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Read an delimited file with interlaced missing reasons into a tibble

Source: R/read.R
read_interlaced_delim.Rd

The read_interlaced_*(), family of functions extend readr's read_delim(), read_csv, etc. functions for use on data sources where values are interlaced with missing reasons. These functions return a tibble with interlaced columns.

Usage

read_interlaced_delim(
  file,
  delim = NULL,
  quote = "\"",
  escape_backslash = FALSE,
  escape_double = TRUE,
  col_names = TRUE,
  col_types = NULL,
  col_select = NULL,
  id = NULL,
  locale = readr::default_locale(),
  na = na_col_none(),
  comment = "",
  trim_ws = FALSE,
  skip = 0,
  n_max = Inf,
  guess_max = min(1000, n_max),
  name_repair = "unique",
  progress = readr::show_progress(),
  show_col_types = readr::should_show_types(),
  skip_empty_rows = TRUE
)

read_interlaced_csv(
  file,
  col_names = TRUE,
  col_types = NULL,
  col_select = NULL,
  id = NULL,
  locale = readr::default_locale(),
  na = na_col_none(),
  quote = "\"",
  comment = "",
  trim_ws = TRUE,
  skip = 0,
  n_max = Inf,
  guess_max = min(1000, n_max),
  name_repair = "unique",
  progress = readr::show_progress(),
  show_col_types = readr::should_show_types(),
  skip_empty_rows = TRUE
)

read_interlaced_csv2(
  file,
  col_names = TRUE,
  col_types = NULL,
  col_select = NULL,
  id = NULL,
  locale = readr::default_locale(),
  na = na_col_none(),
  quote = "\"",
  comment = "",
  trim_ws = TRUE,
  skip = 0,
  n_max = Inf,
  guess_max = min(1000, n_max),
  name_repair = "unique",
  progress = readr::show_progress(),
  show_col_types = readr::should_show_types(),
  skip_empty_rows = TRUE
)

read_interlaced_tsv(
  file,
  col_names = TRUE,
  col_types = NULL,
  col_select = NULL,
  id = NULL,
  locale = readr::default_locale(),
  na = na_col_none(),
  quote = "\"",
  comment = "",
  trim_ws = TRUE,
  skip = 0,
  n_max = Inf,
  guess_max = min(1000, n_max),
  name_repair = "unique",
  progress = readr::show_progress(),
  show_col_types = readr::should_show_types(),
  skip_empty_rows = TRUE
)

interlaced_vroom(
  file,
  delim = NULL,
  col_names = TRUE,
  col_types = NULL,
  col_select = NULL,
  id = NULL,
  skip = 0,
  n_max = Inf,
  na = na_col_none(),
  quote = "\"",
  comment = "",
  skip_empty_rows = TRUE,
  trim_ws = TRUE,
  escape_double = TRUE,
  escape_backslash = FALSE,
  locale = vroom::default_locale(),
  guess_max = 100,
  progress = vroom::vroom_progress(),
  show_col_types = NULL,
  .name_repair = "unique"
)

Arguments

file

Either a path to a file, a connection, or literal data (either a single string or a raw vector).

Files ending in .gz, .bz2, .xz, or .zip will be automatically uncompressed. Files starting with http://, https://, ftp://, or ftps:// will be automatically downloaded. Remote gz files can also be automatically downloaded and decompressed.

Literal data is most useful for examples and tests. To be recognised as literal data, the input must be either wrapped with I(), be a string containing at least one new line, or be a vector containing at least one string with a new line.

Using a value of clipboard() will read from the system clipboard.

delim

Single character used to separate fields within a record.

quote

Single character used to quote strings.

escape_backslash

Does the file use backslashes to escape special characters? This is more general than escape_double as backslashes can be used to escape the delimiter character, the quote character, or to add special characters like \\n.

escape_double

Does the file escape quotes by doubling them? i.e. If this option is TRUE, the value """" represents a single quote, \".

col_names

Either TRUE, FALSE or a character vector of column names.

If TRUE, the first row of the input will be used as the column names, and will not be included in the data frame. If FALSE, column names will be generated automatically: X1, X2, X3 etc.

If col_names is a character vector, the values will be used as the names of the columns, and the first row of the input will be read into the first row of the output data frame.

Missing (NA) column names will generate a warning, and be filled in with dummy names ...1, ...2 etc. Duplicate column names will generate a warning and be made unique, see name_repair to control how this is done.

col_types

One of NULL, a cols() specification, or a string. See vignette("readr") for more details.

If NULL, all column types will be inferred from guess_max rows of the input, interspersed throughout the file. This is convenient (and fast), but not robust. If the guessed types are wrong, you'll need to increase guess_max or supply the correct types yourself.

Column specifications created by list() or cols() must contain one column specification for each column. If you only want to read a subset of the columns, use cols_only().

Alternatively, you can use a compact string representation where each character represents one column:

  • c = character

  • i = integer

  • n = number

  • d = double

  • l = logical

  • f = factor

  • D = date

  • T = date time

  • t = time

  • ? = guess

  • _ or - = skip

By default, reading a file without a column specification will print a message showing what readr guessed they were. To remove this message, set show_col_types = FALSE or set options(readr.show_col_types = FALSE).

col_select

Columns to include in the results. You can use the same mini-language as dplyr::select() to refer to the columns by name. Use c() to use more than one selection expression. Although this usage is less common, col_select also accepts a numeric column index. See ?tidyselect::language for full details on the selection language.

id

The name of a column in which to store the file path. This is useful when reading multiple input files and there is data in the file paths, such as the data collection date. If NULL (the default) no extra column is created.

locale

The locale controls defaults that vary from place to place. The default locale is US-centric (like R), but you can use locale() to create your own locale that controls things like the default time zone, encoding, decimal mark, big mark, and day/month names.

na

A NA col spec defined by na_cols() or a character or numeric vector of values to interpret as missing values.

comment

A string used to identify comments. Any text after the comment characters will be silently ignored.

trim_ws

Should leading and trailing whitespace (ASCII spaces and tabs) be trimmed from each field before parsing it?

skip

Number of lines to skip before reading data. If comment is supplied any commented lines are ignored after skipping.

n_max

Maximum number of lines to read.

guess_max

Maximum number of lines to use for guessing column types. Will never use more than the number of lines read. See vignette("column-types", package = "readr") for more details.

name_repair, .name_repair

Handling of column names. The default behaviour is to ensure column names are "unique". Various repair strategies are supported:

  • "minimal": No name repair or checks, beyond basic existence of names.

  • "unique" (default value): Make sure names are unique and not empty.

  • "check_unique": No name repair, but check they are unique.

  • "unique_quiet": Repair with the unique strategy, quietly.

  • "universal": Make the names unique and syntactic.

  • "universal_quiet": Repair with the universal strategy, quietly.

  • A function: Apply custom name repair (e.g., name_repair = make.names for names in the style of base R).

  • A purrr-style anonymous function, see rlang::as_function().

This argument is passed on as repair to vctrs::vec_as_names(). See there for more details on these terms and the strategies used to enforce them.

progress

Display a progress bar? By default it will only display in an interactive session and not while knitting a document. The automatic progress bar can be disabled by setting option readr.show_progress to FALSE.

show_col_types

If FALSE, do not show the guessed column types. If TRUE always show the column types, even if they are supplied. If NULL (the default) only show the column types if they are not explicitly supplied by the col_types argument.

skip_empty_rows

Should blank rows be ignored altogether? i.e. If this option is TRUE then blank rows will not be represented at all. If it is FALSE then they will be represented by NA values in all the columns.

Value

A tibble(), with interlaced columns.

Examples

# Beep boop