datawizard (version 0.4.0)

standardize: Standardization (Z-scoring)

Description

Performs a standardization of data (z-scoring), i.e., centering and scaling, so that the data is expressed in terms of standard deviation (i.e., mean = 0, SD = 1) or Median Absolute Deviance (median = 0, MAD = 1). When applied to a statistical model, this function extracts the dataset, standardizes it, and refits the model with this standardized version of the dataset. The normalize() function can also be used to scale all numeric variables within the 0 - 1 range.

For model standardization, see effectsize::standardize.default()

Usage

standardize(x, ...)
standardise(x, ...)
# S3 method for numeric
standardize(
  x,
  robust = FALSE,
  two_sd = FALSE,
  weights = NULL,
  reference = NULL,
  center = NULL,
  scale = NULL,
  verbose = TRUE,
  ...
)
# S3 method for factor
standardize(
  x,
  robust = FALSE,
  two_sd = FALSE,
  weights = NULL,
  force = FALSE,
  verbose = TRUE,
  ...
)
# S3 method for data.frame
standardize(
  x,
  robust = FALSE,
  two_sd = FALSE,
  weights = NULL,
  reference = NULL,
  center = NULL,
  scale = NULL,
  remove_na = c("none", "selected", "all"),
  force = FALSE,
  append = FALSE,
  select = NULL,
  exclude = NULL,
  ignore_case = FALSE,
  verbose = TRUE,
  ...
)
unstandardize(x, ...)
unstandardise(x, ...)
# S3 method for numeric
unstandardize(
  x,
  center = NULL,
  scale = NULL,
  reference = NULL,
  robust = FALSE,
  two_sd = FALSE,
  ...
)
# S3 method for data.frame
unstandardize(
  x,
  center = NULL,
  scale = NULL,
  reference = NULL,
  robust = FALSE,
  two_sd = FALSE,
  select = NULL,
  exclude = NULL,
  ...
)

Arguments

x

A (grouped) data frame, a vector or a statistical model (for unstandardize() cannot be a model).

...

Arguments passed to or from other methods.

robust

Logical, if TRUE, centering is done by subtracting the median from the variables and dividing it by the median absolute deviation (MAD). If FALSE, variables are standardized by subtracting the mean and dividing it by the standard deviation (SD).

two_sd

If TRUE, the variables are scaled by two times the deviation (SD or MAD depending on robust). This method can be useful to obtain model coefficients of continuous parameters comparable to coefficients related to binary predictors, when applied to the predictors (not the outcome) (Gelman, 2008).

weights

Can be NULL (for no weighting), or:

• For model: if TRUE (default), a weighted-standardization is carried out.

• For data.frames: a numeric vector of weights, or a character of the name of a column in the data.frame that contains the weights.

• For numeric vectors: a numeric vector of weights.

reference

A data frame or variable from which the centrality and deviation will be computed instead of from the input variable. Useful for standardizing a subset or new data according to another data frame.

center, scale

• For standardize(): Numeric values, which can be used as alternative to reference to define a reference centrality and deviation. If scale and center are of length 1, they will be recycled to match the length of selected variables for standardization. Else, center and scale must be of same length as the number of selected variables. Values in center and scale will be matched to selected variables in the provided order, unless a named vector is given. In this case, names are matched against the names of the selected variables.

• For unstandardize(): center and scale correspond to the center (the mean / median) and the scale (SD / MAD) of the original non-standardized data (for data frames, should be named, or have column order correspond to the numeric column). However, one can also directly provide the original data through reference, from which the center and the scale will be computed (according to robust and two_sd). Alternatively, if the input contains the attributes center and scale (as does the output of standardize()), it will take it from there if the rest of the arguments are absent.

verbose

Toggle warnings and messages on or off.

force

Logical, if TRUE, forces standardization of factors and dates as well. Factors are converted to numerical values, with the lowest level being the value 1 (unless the factor has numeric levels, which are converted to the corresponding numeric value).

remove_na

How should missing values (NA) be treated: if "none" (default): each column's standardization is done separately, ignoring NAs. Else, rows with NA in the columns selected with select / exclude ("selected") or in all columns ("all") are dropped before standardization, and the resulting data frame does not include these cases.

append

Logical or string. If TRUE, standardized variables get new column names (with the suffix "_z") and are appended (column bind) to x, thus returning both the original and the standardized variables. If FALSE, original variables in x will be overwritten by their standardized versions. If a character value, standardized variables are appended with new column names (using the defined suffix) to the original data frame.

select

Variables that will be included when performing the required tasks. Can be either

• a variable specified as a literal variable name (e.g., column_name),

• a string with the variable name (e.g., "column_name"), or a character vector of variable names (e.g., c("col1", "col2", "col3")),

• a formula with variable names (e.g., ~column_1 + column_2),

• a vector of positive integers, giving the positions counting from the left (e.g. 1 or c(1, 3, 5)),

• a vector of negative integers, giving the positions counting from the right (e.g., -1 or -1:-3),

• or one of the following select-helpers: starts_with(""), ends_with(""), contains(""), a range using : or regex("").

If NULL, selects all columns.

exclude

See select, however, column names matched by the pattern from exclude will be excluded instead of selected. If NULL (the default), excludes no columns.

ignore_case

Logical, if TRUE and when one of the select-helpers or a regular expression is used in select, ignores lower/upper case in the search pattern when matching against variable names.

Value

The standardized object (either a standardize data frame or a statistical model fitted on standardized data).

See Also

See center() for grand-mean centering of variables.

Other transform utilities: data_rescale(), data_reverse(), normalize(), ranktransform()

Examples

# NOT RUN {
d <- iris[1:4, ]

# vectors
standardise(d$Petal.Length)

# Data frames
# overwrite
standardise(d, select = c("Sepal.Length", "Sepal.Width"))

# append
standardise(d, select = c("Sepal.Length", "Sepal.Width"), append = TRUE)

# append, suffix
standardise(d, select = c("Sepal.Length", "Sepal.Width"), append = "_std")

# standardizing with reference center and scale
d <- data.frame(
  a = c(-2, -1, 0, 1, 2),
  b = c(3, 4, 5, 6, 7)
)

# default standardization, based on mean and sd of each variable
standardize(d) # means are 0 and 5, sd ~ 1.581139

# standardization, based on mean and sd set to the same values
standardize(d, center = c(0, 5), scale = c(1.581, 1.581))

# standardization, mean and sd for each variable newly defined
standardize(d, center = c(3, 4), scale = c(2, 4))

# standardization, taking same mean and sd for each variable
standardize(d, center = 1, scale = 3)
# }