %<>% decorate('z: [linetype: [6, 5, 4, 3, 2, 1]]')
x %<>% decorate('z: [alpha: [ .9, .8, .7, .6, .5, .4]]')
x %<>% decorate('z: [size: [1, 1.5, 2, 2.5, 3, 3.5]]')
x %>% ggplot(aes(
 x, y,
  color = z,
  fill = z,
  shape = z,
  linetype = z, 
  alpha = z,
  size = z,
)) + 
  geom_point() +
  geom_line(size = 1)
file <- system.file(package = 'yamlet', 'extdata','quinidine.csv')
library(ggplot2)
library(dplyr)
library(magrittr)
# par(ask = FALSE)

x <- decorate(file)
x %<>% filter(!is.na(conc))

# Manipulate class to switch among ggplot methods.
class(x)
class(data.frame(x))
class(as_decorated(data.frame(x)))

# The bare data.frame gives boring labels and un-ordered groups.
map <- aes(x = time, y = conc, color = Heart)
data.frame(x) %>% ggplot(map) + geom_point()

# Decorated data.frame uses supplied labels.
# Notice CHF levels are still not ordered. (Moderate first.)
x %>% ggplot(map) + geom_point()

# If we resolve Heart, CHF levels are ordered.
x %<>% resolve(Heart)
x %>% ggplot(map) + geom_point()

# We can map aesthetics as decorations.
x %<>% decorate('Heart: [ color: [gold, purple, green]]')
x %>% ggplot(map) + geom_point()

# Colors are matched to particular levels. Purple drops out here:
x %>% filter(Heart != 'Moderate') %>% ggplot(map) + geom_point()

# We can resolve other columns for a chance to enrich the output with units.
x %<>% resolve
suppressWarnings( # because this complains for columns with no units
  x <- modify(x, title = paste0(label, '\n(', units, ')'))
)
x %>% ggplot(map) + geom_point()

# Or something fancier.
x %<>% modify(conc, title = 'conc_serum. (mg*L^-1.)')
x %>% ggplot(map) + geom_point()

# The y-axis title is deliberately given in spork syntax for elegant coercion:
library(spork)
x %<>% modify(conc, expression = as.expression(as_plotmath(as_spork(title))))
x %>% ggplot(map) + geom_point()
# Add a fancier label for Heart, and facet by a factor:
x %<>% modify(Heart, expression = as.expression(as_plotmath(as_spork('CHF^\\*'))))
x %>% ggplot(map) + geom_point() + facet_wrap(~Creatinine)

# ggready handles the units and plotmath implicitly for a 'standard' display:
x %>% ggready %>% ggplot(map) + geom_point() + facet_wrap(~Creatinine)

# Notice that instead of over-writing the label
# attribute, we are creating a stack of label
# substitutes (title, expression) so that
# label is still available as an argument
# if we want to try something else.  The
# print method by default looks for all of these.
# Precedence is expression, title, label, column name.
# Precedence can be controlled using
# options(decorated_ggplot_search = c(a, b, ...) ).

# Here we try a dataset with conditional labels and units.

file <- system.file(package = 'yamlet', 'extdata','phenobarb.csv')
x <- file %>% decorate %>% resolve
# Note that value has two elements for label and guide.
x %>% decorations(value)

# The print method defaults to the first, with warning.
map <- aes(x = time, y = value, color = event)

x %>% ggplot(map) + geom_point()


# If we subset appropriately, the relevant value is substituted.
x %>% filter(event == 'conc') %>% ggplot(map) + geom_point()

x %>% filter(event == 'conc') %>%
ggplot(aes(x = time, y = value, color = ApgarInd)) + geom_point()

x %>% filter(event == 'dose') %>%
ggplot(aes(x = time, y = value, color = Wt)) +
geom_point() +
scale_y_log10() +
scale_color_gradientn(colours = rainbow(4))

