,
Daniel Antal [ctb] | Title: | Functions for Declared Missing Values |
|---|---|
| Description: | A zero dependency package containing functions to declare labels and missing values, coupled with associated functions to create (weighted) tables of frequencies and various other summary measures. Some of the base functions have been rewritten to make use of the specific information about the missing values, most importantly to distinguish between empty and declared NA values. Some functions have similar functionality with the corresponding ones from packages "haven" and "labelled". The aim is to ensure as much compatibility as possible with these packages, while offering an alternative in the objects of class "declared". |
| Authors: | Adrian Dusa [aut, cre, cph] ,
Daniel Antal [ctb] |
| Maintainer: | Adrian Dusa <[email protected]> |
| License: | GPL (>= 3) |
| Version: | 0.25.1 |
| Built: | 2024-11-10 06:01:14 UTC |
| Source: | https://github.com/dusadrian/declared |
The labelled vectors are mainly used to analyse social science data, and the missing values declaration is an important step in the analysis.
as.declared(x, ...) declared( x, labels = NULL, na_values = NULL, na_range = NULL, label = NULL, measurement = NULL, llevels = FALSE, ... ) is.declared(x) anyNAdeclared(x)as.declared(x, ...) declared( x, labels = NULL, na_values = NULL, na_range = NULL, label = NULL, measurement = NULL, llevels = FALSE, ... ) is.declared(x) anyNAdeclared(x)
x |
A numeric vector to label, or a declared labelled vector
(for |
... |
Other arguments used by various other methods |
labels |
A named vector or |
na_values |
A vector of values that should also be considered as missing |
na_range |
A numeric vector of length two giving the (inclusive) extents
of the range. Use |
label |
A short, human-readable description of the vector |
measurement |
Optional, user specified measurement level |
llevels |
Logical, when |
The declared objects are very similar to the haven_labelled_spss objects
from package haven. It has exactly the same arguments, but it features
a fundamental difference in the treatment of (declared) missing values.
In package haven, existing values are treated as if they were missing. By contrast, in package declared the NA values are treated as if they were existing values.
This difference is fundamental and points to an inconsistency in package
haven: while existing values can be identified as missing using the
function is.na(), they are in fact present in the vector and other
packages (most importantly the base ones) do not know these values should be
treated as missing.
Consequently, the existing values are interpreted as missing only by package haven. Statistical procedures will use those values as if they were valid values.
Package declared approaches the problem in exactly the opposite way: instead of treating existing values as missing, it treats (certain) NA values as existing. It does that by storing an attribute containing the indices of those NA values which are to be treated as declared missing values, and it refreshes this attribute each time the declared object is changed.
This is a trade off and has important implications when subsetting datasets: all declared variables get this attribute refreshed, which consumes some time depending on the number of variables in the data.
The generic function as.declared() attempts to coerce only the compatible
types of objects, namely haven_labelled and factors. Dedicated class
methods can be written for any other type of object, and users are free to
write their own. To end of with a declared object, additional metadata is
needed such as value labels, which values should be treated as missing etc.
The measurement level is optional and, for the moment, purely aesthetic. It might however be useful to (automatically) determine if a declared object is suitable for a certain statistical analysis, for instance regression requires quantitative variables, while some declared objects are certainly categorical despite using numbers to denote categories.
It distinguishes between "categorial" and "quantitative" types of
variables, and additionally recognizes "nominal" and "ordinal" as
categorical, and similarly recognizes "interval", "ratio",
"discrete" and "continuous" as quantitative.
declared() and as.declared() return labelled vector of class
"declared". When applied to a data frame, as.declared() will return a
corresponding data frame with declared variables. is.declared() and
anyNAdeclared() return a logical value.
x <- declared( c(1:5, -1), labels = c(Good = 1, Bad = 5, DK = -1), na_values = -1 ) x is.na(x) x > 0 x == -1 # Values are actually placeholder for categories, # so labels work as if they were factors: x == "DK" # when newly added values are already declared as missing, # they are automatically coerced c(x, 2, -1) # switch NAs with their original values undeclare(x) as.character(x) # Returning values instead of categories as.character(x, values = TRUE) anyNAdeclared(x) # contains declared missing values anyNAdeclared(c(1:5, NA)) # no declared missing valuesx <- declared( c(1:5, -1), labels = c(Good = 1, Bad = 5, DK = -1), na_values = -1 ) x is.na(x) x > 0 x == -1 # Values are actually placeholder for categories, # so labels work as if they were factors: x == "DK" # when newly added values are already declared as missing, # they are automatically coerced c(x, 2, -1) # switch NAs with their original values undeclare(x) as.character(x) # Returning values instead of categories as.character(x, values = TRUE) anyNAdeclared(x) # contains declared missing values anyNAdeclared(c(1:5, NA)) # no declared missing values
Convert declared labelled objects to haven labelled objects
as.haven(x, ...)as.haven(x, ...)
