Compiling outputs from lists
compile_data(data, output_type = "list", list_element)
List of elements
Type of desired output. For graphs or models, use "list", for parameters, use "dataframe".
Which elements of the sublists do you wish to compile?
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.
# \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"
)
#> Warning: `fit_many()` was deprecated in photosynthesis 2.1.3.
#>

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# 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]])
#> Warning: Removed 12 rows containing missing values (`geom_line()`).
# }