# print.decorated_ggplot will attempt to honor coordinated aesthetics.
x <- data.frame(x = c(1:6, 3:8), y = c(1:6,1:6), z = letters[c(1:6,1:6)])
x %<>% decorate('z: [color: ["red", "blue", "green", "gold", "black", "magenta"]]')
x %<>% decorate('z: [fill: ["red", "blue", "green", "gold", "black", "magenta"]]')
x %<>% decorate('z: [shape: [20, 21, 22, 23, 24, 25]]')
x %<>% decorate('z: [linetype: [6, 5, 4, 3, 2, 1]]')
x %<>% decorate('z: [alpha: [ .9, .8, .7, .6, .5, .4]]')
x %<>% decorate('z: [size: [1, 1.5, 2, 2.5, 3, 3.5]]')
x %>% ggplot(aes(
 x, y,
  color = z,
  fill = z,
  shape = z,
  linetype = z, 
  alpha = z,
  size = z,
)) + 
  geom_point() +
  geom_line(size = 1)

Groups by Decorations for Data Frame

Description

Invokes group_by using whatever groups are recovered by decorations_groups.

Usage

## S3 method for class 'data.frame'
group_by_decorations(x, ...)
## S3 method for class 'data.frame'
group_by_decorations(x, ...)

Arguments

`x`	grouped_df
`...`	ignored

Value

list of symbols

Examples

library(magrittr)
library(dplyr)
Theoph %>% group_vars # nothing!
Theoph %<>% decorate_groups(Subject, Time) 
Theoph %<>% group_by_decorations
Theoph %>% group_vars # something
rm(Theoph)

library(magrittr)
library(dplyr)
Theoph %>% group_vars # nothing!
Theoph %<>% decorate_groups(Subject, Time) 
Theoph %<>% group_by_decorations
Theoph %>% group_vars # something
rm(Theoph)

Import and Export Documented Tables as CSV

Description

Imports or exports documented tables as comma-separated variable. Generic, with methods that extend as.csv.

Usage

io_csv(x, ...)
io_csv(x, ...)

Arguments

`x`	object
`...`	passed arguments

Value

See methods.

Examples

# generate some decorated data
file <- system.file(package = 'yamlet', 'extdata','quinidine.csv')
x <- decorate(file)

# get a temporary filepath
out <- file.path(tempdir(), 'out.csv')

# save file using io_csv (returns filepath)
foo <- io_csv(x, out)
stopifnot(identical(out, foo))

# read using this filepath
y <- io_csv(foo)

# lossless round-trip (ignoring source attribute)
attr(x, 'source') <- NULL
attr(y, 'source') <- NULL
stopifnot(identical(x, y))
# generate some decorated data
file <- system.file(package = 'yamlet', 'extdata','quinidine.csv')
x <- decorate(file)

# get a temporary filepath
out <- file.path(tempdir(), 'out.csv')

# save file using io_csv (returns filepath)
foo <- io_csv(x, out)
stopifnot(identical(out, foo))

# read using this filepath
y <- io_csv(foo)

# lossless round-trip (ignoring source attribute)
attr(x, 'source') <- NULL
attr(y, 'source') <- NULL
stopifnot(identical(x, y))

Import and Export Documented Tables

Description

Imports or exports documented tables. Generic, with methods that extend read.table and write.table.

Usage

io_table(x, ...)
io_table(x, ...)

Arguments

`x`	object
`...`	passed arguments

Value

See methods.

Examples

# generate some decorated data
file <- system.file(package = 'yamlet', 'extdata','quinidine.csv')
x <- decorate(file)

# get a temporary filepath
out <- file.path(tempdir(), 'out.tab')

# save file using io_table (returns filepath)
foo <- io_table(x, out)
stopifnot(identical(out, foo))

# read using this filepath
y <- io_table(foo, as.is = TRUE)

# lossless round-trip
attr(x, 'source') <- NULL
rownames(x) <- NULL
rownames(y) <- NULL
stopifnot(identical(x, y))
# generate some decorated data
file <- system.file(package = 'yamlet', 'extdata','quinidine.csv')
x <- decorate(file)

# get a temporary filepath
out <- file.path(tempdir(), 'out.tab')

# save file using io_table (returns filepath)
foo <- io_table(x, out)
stopifnot(identical(out, foo))

# read using this filepath
y <- io_table(foo, as.is = TRUE)

# lossless round-trip
attr(x, 'source') <- NULL
rownames(x) <- NULL
rownames(y) <- NULL
stopifnot(identical(x, y))

Test if Class is dvec

Description

Tests whether x inherits 'dvec'.

