Title: | Fast and Efficient Processing of PAM Data |
---|---|
Description: | Processing Chlorophyll Fluorescence & P700 Absorbance data generated by WALZ hardware. Four models are provided for the regression of Pi curves, which can be compared with each other in order to select the most suitable model for the data set. Control plots ensure the successful verification of each regression. Bundled output of alpha, ETRmax, Ik etc. enables fast and reliable further processing of the data. |
Authors: | Julien Böhm [cre, aut]
|
Maintainer: | Julien Böhm <[email protected]> |
License: | GPL-3 |
Version: | 1.0.2 |
Built: | 2025-02-25 11:34:20 UTC |
Source: | https://github.com/cran/pam |
Generates a plot of ETR data with different regression model predictions and a summary table.
combo_plot_control(title, data, model_results, name_list, color_list)
combo_plot_control(title, data, model_results, name_list, color_list)
title |
Character. Plot title. |
data |
Data frame. ETR and PAR data. |
model_results |
List. Regression data and parameters. |
name_list |
List. Names for models (legend and table). |
color_list |
List. Colors for model lines. |
A detailed documentation can be found under https://github.com/biotoolbox/pam?tab=readme-ov-file#combo_control_plot.
A plot with ETR data, regression results, and a summary table.
#' @examples path <- file.path(system.file("extdata", package = "pam"), "20240925.csv") data <- read_dual_pam_data(path)
model_results_eilers_peeters <- eilers_peeters_generate_regression_ETR_I(data) model_results_platt <- platt_generate_regression_ETR_I(data) model_results <- list(eilers_peeters_modified(model_results), platt_modified(model_results)) name_list <- c("Eilers-Peeters", "Platt") color_list <- c("red", "pink") plot <- combo_plot_control("test", data, model_results, name_list, color_list)
Compares multiple regression models for electron transport rate (ETR) data using predefined performance metrics.
compare_regression_models_ETR_I(data_dir)
compare_regression_models_ETR_I(data_dir)
data_dir |
A character string specifying the directory containing input data files. |
This function compares the performance of the following models:
Eilers-Peeters (1988)
Platt (1980)
Vollenweider (1965)
Walsby (1997)
Models are ranked based on the deviation between observed and predicted values. The results guide users in selecting the most appropriate model for their dataset. Start values for parameters cannot be adjusted within this function. A detailed documentation can be found under https://github.com/biotoolbox/pam?tab=readme-ov-file#walsby_modified
A vector with total points assigned to each regression model based on their performance. Models are ranked as follows:
1st place: 3 points
2nd place: 2 points
3rd place: 1 point
4th place: 0 points
If regression is not possible for a model, no points are awarded for any of the models for the respective file.
Eilers, P. H. C., & Peeters, J. C. H. (1988). A model for the relationship between light intensity and the rate of photosynthesis in phytoplankton. Ecological Modelling, 42(3-4), 199-215. Available at: doi:10.1016/0304-3800(88)90057-9
Platt, T., Gallegos, C. L., & Harrison, W. G. (1980). Photoinhibition of photosynthesis in natural assemblages of marine phytoplankton. Journal of Marine Research, 38(4). Available at: https://elischolar.library.yale.edu/journal_of_marine_research/1525/.
Romoth, K., Nowak, P., Kempke, D., Dietrich, A., Porsche, C., & Schubert, H. (2019). Acclimation limits of Fucus evanescens along the salinity gradient of the southwestern Baltic Sea. Botanica Marina, 62(1), 1-12. Available at: doi:10.1515/bot-2018-0098.
Vollenweider, R. A. (1965). Calculation models of photosynthesis-depth curves and some implications regarding day rate estimates in primary production measurements. In C. R. Goldman (Ed.), Primary Productivity in Aquatic Environments (pp. 427-457). Mem. Ist. Ital. Idrobiol., 18 Suppl., University of California Press, Berkeley.
