vollenweider_generate_regression_ETR_II: Vollenweider Regression for ETR II

In pam: Fast and Efficient Processing of PAM Data

Vollenweider Regression for ETR II

Description

Fits the Vollenweider (1965) regression model using original naming conventions from the publication.

Usage

vollenweider_generate_regression_ETR_II(
  data,
  pmax_start_value = vollenweider_default_start_value_pmax,
  a_start_value = vollenweider_default_start_value_a,
  alpha_start_value = vollenweider_default_start_value_alpha,
  n_start_value = vollenweider_default_start_value_n
)

Arguments

data	A data.table from read function (e.g.read_dual_pam_data).
pmax_start_value	Numeric. Initial value for p_{max}. Default: pmax_start_values_vollenweider_default.
a_start_value	Numeric. Initial value for a. Default: a_start_values_vollenweider_default.
alpha_start_value	Numeric. Initial value for \alpha. Default: alpha_start_values_vollenweider_default.
n_start_value	Numeric. Initial value for n. Default: n_start_values_vollenweider_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.

• pmax: Maximum electron transport rate without photoinhibition (p_{max}).

• a: Parameter a.

• alpha: Parameter \alpha.

• n: Parameter n.

• popt: Maximum electron transport rate with photoinhibition (p_{opt}).

• ik: Transition point from light limitation to light saturation without photoinhibition (I_k).

• iik: Transition point from light limitation to light saturation with photoinhibition (I_k^\prime).

• pmax_popt_and_ik_iik_ratio: Ratio of p_{max} / p_{opt} and I_k / I_k^\prime.

References

Vollenweider, R. A. (1965). Calculation models of photosynthesis-depth curves and some implications regarding day rate estimates in primary production measurements, p. 427-457. In C. R. Goldman [ed.], Primary Productivity in Aquatic Environments. Mem. Ist. Ital. Idrobiol., 18 Suppl., University of California Press, Berkeley.

Examples

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

result <- vollenweider_generate_regression_ETR_II(data)

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