photosynthesis (version 2.1.5)

fit_many: Fitting many functions across groups

Description

We are no longer updating this function. Please use generic methods like map instead. See vignette("light-response") for an example.

Usage

fit_many(data, funct, group, progress = TRUE, ...)

Value

fit_many fits a function across every instance of a grouping variable.

Arguments

data

Dataframe

funct

Function to fit

group

Grouping variables

progress

Flag. Show progress bar?

...

Arguments for the function to fit. Use ?functionname to read the help file on available arguments for a given function.

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"
)

# Print the parameters
# First set of double parentheses selects an individual group value
# Second set selects an element of the sublist
fits[[3]][[1]]

# Print the graph
fits[[3]][[2]]

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


# Compile parameters into dataframe for analysis
fits_pars = compile_data(fits,
  output_type = "dataframe",
  list_element = 1
)
# }