Walsby, A. E. (1997). Numerical integration of phytoplankton photosynthesis through time and depth in a water column. New Phytologist, 136(2), 189-209. Available at: doi:10.1046/j.1469-8137.1997.00736.x.
path <- file.path(system.file("extdata", package = "pam")) points <- compare_regression_models_ETR_I(path)
path <- file.path(system.file("extdata", package = "pam")) points <- compare_regression_models_ETR_I(path)
Compares multiple regression models for electron transport rate (ETR) data using predefined performance metrics.
compare_regression_models_ETR_II(data_dir)
compare_regression_models_ETR_II(data_dir)
data_dir |
A character string specifying the directory containing input data files. |
This function compares the performance of the following models:
Eilers-Peeters (1988)
Platt (1980)
Vollenweider (1965)
Walsby (1997)
Models are ranked based on the deviation between observed and predicted values. The results guide users in selecting the most appropriate model for their dataset. Start values for parameters cannot be adjusted within this function. A detailed documentation can be found in the README.
A vector with total points assigned to each regression model based on their performance. Models are ranked as follows:
1st place: 3 points
2nd place: 2 points
3rd place: 1 point
4th place: 0 points
If regression is not possible for a model, no points are awarded for any of the models for the respective file.
Eilers, P. H. C., & Peeters, J. C. H. (1988). A model for the relationship between light intensity and the rate of photosynthesis in phytoplankton. Ecological Modelling, 42(3-4), 199-215. Available at: doi:10.1016/0304-3800(88)90057-9
Platt, T., Gallegos, C. L., & Harrison, W. G. (1980). Photoinhibition of photosynthesis in natural assemblages of marine phytoplankton. Journal of Marine Research, 38(4). Available at: https://elischolar.library.yale.edu/journal_of_marine_research/1525/.
Romoth, K., Nowak, P., Kempke, D., Dietrich, A., Porsche, C., & Schubert, H. (2019). Acclimation limits of Fucus evanescens along the salinity gradient of the southwestern Baltic Sea. Botanica Marina, 62(1), 1-12. Available at: doi:10.1515/bot-2018-0098.
Vollenweider, R. A. (1965). Calculation models of photosynthesis-depth curves and some implications regarding day rate estimates in primary production measurements. In C. R. Goldman (Ed.), Primary Productivity in Aquatic Environments (pp. 427-457). Mem. Ist. Ital. Idrobiol., 18 Suppl., University of California Press, Berkeley.
Walsby, A. E. (1997). Numerical integration of phytoplankton photosynthesis through time and depth in a water column. New Phytologist, 136(2), 189-209. Available at: doi:10.1046/j.1469-8137.1997.00736.x.
path <- file.path(system.file("extdata", package = "pam")) points <- compare_regression_models_ETR_II(path)
path <- file.path(system.file("extdata", package = "pam")) points <- compare_regression_models_ETR_II(path)
Default start value
eilers_peeters_default_start_value_a
eilers_peeters_default_start_value_a
An object of class numeric
of length 1.
Default start value
eilers_peeters_default_start_value_b
eilers_peeters_default_start_value_b
An object of class numeric
of length 1.
Default start value
eilers_peeters_default_start_value_c
eilers_peeters_default_start_value_c
An object of class numeric
of length 1.
Fits a regression model for ETR I based on Eilers-Peeters (1988), considering photoinhibition.
eilers_peeters_generate_regression_ETR_I( data, a_start_value = eilers_peeters_default_start_value_a, b_start_value = eilers_peeters_default_start_value_b, c_start_value = eilers_peeters_default_start_value_c )
eilers_peeters_generate_regression_ETR_I( data, a_start_value = eilers_peeters_default_start_value_a, b_start_value = eilers_peeters_default_start_value_b, c_start_value = eilers_peeters_default_start_value_c )
data |
A |
a_start_value |
Numeric. Starting value for |
b_start_value |
Numeric. Starting value for |
c_start_value |
Numeric. Starting value for |
A detailed documentation can be found under https://github.com/biotoolbox/pam?tab=readme-ov-file#eilers_peeters_generate_regression_etr_i-and-eilers_peeters_generate_regression_etr_ii.
