remove_points: Remove specific points from an exdf object

In PhotoGEA: Photosynthetic Gas Exchange Analysis

Remove specific points from an exdf object

Description

Removes all points from an exdf object that satisfy a set of conditions.

Usage

  remove_points(exdf_obj, ..., method = 'remove')

Arguments

exdf_obj	An exdf object.
...	Each optional argument should be a list of named elements that specify points to be removed from exdf_obj. For example, list(species = 'soybean', plot = c('1a', '1b')) specifies the set of points where (1) species is 'soybean' and (2) plot is '1a' or '1b'.
method	Specify whether to remove points ('remove') or designate them as being excluded from subsequent fits ('exclude'); see below for more details.

Value

This function returns an exdf object formed from exdf_obj, where the result depends on the value of method.

When method is 'remove', the returned object is a modified copy of exdf_obj where all rows that meet the conditions specified by the optional arguments have been removed.

When method is 'exclude', the returned object is a modified copy of exdf_obj with a new column called include_when_fitting. The value of this column is FALSE for all rows that meet the conditions specified by the optional arguments, and TRUE otherwise. Points where this column is FALSE will not be used for fitting by fit_c3_aci or other fitting functions.

See Also

exdf

Examples

# Create an exdf object by reading a Licor Excel file
licor_file <- read_gasex_file(
  PhotoGEA_example_file_path('ball_berry_1.xlsx')
)

# Print the number of points in the data set
nrow(licor_file)

# Remove the following:
# - All points where `obs` is 28 (1 point)
# - All points where `species` is `soybean` and `plot` is `1a` or `1b` (14 points)
licor_file_2 <- remove_points(
  licor_file,
  list(obs = 28),
  list(species = 'soybean', plot = c('1a', '1b')),
  method = 'remove'
)

# There should now be 15 fewer points remaining in the data set
nrow(licor_file_2)

# We can also specify the same points for exclusion rather than removal:
licor_file_3 <- remove_points(
  licor_file,
  list(obs = 28),
  list(species = 'soybean', plot = c('1a', '1b')),
  method = 'exclude'
)

print(licor_file_3[, c('species', 'plot', 'include_when_fitting')])

# The number of points where `include_when_fitting` is TRUE should be the same
# as the number of remaining rows when using the `remove` method
sum(licor_file_3[, 'include_when_fitting'])

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