| 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 
[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