x |
A declared labelled vector |
... |
Other arguments used by various methods |
This is a function that reverses the process of as.declared(), making
a round trip between declared and haven_labelled_spss classes.
A labelled vector of class "haven_labelled_spss".
x <- declared( c(1:5, -1), labels = c(Good = 1, Bad = 5, DK = -1), na_values = -1 ) x as.haven(x)x <- declared( c(1:5, -1), labels = c(Good = 1, Bad = 5, DK = -1), na_values = -1 ) x as.haven(x)
A function to obtain a version of the object with all information about declared missing values, dropped
undeclare(x, drop = FALSE, ...) drop_na(x, drop_labels = TRUE)undeclare(x, drop = FALSE, ...) drop_na(x, drop_labels = TRUE)
x |
A labelled object with declared missing values |
drop |
Logical, drop all attributes |
... |
Other internal arguments |
drop_labels |
Logical, drop the labels for the declared missing values |
The function undeclare() replaces the NA entries into their original
numeric values, and drops all attributes related to missing values:
na_values, na_range and na_index, and it preserves the labels referring
to the missing values.
The result can be a regular vector (dropping all attributes, including the
class "declared") by activating the argument drop.
Function drop_na() transforms the declared missing values in regular empty
NAs, and the labels referring to the missing values are deleted by default.
Function drop() deletes all attributes.
A declared labelled object.
Other labelling functions:
labels(),
measurement()
x <- declared( c(-2, 1:5, -1), labels = c("Good" = 1, "Bad" = 5, "DK" = -1), na_values = c(-1, -2), label = "Test variable" ) x undeclare(x) drop_na(x) drop(x) undeclare(x, drop = TRUE) # similar to: drop(undeclare(x))x <- declared( c(-2, 1:5, -1), labels = c("Good" = 1, "Bad" = 5, "DK" = -1), na_values = c(-1, -2), label = "Test variable" ) x undeclare(x) drop_na(x) drop(x) undeclare(x, drop = TRUE) # similar to: drop(undeclare(x))
Functions that indicate which elements are empty NA missing values, in
contrast to declared missing values.
is.empty(x) anyNAempty(x)is.empty(x) anyNAempty(x)
x |
A vector |
All missing values, declared or undeclared, as stored as regular NA
values, therefore the base function is_na() does not differentiate
between them.
These functions are specifically adapted to objects of class "declared",
to return a truth value only for those elements that are completely missing
with no reason.
A logical vector.
x <- declared( c(1:2, -91), labels = c(Good = 1, Bad = 2, Missing = -91), na_values = -91 ) x is.empty(x) # FALSE FALSE FALSE anyNAempty(x) # FALSE x <- c(x, NA) is.empty(x) # FALSE FALSE FALSE TRUE anyNAempty(x) # TRUEx <- declared( c(1:2, -91), labels = c(Good = 1, Bad = 2, Missing = -91), na_values = -91 ) x is.empty(x) # FALSE FALSE FALSE anyNAempty(x) # FALSE x <- c(x, NA) is.empty(x) # FALSE FALSE FALSE TRUE anyNAempty(x) # TRUE
Functions to extract information about the declared variable / value labels, or to declare such values if they are present in the data.
label(x) label(x, ...) <- value labels(x) <- valuelabel(x) label(x, ...) <- value labels(x) <- value
x |
Any vector of values that should be declared as missing
(for |
... |
Other arguments, for internal use. |
value |
The variable label, or a list of (named) variable labels |
The function labels() is a adaptation of the base function to the objects
of class declared. In addition to the regular arguments, it has two
additional (logical) arguments called prefixed (FALSE by default), to
retrieve the value labels prefixed with their values, and print_as_df
(TRUE by default) to print the result as a data frame.
labels() will return a named vector.
label() will return a single character string.
