Skip to contents padding-top: 70px;

Check response curve data for common issues

check_response_curve_data.Rd

Checks to make sure an exdf object representing response curve data has the expected number of rows and does not contain infinite values.

Usage

check_response_curve_data(
    licor_exdf,
    identifier_columns,
    expected_npts = 0,
    driving_column = NULL,
    driving_column_tolerance = 1.0,
    col_to_ignore_for_inf = 'gmc',
    error_on_failure = TRUE
  )

Arguments

licor_exdf

An exdf object representing data from a Licor gas exchange measurement system.

identifier_columns

A vector or list of strings representing the names of columns in licor_exdf that, taken together, uniquely identify each curve. This often includes names like plot, event, replicate, etc.

expected_npts

The number of points that should be in each response curve. If expected_npts == 0, then all response curves are expected to have the same (unspecified) number of points. If expected_npts < 0, then this check will be skipped.

driving_column

The name of a column that is systematically varied to produce each curve; for example, in a light response curve, this would typically by Qin. If driving_column is NULL, then this check will be skipped.

driving_column_tolerance

An absolute tolerance for the deviation of each value of driving_column away from its mean across all the curves; the driving_column_tolerance can be set to Inf to disable this check.

col_to_ignore_for_inf

Any columns to ignore while checking for infinite values. Mesophyll conductance (gmc) is often set to infinity intentionally so should be ignored when performing this check. To completely disable this check, set col_to_ignore_for_inf to NULL.

error_on_failure

A logical value indicating whether to send an error message when an issue is detected. See details below.

Details

This function makes a few basic checks to ensure that the Licor data includes the expected information and does not include any mistakes. If no problems are detected, this function will be silent with no return value. If a problem is detected and error_on_failure is TRUE, then it will print information about the issue and throw an error; if a problem is detected and error_on_failure is FALSE, then it will print information and only throw a warning.

This function will perform the following checks, some of which are optional:

  • If col_to_ignore_for_inf is not NULL, no numeric columns in licor_exdf should have infinite values, with the exception of columns designated in col_to_ignore_for_inf.

  • All elements of identifier_columns should be present as columns in licor_exdf. If driving_column is not NULL, it should also be present as a column in licor_exdf.

  • licor_exdf will be split into chunks according to the values of its identifier_columns. If this exdf file represents response curves, then each chunk should represent a single curve and a few additional checks can be performed:

    • If expected_npts >= 0, then each chunk should have the same number of points. If expected_npts > 0, then each chunk should have expected_npts points.

    • If driving_column is not NULL, then each code chunk should have the same sequence of values in this column. To allow for small variations, a nonzero driving_column_tolerance can be specified.

Examples

# Read an example Licor file included in the PhotoGEA package and check it.
# This file includes several 7-point light-response curves that can be uniquely
# identified by the values of its 'species' and 'plot' columns. Since these are
# light-response curves, each one follows a pre-set sequence of `Qin` values.
licor_file <- read_gasex_file(
  PhotoGEA_example_file_path('ball_berry_1.xlsx')
)

# Make sure there are no infinite values and that all curves have the same
# number of points
check_response_curve_data(licor_file, c('species', 'plot'))

# Make sure there are no inifinite values and that all curves have 7 points
check_response_curve_data(licor_file, c('species', 'plot'), 7)

# Make sure there are no infinite values, that all curves have 7 points, and
# that the values of the `Qin` column follow the same sequence in all curves
# (to within 1.0 micromol / m^2 / s)
check_response_curve_data(licor_file, c('species', 'plot'), 7, 'Qin', 1.0)