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Combine records helper functions

Source: R/combine_records_class.R
combine_records_helper_functions.Rd

This page documents helper functions for use with combine_records().

Usage

.mode(ties = FALSE, na.rm = TRUE)

.mean()

.median()

.collapse(separator, na_string = "NA")

.select_max(max_col, use_abs = FALSE, keep_NA = FALSE)

.select_min(min_col, use_abs = FALSE, keep_NA = FALSE)

.select_match(match_col, search_col, separator, na_string = "NA")

.select_exact(match_col, match, separator, na_string = "NA")

.unique(separator, na_string = "NA", digits = 6, drop_na = FALSE, sort = FALSE)

.prioritise(match_col, priority, separator, no_match = NA, na_string = "NA")

.nothing()

.count()

.select_grade(grade_col, keep_NA = FALSE, upper_case = TRUE)

Arguments

ties

(logical) If TRUE then all records matching the tied groups are returned. Otherwise the first record is returned.

na.rm

(logical) If TRUE then NA is ignored

separator

(character, NULL) if !NULL this string is used to collapse matches with the same priority

na_string

(character) NA values are replaced with this string

max_col

(character) the column name to search for the maximum value.

use_abs

(logical) If TRUE then the sign of the values is ignored.

keep_NA

(logical) If TRUE keeps records with NA values

min_col

(character) the column name to search for the minimum value.

match_col

(character) the column with labels to prioritise

search_col

(character) the name of a column to use as a reference for locating values in the matching column.

match

(character) a value to search for in the matching column.

digits

(numeric) the number of digits to use when converting numerical values to characters when determining if values are unique.

sort

(logical) sort the values before collapsing.

priority

(character) a list of labels in priority order

no_match

(character, NULL) if !NULL then annotations not matching any of the priority labels are replaced with this value

grade_col

(character) the name of a column containing grades

upper_case

(logical) If TRUE then grades are compared to upper case letters to determine their ordering, otherwise lower case.

Value

A function for use with combine_records()

Functions

  • .mode(): returns the most common value, excluding NA. If ties == TRUE then all tied values are returned, otherwise the first value in a sorted unique list is returned (equal to min if numeric). If na.rm = FALSE then NA are included when searching for the modal value and placed last if ties = FALSE (values are returned preferentially over NA).

  • .mean(): calculates the mean value, excluding NA if na.rm = TRUE

  • .median(): calculates the median value, excluding NA if na.rm = TRUE

  • .collapse(): collapses multiple matching records into a single string using the provided separator.

  • .select_max(): selects a record based on the index of the maximum value in a another column.

  • .select_min(): selects a record based on the index of the minimum in a second column.

  • .select_match(): returns all records based on the indices of identical matches in a second column and collapses them useing the provided separator.

  • .select_exact(): returns records based on the index of identical value matching the match parameter within the current column, and collapses them using the provided separator if necessary.

  • .unique(): collapses a set of records to a set of unique values using the provided separator. digits can be provided for numeric columns to control the precision used when determining unique values.

  • .prioritise(): reduces a set of annotations by prioritising values according to the input. If there are multiple matches with the same priority then they are collapsed using a separator.

  • .nothing(): a pass-through function to allow some annotation table columns to remain unchanged.

  • .count(): adds a new column indicating the number of annotations that match the given grouping variable.

  • .select_grade(): returns records based on the index of the best grade in a second list. The best grade is defined as "A" for upper_case = TRUE or "a" for upper_case = FALSE and the worst grade is "Z" or "z". Any non-exact matches to a character in LETTERS or letters are replaced with NA.

Examples


# Select matching records
M <- combine_records(
    group_by = "example",
    default_fcn = .select_match(
        match_col = "match_column",
        match = "find_me",
        separator = ", ",
        na_string = "NA"
    )
)
#> Error in .select_match(match_col = "match_column", match = "find_me",     separator = ", ", na_string = "NA"): unused argument (match = "find_me")

# Collapse unique values
M <- combine_records(
    group_by = "example",
    default_fcn = .unique(
        digits = 6,
        separator = ", ",
        na_string = "NA",
        sort = FALSE
    )
)

# Prioritise by source
M <- combine_records(
    group_by = "InChiKey",
    default_fcn = .prioritise(
        match_col = "source",
        priority = c("CD", "LS"),
        separator = "  || "
    )
)

# Do nothing to all columns
M <- combine_records(
    group_by = "InChiKey",
    default_fcn = .nothing()
)

# Add a column with the number of records with a matching inchikey
M <- combine_records(
    group_by = "InChiKey",
    fcns = list(
        count = .count()
    )
)

# Select annotation with highest (best) grade
M <- combine_records(
    group_by = "InChiKey",
    default_fcn = .select_grade(
        grade_col = "grade",
        keep_NA = FALSE,
        upper_case = TRUE
    )
)