Usage

is_dvec(x)
is_dvec(x)

Arguments

x

object

Value

logical

Examples

is_dvec(1L)
is_dvec(as_dvec(1L))
is_dvec(1L)
is_dvec(as_dvec(1L))

Try To Look Like Another Equal-length Variable

Description

Tries to mimic another vector or factor. If meaningful and possible, x acquires a guide attribute with labels from corresponding values in y. Any codelist attribute is removed. No guide is created for zero-length x. If x is a factor, unused levels are removed.

Usage

## Default S3 method:
mimic(x, y = x, ...)
## Default S3 method:
mimic(x, y = x, ...)

Arguments

`x`	vector-like
`y`	vector-like, same length as x
`...`	passed to `link{factor}`

Value

same class as x

Examples

library(magrittr)
library(dplyr)
let <- letters[1:5]
LET <- LETTERS[1:5]
int <- 0L:4L
num <- as.numeric(int)
fac <- factor(let)
css <- classified(let)

# any of these can mimic any other
str(mimic(LET, let))
str(mimic(num, let))
str(mimic(let, num))

# factors get a guide and classifieds get a named codelist
str(mimic(fac, int))
str(mimic(css, int))

# int can 'pick up' the factor levels as guide names
str(mimic(int, css))

# if two variables mean essentially the same thing,
# mimic lets you save space
x <- data.frame(id = 1:2, ID = c('A','B'))
x
x %<>% mutate(id = mimic(id, ID)) %>% select(-ID)
x
# ID still available, in principle:
x %>% as_decorated %>% resolve
library(magrittr)
library(dplyr)
let <- letters[1:5]
LET <- LETTERS[1:5]
int <- 0L:4L
num <- as.numeric(int)
fac <- factor(let)
css <- classified(let)

# any of these can mimic any other
str(mimic(LET, let))
str(mimic(num, let))
str(mimic(let, num))

# factors get a guide and classifieds get a named codelist
str(mimic(fac, int))
str(mimic(css, int))

# int can 'pick up' the factor levels as guide names
str(mimic(int, css))

# if two variables mean essentially the same thing,
# mimic lets you save space
x <- data.frame(id = 1:2, ID = c('A','B'))
x
x %<>% mutate(id = mimic(id, ID)) %>% select(-ID)
x
# ID still available, in principle:
x %>% as_decorated %>% resolve

Modify Attributes of Indicated Components by Default

Description

Modifies the attributes of each indicated element (all elements by default). Tries to assign the value of an expression to the supplied label, with existing attributes and the object itself (.) available as arguments. Gives a warning if the supplied label is considered reserved. Intends to support anything with one or more non-empty names.

Usage

## Default S3 method:
modify(
  x,
  ...,
  .reserved = getOption("yamlet_modify_reserved", c("class", "levels", "labels",
    "names"))
)
## Default S3 method:
modify(
  x,
  ...,
  .reserved = getOption("yamlet_modify_reserved", c("class", "levels", "labels",
    "names"))
)

Arguments

`x`	object
`...`	indicated columns, or name-value pairs
`.reserved`	reserved labels that warn on assignment

Details

The name of the component itself is available during assignments as attribute 'name' (any pre-existing attribute 'name' is temporarily masked). After all assignments are complete, the value of 'name' is enforced at the object level. Thus, modify expressions can modify component names.

As currently implemented, the expression is evaluated by eval_tidy, with attributes supplied as the data argument. Thus, names in the expression may be disambiguated, e.g. with .data. See examples.

