Package: photobiologyPlants 0.6.1-1.9000

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_0.6.1-1.9000.tar.gz
photobiologyPlants_0.6.1-1.9000.zip(r-4.7)photobiologyPlants_0.6.1-1.9000.zip(r-4.6)photobiologyPlants_0.6.1-1.9000.zip(r-4.5)
photobiologyPlants_0.6.1-1.9000.tgz(r-4.6-any)photobiologyPlants_0.6.1-1.9000.tgz(r-4.5-any)
photobiologyPlants_0.6.1-1.9000.tar.gz(r-4.7-any)photobiologyPlants_0.6.1-1.9000.tar.gz(r-4.6-any)
photobiologyPlants_0.6.1-1.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
photobiologyPlants/json (API)
NEWS

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

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

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

Datasets:

On CRAN:

Conda:

5.85 score 65 scripts 238 downloads 48 exports 33 dependencies

Last updated from:1e54ff277e. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK168
source / vignettesOK210
linux-release-x86_64OK120
macos-release-arm64OK104
macos-oldrel-arm64OK126
windows-develOK113
windows-releaseOK127
windows-oldrelOK94
wasm-releaseOK123

Exports:B_GD_CO2D_waterET_refET_ref_dayFR_ePARFR_PARFR_RpFRgs_c_from_gs_wgs_c_from_sizegs_from_sizegs_mol2volgs_vol2molgs_w_from_gs_cgs_w_from_sizemolar_volnet_irradiancePfr_PtotPfr_Ptot_R_FRPhy_reaction_ratesPhy_SigmaPhy_Sigma_FRPhy_Sigma_Rpsychrometric_constantR_FRR_RpFRrs_from_sizeUV_PARUVA_PARUVA_UVUVA1_UVUVA1_UVAUVA2_UVUVA2_UVAUVAlw_UVUVAsw_UVUVB_PARUVB_UVUVB_UVAwater_dpwater_fpwater_mvc2vpwater_RH2vpwater_vp_satwater_vp_sat_slopewater_vp2mvcwater_vp2RHxPAR_irrad

Dependencies:bitopscaToolsclicpp11dplyrgenericsgluelatticelifecyclelubridatemagrittrphotobiologyphotobiologyWavebandspillarpkgconfigplyrpolynompurrrR6Rcpprlangsplus2RstringistringrSunCalcMeeustibbletidyrtidyselecttimechangeutf8vctrswithrzoo

User Guide

Pedro J. Aphalo

Rendered fromuser-guide.Rmdusingknitr::rmarkdownon May 12 2026.

Last update: 2025-11-03
Started: 2018-02-02

User Guide: 0 The R for Photobiology Suite

Pedro J. Aphalo

Rendered fromr4p-introduction.Rmdusingknitr::rmarkdownon May 12 2026.

Last update: 2025-07-26
Started: 2023-10-21

Readme and manuals

Help Manual

Help pageTopics
photobiologyPlants: Plant Photobiology Related Functions and DataphotobiologyPlants-package photobiologyPlants
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
Diffusion coefficients in airD_CO2 D_water
EvapotranspirationET_ref ET_ref_day
Convert stomatal conductancegs_c_from_gs_w gs_mol2vol gs_vol2mol gs_w_from_gs_c
Fluorescence emission spectra of leaves.leaf_fluorescence.mspct
McCree's action spectra for whole-leaf photosynthesis.McCree_photosynthesis.mspct
Molar volume of an ideal gasmolar_vol
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
Constrained extended PAR from spectral irradiancephoton irradiances xPAR_irrad xPAR_irrad.default xPAR_irrad.source_mspct xPAR_irrad.source_spct
Calculate photon ratios from spectral irradianceB_G FR_ePAR FR_PAR FR_RpFR photon ratios R_FR R_RpFR UVA1_UV UVA1_UVA UVA2_UV UVA2_UVA UVAlw_UV UVAsw_UV UVA_PAR UVA_UV UVB_PAR UVB_UV UVB_UVA UV_PAR
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
Stomatal conductance from sizes and densitygs_c_from_size gs_from_size gs_w_from_size rs_from_size
Spectral optical data for 'Solidago altissima' leavesSolidago_altissima.mspct
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