platt_generate_regression_ETR_II: Platt Regression for ETR II

In pam: Fast and Efficient Processing of PAM Data

Platt Regression for ETR II

Description

Fits the Platt (1980) regression model using original naming conventions.

Usage

platt_generate_regression_ETR_II(
  data,
  alpha_start_value = platt_default_start_value_alpha,
  beta_start_value = platt_default_start_value_beta,
  ps_start_value = platt_default_start_value_ps
)

Arguments

data	A data.table from from read function (e.g.read_dual_pam_data).
alpha_start_value	Numeric. Initial value for \alpha. Default: alpha_start_value_platt_default.
beta_start_value	Numeric. Initial value for \beta. Default: beta_start_value_platt_default.
ps_start_value	Numeric. Initial value for P_s. Default: ps_start_value_platt_default.

Details

A detailed documentation can be found under https://github.com/biotoolbox/pam/tree/main#functions.

Value

A list containing:

• etr_regression_data: Predicted ETR values.

• residual_sum_of_squares: Difference between observed and predicted ETR values, expressed as the sum of squared residuals.

• root_mean_squared_error: Difference between observed and predicted ETR values, expressed as the root mean squared error.

• relative_root_mean_squared_error: Difference between observed and predicted ETR values, expressed as the relative root mean squared error, normalized by the mean.

• ps: Maximum electron transport rate without photoinhibition (P_s).

• alpha: Initial slope of the light curve (\alpha).

• beta: Photoinhibition (\beta).

• pm: Maximum electron transport rate with photoinhibition (P_m).

• ik: Transition PAR with photoinhibition (I_k).

• is: Transition PAR without photoinhibition (I_s).

• im: PAR at maximum ETR with photoinhibition (I_m).

• ib: (I_b)

References

Platt, T., Gallegos, C. L., & Harrison, W. G. (1980). Photoinhibition of photosynthesis in natural assemblages of marine phytoplankton. Journal of Marine Research, 38(4). Retrieved from https://elischolar.library.yale.edu/journal_of_marine_research/1525/.

Examples

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

result <- platt_generate_regression_ETR_II(data)

pam documentation built on April 30, 2026, 5:06 p.m.