Other labelling functions:
drop_undeclare,
measurement()
x <- declared( c(-2, 1:5, -1), labels = c("Good" = 1, "Bad" = 5, "DK" = -1), na_values = c(-1, -2), label = "Test variable" ) x labels(x) labels(x, prefixed = TRUE) labels(x) <- c("Good" = 1, "Bad" = 5, "DK" = -1, "Not applicable" = -2) label(x) label(x) <- "This is a proper label" xx <- declared( c(-2, 1:5, -1), labels = c("Good" = 1, "Bad" = 5, "DK" = -1), na_values = c(-1, -2), label = "Test variable" ) x labels(x) labels(x, prefixed = TRUE) labels(x) <- c("Good" = 1, "Bad" = 5, "DK" = -1, "Not applicable" = -2) label(x) label(x) <- "This is a proper label" x
Functions to extract information about the measurement levels of a variable (if already present), or to specify such measurement levels.
measurement(x) measurement(x) <- valuemeasurement(x) measurement(x) <- value
x |
A declared vector. |
value |
A single character string of measurement levels, separated by commas. |
This function creates an attribute called "measurement" to a declared
object. This is an optional feature, at this point for purely aesthetic
reasons, but it might become useful in the future to (automatically)
determine if a declared object is suitable for a certain statistical
analysis, for instance regression requires quantitative variables, while some
declared objects are certainly categorical despite using numbers to denote
categories.
It distinguishes between "categorical" and "quantitative" types of
variables, and additionally recognizes "nominal" and "ordinal" as
categorical, and similarly recognizes "interval", "ratio",
"discrete" and "continuous" as quantitative.
The words "qualitative" is treated as a synonym for "categorical",
and the words "metric" and "numeric" are treated as synonyms for
"quantitative", respectively.
A character vector.
Other labelling functions:
drop_undeclare,
labels()
x <- declared( c(-2, 1:5, -1), labels = c(Good = 1, Bad = 5, DK = -1), na_values = c(-1, -2), label = "Test variable" ) x measurement(x) # automatically recognized as categorical measurement(x) <- "ordinal" measurement(x) # the same with measurement(x) <- "categorical, ordinal" set.seed(1890) x <- declared( sample(c(18:90, -91), 20, replace = TRUE), labels = c("No answer" = -91), na_values = -91, label = "Respondent's age" ) # automatically recognized as quantitative measurement(x) <- "discrete" measurement(x) # the same with measurement(x) <- "metric, discrete"x <- declared( c(-2, 1:5, -1), labels = c(Good = 1, Bad = 5, DK = -1), na_values = c(-1, -2), label = "Test variable" ) x measurement(x) # automatically recognized as categorical measurement(x) <- "ordinal" measurement(x) # the same with measurement(x) <- "categorical, ordinal" set.seed(1890) x <- declared( sample(c(18:90, -91), 20, replace = TRUE), labels = c("No answer" = -91), na_values = -91, label = "Respondent's age" ) # automatically recognized as quantitative measurement(x) <- "discrete" measurement(x) # the same with measurement(x) <- "metric, discrete"
Functions to extract information about the declared missing values, or to declare such values if they are present in the data.
missing_range(x) missing_range(x) <- value missing_values(x) missing_values(x) <- valuemissing_range(x) missing_range(x) <- value missing_values(x) missing_values(x) <- value
x |
A vector. |
value |
Any vector of values that should be declared as missing
(for |
missing_values() will return a vector of one or more values.
missing_range() will return a numeric vector of length 2.
