messy_linelist: Create messy line list data

In simulist: Simulate Disease Outbreak Line List and Contacts Data

Create messy line list data

Description

Take line list output from sim_linelist() and replace elements of the ⁠<data.frame>⁠ with missing values (e.g. NA), introduce spelling mistakes and inconsistencies, as well as coerce date types.

Usage

messy_linelist(linelist, ...)

Arguments

linelist

Line list ⁠<data.frame>⁠ output from sim_linelist().

...

<dynamic-dots> Named elements to replace default settings. Only if names match exactly are elements replaced, otherwise the function errors. Accepted arguments and their defaults are: prop_missing A numeric between 0 and 1 for the proportion of missing values introduced. Default is 0.1 (10%). missing_value A single atomic R object used to represent missing values. Default is NA. prop_spelling_mistakes A numeric between 0 and 1 used to specify the proportion of spelling mistakes in character columns. Default is 0.1 (10%). inconsistent_sex A logical boolean to specify whether the ⁠$sex⁠ column uses "m" and "f", or inconsistently uses "m", "f", "M", "F", "male", "female", "Male" or "Female". Default is TRUE so sexes are sampled from the options. sex_as_numeric A logical boolean used to specify whether the values in the ⁠$sex⁠ column should be encoded as numeric values (0 and 1). Default is FALSE. sex_as_numeric cannot be TRUE if inconsistent_sex = TRUE. numeric_as_char A logical boolean used to specify whether numeric columns should be coerced to character. Default is TRUE. date_as_char A logical boolean used to specify whether Date columns should be coerced to character. Default is TRUE. inconsistent_dates A logical boolean used to specify whether the values in Date columns are inconsistently formatted (e.g. "%Y-%m-%d", "%Y/%m/%d", "%d-%m-%Y", or "%d %B %Y"). Default is FALSE. prop_int_as_word A numeric between 0 and 1 for the proportion of elements in integer columns should that are coerced to words (see english::words()). Default is 0.5 (50%). prop_duplicate_row A numeric between 0 and 1 for the proportion of rows to duplicate. Default is 0.01 (1%). If prop_duplicate_row > 0 then it is guaranteed that at least one row will be duplicated. inconsistent_id A logical boolean used to specify whether the ⁠$id⁠ column has inconsistent formatting by appending random prefixes and suffixes to a random sample (~10%) of IDs. Default is FALSE, so IDs are numbers (numeric, characters or words depending on prop_int_as_word and numeric_as_char).

Details

By default messy_linelist():

• Introduces 10% of values missing, i.e. converts to NA.

• Introduces spelling mistakes in 10% of character columns.

• Introduce inconsistency in the reporting of ⁠$sex⁠.

• Converts numeric columns (double & integer) to character.

• Converts Date columns to character.

• Converts 50% of integers to (English) words.

• Duplicates 1% of rows.

Setting missing_value to something other than NA will likely cause type coercion in the line list ⁠<data.frame>⁠ columns, most likely to character.

When setting sex_as_numeric to TRUE, male is set to 0 and female to 1. Only one of inconsistent_sex or sex_as_numeric can be TRUE, otherwise the function will error.

If numeric_as_char = TRUE and sex_as_numeric = TRUE then the sex encoded as 0 or 1 is converted to character. If prop_spelling_mistake > 0 and numeric_as_char = TRUE the columns that are converted from numeric to character do not have spelling mistakes introduced, because they are numeric characters stored as character strings. If prop_spelling_mistake > 0 and date_as_char = TRUE spelling mistakes are not introduced into dates.

The Date columns can be converted into an inconsistent format by setting inconsistent_dates = TRUE and it requires date_as_char = TRUE, if the latter is FALSE the function will error.

If numeric_as_char = FALSE and prop_int_as_word > 0 then the integer columns are converted to character string (either character numbers or words) but the other numeric columns are not coerced. Spelling mistakes are not introduced into integers converted to words when prop_spelling_mistakes > 0 and prop_int_as_word > 0.

Rows are duplicated after other messy modifications so the duplicated row contains identical messy elements.

Value

A messy line list ⁠<data.frame>⁠.

Examples

linelist <- sim_linelist()
messy_linelist <- messy_linelist(linelist)

# increasing proportion of missingness to 30% with a missing value of -99
messy_linelist <- messy_linelist(
  linelist,
  prop_missing = 0.3,
  missing_value = -99
)

# increasing proportion of spelling mistakes to 50%
messy_linelist <- messy_linelist(linelist, prop_spelling_mistakes = 0.5)

# encode `$sex` as `numeric`
messy_linelist <- messy_linelist(
  linelist,
  sex_as_numeric = TRUE,
  inconsistent_sex = FALSE
)

# inconsistently formatted dates
messy_linelist <- messy_linelist(linelist, inconsistent_dates = TRUE)

simulist documentation built on April 12, 2025, 1:34 a.m.