Nothing
## -----------------------------------------------------------------------------
library(plantecowrap)
## -----------------------------------------------------------------------------
#Read in data from package
data <- read.csv(system.file("extdata", "example_1.csv",
package = "plantecowrap"),
stringsAsFactors = FALSE)
#Fit ACi curves
fits <- fitacis2(data = data,
varnames = list(ALEAF = "A",
Tleaf = "Tleaf",
Ci = "Ci",
PPFD = "PPFD",
Rd = "Rd",
Press = "Press"),
group1 = "Treat",
fitTPU = FALSE,
fitmethod = "bilinear",
gm25 = 10000, #Allows fitting on an ACi rather than ACc-basis
Egm = 0)
#Get ACi outputs
outputs <- acisummary(data, group1 = "Treat", fits = fits)
#Fit temperature response
#Note that this will return NA warnings because it runs through
#1000 sets of starting parameters for Vcmax and Jmax
tresp <- fit_topt_VJ(outputs)
#See parameters
tresp[[2]]
#See plot
tresp[[3]]
## -----------------------------------------------------------------------------
#Read in data from package
data2 <- read.csv(system.file("extdata", "example_2.csv",
package = "plantecowrap"),
stringsAsFactors = FALSE)
#Fit ACi curves
fits2 <- fitacis2(data = data2,
varnames = list(ALEAF = "A",
Tleaf = "Tleaf",
Ci = "Ci",
PPFD = "PPFD",
Rd = "Rd",
Press = "Press"),
group1 = "Grouping",
fitTPU = FALSE,
fitmethod = "bilinear",
gm25 = 10000,
Egm = 0)
#Get ACi outputs
outputs <- acisummary(data2, group1 = "Grouping", fits = fits2)
#NOTE: if fitacis2 fails to fit a curve, some output elements will be "Failed"
#and need to be removed before acisummary() is run
#Split grouping variable
outputs <- separate(outputs, col = "ID", into = c("Treat", "Block"), sep = "_")
#Note that this will return NA warnings because it runs through
#1000 sets of starting parameters for Vcmax and Jmax. Some of
#these sets will not work and return the NA warning.
tresps <- fit_topt_VJs(data = outputs,
group = "Block")
#Get parameters
pars <- get_t_pars(tresps)
#Get graphs
graphs <- get_t_graphs(tresps)
#Print graphs
#To print to current working directory, set path = "./".
print_graphs(graphs,
path = tempdir())
#View parameters
pars
#View graphs
#Note that the second graph is strange because A was simply multiplied by
#2 for the sample dataset
graphs[[1]]
graphs[[2]]
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.