x <- declared(c(-2, 1:5, -1), labels = c(Good = 1, Bad = 5, DK = -1, NotApplicable = -2), na_values = c(-1, -2) ) x missing_values(x) missing_range(x) <- c(-10, -7) missing_range(x)x <- declared(c(-2, 1:5, -1), labels = c(Good = 1, Bad = 5, DK = -1, NotApplicable = -2), na_values = c(-1, -2) ) x missing_values(x) missing_range(x) <- c(-10, -7) missing_range(x)
Functions to compute weighted tables or summaries, based on a vector of
frequency weights. These are reimplementations of various existing functions,
adapted to objects of class "declared" (see Details below)
w_IQR(x, wt = NULL, na.rm = FALSE, ...) w_fivenum(x, wt = NULL, na.rm = FALSE) w_mean(x, wt = NULL, trim = 0, na.rm = TRUE) w_median(x, wt = NULL, na.rm = TRUE, ...) w_mode(x, wt = NULL) w_quantile(x, wt = NULL, probs = seq(0, 1, 0.25), na.rm = TRUE, ...) w_sd(x, wt = NULL, method = NULL, na.rm = TRUE) w_standardize(x, wt = NULL, na.rm = TRUE) w_summary(x, wt = NULL, ...) w_table( x, y = NULL, wt = NULL, values = FALSE, valid = TRUE, observed = TRUE, margin = NULL, vlabel = FALSE ) w_var(x, wt = NULL, method = NULL, na.rm = TRUE)w_IQR(x, wt = NULL, na.rm = FALSE, ...) w_fivenum(x, wt = NULL, na.rm = FALSE) w_mean(x, wt = NULL, trim = 0, na.rm = TRUE) w_median(x, wt = NULL, na.rm = TRUE, ...) w_mode(x, wt = NULL) w_quantile(x, wt = NULL, probs = seq(0, 1, 0.25), na.rm = TRUE, ...) w_sd(x, wt = NULL, method = NULL, na.rm = TRUE) w_standardize(x, wt = NULL, na.rm = TRUE) w_summary(x, wt = NULL, ...) w_table( x, y = NULL, wt = NULL, values = FALSE, valid = TRUE, observed = TRUE, margin = NULL, vlabel = FALSE ) w_var(x, wt = NULL, method = NULL, na.rm = TRUE)
x |
A numeric vector for summaries, or declared / factor for frequency tables |
wt |
A numeric vector of frequency weights |
na.rm |
Logical, should the empty missing values be removed? |
... |
Further arguments passed to or from other methods. |
trim |
A fraction (0 to 0.5) of observations to be trimmed from each end of x before the mean is computed. Values of trim outside that range are taken as the nearest endpoint. |
probs |
Numeric vector of probabilities with values in [0,1] |
method |
Character, specifying how the result is scaled, see 'Details' below. |
y |
An optional variable, to create crosstabs; must have the same length as x |
values |
Logical, print the values in the table rows |
valid |
Logical, print separate percent distribution for valid values, if any missing values are present; for cross tables, use valid values only |
observed |
Logical, print the observed categories only |
margin |
Numeric, indicating the margin to calculate crosstab proportions: 0 from the total, 1 from row totals and 2 from column totals |
vlabel |
Logical, print the variable label, if existing |
Weighted summaries
A frequency table is usually performed for a categorical variable, displaying the frequencies of the respective categories. Note that general variables containing text are not necessarily factors, despite having a small number of characters.
A general table of frequencies, using the base function table(), ignores
the defined missing values (which are all stored as NAs). The
reimplementation of this function in w_table() takes care of this detail,
and presents frequencies for each separately defined missing values. Similar
reimplementations for the other functions have the same underlying objective.
It is also possible to perform a frequency table for numerical variables, if the number of values is limited (an arbitrary and debatable upper limit of 15 is used). An example of such variable can be the number of children, where each value can be interpreted as a class, containing a single value (for instance 0 meaning the category of people with no children).
Objects of class declared are not pure categorical variables (R factors)
but they are nevertheless interpreted as if they were factors, to allow
producing frequency tables. Given the high similarity with package
haven, objects of class haven_labelled_spss are automatically
coerced to objects of class declared and treated accordingly.
The argument values makes sense only when the input is of family class
declared, otherwise for regular (base R) factors the values are
just a sequence of numbers.
The later introduced argument observed is useful in situations when a
variable has a very large number of potential values, and a smaller subset of
actually observed ones. As an example, the variable “Occupation” has
hundreds of possible values in the ISCO08 codelist, and not all of them might
be actually observed. When activated, this argument restricts the printed
frequency table to the subset of observed values only.
The argument method can be one of "unbiased" or "ML".
When this is set to "unbiased", the result is an unbiased estimate
using Bessel's correction. When this is set to "ML", the result is the
maximum likelihood estimate for a Gaussian distribution.
The argument wt refers only to frequency weights. Users should be
aware of the differences between frequency weights, analytic weights,
probability weights, design weights, post-stratification weights etc. For
purposes of inferential testing, Thomas Lumley's package survey
should be employed.
If no frequency weights are provided, the result is identical to the corresponding base functions.
The function w_quantile() extensively borrowed ideas from packages
stats and Hmisc, to ensure a constant interpolation that would
produce the same quantiles if no weights are provided or if all
weights are equal to 1.