Value

same class as x

Examples

library(magrittr)
library(dplyr)
file <- system.file(package = 'yamlet', 'extdata','quinidine.csv')
x <- decorate(file)

# modify selected columns
x %<>% modify(title = paste(label, '(', guide, ')'), time)
x %>% select(time, conc) %>% decorations

# modify (almost) all columns
x %<>% modify(title = paste(label, '(', guide, ')'), -Subject)
x %>% select(time, conc) %>% decorations

# use column itself
x %<>% modify(`defined values` = sum(!is.na(.)))
x %>% select(time) %>% decorations

# rename column
x %<>% modify(time, name = label)
names(x)

# warn if assignment fails
## Not run: 
\donttest{
x %<>% modify(title = foo, time)
}
## End(Not run)

# support lists
list(a = 1, b = 1:10, c = letters) %>%
modify(length = length(.), b:c)

x %<>% select(Subject) %>% modify(label = NULL, `defined values` = NULL)

# distinguish data and environment
location <- 'environment'
x %>% modify(where = location) %>% decorations
x %>% modify(where = .env$location) %>% decorations
## Not run: 
\donttest{
x%>% modify(where = .data$location) %>% decorations
}
## End(Not run)
x %>% modify(location = 'attributes', where = location) %>% decorations
x %>% modify(location = 'attributes', where = .data$location) %>% decorations

library(magrittr)
library(dplyr)
file <- system.file(package = 'yamlet', 'extdata','quinidine.csv')
x <- decorate(file)

# modify selected columns
x %<>% modify(title = paste(label, '(', guide, ')'), time)
x %>% select(time, conc) %>% decorations

# modify (almost) all columns
x %<>% modify(title = paste(label, '(', guide, ')'), -Subject)
x %>% select(time, conc) %>% decorations

# use column itself
x %<>% modify(`defined values` = sum(!is.na(.)))
x %>% select(time) %>% decorations

# rename column
x %<>% modify(time, name = label)
names(x)

# warn if assignment fails
## Not run: 
\donttest{
x %<>% modify(title = foo, time)
}
## End(Not run)

# support lists
list(a = 1, b = 1:10, c = letters) %>%
modify(length = length(.), b:c)

x %<>% select(Subject) %>% modify(label = NULL, `defined values` = NULL)

# distinguish data and environment
location <- 'environment'
x %>% modify(where = location) %>% decorations
x %>% modify(where = .env$location) %>% decorations
## Not run: 
\donttest{
x%>% modify(where = .data$location) %>% decorations
}
## End(Not run)
x %>% modify(location = 'attributes', where = location) %>% decorations
x %>% modify(location = 'attributes', where = .data$location) %>% decorations

Substitute Expressions, Titles, Labels and Aesthetics in ggplots

Description

Default labels (e.g. mappings for x, y, etc.) will be used to search data for more meaningful labels, taking first available from attributes with names in search. Likewise, if mappings for colour (color), fill, size, etc. (see defaults for discrete) indicate columns that have these defined as attributes, an attempt is made to add a corresponding discrete scale if one does not exist already. Values are recycled if necessary and are specific by ordinal position to the corresponding level of the corresponding variable. Levels are defined in increasing priority by sort(unique(x)), any guide attribute, any factor levels, any codelist attribute, or any plotmath attribute.

Usage

## S3 method for class 'decorated_ggplot'
print(
  x,
  ...,
  search = getOption("yamlet_decorated_ggplot_search", c("expression", "title", "label")),
  discrete = getOption("yamlet_decorated_ggplot_discrete", c("colour", "fill", "size",
    "shape", "linetype", "linewidth", "alpha")),
  drop = getOption("yamlet_decorated_ggplot_drop", TRUE)
)
## S3 method for class 'decorated_ggplot'
print(
  x,
  ...,
  search = getOption("yamlet_decorated_ggplot_search", c("expression", "title", "label")),
  discrete = getOption("yamlet_decorated_ggplot_discrete", c("colour", "fill", "size",
    "shape", "linetype", "linewidth", "alpha")),
  drop = getOption("yamlet_decorated_ggplot_drop", TRUE)
)

Arguments

`x`	class 'decorated_ggplot' from `ggplot.decorated`
`...`	ignored
`search`	attribute names from which to seek label substitutes
`discrete`	discrete aesthetics to map from data decorations where available
`drop`	should unused factor levels be omitted from data-driven discrete scales?