A list containing:
etr_regression_data
: Predicted ETR values.
sdiff
: Deviation between actual and predicted values.
a
, b
, c
: Fitted parameters.
pm
: Maximum ETR ().
s
: Initial slope ().
ik
: Transition point from light limitation to light saturation ().
im
: PAR at maximum ETR ().
w
: Peak sharpness ().
Eilers, P. H. C., & Peeters, J. C. H. (1988). A model for the relationship between light intensity and the rate of photosynthesis in phytoplankton. Ecological Modelling, 42(3-4), 199-215. Available at: doi:10.1016/0304-3800(88)90057-9
path <- file.path(system.file("extdata", package = "pam"), "20240925.csv") data <- read_dual_pam_data(path) result <- eilers_peeters_generate_regression_ETR_I(data)
path <- file.path(system.file("extdata", package = "pam"), "20240925.csv") data <- read_dual_pam_data(path) result <- eilers_peeters_generate_regression_ETR_I(data)
Fits a regression model for ETR II based on Eilers-Peeters (1988), considering photoinhibition.
eilers_peeters_generate_regression_ETR_II( data, a_start_value = eilers_peeters_default_start_value_a, b_start_value = eilers_peeters_default_start_value_b, c_start_value = eilers_peeters_default_start_value_c )
eilers_peeters_generate_regression_ETR_II( data, a_start_value = eilers_peeters_default_start_value_a, b_start_value = eilers_peeters_default_start_value_b, c_start_value = eilers_peeters_default_start_value_c )
data |
A |
a_start_value |
Numeric. Starting value for |
b_start_value |
Numeric. Starting value for |
c_start_value |
Numeric. Starting value for |
A detailed documentation can be found under https://github.com/biotoolbox/pam?tab=readme-ov-file#eilers_peeters_generate_regression_etr_i-and-eilers_peeters_generate_regression_etr_ii.
A list containing:
etr_regression_data
: Predicted ETR values.
sdiff
: Deviation between actual and predicted values.
a
, b
, c
: Fitted parameters.
pm
: Maximum ETR ().
s
: Initial slope ().
ik
: Transition point from light limitation to light saturation ().
im
: PAR at maximum ETR ().
w
: Peak sharpness ().
Eilers, P. H. C., & Peeters, J. C. H. (1988). A model for the relationship between light intensity and the rate of photosynthesis in phytoplankton. Ecological Modelling, 42(3-4), 199-215. Available at: doi:10.1016/0304-3800(88)90057-9
path <- file.path(system.file("extdata", package = "pam"), "20240925.csv") data <- read_dual_pam_data(path) result <- eilers_peeters_generate_regression_ETR_II(data)
path <- file.path(system.file("extdata", package = "pam"), "20240925.csv") data <- read_dual_pam_data(path) result <- eilers_peeters_generate_regression_ETR_II(data)
This function enhances the Eilers and Peeters (1988) 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.
eilers_peeters_modified(model_result)
eilers_peeters_modified(model_result)
model_result |
A list containing the results of the model, including parameters such as |
A detailed documentation can be found under https://github.com/biotoolbox/pam?tab=readme-ov-file#eilers_peeters_modified
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
: The obtained parameter a
.
b
: The obtained parameter b
.
c
: The obtained parameter c
.
d
: Not available, set to NA_real_
.
alpha
: The initial slope of the light curve, transferred unchanged as s
.
beta
: Not available, set to NA_real_
.
etrmax_with_photoinhibition
: The maximum electron transport rate with photoinhibition, transferred as pm
.
etrmax_without_photoinhibition
: Not available, set to NA_real_
.
