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Type: Package
Title: Rapid A/Ci Response (RACiR) Data Analysis
Version: 2.0.0
Date: 2020-07-29
Maintainer: Joseph Stinziano <josephstinziano@gmail.com>
Description: Contains functions useful for reading in Licor 6800 files, correcting and analyzing rapid A/Ci response (RACiR) data. Requires some user interaction to adjust the calibration (empty chamber) data file to a useable range. Calibration uses a 1st to 5th order polynomial as suggested in Stinziano et al. (2017) <doi:10.1111/pce.12911>. Data can be processed individually or batch processed for all files paired with a given calibration file. RACiR is a trademark of LI-COR Biosciences, and used with permission.
URL: https://github.com/jstinzi/racir
BugReports: https://github.com/jstinzi/racir/issues
License: MIT + file LICENSE
Depends: R (≥ 4.0.0)
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
Imports: utils, stats, graphics
NeedsCompilation: no
Packaged: 2020-07-29 15:48:49 UTC; Joseph Stinziano
Author: Joseph Stinziano ORCID iD [aut, cre]
Repository: CRAN
Date/Publication: 2020-08-03 11:30:03 UTC

Corrects rapid A/Ci response (RACiR) data from leaves using empty chamber data.

Description

racircal Corrects your RACiR data based on calibration data. Produces corrected A vs. Ci graph. Output is a data frame with corrected RACiR data using variable names Acor and Cicor for the corrected A and Ci values.

Usage

racircal(
  data,
  caldata,
  mincut,
  maxcut,
  title,
  varnames = list(A = "A", Ca = "Ca", CO2_r = "CO2_r", E = "E", gtc = "gtc")
)

Arguments

data

Data frame with the RACiR response data

caldata

Data frame with the calibration data

mincut

Minimum cutoff value for reference CO2 (CO2_r). Used to cut out the data from the initial chamber mixing. Default value is set to the minimum COR_r value.

maxcut

Maximum cutoff value for reference CO2 (CO2_r). Used to cut out the data from the end of the response. Not needed in all cases. Default value is set to the maximum COR_r value.

title

Title of output graph - useful for batch RACiR corrections.

varnames

Variable names - this allows for the use of this code with other machines and setups where variable names may differ.

Value

racircal returns a data frame with corrected RACiR data

Examples


#Read in data
data <- read_6800(system.file("extdata", "poplar_2", package = "racir"))
caldata <- read_6800(system.file("extdata", "cal", package = "racir"))
#Correct data
data_corrected <- racircal(data = data, caldata = caldata,
                           mincut = 350, maxcut = 780, title = "Test")

Corrects rapid A/Ci response (RACiR) data from leaves using empty chamber data.

Description

racircal_advanced Interval correction for RACiR data.

Usage

racircal_advanced(
  data,
  caldata,
  mincut,
  maxcut,
  title,
  digits,
  varnames = list(A = "A", Ca = "Ca", CO2_r = "CO2_r", E = "E", gtc = "gtc")
)

Arguments

data

Data frame with the RACiR response data

caldata

Data frame with the calibration data

mincut

Minimum cutoff value for reference CO2 (CO2_r). Used to cut out the data from the initial chamber mixing. Default value is set to the minimum COR_r value.

maxcut

Maximum cutoff value for reference CO2 (CO2_r). Used to cut out the data from the end of the response. Not needed in all cases. Default value is set to the maximum COR_r value.

title

Title of output graph - useful for batch RACiR corrections.

digits

Specifies rounding for groups. Defaults to -2 (100s). Effectively uses 100 ppm intervals (e.g. data matching >50 ppm to 150 ppm would be assigned to an interval centered around 100 ppm for reference CO2).

varnames

Variable names - this allows for the use of this code with other machines and setups where variable names may differ.

Value

racircal_advanced racircalcheck allows visual checking of RACiR calibration data

Examples


#Read in data
data <- read_6800(system.file("extdata", "poplar_2", package = "racir"))
caldata <- read_6800(system.file("extdata", "cal", package = "racir"))
#Correct data
data_corrected <- racircal_advanced(data = data, caldata = caldata,
                                    mincut = 350, maxcut = 780,
                                    digits = -2, title = "Test")

Corrects a batch of rapid A/Ci response (RACiR) data

Description

racircalbatch Corrects your RACiR data files based on a calibration file. Produces diagnostic graphs of A vs. Ci for quality control. Output includes a list of data frames with corrected data.

Usage

racircalbatch(
  caldata,
  data,
  mincut,
  maxcut,
  title,
  varnames = list(A = "A", Ca = "Ca", CO2_r = "CO2_r", E = "E", gtc = "gtc")
)

Arguments

caldata

Data frame with the calibration data

data

List of data frames with the RACiR response data

mincut

Minimum cutoff value for reference CO2 (CO2_r). Used to cut out the data from the initial chamber mixing. Default value is set to the minimum COR_r value.

maxcut

Maximum cutoff value for reference CO2 (CO2_r). Used to cut out the data from the end of the response. Not needed in all cases. Default value is set to the maximum COR_r value.

title

Vector for titles of output graph - useful for batch RACiR corrections. Length must be equal to data list length

varnames

Variable names - this allows for the use of this code with other machines and setups where variable names may differ.

