Introduction | Light environment | Photon ratios | Photoreceptors | Phytochromes: photoequilibrium | Phytochromes: reaction rates | Phytochromes: absorption cross section at given wavelengths | Cryptochromes: spectral absorbance | Phototropins: spectral absorbance | UVR8: spectral absorbance | Zeitloupe proteins: spectral absorbance | Mass pigments | Carotenoids | Chlorophylls | Fluorescence | Leaves | Optical properties | Fluorescence: UV excited | Photosynthesis: action spectra | Photosynthesis: plastoquinone redox state | Stomatal conductance | Vegetation | Reference evapotranspiration | Water vapour in air
Package: photobiologyPlants 0.6.2.9000
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:
photobiologyPlants_0.6.2.9000.tar.gz
photobiologyPlants_0.6.2.9000.zip(r-4.7-any)photobiologyPlants_0.6.2.9000.zip(r-4.6-any)photobiologyPlants_0.6.2.9000.zip(r-4.5-any)
photobiologyPlants_0.6.2.9000.tgz(r-4.6-any)photobiologyPlants_0.6.2.9000.tgz(r-4.5-any)
photobiologyPlants_0.6.2.9000.tar.gz(r-4.7-any)photobiologyPlants_0.6.2.9000.tar.gz(r-4.6-any)
photobiologyPlants_0.6.2.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
photobiologyPlants/json (API)
| # 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:
- Betula_ermanii.mspct - Spectral data for 'Betula ermanii' leaves
- carotenoids.mspct - Absorbance spectra for carotenoids.
- chlorophylls_fluorescence.mspct - Fluorescence emission spectra for chlorophylls.
- chlorophylls.mspct - Absorbance spectra for chlorophylls.
- CRYs.mspct - CRY1, CRY2 and CRY3 absorbance spectra.
- leaf_fluorescence.mspct - Fluorescence emission spectra of leaves.
- McCree_photosynthesis.mspct - McCree's action spectra for whole-leaf photosynthesis.
- PHOTs.mspct - PHOT1 and PHOT2 absorbance spectra.
- PHYs.mspct - Tabulated data for Phytochrome Sigma
- phytochrome.spct - Tabulated data for Phytochrome Sigma
- PS1_PS2_k.spct - Coefficients for redox state of the plastoquinone pool
- Solidago_altissima.mspct - Spectral optical data for 'Solidago altissima' leaves
- UVR8s.mspct - UVR8 absorbance spectrum
- ZTLs.mspct - ZTL absorbance spectra.
Last updated from:652c2584cb. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 150 | ||
| source / vignettes | OK | 229 | ||
| linux-release | OK | 162 | ||
| macos-release | OK | 114 | ||
| macos-oldrel | OK | 98 | ||
| windows-devel | OK | 88 | ||
| windows-release | OK | 85 | ||
| windows-oldrel | OK | 98 | ||
| wasm-release | OK | 103 |
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_photoconversionPhy_reaction_ratesPhy_SigmaPhy_Sigma_FRPhy_Sigma_RPQ_redox_statepsychrometric_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
Last update: 2026-09-17
Started: 2018-02-02
User Guide: 0 The R for Photobiology Suite
Introduction | References | Packages in the suite | Acknowledgements
Last update: 2025-07-26
Started: 2023-10-21
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| photobiologyPlants: Plant Photobiology Related Functions and Data | photobiologyPlants-package photobiologyPlants |
| Spectral data for 'Betula ermanii' leaves | Betula_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 air | D_CO2 D_water |
| Evapotranspiration | ET_ref ET_ref_day |
| Convert stomatal conductance | gs_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 gas | molar_vol |
| Net radiation flux | net_irradiance |
| Calculate phytochrome photoequilibrium | Pfr_Ptot Pfr_Ptot.default Pfr_Ptot.numeric Pfr_Ptot.source_mspct Pfr_Ptot.source_spct |
| Pr:Ptot ratio (photoequilibrium) from R:FR photon ratio. | Pfr_Ptot_R_FR |
| Constrained extended PAR from spectral irradiance | photon irradiances xPAR_irrad xPAR_irrad.default xPAR_irrad.source_mspct xPAR_irrad.source_spct |
| Calculate photon ratios from spectral irradiance | B_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 photoconversion rates | Phy_photoconversion Phy_photoconversion.default Phy_photoconversion.source_mspct Phy_photoconversion.source_spct |
| Phytochrome reaction rates | Phy_reaction_rates |
| Phytochrome Sigma as a function of wavelength | Phy_Sigma |
| Pfr Sigma as a function of wavelength | Phy_Sigma_FR |
| Pr Sigma as a function of wavelength | Phy_Sigma_R |
| Tabulated data for Phytochrome Sigma | PHYs.mspct phytochrome.spct |
| Redox state of the plastoquinone pool | PQ_redox_state PQ_redox_state.default PQ_redox_state.source_mspct PQ_redox_state.source_spct |
| Coefficients for redox state of the plastoquinone pool | PS1_PS2_k.spct |
| Stomatal conductance from sizes and density | gs_c_from_size gs_from_size gs_w_from_size rs_from_size |
| Spectral optical data for 'Solidago altissima' leaves | Solidago_altissima.mspct |
| UVR8 absorbance spectrum | UVR8s.mspct |
| Water vapour pressure | psychrometric_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 |