ik_with_photoinhibition
: PAR where the transition point from light limitation to light saturation is achieved with photoinhibition, transferred as ik
.
ik_without_photoinhibition
: Not available, set to NA_real_
.
im_with_photoinhibition
: The PAR at which the maximum electron transport rate is achieved with photoinhibition, transferred as im
.
w
: The sharpness of the peak, transferred as w
.
ib
: Not available, set to NA_real_
.
etrmax_with_without_ratio
: Not available, set to NA_real_
.
path <- file.path(system.file("extdata", package = "pam"), "20240925.csv") data <- read_dual_pam_data(path) result <- eilers_peeters_generate_regression_ETR_II(data) modified_result <- eilers_peeters_modified(result)
path <- file.path(system.file("extdata", package = "pam"), "20240925.csv") data <- read_dual_pam_data(path) result <- eilers_peeters_generate_regression_ETR_II(data) modified_result <- eilers_peeters_modified(result)
Default start value
platt_default_start_value_alpha
platt_default_start_value_alpha
An object of class numeric
of length 1.
Default start value
platt_default_start_value_beta
platt_default_start_value_beta
An object of class numeric
of length 1.
Default start value
platt_default_start_value_ps
platt_default_start_value_ps
An object of class numeric
of length 1.
Fits the Platt (1980) regression model using original naming conventions.
platt_generate_regression_ETR_I( 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 )
platt_generate_regression_ETR_I( 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 )
data |
A |
alpha_start_value |
Numeric. Initial value for |
beta_start_value |
Numeric. Initial value for |
ps_start_value |
Numeric. Initial value for |
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 .
A list containing:
etr_regression_data
: Predicted ETR values.
sdiff
: Deviation between actual and predicted ETR.
ps
: Maximum electron transport rate without photoinhibition ().
alpha
: Initial slope of the light curve ().
beta
: Photoinhibition ().
pm
: Maximum electron transport rate with photoinhibition ().
ik
: Transition PAR with photoinhibition ().
is
: Transition PAR without photoinhibition ().
im
: PAR at maximum ETR with photoinhibition ().
ib
: ()
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/.
path <- file.path(system.file("extdata", package = "pam"), "20240925.csv") data <- read_dual_pam_data(path) result <- platt_generate_regression_ETR_I(data)
path <- file.path(system.file("extdata", package = "pam"), "20240925.csv") data <- read_dual_pam_data(path) result <- platt_generate_regression_ETR_I(data)
Fits the Platt (1980) regression model using original naming conventions.
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 )
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 )
data |
A |
alpha_start_value |
Numeric. Initial value for |
beta_start_value |
Numeric. Initial value for |
ps_start_value |
Numeric. Initial value for |
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.
A list containing:
etr_regression_data
: Predicted ETR values.
sdiff
: Deviation between actual and predicted ETR.
ps
: Maximum electron transport rate without photoinhibition ().
alpha
: Initial slope of the light curve ().
beta
: Photoinhibition ().
pm
: Maximum electron transport rate with photoinhibition ().
ik
: Transition PAR with photoinhibition ().
is
: Transition PAR without photoinhibition ().
im
: PAR at maximum ETR with photoinhibition ().
ib
: ()
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/.
path <- file.path(system.file("extdata", package = "pam"), "20240925.csv") data <- read_dual_pam_data(path) result <- platt_generate_regression_ETR_II(data)
path <- file.path(system.file("extdata", package = "pam"), "20240925.csv") data <- read_dual_pam_data(path) result <- platt_generate_regression_ETR_II(data)
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.
platt_modified(model_result)
platt_modified(model_result)
model_result |
A list containing the results of the model, including parameters such as |
A detailed documentation can be found under https://github.com/biotoolbox/pam?tab=readme-ov-file#platt_modified
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
.
