pam (version 2.0.2)

platt_generate_regression_ETR_II: 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
)

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: (\(I_b\))

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?tab=readme-ov-file#platt_generate_regression_etr_i-and-platt_generate_regression_etr_ii.

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

result <- platt_generate_regression_ETR_II(data)