print_graphs {plantecowrap}

Printing graphs from a list of graphs

Description

Printing graphs from a list of graphs

Usage

print_graphs(data, path, height = 5, width = 5, res = 600, units = "in", ...)

Arguments

data

List of graphs to output as .jpeg files

path

File path for printing out graphs. Use "./" to set to current working directory.

height

Height of output graphs. Defaults to 5.

width

Width of output graphs. Defaults to 5.

res

Resolution of output graphs. Defaults to 600.

units

Units of height and width. Defaults to "in".

...

Further arguments, specifically for jpeg().

Value

print_graphs creates jpeg files from a list of graphs based on the graph names. Used in combination with get_t_graphs. Output is a series of .jpeg files in the working directory.

Examples

#Read in data
data <- read.csv(system.file("extdata", "example_2.csv",
package = "plantecowrap"), stringsAsFactors = FALSE)
#Fit ACi Curves then fit temperature responses
fits <- fitacis2(data = data,
                 varnames = list(ALEAF = "A",
                                 Tleaf = "Tleaf",
                                 Ci = "Ci",
                                 PPFD = "PPFD",
                                 Rd = "Rd",
                                 Press = "Press"),
                 group1 = "Grouping",
                 fitTPU = FALSE,
                 fitmethod = "bilinear",
                 gm25 = 10000,
                 Egm = 0)
#Extract coefficients
outputs <- acisummary(data, group1 = "Grouping", fits = fits)
#Plot curve fits
for (i in 1:length(fits)) {
  plot(fits[[i]])
}
#Separate out grouping variable
outputs <- separate(outputs, col = "ID", c("Treat", "Block"), sep = "_")
#Fit the Topt model from Medlyn et al. 2002 for all individuals
#Output is a list of lists for each individual
#There is also a fit_topt_VJ for single temperature response
#fitting
out <- fit_topt_VJs(data = outputs,
                    group = "Block", #this grouping variable is for
                    #each individual
                    varnames = list(Vcmax = "Vcmax",
                                    Jmax = "Jmax",
                                    Tleaf = "Tleaf"),
                    limit_jmax = 100000,
                    limit_vcmax = 100000)
#Let's get the graphs out into a list
#You can get a graph using: graph[1]
graphs <- get_t_graphs(out)
#Print graphs out as jpegs into folder
print_graphs(graphs, path = tempdir())