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)
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)
This function creates a control plot for the used model based on the provided data and model results.
plot_control(data, model_result, title, color = "black")
plot_control(data, model_result, title, color = "black")
data |
A 'data.table' containing the original ETR and yield data for the plot. |
model_result |
A list containing the fitting results of the used model and the calculated paramters (alpha, ik...). |
title |
A character string that specifies the title of the plot. |
color |
A color specification for the regression line in the plot. |
A detailed documentation can be found under https://github.com/biotoolbox/pam?tab=readme-ov-file#plot_control
A plot displaying the original ETR and Yield values and the regression data. A table below the plot shows the calculated data (alpha, ik...)
path <- file.path(system.file("extdata", package = "pam"), "20240925.csv") data <- read_dual_pam_data(path) result <- eilers_peeters_generate_regression_ETR_I(data) plot_control(data, result, "Control Plot")
path <- file.path(system.file("extdata", package = "pam"), "20240925.csv") data <- read_dual_pam_data(path) result <- eilers_peeters_generate_regression_ETR_I(data) plot_control(data, result, "Control Plot")
Reads raw CSV files generated by DualPAM software, calculates electron transport rate (ETR) values, and returns a cleaned dataset. Customization may be needed for non-DualPAM devices.
read_dual_pam_data( csv_path, remove_recovery = TRUE, etr_factor = 0.84, fraction_photosystem_I = 0.5, fraction_photosystem_II = 0.5 )
read_dual_pam_data( csv_path, remove_recovery = TRUE, etr_factor = 0.84, fraction_photosystem_I = 0.5, fraction_photosystem_II = 0.5 )
csv_path |
File path to the CSV file. |
remove_recovery |
Logical. Removes recovery measurements if |
etr_factor |
Numeric. Factor for ETR calculation. Default is |
fraction_photosystem_I |
Numeric. Relative distribution of absorbed PAR to photosystem I. Default is |
fraction_photosystem_II |
Numeric. Relative distribution of absorbed PAR to photosystem II. Default is |
Calculates ETR using:
A detailed documentation can be found under https://github.com/biotoolbox/pam?tab=readme-ov-file#read_dual_pam_data
A 'data.table' with processed data and calculated ETR values.
Heinz Walz GmbH. (2024). DUAL-PAM-100 DUAL-PAM/F MANUAL, 5th Edition, April 2024, Chapter 7 (pp. 162-172). Heinz Walz GmbH, Effeltrich, Germany. Available at: https://www.walz.com/files/downloads/manuals/dual-pam-100/DualPamEd05.pdf
path <- file.path(system.file("extdata", package = "pam"), "20240925.csv") data <- read_dual_pam_data(path)
path <- file.path(system.file("extdata", package = "pam"), "20240925.csv") data <- read_dual_pam_data(path)
Default start value
vollenweider_default_start_value_a
vollenweider_default_start_value_a
An object of class numeric
of length 1.
Default start value
vollenweider_default_start_value_alpha
vollenweider_default_start_value_alpha
An object of class numeric
of length 1.
Default start value
vollenweider_default_start_value_n
vollenweider_default_start_value_n
An object of class numeric
of length 1.
Default start value
vollenweider_default_start_value_pmax
vollenweider_default_start_value_pmax
An object of class numeric
of length 1.
Fits the Vollenweider (1965) regression model using original naming conventions from the publication.
vollenweider_generate_regression_ETR_I( data, pmax_start_value = vollenweider_default_start_value_a, a_start_value = vollenweider_default_start_value_a, alpha_start_value = vollenweider_default_start_value_alpha, n_start_value = vollenweider_default_start_value_n )
vollenweider_generate_regression_ETR_I( data, pmax_start_value = vollenweider_default_start_value_a, a_start_value = vollenweider_default_start_value_a, alpha_start_value = vollenweider_default_start_value_alpha, n_start_value = vollenweider_default_start_value_n )
data |
A |
pmax_start_value |
Numeric. Initial value for |
a_start_value |
Numeric. Initial value for |
alpha_start_value |
Numeric. Initial value for |
n_start_value |
Numeric. Initial value for |
A detailed documentation can be found under https://github.com/biotoolbox/pam?tab=readme-ov-file#vollenweider_generate_regression_etr_i-and-vollenweider_generate_regression_etr_ii.
