Package 'readMDTable'

Title: Read Markdown Tables into Tibbles
Description: Efficient reading of raw markdown tables into tibbles. Designed to accept content from strings, files, and URLs with the ability to extract and read multiple tables from markdown for analysis.
Authors: Jordan Bradford [aut, cre, cph]
Maintainer: Jordan Bradford <[email protected]>
License: GPL (>= 3)
Version: 0.2.0.9000
Built: 2024-10-30 06:45:02 UTC
Source: https://github.com/jrdnbradford/readmdtable

Help Index

Extract Markdown Tables from Markdown Files

Description

Extract Markdown Tables from Markdown Files

Usage

extract_md_tables(file, warn = TRUE, ...)

Arguments

file

Either a path to a file, a connection, or literal data (either a single string or a raw vector). Files starting with ⁠http://⁠, ⁠https://⁠, ⁠ftp://⁠, or ⁠ftps://⁠ will be automatically downloaded.
warn

Boolean. Should warnings be raised about possible issues with the passed file? Defaults to TRUE.
...

Arguments passed on to readr::read_delim

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

Character vector of strings to interpret as missing values. Set this option to character() to indicate no missing values.

quoted_na

[Deprecated] Should missing values inside quotes be treated as missing values (the default) or strings. This parameter is soft deprecated as of readr 2.0.0.

comment

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

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

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.

num_threads

The number of processing threads to use for initial parsing and lazy reading of data. If your data contains newlines within fields the parser should automatically detect this and fall back to using one thread only. However if you know your file has newlines within quoted fields it is safest to set num_threads = 1 explicitly.

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.

lazy

Read values lazily? By default, this is FALSE, because there are special considerations when reading a file lazily that have tripped up some users. Specifically, things get tricky when reading and then writing back into the same file. But, in general, lazy reading (lazy = TRUE) has many benefits, especially for interactive use and when your downstream work only involves a subset of the rows or columns.

Learn more in should_read_lazy() and in the documentation for the altrep argument of vroom::vroom().

Details

extract_md_tables attempts to capture all the markdown tables from file utilizing a regular expression and therefore requires that the tables follow the markdown table format much more closely than readMDTable::read_md_table.

Value

A tibble or list of tibbles.

Examples

md <-
"# Heading 1

We'll split the `mtcars` dataset for testing `extract_md_tables`.

## Heading 2

|model              |mpg |cyl|disp |hp |drat|wt   |qsec |vs |am |gear|carb|
|-------------------|----|---|-----|---|----|-----|-----|---|---|----|----|
|Mazda RX4          |21  |6  |160  |110|3.9 |2.62 |16.46|0  |1  |4   |4   |
|Mazda RX4 Wag      |21  |6  |160  |110|3.9 |2.875|17.02|0  |1  |4   |4   |
|Datsun 710         |22.8|4  |108  |93 |3.85|2.32 |18.61|1  |1  |4   |1   |
|Hornet 4 Drive     |21.4|6  |258  |110|3.08|3.215|19.44|1  |0  |3   |1   |

## Another Heading 2
Another paragraph.

With some lines.

Like this one.

|model              |mpg |cyl|disp |hp |drat|wt   |qsec |vs |am |gear|carb|
|-------------------|----|---|-----|---|----|-----|-----|---|---|----|----|
|Hornet Sportabout  |18.7|8  |360  |175|3.15|3.44 |17.02|0  |0  |3   |2   |
|Valiant            |18.1|6  |225  |105|2.76|3.46 |20.22|1  |0  |3   |1   |
|Duster 360         |14.3|8  |360  |245|3.21|3.57 |15.84|0  |0  |3   |4   |
|Merc 240D          |24.4|4  |146.7|62 |3.69|3.19 |20   |1  |0  |4   |2   |

Just some paragraph text here.

|model              |mpg |cyl|disp |hp |drat|wt   |qsec |vs |am |gear|carb|
|-------------------|----|---|-----|---|----|-----|-----|---|---|----|----|
|Cadillac Fleetwood |10.4|8  |472  |205|2.93|5.25 |17.98|0  |0  |3   |4   |
|Lincoln Continental|10.4|8  |460  |215|3   |5.424|17.82|0  |0  |3   |4   |
|Chrysler Imperial  |14.7|8  |440  |230|3.23|5.345|17.42|0  |0  |3   |4   |
|Fiat 128           |32.4|4  |78.7 |66 |4.08|2.2  |19.47|1  |1  |4   |1   |