Value

racircalbatch calibrates a batch of RACiR data

Examples


#Create a list of files
files <- c(system.file("extdata", "poplar_1", package = "racir"),
          system.file("extdata", "poplar_2", package = "racir"))
data <- vector("list", length(files))
for(i in seq_along(files)){
 data[[i]] <- read_6800(files[i])
 names(data)[i] <- files[i]
}

caldata <- read_6800(system.file("extdata", "cal", package = "racir"))
output <- racircalbatch(caldata = caldata, data = data,
                       mincut = 300, maxcut = 780, title = files)

Corrects a batch of rapid A/Ci response (RACiR) data

Description

racircalbatch_advanced Corrects your RACiR data files based on a calibration file. Produces diagnostic graphs of A vs. Ci for quality control. Output includes a list of data frames with corrected data.

Usage

racircalbatch_advanced(
  caldata,
  data,
  mincut,
  maxcut,
  digits,
  title,
  varnames = list(A = "A", Ca = "Ca", CO2_r = "CO2_r", E = "E", gtc = "gtc")
)

Arguments

caldata

Data frame with the calibration data

data

List of data frames with the RACiR response data

mincut

Minimum cutoff value for reference CO2 (CO2_r). Used to cut out the data from the initial chamber mixing. Default value is set to the minimum COR_r value.

maxcut

Maximum cutoff value for reference CO2 (CO2_r). Used to cut out the data from the end of the response. Not needed in all cases. Default value is set to the maximum COR_r value.

digits

Specifies rounding for groups. Defaults to -2 (100s). Effectively uses 100 ppm intervals (e.g. data matching >50 ppm to 150 ppm would be assigned to an interval centered around 100 ppm for reference CO2).

title

Vector for titles of output graph - useful for batch RACiR corrections. Length must be equal to data list length

varnames

Variable names - this allows for the use of this code with other machines and setups where variable names may differ.

Value

racircalbatch_advanced uses racircal_advanced on many files

Examples


#Create a list of files
files <- c(system.file("extdata", "poplar_1", package = "racir"),
          system.file("extdata", "poplar_2", package = "racir"))
data <- vector("list", length(files))
for(i in seq_along(files)){
 data[[i]] <- read_6800(files[i])
 names(data)[i] <- files[i]
}

caldata <- read_6800(system.file("extdata", "cal", package = "racir"))
output <- racircalbatch_advanced(caldata = caldata, data = data,
                                mincut = 300, maxcut = 780, title = files)

Allows visual checking of rapid A/Ci response (RACiR) calibration data using empty chamber data.

Description

racircalcheck Used to check range of calibration file. Produces diagnostic graphs of A vs. Ci for quality control. Output includes plots for checking and confirming cutoff values, and a plot with the fit, as well as information as to which polynomial fit the data best.

Usage

racircalcheck(
  data,
  mincut,
  maxcut,
  varnames = list(A = "A", Ca = "Ca", CO2_r = "CO2_r", E = "E", gtc = "gtc")
)

Arguments

data

Data frame with the calibration (empty chamber) rapid A/Ci response

mincut

Minimum cutoff value for reference CO2 (CO2_r). Used to cut out the data from the initial chamber mixing. Default value is set to the minimum COR_r value.

maxcut

Maximum cutoff value for reference CO2 (CO2_r). Used to cut out the data from the end of the response. Not needed in all cases. Default value is set to the maximum COR_r value.

varnames

Variable names - this allows for the use of this code with other machines and setups where variable names may differ.

Value

racircalcheck allows visual checking of RACiR calibration data

Examples


#Read in the file
data <- read_6800(system.file("extdata", "cal", package = "racir"))
#Run calibration check
racircalcheck(data = data,
              mincut = 350,
              maxcut = 780)

Allows visual checking of rapid A/Ci response (RACiR) calibration data using empty chamber data.

Description

racircalcheck_advanced Used to check range of calibration file. Produces diagnostic graphs of A vs. Ci for quality control.

Usage

racircalcheck_advanced(
  data,
  mincut,
  maxcut,
  digits,
  varnames = list(A = "A", Ca = "Ca", CO2_r = "CO2_r", E = "E", gtc = "gtc")
)

Arguments

data

Data frame with the calibration (empty chamber) rapid A/Ci response

mincut

Minimum cutoff value for reference CO2 (CO2_r). Used to cut out the data from the initial chamber mixing. Default value is set to the minimum COR_r value.

maxcut

Maximum cutoff value for reference CO2 (CO2_r). Used to cut out the data from the end of the response. Not needed in all cases. Default value is set to the maximum COR_r value.

digits

Specifies rounding for groups. Defaults to -2 (100s). Effectively uses 100 ppm intervals (e.g. data matching >50 ppm to 150 ppm would be assigned to an interval centered around 100 ppm for reference CO2).

varnames

Variable names - this allows for the use of this code with other machines and setups where variable names may differ.

Value

racircalcheck_advanced returns a data frame with corrected RACiR data

Examples


#Read in data
data <- read_6800(system.file("extdata", "poplar_2", package = "racir"))
caldata <- read_6800(system.file("extdata", "cal", package = "racir"))
#Correct data
racircalcheck_advanced(data = data, mincut = 350, maxcut = 780)

Reads files from the Li-Cor 6800

Description

read_6800 Reads Li-Cor 6800 files, which are delimited by spaces and tabs.

Usage

read_6800(x)

Arguments

x

A Li-Cor 6800 data file name of the form: "mydata".

Value

read_6800 imports a Li-Cor 6800 file as a data frame

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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