A list containing:
etr_regression_data
: Predicted ETR values.
sdiff
: Deviation between actual and predicted ETR.
pmax
: Maximum electron transport rate ().
a
: Parameter .
alpha
: Parameter .
n
: Parameter .
popt
: Maximum electron transport rate with photoinhibition ().
ik
: Transition point from light limitation to light saturation without photoinhibition ().
iik
: Transition point from light limitation to light saturation with photoinhibition ().
pmax_popt_and_ik_iik_ratio
: Ratio of to
and
to
.
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.
path <- file.path(system.file("extdata", package = "pam"), "20240925.csv") data <- read_dual_pam_data(path) result <- vollenweider_generate_regression_ETR_I(data)
path <- file.path(system.file("extdata", package = "pam"), "20240925.csv") data <- read_dual_pam_data(path) result <- vollenweider_generate_regression_ETR_I(data)
Fits the Vollenweider (1965) regression model using original naming conventions from the publication.
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 )
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 )
data |
A |
pmax_start_value |
Numeric. Initial value for |
a_start_value |
Numeric. Initial value for |
alpha_start_value |
Numeric. Initial value for |
n_start_value |
Numeric. Initial value for |
A detailed documentation can be found under https://github.com/biotoolbox/pam?tab=readme-ov-file#vollenweider_generate_regression_etr_i-and-vollenweider_generate_regression_etr_ii.
A list containing:
etr_regression_data
: Predicted ETR values.
sdiff
: Deviation between actual and predicted ETR.
pmax
: Maximum electron transport rate ().
a
: Parameter .
alpha
: Parameter .
n
: Parameter .
popt
: Maximum electron transport rate with photoinhibition ().
ik
: Transition point from light limitation to light saturation without photoinhibition ().
iik
: Transition point from light limitation to light saturation with photoinhibition ().
pmax_popt_and_ik_iik_ratio
: Ratio of to
and
to
.
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.
path <- file.path(system.file("extdata", package = "pam"), "20240925.csv") data <- read_dual_pam_data(path) result <- vollenweider_generate_regression_ETR_II(data)
path <- file.path(system.file("extdata", package = "pam"), "20240925.csv") data <- read_dual_pam_data(path) result <- vollenweider_generate_regression_ETR_II(data)
This function adds parameters that were not originally included in the Vollenweider (1965) model, but were introduced by other models, and renames the parameters to a standardized one for all models.
vollenweider_modified(model_result)
vollenweider_modified(model_result)
model_result |
A list containing the results of the model, including parameters such as |
A detailed documentation can be found under https://github.com/biotoolbox/pam?tab=readme-ov-file#vollenweider_modified
A modified model result as a list containing 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
, here equal to etrmax_without_photoinhibition
.
b
: Obtained parameter b
, transferred as a
.
c
: Obtained parameter c
, here transferred as alpha
.
d
: Obtained parameter d
, here transferred as n
.
alpha
: The initial slope of the light curve.
beta
: Not available, here set to NA_real_
.
etrmax_with_photoinhibition
: The maximum electron transport rate with photoinhibition, transferred as popt
.
etrmax_without_photoinhibition
: The maximum electron transport rate without photoinhibition, transferred as pmax
.
ik_with_photoinhibition
: PAR where the transition point from light limitation to light saturation is achieved taking photoinhibition into account, transferred as iik
.
ik_without_photoinhibition
: PAR where the transition point from light limitation to light saturation is achieved not taking photoinhibition into account, transferred as ik
.
