gnxmanu / ccpp

A Concentration Calculation and Plotting Package for Los Gatos Gas Analyzer

CCPP

An R Concentration Calculation and Plotting Package (CCPP) for Los Gatos Gas Analyzer (LGGA).

Description

Built for an individual LGGA day/run with control in triplicates and four sample replicates.

Getting Started

Dependencies

• Packages: readxl, tcltk, ggplot2, data.table, plotly, tidyr, dplyr, stringr, lubridate, readr.
• Excel file (.xlsx) (from template) with injection times
• Logs from LGGA (.txt)

Installing

# install.packages("devtools")
devtools::install_github("gnxmanu/CCPP")

or

# install.packages("remotes")
remotes::install_github("gnxmanu/CCPP")

Executing program

• User will be prompted for required .xsls and .txt files as well as for the directory to export products.
• The function runs on predetermined parameters, though they can be specified out of default (see below).

library(CCPP)
CCPPs()

• A folder tree will be created in the indicated directory.

.
├── Figures
│   └── Day
│        └── CH4
│             └── All
│             └── All_base_peaks
│             └── All_WithoutControls
│             └── ZoomInToPlateaus
│        └── CO2
│             └── All
│             └── All_base_peaks
│             └── All_WithoutControls
│             └── ZoomInToPlateaus
├── CalculatedConcentrations.csv

• All plots (10 per species) will be exported in their respective folders (dates are printed as parent folder names and species and variant to child folders).
• A .csv is created with the calculated concentrations (corrected for dilution and considering plateaus), as well as some summary data.

Arguments

Option	Description	Type	Default	Required?
path_main	Export path. If NULL, it asks the user in GUI.	string	NULL	No
path_day1	Import path of 'LGGA log.txt' for day 1. If NULL, it asks the user in GUI.	string	NULL	No
path_day2	Import path of 'LGGA log.txt' for day 2. If NULL, it asks the user in GUI.	string	NULL	No
path_day3	Import path of 'LGGA log.txt' for day 3. If NULL, it asks the user in GUI.	string	NULL	No
interval	Length of interval to average on. If NULL, 10 seconds.	integer	10	No
base_interval	Offset before injection time input by the user	integer	20	No
peak_interval	Offset before injection time input by the user	integer	20	No
V_sample	Injected sample volume [L] (V_s).	integer	100E-6	No
V_loop	Loop volume [L] (V_L). Equivalent to 92 mL.	integer	92E-3	No
offset_initial_final	Injection offset to discriminate raw data.	integer	60	No

Authors

Manuel V.

@gnxmanu

Version History

• v0.1 –––––– (Alpha Release. September 13, 2021
• v0.2.1 –––– Beta Release. October 23, 2021
• v0.2.2 –––– Beta Release. November 15, 2021
• v1.0 –––––– Public Release. 31 January 2022

License

This project is licensed under the [MIT] License - see the LICENSE.md file for details.

Future Updates

• Alpha Release
  • Alpha version on github

• v.1.0
  • Remove: "* New names:"
  • Remove: "* `` -> ...1"
  • Remove: "Scale for 'y' is already present. Adding another scale for 'y', which will replace the existing scale."
  • Remove: "There were 50 or more warnings (use warnings() to see the first 50)"
  • Print parameters into resulting .csv and plots
  • Rename variables
  • Fix pacman or utilise if/require iteratively on a string
  • Confirm packages utilisation
  • Loops for each injection and for each day (calculations and plotting)
  • Input and loop that will allow any controls and samples replicates as well as day-runs
  • Introduce website
  • Present example study case
  • Add rectangle shading to denote flush, inyection and stabilisation stages