Other arguments can be passed to the stats function quantile() via the
three dots ... argument, and their extensive explanation is found in the
corresponding stats function's help page.
For all functions, the argument na.rm refers to the empty missing values
and its default is set to TRUE. The declared missing values are automatically
eliminated from the summary statistics, even if this argument is deactivated.
The function w_mode() returns the weighted mode of a variable. Unlike the
other functions where the prefix w_ signals a weighted version of the
base function with the same name, this has nothing to do with the base
function mode() which refers to the storage mode / type of an R object.
A vector of (weighted) values.
Adrian Dusa
set.seed(215) # a pure categorical variable x <- factor(sample(letters[1:5], 215, replace = TRUE)) w_table(x) # simulate number of children x <- sample(0:4, 215, replace = TRUE) w_table(x) # simulate a Likert type response scale from 1 to 7 values <- sample(c(1:7, -91), 215, replace = TRUE) x <- declared(values, labels = c("Good" = 1, "Bad" = 7)) w_table(x) # Defining missing values missing_values(x) <- -91 w_table(x) # Defined missing values with labels values <- sample(c(1:7, -91, NA), 215, replace = TRUE) x <- declared( values, labels = c("Good" = 1, "Bad" = 7, "Don't know" = -91), na_values = -91 ) w_table(x) # Including the values in the table of frequencies w_table(x, values = TRUE) # An example involving multiple variables DF <- data.frame( Area = declared( sample(1:2, 215, replace = TRUE, prob = c(0.45, 0.55)), labels = c(Rural = 1, Urban = 2) ), Gender = declared( sample(1:2, 215, replace = TRUE, prob = c(0.55, 0.45)), labels = c(Males = 1, Females = 2) ), Age = sample(18:90, 215, replace = TRUE), Children = sample(0:5, 215, replace = TRUE) ) w_table(DF$Gender) w_sd(DF$Age) # Weighting: observed proportions op <- proportions(with(DF, table(Gender, Area))) # Theoretical proportions: 53% Rural, and 50.2% Females tp <- rep(c(0.53, 0.47), each = 2) * rep(c(0.498, 0.502), 2) # Corrections by strata fweights <- tp / op DF$fweight <- fweights[match(10 * DF$Area + DF$Gender, c(11, 12, 21, 22))] with(DF, w_table(Gender, wt = fweight)) with(DF, w_mean(Age, wt = fweight)) with(DF, w_quantile(Age, wt = fweight))set.seed(215) # a pure categorical variable x <- factor(sample(letters[1:5], 215, replace = TRUE)) w_table(x) # simulate number of children x <- sample(0:4, 215, replace = TRUE) w_table(x) # simulate a Likert type response scale from 1 to 7 values <- sample(c(1:7, -91), 215, replace = TRUE) x <- declared(values, labels = c("Good" = 1, "Bad" = 7)) w_table(x) # Defining missing values missing_values(x) <- -91 w_table(x) # Defined missing values with labels values <- sample(c(1:7, -91, NA), 215, replace = TRUE) x <- declared( values, labels = c("Good" = 1, "Bad" = 7, "Don't know" = -91), na_values = -91 ) w_table(x) # Including the values in the table of frequencies w_table(x, values = TRUE) # An example involving multiple variables DF <- data.frame( Area = declared( sample(1:2, 215, replace = TRUE, prob = c(0.45, 0.55)), labels = c(Rural = 1, Urban = 2) ), Gender = declared( sample(1:2, 215, replace = TRUE, prob = c(0.55, 0.45)), labels = c(Males = 1, Females = 2) ), Age = sample(18:90, 215, replace = TRUE), Children = sample(0:5, 215, replace = TRUE) ) w_table(DF$Gender) w_sd(DF$Age) # Weighting: observed proportions op <- proportions(with(DF, table(Gender, Area))) # Theoretical proportions: 53% Rural, and 50.2% Females tp <- rep(c(0.53, 0.47), each = 2) * rep(c(0.498, 0.502), 2) # Corrections by strata fweights <- tp / op DF$fweight <- fweights[match(10 * DF$Area + DF$Gender, c(11, 12, 21, 22))] with(DF, w_table(Gender, wt = fweight)) with(DF, w_mean(Age, wt = fweight)) with(DF, w_quantile(Age, wt = fweight))