im_with_photoinhibition
: The PAR at which the maximum electron transport rate is achieved by taking photoinhibition into account, determined using the regression data from the model.
w
: Not available, here 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
.
path <- file.path(system.file("extdata", package = "pam"), "20240925.csv") data <- read_dual_pam_data(path) result <- vollenweider_generate_regression_ETR_II(data) modified_result <- vollenweider_modified(result)
path <- file.path(system.file("extdata", package = "pam"), "20240925.csv") data <- read_dual_pam_data(path) result <- vollenweider_generate_regression_ETR_II(data) modified_result <- vollenweider_modified(result)
Default start value
walsby_default_start_value_alpha
walsby_default_start_value_alpha
An object of class numeric
of length 1.
Default start value
walsby_default_start_value_beta
walsby_default_start_value_beta
An object of class numeric
of length 1.
Default start value
walsby_default_start_value_etr_max
walsby_default_start_value_etr_max
An object of class numeric
of length 1.
Fits a modified Walsby (1997) regression model without the respiration term, using Romoth (2019) naming conventions.
Calculates without accounting for photoinhibition.
walsby_generate_regression_ETR_I( data, etr_max_start_value = walsby_default_start_value_etr_max, alpha_start_value = walsby_default_start_value_alpha, beta_start_value = walsby_default_start_value_alpha )
walsby_generate_regression_ETR_I( data, etr_max_start_value = walsby_default_start_value_etr_max, alpha_start_value = walsby_default_start_value_alpha, beta_start_value = walsby_default_start_value_alpha )
data |
A |
etr_max_start_value |
Numeric. Initial value for |
alpha_start_value |
Numeric. Initial value for |
beta_start_value |
Numeric. Initial value for |
A detailed documentation can be found under https://github.com/biotoolbox/pam?tab=readme-ov-file#walsby_generate_regression_etr_i-and-walsby_generate_regression_etr_ii.
A list containing:
etr_regression_data
: Predicted ETR values.
sdiff
: Deviation between actual and predicted ETR.
etr_max
: Maximum ETR ().
alpha
: Initial slope ().
beta
: Photoinhibition factor ().
Walsby, A. E. (1997). Numerical integration of phytoplankton photosynthesis through time and depth in a water column. New Phytologist, 136(2), 189-209. Available at: doi:10.1046/j.1469-8137.1997.00736.x
Romoth, K., Nowak, P., Kempke, D., Dietrich, A., Porsche, C., & Schubert, H. (2019). Acclimation limits of Fucus evanescens along the salinity gradient of the southwestern Baltic Sea. Botanica Marina, 62(1), 1-12. Available at: doi:10.1515/bot-2018-0098
path <- file.path(system.file("extdata", package = "pam"), "20240925.csv") data <- read_dual_pam_data(path) result <- walsby_generate_regression_ETR_I(data)
path <- file.path(system.file("extdata", package = "pam"), "20240925.csv") data <- read_dual_pam_data(path) result <- walsby_generate_regression_ETR_I(data)
Fits a modified Walsby (1997) regression model without the respiration term, using Romoth (2019) naming conventions.
Calculates without accounting for photoinhibition.
walsby_generate_regression_ETR_II( data, etr_max_start_value = walsby_default_start_value_etr_max, alpha_start_value = walsby_default_start_value_alpha, beta_start_value = walsby_default_start_value_beta )
walsby_generate_regression_ETR_II( data, etr_max_start_value = walsby_default_start_value_etr_max, alpha_start_value = walsby_default_start_value_alpha, beta_start_value = walsby_default_start_value_beta )
data |
A |
etr_max_start_value |
Numeric. Initial value for |
alpha_start_value |
Numeric. Initial value for |
beta_start_value |
Numeric. Initial value for |
A detailed documentation can be found under https://github.com/biotoolbox/pam?tab=readme-ov-file#walsby_generate_regression_etr_i-and-walsby_generate_regression_etr_ii.
