Package: fluorojip 0.1.1

Joao Everthon da Silva Ribeiro

fluorojip: Analysis of Chlorophyll a Fluorescence Transient Parameters

Computes chlorophyll a fluorescence transient parameters from fluorescence summary data, including minimum and maximum fluorescence, selected transient steps, and area. Provides standard photosynthetic performance indices and fluxes per reaction center and per cross section. Includes helpers to read exported trace tables in supported 'csv' formats and validation workflows based on bundled example files, as well as visualization tools and an interactive 'shiny' interface. The implemented calculations are based on Strasser et al. (2004) <doi:10.1007/978-1-4020-3218-9_12> and Stirbet and Govindjee (2011) <doi:10.1016/j.jphotobiol.2010.12.010>.

Authors:Joao Everthon da Silva Ribeiro [aut, cre], Toshik Iarley da Silva [aut], Ronald Maldonado Rodriguez [aut]

fluorojip_0.1.1.tar.gz
fluorojip_0.1.1.tar.gz(r-4.7-any)fluorojip_0.1.1.tar.gz(r-4.6-any)
fluorojip_0.1.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
fluorojip/json (API)

# Install 'fluorojip' in R:

install.packages('fluorojip', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

example_fluorojip - Example OJIP summary data

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.00 score 473 downloads 17 exports 19 dependencies

Last updated from:2a9e6adbac. Checks:4 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	136
source / vignettes	OK	191
linux-release-x86_64	OK	117
wasm-release	OK	119

Exports:calc_fluorojip calc_fluorojip_file calc_fluorojip_fluorpen calc_fluorojip_handypea fluorojip_example_biolyzer_file fluorpen_to_ojip handypea_to_ojip normalized_jiptable plot_3d_fluorojip plot_heatmap_fluorojip plot_param_3d plot_param_heatmap plot_param_surface3d read_fluorpen_xlsx read_handypea_csv run_fluorojip_app write_normalized_jiptable

Dependencies:cellranger cli cpp11 crayon glue hms lifecycle magrittr pillar pkgconfig prettyunits progress R6 readxl rematch rlang tibble utf8 vctrs

Introduction to fluorojip

Rendered fromfluorojip-intro.Rmdusingknitr::rmarkdown

Last update: 2026-04-09
Started: 2026-04-09

Help page	Topics
Compute chlorophyll a fluorescence OJIP / JIP-test parameters	calc_fluorojip
Read a summary table and compute FluorOJIP parameters	calc_fluorojip_file
Calculate FluorOJIP parameters from a FluorPen workbook	calc_fluorojip_fluorpen
Calculate FluorOJIP parameters from a supported exported table	calc_fluorojip_handypea
Example OJIP summary data	example_fluorojip
Get the bundled Biolyzer validation workbook path	fluorojip_example_biolyzer_file
Convert FluorPen traces to an OJIP summary table	fluorpen_to_ojip
Convert a supported CSV trace export to an OJIP summary table	handypea_to_ojip
Build a normalized JIP parameter table	normalized_jiptable
Plot a 3D scatter plot of OJIP parameters	plot_3d_fluorojip plot_param_3d plot_param_surface3d
Plot a heatmap of OJIP parameters	plot_heatmap_fluorojip plot_param_heatmap
Read a FluorPen Excel export	read_fluorpen_xlsx
Read a supported Biolyzer-exported CSV trace table	read_handypea_csv
Run the fluorojip Shiny application	run_fluorojip_app
Write a normalized JIP parameter table	write_normalized_jiptable

Package: fluorojip 0.1.1

fluorojip: Analysis of Chlorophyll a Fluorescence Transient Parameters

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)