Value

see print.ggplot

Examples

example(ggplot.decorated)
example(ggplot.decorated)

Read Yamlet

Description

Reads yamlet from file. Similar to io_yamlet.character but also reads text fragments.

Usage

read_yamlet(
  x,
  ...,
  default_keys = getOption("yamlet_default_keys", list("label", "guide"))
)
read_yamlet(
  x,
  ...,
  default_keys = getOption("yamlet_default_keys", list("label", "guide"))
)

Arguments

`x`	file path for yamlet, or vector of yamlet in storage syntax
`...`	passed to `as_yamlet`
`default_keys`	character: default keys for the first n anonymous members of each element

Value

yamlet: a named list with default keys applied

Examples

library(csv)
file <- system.file(package = 'yamlet', 'extdata','quinidine.csv')
meta <- system.file(package = 'yamlet', 'extdata','quinidine.yaml')
x <- as.csv(file)
y <- read_yamlet(meta)
x <- decorate(x, meta = y)
stopifnot(identical(x, decorate(file)))
library(csv)
file <- system.file(package = 'yamlet', 'extdata','quinidine.csv')
meta <- system.file(package = 'yamlet', 'extdata','quinidine.yaml')
x <- as.csv(file)
y <- read_yamlet(meta)
x <- decorate(x, meta = y)
stopifnot(identical(x, decorate(file)))

Resolve Guide for Decorated

Description

Resolves implicit usage of default key 'guide' to explicit usage for decorated class. Calls explicit_guide, classified, and make_title.

Usage

## S3 method for class 'decorated'
resolve(x, ...)
## S3 method for class 'decorated'
resolve(x, ...)

Arguments

`x`	decorated
`...`	passed to `explicit_guide`, `classified`, and `make_title`

Value

decorated

Examples

# generate some decorated data
library(magrittr)
file <- system.file(package = 'yamlet', 'extdata','quinidine.csv')
x <- decorate(file)
x %>% decorations(Age, glyco)

# resolve everything, and show selected decorations
x %>% resolve %>% decorations(Age, glyco)

# resolve selectively, and show selected decorations
x %>% resolve(glyco) %>% decorations(Age, glyco)
# generate some decorated data
library(magrittr)
file <- system.file(package = 'yamlet', 'extdata','quinidine.csv')
x <- decorate(file)
x %>% decorations(Age, glyco)

# resolve everything, and show selected decorations
x %>% resolve %>% decorations(Age, glyco)

# resolve selectively, and show selected decorations
x %>% resolve(glyco) %>% decorations(Age, glyco)

Render Scripted Attributes of Indicated Components by Default

Description

Modifies specific attributes of each indicated element (all elements by default).

Usage

## Default S3 method:
scripted(
  x,
  ...,
  open = getOption("yamlet_append_units_open", " ("),
  close = getOption("yamlet_append_units_close", ")"),
  format = getOption("yamlet_format", ifelse(knitr::is_latex_output(), "latex", "html"))
)
## Default S3 method:
scripted(
  x,
  ...,
  open = getOption("yamlet_append_units_open", " ("),
  close = getOption("yamlet_append_units_close", ")"),
  format = getOption("yamlet_format", ifelse(knitr::is_latex_output(), "latex", "html"))
)

Arguments

`x`	object
`...`	indicated columns, or name-value pairs; passed to `resolve` and `selected`
`open`	character to precede units
`close`	character to follow units
`format`	one of 'latex' or 'html'

Details

The goal here is to render labels and units (where present) in a way that supports subscripts and superscripts for both plots and tables in either html or latex contexts.

