check_required_variables: Make sure required variables exist

In PhotoGEA: Photosynthetic Gas Exchange Analysis

Make sure required variables exist

Description

Checks whether the input table has the required variables.

Usage

  check_required_variables(x, required_variables, check_NA = TRUE)

  ## S3 method for class 'data.frame'
check_required_variables(x, required_variables, check_NA = TRUE)

  ## S3 method for class 'exdf'
check_required_variables(x, required_variables, check_NA = TRUE)

Arguments

x	A table-like R object such as a data frame or an exdf.
required_variables	A set of variables that must each be included in x as columns.
check_NA	A logical value indicating whether to check for columns that are all NA; see below.

Details

check_required_variables is generic, with methods defined for data frames and exdf objects.

When x is an exdf, the required_variables input argument must be a list of named strings, where the name of each element specifies the name of a column that must be included in x, while the value of each column specifies the corresponding units for that column. If the value is NA, no unit checking will be performed.

When x is a data.frame, the required_variables input argument can be specified as a list (as if x were an exdf object) or as a character vector specifying the names of columns that should be included in x.

The required variables will be checked as follows:

• If any required variable columns are missing from the table, an informative error message will be thrown.

• If check_NA is TRUE and any required variable columns are entirely NA, an informative error message will be thrown.

• If any required variable colums have incorrect units, an informative error message will be thrown. (Only applies to exdf objects.)

Otherwise, check_required_variables will have no output and produce no messages.

This function is used internally by many other functions from the PhotoGEA package to check for important columns and make sure they have the correct units. For example, see the code for apply_gm by typing PhotoGEA::apply_gm in the R terminal.

Value

The check_required_variables function does not return anything.

See Also

exdf

Examples

# Create a simple exdf object
simple_exdf <- exdf(
  data.frame(A = c(3, 2, 7, 9), B = c(4, 5, 1, 8)),
  data.frame(A = 'm', B = 's', stringsAsFactors = FALSE),
  data.frame(A = 'Cat1', B = 'Cat2', stringsAsFactors = FALSE)
)

# Confirm that columns named `A` and `B` are in the object, and that they have
# units of `m` and `s`, respectively.
check_required_variables(simple_exdf, list(A = 'm', B = 's'))

# Confirm that columns named `A` and `B` are in the object, but only check units
# for the `A` column.
check_required_variables(simple_exdf, list(A = 'm', B = NA))

# Use the data frame method on `simple_exdf$main_data` to confirm that columns
# named `A` and `B` are present
check_required_variables(simple_exdf$main_data, c('A', 'B'))

PhotoGEA documentation built on April 11, 2025, 5:48 p.m.