|model              |mpg |cyl|disp |hp |drat|wt   |qsec |vs |am |gear|carb|
|-------------------|----|---|-----|---|----|-----|-----|---|---|----|----|
|Porsche 914-2      |26  |4  |120.3|91 |4.43|2.14 |16.7 |0  |1  |5   |2   |
|Lotus Europa       |30.4|4  |95.1 |113|3.77|1.513|16.9 |1  |1  |5   |2   |
|Ford Pantera L     |15.8|8  |351  |264|4.22|3.17 |14.5 |0  |1  |5   |4   |
|Ferrari Dino       |19.7|6  |145  |175|3.62|2.77 |15.5 |0  |1  |5   |6   |
|Maserati Bora      |15  |8  |301  |335|3.54|3.57 |14.6 |0  |1  |5   |8   |
|Volvo 142E         |21.4|4  |121  |109|4.11|2.78 |18.6 |1  |1  |4   |2   |"

# Extract tables from the markdown file
tables <- extract_md_tables(md)

# Display the 2nd table in the list
tables[[2]]

Read a Markdown Table into a Tibble

Description

Read a Markdown Table into a Tibble

Usage

read_md_table(file, warn = TRUE, ...)

Arguments

file

Either a path to a file, a connection, or literal data (either a single string or a raw vector). Files starting with ⁠http://⁠, ⁠https://⁠, ⁠ftp://⁠, or ⁠ftps://⁠ will be automatically downloaded.
warn

Boolean. Should warnings be raised about possible issues with the passed file? Defaults to TRUE.
...

Arguments passed on to readr::read_delim

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

Character vector of strings to interpret as missing values. Set this option to character() to indicate no missing values.

quoted_na

[Deprecated] Should missing values inside quotes be treated as missing values (the default) or strings. This parameter is soft deprecated as of readr 2.0.0.

comment

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

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

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.

num_threads

The number of processing threads to use for initial parsing and lazy reading of data. If your data contains newlines within fields the parser should automatically detect this and fall back to using one thread only. However if you know your file has newlines within quoted fields it is safest to set num_threads = 1 explicitly.

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.

lazy

Read values lazily? By default, this is FALSE, because there are special considerations when reading a file lazily that have tripped up some users. Specifically, things get tricky when reading and then writing back into the same file. But, in general, lazy reading (lazy = TRUE) has many benefits, especially for interactive use and when your downstream work only involves a subset of the rows or columns.

Learn more in should_read_lazy() and in the documentation for the altrep argument of vroom::vroom().

Details

read_md_table reads a markdown table into a tibble from a string, file, or URL. It uses readr::read_delim to efficiently read in data.

read_md_table expects file to be a markdown table. If file is a markdown file that contains more than just a table or tables, the table(s) should be extracted with extract_md_tables before reading them in.

If warn is TRUE, read_md_table will warn if there are potential issues with the provided markdown table. Depending on the issue, read_md_table may still correctly read the table. For instance, if the row separating the header from the other rows is malformed or any rows have missing leading or trailing pipes, warnings will be raised but the data will be read correctly. readr::read_delim will provide its own warnings if there are potential issues.

Value

A tibble created from the markdown table.

Examples

# Read from a file
read_md_table(read_md_table_example("mtcars.md"))

# Read from a string
read_md_table("| H1 | H2 | \n|-----|-----|\n| R1C1 | R1C2 |\n| R2C1 | R2C2 |")


# Read from a URL
read_md_table(
  "https://raw.githubusercontent.com/jrdnbradford/readMDTable/main/inst/extdata/iris.md"
)


# Get warnings for malformed tables
read_md_table(
  "| Name  | Age | City        | Date       |
   |-------|-----|-------------|------------|
   | Alice | 30  | New York    | 2021/01/08 |
   | Bob   | 25  | Los Angeles | 2023/07/22 |
     Carol | 27  | Chicago     | 2022/11/01  "
)

Get Path to readMDTable Examples

Description

Get Path to readMDTable Examples

Usage

read_md_table_example(file = NULL)

Arguments

file

Name of file. If NULL, the example files will be listed.

Details

readMDTable comes with a number of well-known datasets as example markdown tables in the inst/extdata directory. read_md_table_example will list the file names or return the path of a specified file.

Value

Vector of example file names if file is NULL, else the path to the example markdown table file.

Examples

# List the available example files
read_md_table_example()

# Get the path to the mtcars example file
read_md_table_example("mtcars.md")

# Read in an example file
mtcars_path <- read_md_table_example("mtcars.md")
read_md_table(mtcars_path)