The current implementation writes an 'expression' attribute to support figure labels and a 'title' attribute to support tables. print.decorated_ggplot will attempt to honor the expression attribute if it exists. tablet.data.frame will attempt to honor the title attribute if it exists (see Details there). An attempt is made to guess the output format (html or latex).

In addition to the 'title' and 'expression' attributes, scripted() writes a 'plotmath' attribute to store plotmath versions of factor levels, where present. print.decorated_ggplot should prefer these over their latex and html counterparts. Furthermore, factor levels (and codelists, where present) are converted to their latex or html equivalents. None of this happens if a 'plotmath' attribute already exists, thus preventing the same variable from being accidentally transformed twice.

To flexibly support latex, html, and plotmath, this function expects column labels and units to be encoded in "spork" syntax. See as_spork for details and examples. Briefly, "_" precedes a subscript, "^" precedes a superscript, and "." is used to force the termination of either a superscript or a subscript where necessary. For best results, units should be written using *, /, and ^; e.g. "kg*m^2/s^2" not "kg m2 s-2" (although both are valid: see is_parseable). A literal backslash followed by "n" represents a newline. Greek letters are represented by their names, except where names are enclosed in backticks.

scripted() always calls resolve() for the indicated columns, to make units present where appropriate.

Value

'scripted', a superclass of x

Examples

library(magrittr)
library(ggplot2)
x <- data.frame(time = 1:10, work = (1:10)^1.5)
x %<>% decorate('
  time: [ Time_elapsed, h ]
  work: [ Work_total_observed, kg*m^2/s^2 ]
')

x %>% decorations
x %>% ggplot(aes(time, work)) + geom_point()
x %>% scripted %>% ggplot(aes(time, work)) + geom_point()
x %>% scripted(format = 'html') %$% work %>% attr('title')
testthat::expect_equal(scripted(x), scripted(scripted(x)))
library(magrittr)
library(ggplot2)
x <- data.frame(time = 1:10, work = (1:10)^1.5)
x %<>% decorate('
  time: [ Time_elapsed, h ]
  work: [ Work_total_observed, kg*m^2/s^2 ]
')

x %>% decorations
x %>% ggplot(aes(time, work)) + geom_point()
x %>% scripted %>% ggplot(aes(time, work)) + geom_point()
x %>% scripted(format = 'html') %$% work %>% attr('title')
testthat::expect_equal(scripted(x), scripted(scripted(x)))

Write Yamlet

Description

Writes yamlet to file. Similar to io_yamlet.yamlet but returns invisible storage format instead of invisible storage location.

Usage

write_yamlet(
  x,
  con = stdout(),
  eol = "\n",
  useBytes = FALSE,
  default_keys = getOption("yamlet_default_keys", list("label", "guide")),
  fileEncoding = getOption("encoding"),
  block = FALSE,
  ...
)
write_yamlet(
  x,
  con = stdout(),
  eol = "\n",
  useBytes = FALSE,
  default_keys = getOption("yamlet_default_keys", list("label", "guide")),
  fileEncoding = getOption("encoding"),
  block = FALSE,
  ...
)

Arguments

`x`	something that can be coerced to class 'yamlet', like a yamlet object or a decorated data.frame
`con`	passed to `writeLines`
`eol`	end-of-line; passed to `writeLines` as `sep`
`useBytes`	passed to `writeLines`
`default_keys`	character: default keys for the first n anonymous members of each element
`fileEncoding`	if `con` is character, passed to `file` as `encoding`
`block`	whether to write block scalars
`...`	passed to `as_yamlet` and to `as.character.yamlet`

Value

invisible character representation of yamlet (storage syntax)

