Help for package licoread

Title:

Reads Raw Files from Li-COR Gas Analyzers

Version:

0.2.0

Date:

2025-05-08

Description:

Reads raw files from Li-COR gas analyzers and produces a dataframe that can directly be used with 'fluxible' https://cran.r-project.org/package=fluxible.

License:

GPL (≥ 3)

Encoding:

UTF-8

RoxygenNote:

7.3.2

Suggests:

knitr, rmarkdown, testthat (≥ 3.0.0)

Config/testthat/edition:

Imports:

dplyr, jsonlite, lubridate, purrr, readr, rlang, stringr, tibble, tidyr, yaml

URL:

https://jogaudard.github.io/licoread/

BugReports:

https://github.com/jogaudard/licoread/issues

VignetteBuilder:

knitr

NeedsCompilation:

Packaged:

2025-05-08 16:31:58 UTC; jga051

Author:

Joseph Gaudard

[aut, cre]

Maintainer:

Joseph Gaudard <joseph.gaudard@pm.me>

Depends:

R (≥ 4.1.0)

Repository:

CRAN

Date/Publication:

2025-05-08 16:50:09 UTC

to read the raw data

Description

to read the raw data

Usage

data_82z(filepath, data_file, data_name, gases, filename)

Arguments

filepath

name and path to the 82z archive

data_file

name of the file with raw data

data_name

vector of colnames

gases

list of gases

filename

name of the 82z archive

Value

a long df with the actual data contained in the data file

create colnames for data tibble

Description

create colnames for data tibble

Usage

data_name_82z(filepath, data_file)

Arguments

filepath

name and path to the 82z archive

data_file

name of the file with raw data

Value

a character vector or the colnames of the data file

makes df from 81x files compatible with fluxible

Description

makes df from 81x files compatible with fluxible

Usage

fluxible_81x(df, focus_gas, id_cols, datetime_col)

Arguments

df

input dataframe from licoread

focus_gas

gas to select

id_cols

columns to identify unique fluxes

datetime_col

column containing datetime information

Value

a df with the focus gas column renamed as "f_conc" and f_fluxid in chronological order of datetime

makes df from 82z files compatible with fluxible

Description

makes df from 82z files compatible with fluxible

Usage

fluxible_82z(df, focus_gas)

Arguments

df

input dataframe from licoread

focus_gas

gas to select

Value

an unnested df with only the selected gas

reads Li-COR files in a given location

Description

reads Li-COR files in a given location

Usage

licoread(
  location,
  file_type = "auto",
  file_type_list = c("82z", "81x", "auto"),
  data_file = "data.csv",
  meta_file = "metadata.json",
  regex_file = "(\\w*-)*\\w*(?=([.]82z$))",
  sample = FALSE
)

Arguments

location

location of the files

file_type

type of file (82z or 81x). If "auto" (default), the function will try to detect it by itself.

file_type_list

list of file types

data_file

name of the file with raw data

meta_file

name of the file with meta data

regex_file

regex expression matching the name of the 82z file. Here in case the user has a different than the default and for easier updates.

sample

sample = n randomly selects n files to be imported. This allows for testing the setup before importing a potentially large list of files which will take time and be difficult to handle.

Value

a tibble (nested or not depending on raw data) containing all the data from the raw files present at the location provided

Examples

path_82z <- system.file("extdata/82z", package = "licoread")
licoread(path_82z)

finds out the file type for licoread

Description

finds out the file type for licoread

Usage

licoread_auto(file_list)

Arguments

file_list

list of files found in the location

Value

a single character string indicating the file type

selects the focus gas and makes a df to use in fluxible

Description

selects the focus gas and checks the columns needed for the fluxible workflow

Usage

licoread_to_fluxible(
  df,
  focus_gas,
  datetime_col,
  id_cols = c("File Name", "Obs#"),
  file_type = "auto",
  file_type_list = c("82z", "81x", "auto")
)

Arguments

df

input dataframe from licoread

focus_gas

gas to select

datetime_col

column containing datetime information if date and time are in two different columns, provide a character vector of the form c("date", "time")

id_cols

columns to identify unique fluxes

file_type

type of file (82z or 81x). If "auto" (default), the function will try to detect it by itself.

file_type_list

list of file types

Value

an unnested df with only the selected gas

Examples

path_82z <- system.file("extdata/82z", package = "licoread")
gas_df_82z <- licoread(path_82z)
licoread_to_fluxible(gas_df_82z, "LI-7810_CH4_DRY",
datetime_col = c("LI-8250_DATE", "LI-8250_TIME"))

lists gases present in the dataset

Description

prints a character vector of the gases present in the dataset. This is to be used to obtain the exact names of the gases before using licoread_to_fluxible.

Usage

list_gases(df, file_type = "auto", file_type_list = c("82z", "81x", "auto"))

Arguments

df

the dataframe as imported with licoread

file_type

type of file (currently works only for 82z). If "auto" (default), the function will try to detect it by itself.

file_type_list

list of file types

Value

a character vector of the gases present in the dataset

Examples

path_82z <- system.file("extdata/82z", package = "licoread")
gas_df_82z <- licoread(path_82z)
list_gases(gas_df_82z)

read meta data file inside 82z archive

Description

read meta data file inside 82z archive

Usage

metadata_82z(filepath, meta_file)

Arguments

filepath

name and path to the 82z archive

meta_file

name of the file with meta data

Value

a tibble with the metadata from one observation

to get a vector of names of a df, matching a regex

Description

to get a vector of names of a df, matching a regex

Usage

names_df(df, regname = "name\\d")

Arguments

df

the df to get the names from

regname

the regex expression to match

Value

a df with the names of the meta df

reading a single measurement from 81x file

Description

reads a single measurement from a licor .81x file

Usage

oneobs_81x(start, end, all_obs, file)

Arguments

start

line number at which the measurement starts

end

line number at which the measurement ends

all_obs

list of all the lines from the full file

file

filepath to the 81x files

Value

a df with 1 row with the meta data of the measurement and raw data nested

to read one measurement from the 82z archive

Description

to read one measurement from the 82z archive

Usage

oneobs_82z(filepath, data_file, meta_file, regex_file)

Arguments

filepath

path to the 82z archive

data_file

name of the file with raw data

meta_file

name of the file with meta data

regex_file

regex expression matching the name of the 82z file. Here in case the user has a different than the default and for easier updates.

Value

a tibble with all the data and metadata from one observation (one file)

reads 81x licor file

Description

reads a .81x file with several measurements

Usage

read_81x_onefile(file)

Arguments

file

filepath the the 81x file to read

Value

a nested tibble with the meta data from each measurements as row and the raw data nested

to create a nested tibble with the units of data

Description

to create a nested tibble with the units of data

Usage

units_82z(filepath, data_file, data_name, filename)

Arguments

filepath

name and path to the 82z archive

data_file

name of the file with raw data

data_name

vector of colnames

filename

name of the 82z archive

Value

a tibble with the units of the variables contained in the raw data