compile_data: Compiling outputs from lists

In cdmuir/photosynthesis: Tools for Plant Ecophysiology & Modeling

Compiling outputs from lists

Description

Compiling outputs from lists

Usage

compile_data(data, output_type = "list", list_element)

Arguments

data	List of elements
output_type	Type of desired output. For graphs or models, use "list", for parameters, use "dataframe".
list_element	Which elements of the sublists do you wish to compile?

Value

compile_data converts the outputs of fit_many into a form more readily usable for analysis. Can be used to create dataframe of all fitted parameters, a list of model outputs, a list of graphs for plotting. This function is NOT restricted to compiling outputs from plantecophystools but could be used to compile elements from ANY list of lists.

Examples

# Read in your data
# Note that this data is coming from data supplied by the package
# hence the complicated argument in read.csv()
# This dataset is a CO2 by light response curve for a single sunflower
data <- read.csv(system.file("extdata", "A_Ci_Q_data_1.csv",
  package = "photosynthesis"
))

# Define a grouping factor based on light intensity to split the ACi
# curves
data$Q_2 <- as.factor((round(data$Qin, digits = 0)))

# Convert leaf temperature to K
data$T_leaf <- data$Tleaf + 273.15

# Fit many curves
fits <- fit_many(
  data = data,
  varnames = list(
    A_net = "A",
    T_leaf = "T_leaf",
    C_i = "Ci",
    PPFD = "Qin"
  ),
  funct = fit_aci_response,
  group = "Q_2"
)

# Compile graphs into a list for plotting
fits_graphs <- compile_data(fits,
  list_element = 2
)

# Plot one graph from the compiled list
plot(fits_graphs[[1]])

cdmuir/photosynthesis documentation built on April 11, 2025, 3:28 p.m.