Examples

library(csv)
file <- system.file(package = 'yamlet', 'extdata','quinidine.csv')
meta <- system.file(package = 'yamlet', 'extdata','quinidine.yaml')
x <- as.csv(file)
y <- read_yamlet(meta)
x <- decorate(x, meta = y)
identical(x, decorate(file))
tmp <- tempfile()
write_yamlet(x, tmp)
stopifnot(identical(read_yamlet(meta), read_yamlet(tmp)))
library(csv)
file <- system.file(package = 'yamlet', 'extdata','quinidine.csv')
meta <- system.file(package = 'yamlet', 'extdata','quinidine.yaml')
x <- as.csv(file)
y <- read_yamlet(meta)
x <- decorate(x, meta = y)
identical(x, decorate(file))
tmp <- tempfile()
write_yamlet(x, tmp)
stopifnot(identical(read_yamlet(meta), read_yamlet(tmp)))

yamlet: Versatile Curation of Table Metadata

Description

The yamlet package supports storage and retrieval of table metadata in yaml format. The most important function is decorate.character: it lets you 'decorate' your data by attaching attributes retrieved from a file in yaml format. Typically your data will be of class 'data.frame', but it could be anything that is essentially a named list.

Storage Format

Storage format for 'yamlet' is a text file containing well-formed yaml. Technically, it is a map of sequences. Though well formed, it need not be complete: attributes or their names may be missing.

In the simplest case, the data specification consists of a list of column (item) names, followed by semicolons. Perhaps you only have one column:

mpg:

or maybe several:

mpg:
cyl:
disp:

If you know descriptive labels for your columns, provide them (skip a space after the colon).

mpg: fuel economy
cyl: number of cylinders
disp: displacement

If you know units, create a sequence with square brackets.

mpg: [ fuel economy, miles/gallon ]
cyl: number of cylinders
disp: [ displacement , in^3 ]

If you are going to give units, you probably should give a key first, since the first anonymous element is 'label' by default, and the second is 'guide'. (A guide can be units for numeric variables, factor levels/labels for categorical variables, or a format string for dates, times, and datetimes.) You could give just the units but you would have to be specific:

mpg: [units: miles/gallon]

You can over-ride default keys by providing them in your data:

mpg: [units: miles/gallon]
_keys: [label, units]

Notice that stored yamlet can be informationally defective while syntactically correct. If you don't know an item key at the time of data authoring, you can omit it:

race: [race, [white: 0, black: 1, 2, asian: 3 ]]

Or perhaps you know the key but not the value:

race: [race, [white: 0, black: 1, asian: 2, ? other ]]

Notice that race is factor-like; the factor sequence is nested within the attribute sequence. Equivalently:

race: [label: race, guide: [white: 0, black: 1, asian: 2, ? other ]]

If you have a codelist of length one, you should still enclose it in brackets:

sex: [Sex, [ M ]]

To get started using yamlet, see ?as_yamlet.character and examples there. See also ?decorate which adds yamlet values to corresponding items in your data. See also ?print.decorated which uses label attributes, if present, as axis labels.

Note: the quinidine and phenobarb datasets in the examples are borrowed from nlme (?Quinidine, ?Phenobarb), with some reorganization.

Author(s)

Maintainer: Tim Bergsma [email protected]

Display Global Yamlet Options

Description

Displays global yamlet options: those options whose names begin with 'yamlet_'.

