photosynthesis (version 2.1.5)

compile_data: Compiling outputs from lists

Description

Compiling outputs from lists

Usage

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

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.

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?

Examples

# \donttest{
# 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]])
# }