A list containing:
etr_regression_data
: Predicted ETR values.
sdiff
: Deviation between actual and predicted ETR.
etr_max
: Maximum ETR ().
alpha
: Initial slope ().
beta
: Photoinhibition factor ().
Walsby, A. E. (1997). Numerical integration of phytoplankton photosynthesis through time and depth in a water column. New Phytologist, 136(2), 189-209. Available at: doi:10.1046/j.1469-8137.1997.00736.x
Romoth, K., Nowak, P., Kempke, D., Dietrich, A., Porsche, C., & Schubert, H. (2019). Acclimation limits of Fucus evanescens along the salinity gradient of the southwestern Baltic Sea. Botanica Marina, 62(1), 1-12. Available at: doi:10.1515/bot-2018-0098
path <- file.path(system.file("extdata", package = "pam"), "20240925.csv") data <- read_dual_pam_data(path) result <- walsby_generate_regression_ETR_II(data)
path <- file.path(system.file("extdata", package = "pam"), "20240925.csv") data <- read_dual_pam_data(path) result <- walsby_generate_regression_ETR_II(data)
Enhances the Walsby (1997) model by adding parameters from other models and standardizing parameter names.
walsby_modified(model_result)
walsby_modified(model_result)
model_result |
A list of model results including |
A detailed documentation can be found under https://github.com/biotoolbox/pam?tab=readme-ov-file#walsby_modified
A list containing:
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.
etrmax_without_photoinhibition
: The maximum electron transport rate without photoinhibition, transferred as etr_max
.
ik_with_photoinhibition
: PAR where the transition point from light limitation to light saturation is achieved with photoinhibition.
ik_without_photoinhibition
: PAR where the transition point from light limitation to light saturation is achieved without photoinhibition.
im_with_photoinhibition
: PAR at the maximum ETR with photoinhibition.
w
: Not available, set to NA_real_
.
ib
: Not available, set to NA_real_
.
etrmax_with_without_ratio
: Ratio of etrmax_with_photoinhibition
to etrmax_without_photoinhibition
.
path <- file.path(system.file("extdata", package = "pam"), "20240925.csv") data <- read_dual_pam_data(path) result <- walsby_generate_regression_ETR_II(data) modified_result <- walsby_modified(result)
path <- file.path(system.file("extdata", package = "pam"), "20240925.csv") data <- read_dual_pam_data(path) result <- walsby_generate_regression_ETR_II(data) modified_result <- walsby_modified(result)
This function exports the raw input data, regression data, and model parameters into separate CSV files for easy access and further analysis.
write_model_result_csv(dest_dir, name, data, model_result)
write_model_result_csv(dest_dir, name, data, model_result)
dest_dir |
A character string specifying the directory where the CSV files will be saved. |
name |
A character string specifying the base name for the output files. |
data |
A data frame containing the raw input data used in the model. |
model_result |
A list containing the model results, including parameter values and regression data. |
This function generates three CSV files:
raw_data.csv: Contains the original raw data used in the model.
regression_data.csv: Includes the regression data with predicted electron transport rate (ETR) values.
model_result.csv: Summarizes the parameter values derived from the model results (excluding regression data), such as alpha
or beta
.
The 'name' parameter serves as a prefix for each file, ensuring clarity and organization in the output directory. A detailed documentation can be found under https://github.com/biotoolbox/pam?tab=readme-ov-file#write_model_result_csv
No return value, called for side effects
path <- file.path(system.file("extdata", package = "pam"), "20240925.csv") data <- read_dual_pam_data(path) result <- eilers_peeters_generate_regression_ETR_I(data) write_model_result_csv(tempdir(), "20240925", data, result)
path <- file.path(system.file("extdata", package = "pam"), "20240925.csv") data <- read_dual_pam_data(path) result <- eilers_peeters_generate_regression_ETR_I(data) write_model_result_csv(tempdir(), "20240925", data, result)