yamlet_append_units_open: see append_units.default. Controls how labels are constructed for variables with 'units' attributes. In brief, units are wrapped in parentheses, and appended to the label.
yamlet_append_units_close: see append_units.default. Controls how labels are constructed for variables with 'units' attributes. In brief, units are wrapped in parentheses, and appended to the label.
yamlet_append_units_style: see append_units.default. Determines parsing as 'plotmath' or 'latex', or 'plain' for no parsing.
yamlet_append_units_target: see append_units.default. By default, append result is assigned to attribute 'label', but could be something else like 'title'.
yamlet_default_keys: see as_yamlet.character. The first two yaml attributes without specified names are assumed to be 'label' and 'guide'.
yamlet_persistence: see decorate.list and as.integer.classified. By default, persistence of column attributes is implemented by creating 'dvec' objects (decorated vectors) using vctrs methodology.
yamlet_cell_value: see as.data.frame.yamlet. Controls how cells are calculated when converting yamlet (decorations) to a data.frame.
yamlet_import: see decorate.character. Controls how primary data is read from file (default: as.csv()).
yamlet_extension: see decorate.character. Controls what file extension is expected for yaml metadata (default: '.yaml')
yamlet_overwrite: see decorate.list. Controls whether existing decorations are overwritten.
yamlet_exclude_attr: see decorations.data.frame Controls what attributes are excluded from display.
yamlet_with_title: see make_title.dvec and drop_title.dvec. For objects with (implied) units attributes, titles are by default automatically created on resolve() and destroyed on desolve(). Interacts with yamlet_append_units_*.
yamlet_infer_guide: see explicit_guide.yamlet. Identifies the function that will be used to reclassify 'guide' as something more explicit.
yamlet_explicit_guide_overwrite: see explicit_guide.data.frame and explicit_guide.dvec. In the latter case, controls whether existing attributes are overwritten.
yamlet_explicit_guide_simplify: explicit_guide.data.frame and explicit_guide.dvec. Ordinarily, the 'guide' attribute is removed if something more useful can be inferred.
yamlet_decorated_ggplot_search: see print.decorated_ggplot. The print method for decorated_ggplot populates axis labels by searching first for attributes named 'expression', 'title', and 'label'. Customizable.
yamlet_decorated_ggplot_discrete: see print.decorated_ggplot. Discrete aesthetics to map from data decorations where available.
yamlet_decorated_ggplot_drop: see print.decorated_ggplot. Should unused factor levels be omitted from data-driven discrete scales?
yamlet_ggready_parse: see ggready.data.frame, ggready.decorated. Whether to parse axis labels. TRUE by default, but may be problematic if unintended.
yamlet_modify_reserved: see modify.default. A list of reserved labels that warn on reassignment.
yamlet_promote_reserved: see promote.list. Attributes to leave untouched when promoting singularities.
yamlet_promote: see filter.decorated. Whether to promote when filtering 'decorated'.
yamlet_as_units_preserve: as_units.dvec. What attributes to preserve when converting dvec to units. Just 'label' by default. Assign options(yamlet_as_units_preserve = character(0)) to remove all.
yamlet_print_simplify: print.yamlet. Whether to collapse interactively-displayed decorations into a single line for lists that have no (nested) names and have the same length when unlisted. True by default. Can be misleading for lists with fine detail, but in most cases fine detail will likely have names.
yamlet_format: scripted.default. Choice of 'html' or 'latex', guessed if not supplied.
yamlet_warn_conflicted: c.classified. Whether to warn when codelists for combined classified factors have conflicting names (which will be dropped).
yamlet_expand_codelist: explicit_guide.yamlet. If TRUE (default) an empty list as a guide attribute is short-hand for sort(unique(x)).
yamlet_collapse_codelist: implicit_guide.data.frame. An integer (default: Inf) giving the maximum number of (un-named) codelist elements to store explicitly. Else, if sort(unique(x)) has exactly the same values as codelist, implicit_guide will substitute an empty list.

Usage

yamlet_options()
yamlet_options()

Value

list

Examples

yamlet_options()
yamlet_options()

Package 'yamlet'

Help Index

Coerce Units to Decorated Vector

Description

Usage

Arguments

Examples

Coerce Decorated Vector to Units

Description

Usage

Arguments

Examples

Coerce Classified to Integer

Description

Usage

Arguments

Value

See Also

Examples

Sort Decorations

Description

Usage

Arguments

Value

See Also

Examples

Create Classified by Default

Description

Usage

Arguments

Value

See Also

Examples

Create Classified from Factor

Description

Usage

Arguments

Value

See Also

Examples

Capture Groups as Decorations for Data Frame

Description

Usage

Arguments

Value

See Also

Examples

Decorate Character

Description

Usage

Arguments

Value

See Also

Examples

Decorate Data Frame

Description

Usage

Arguments

Details

Value

See Also

Examples

Recover Groups Decorations for Data Frame

Description

Usage

Arguments

Value

See Also

Examples

Retrieve Decorations for Data Frame

Description

Usage

Arguments

Value

See Also

Examples

Desolve Guide for Classified

Description

Usage

Arguments