get_all_fitted_cell_lengths: Calculates all cell lengths for each plant at a given...
In impres-lab/leafkin: Leaf kinematic analysis in R

View source: R/get_all_fitted_cell_lengths.R

get_all_fitted_cell_lengths

R Documentation

Calculates all cell lengths for each plant at a given interval.

Description

This function takes in cell length data. The provided cell length data must be in a data.frame or tibble. The first column are the plant IDs and are used in the LER analysis (header = plant_id). The second column contains the positions of the cell length measurements in the leaf's growth zone (in cm) (header = position). The third column contains the cell length measurements (header = cell_length).

Usage

get_all_fitted_cell_lengths(
  cell_length_data,
  interval_in_cm = 0.1,
  bw_multiplier = 1,
  alternative_bw = 0.5,
  tidy_cell_lengths = TRUE
)

Arguments

`cell_length_data`	data.frame or tibble containing the cell length data.
`interval_in_cm`	specifies the inteval at which cell lengths should be calculated (default = 0.1).
`bw_multiplier`	multiplies the calculated bandwidth with the provided number (default = 1).
`alternative_bw`	sets an alternative bandwidth if no band width could be calculated for the plant (default = 0.5).
`tidy_cell_lengths`	`TRUE` by default, resulting in cell length returned in the tidy format. When `FALSE`, the function will return cell lengths as a human readable wide table.

Details

Using the interval_in_cm variable, you indicate how often (i.e. at which interval) a cell length should be calculated over the entire growth zone. By default, it is set to 0.1 cm.

The bw_multiplier can be used to multiply the bandwidth. Usually, the calculated bandwidth is OK to use. Multiplying it by a number between 0 and 1 will follow the profile more strict. Multiplying the bandwidth with a number larger than 1 will make the fit more loose. Making the multiplier to small could result in an error.

An alternative bandwidth can be specified if, for some plants, no bandwidth could be estimated. Our advise is to use the mean bandwidth of bandwidths which were calculated. You can use the get_pdf_with_cell_length_fit_plots function to extract all these bandwidths and use them to calculate the mean bandwidth. When not specified, the alternative bandwidth is set to 0.5. Normally, the cell lengths are returned in a tidy format. When tidy_cell_lengths is set to FALSE, a human readable wide table is returned.