platt_modified: Platt Model Modification

In pam: Fast and Efficient Processing of PAM Data

Platt Model Modification

Description

This function enhances the Platt (1980) model by adding parameters not originally included in the model, which were introduced by other models. It also renames parameters to a standardized naming convention used across all models.

Usage

platt_modified(model_result)

Arguments

model_result

A list containing the results of the model, including parameters such as etr_max, alpha, and beta.

Details

A detailed documentation can be found under https://github.com/biotoolbox/pam?tab=readme-ov-file#platt_modified

Value

A modified model result as a list with the following elements:

• etr_type: ETR Type based on the model result.

• etr_regression_data: Regression data with ETR predictions based on the fitted model.

• sdiff: The difference between observed and predicted ETR values.

• a: Obtained parameter a, equal to etrmax_without_photoinhibition.

• b: Obtained parameter b, equal to alpha.

• c: Obtained parameter c, equal to beta.

• d: Not available, set to NA_real_.

• alpha: The initial slope of the light curve, transferred unchanged as alpha.

• beta: The photoinhibition of the light curve, transferred unchanged as beta.

• etrmax_with_photoinhibition: The maximum electron transport rate with photoinhibition, transferred as pm.

• etrmax_without_photoinhibition: The maximum electron transport rate without photoinhibition, transferred as ps.

• ik_with_photoinhibition: PAR where the transition point from light limitation to light saturation is achieved with photoinhibition, transferred as ik.

• ik_without_photoinhibition: PAR where the transition point from light limitation to light saturation is achieved without photoinhibition, transferred as is.

• im_with_photoinhibition: The PAR at which the maximum electron transport rate is achieved with photoinhibition, transferred as im.

• w: Not available, set to NA_real_.

• ib: Transferred unchanged as ib.

• etrmax_with_without_ratio: Ratio of etrmax_with_photoinhibition to etrmax_without_photoinhibition, and ik_with_photoinhibition to ik_without_photoinhibition.

Examples

path <- file.path(system.file("extdata", package = "pam"), "20240925.csv")
data <- read_dual_pam_data(path)

result <- platt_generate_regression_ETR_II(data)
modified_result <- platt_modified(result)

pam documentation built on April 4, 2025, 2:12 a.m.