Package: photobiologyPlants 0.6.0

photobiologyPlants: Plant Photobiology Related Functions and Data

Provides functions for quantifying visible (VIS) and ultraviolet (UV) radiation in relation to the photoreceptors Phytochromes, Cryptochromes, and UVR8 which are present in plants. It also includes data sets on the optical properties of plants. Part of the 'r4photobiology' suite, Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.

Authors:Pedro J. Aphalo [aut, cre]

photobiologyPlants_0.6.0.tar.gz
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photobiologyPlants.pdf |photobiologyPlants.html
photobiologyPlants/json (API)
NEWS

# Install 'photobiologyPlants' in R:
install.packages('photobiologyPlants', repos = c('https://aphalo.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/aphalo/photobiologyplants/issues

Pkgdown site:https://docs.r4photobiology.info

Datasets:

On CRAN:

5.50 score 53 scripts 194 downloads 30 exports 32 dependencies

Last updated 5 days agofrom:61c0c7f8f1. Checks:7 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 12 2025
R-4.5-winOKJan 12 2025
R-4.5-linuxOKJan 12 2025
R-4.4-winOKJan 12 2025
R-4.4-macOKJan 12 2025
R-4.3-winOKJan 12 2025
R-4.3-macOKJan 12 2025

Exports:B_GET_refET_ref_daynet_irradiancePfr_PtotPfr_Ptot_R_FRPhy_reaction_ratesPhy_SigmaPhy_Sigma_FRPhy_Sigma_Rpsychrometric_constantR_FRUV_PARUVA_PARUVA_UVUVA1_UVUVA2_UVUVAlw_UVUVAsw_UVUVB_PARUVB_UVUVB_UVAwater_dpwater_fpwater_mvc2vpwater_RH2vpwater_vp_satwater_vp_sat_slopewater_vp2mvcwater_vp2RH

Dependencies:clicpp11dplyrfansigenericsgluelatticelifecyclelubridatemagrittrphotobiologyphotobiologyWavebandspillarpkgconfigplyrpolynompurrrR6Rcpprlangsplus2RstringistringrSunCalcMeeustibbletidyrtidyselecttimechangeutf8vctrswithrzoo

User Guide

Rendered fromuser-guide.Rmdusingknitr::rmarkdownon Jan 12 2025.

Last update: 2025-01-09
Started: 2018-02-02

User Guide: 0 The R for Photobiology Suite

Rendered fromr4p-introduction.Rmdusingknitr::rmarkdownon Jan 12 2025.

Last update: 2024-04-01
Started: 2023-10-21

Readme and manuals

Help Manual

Help pageTopics
photobiologyPlants: Plant Photobiology Related Functions and DataphotobiologyPlants-package photobiologyPlants
Calculate B:G photon ratio from spectral irradiance.B_G
Spectral data for 'Betula ermanii' leavesBetula_ermanii.mspct
Absorbance spectra for carotenoids.carotenoids.mspct
Fluorescence emission spectra for chlorophylls.chlorophylls_fluorescence.mspct
Absorbance spectra for chlorophylls.chlorophylls.mspct
CRY1, CRY2 and CRY3 absorbance spectra.CRYs.mspct
EvapotranspirationET_ref ET_ref_day
Fluorescence emission spectra of leaves.leaf_fluorescence.mspct
McCree's action spectra for whole-leaf photosynthesis.McCree_photosynthesis.mspct
Net radiation fluxnet_irradiance
Calculate phytochrome photoequilibriumPfr_Ptot Pfr_Ptot.default Pfr_Ptot.numeric Pfr_Ptot.source_spct
Pr:Ptot ratio (photoequilibrium) from R:FR photon ratio.Pfr_Ptot_R_FR
PHOT1 and PHOT2 absorbance spectra.PHOTs.mspct
Phytochrome reaction ratesPhy_reaction_rates
Phytochrome Sigma as a function of wavelengthPhy_Sigma
Pfr Sigma as a function of wavelengthPhy_Sigma_FR
Pr Sigma as a function of wavelengthPhy_Sigma_R
Tabulated data for Phytochrome SigmaPHYs.mspct phytochrome.spct
Calculate R:FR photon ratio from spectral irradiance.R_FR
Spectral optical data for 'Solidago altissima' leavesSolidago_altissima.mspct
Calculate UV:PAR photon ratio from spectral irradiance.UV_PAR
Calculate UVA:PAR photon ratio from spectral irradiance.UVA_PAR
Calculate UVA:UV photon ratio from spectral irradiance.UVA_UV
Calculate UVA1:UV photon ratio from spectral irradiance.UVA1_UV
Calculate UVA2:UV photon ratio from spectral irradiance.UVA2_UV
Calculate UVAlw:UV photon ratio from spectral irradiance.UVAlw_UV
Calculate UVAsw:UV photon ratio from spectral irradiance.UVAsw_UV
Calculate UVB:PAR photon ratio from spectral irradiance.UVB_PAR
Calculate UVB:UV photon ratio from spectral irradiance.UVB_UV
Calculate UVB:UVA photon ratio from spectral irradiance.UVB_UVA
UVR8 absorbance spectrumUVR8s.mspct
Water vapour pressurepsychrometric_constant water_dp water_fp water_mvc2vp water_RH2vp water_vp2mvc water_vp2RH water_vp_sat water_vp_sat_slope
ZTL absorbance spectra.ZTLs.mspct