| Title: | Plant Photobiology Related Functions and Data |
|---|---|
| Description: | 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] |
| Maintainer: | Pedro J. Aphalo <[email protected]> |
| License: | GPL (>= 2) |
| Version: | 0.5.0 |
| Built: | 2024-08-30 02:38:14 UTC |
| Source: | https://github.com/aphalo/photobiologyPlants |
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.
Package 'photobiologyPlants' is part of a suite of packages for analysis and plotting of data relevant to photobiology (described at http://www.r4photobiology.info/). The current component package provides functions and data related to plant photoreceptors, light dependent reponses and optical properties of plants.
This work was partly funded by the Academy of Finland (decision 252548). COST Action FA9604 'UV4Growth' facilitated discussions and exchanges of ideas that lead to the development of this package.
Maintainer: Pedro J. Aphalo [email protected] (ORCID)
Aphalo, Pedro J. (2015) The r4photobiology suite. UV4Plants Bulletin, 2015:1, 21-29. doi:10.19232/uv4pb.2015.1.14.
Aphalo, P. J., Albert, A., Bjoern, L. O., McLeod, A. R., Robson, T. M., Rosenqvist, E. (Eds.). (2012). Beyond the Visible: A handbook of best practice in plant UV photobiology (1st ed., p. xxx + 174). Helsinki: University of Helsinki, Department of Biosciences, Division of Plant Biology. ISBN 978-952-10-8363-1 (PDF), 978-952-10-8362-4 (paperback). Open access PDF download available at http://hdl.handle.net/10138/37558
Mancinelli, A.L. (1994) The physiology of phytochrome action. In Photomorphogenesis in plants, 2nd edition. R.E. Kendrick and G.H.M. Kronenberg, eds. Kluwer Academic Publishers, Dordrecht, pp. 211-269. ISBN 978-0-7923-2551-2 (print), 978-94-011-1884-2 (on-line). doi:10.1007/978-94-011-1884-2_10.
Banerjee, R., Schleicher, E., Meier, S., Viana, R. M., Pokorny, R., Ahmad, M., ... Batschauer, A. (2007). The signaling state of Arabidopsis cryptochrome 2 contains flavin semiquinone. J Biol Chem, 282(20), 14916-14922. doi:10.1074/jbc.M700616200.
Package photobiology-package and
photobiologyWavebands-package.
This function returns the blue:green photon ratio of a light source spectrum.
B_G(spct, std = "Sellaro", use.cached.mult = FALSE, use.hinges = TRUE)B_G(spct, std = "Sellaro", use.cached.mult = FALSE, use.hinges = TRUE)
spct |
an object of class "source.spct". |
std |
select which definition of blue and green should be used, defaults to "Sellaro". |
use.cached.mult |
logical indicating whether multiplier values should be cached between calls. |
use.hinges |
logical indicating whether to use hinges to reduce interpolation errors. |
a single numeric dimensionless value giving the B:G photon ratio, with name attribute set to the name of the wavebands, with "(q:q)" appended.
B_G(sun.spct)B_G(sun.spct)
A dataset containing for wavelengths at a 1 nm interval in the range 350 to 1000 nm, tabulated values for total reflectance and total transmittance, for the upper and lower epidermis of leaves of different ages from Erman's birch (Betula ermanii) trees growing in the forest in Japan.
The variables in each spectrum are as follows:
w.length (nm)
Rfr
Tfr
Betula_ermanii.mspctBetula_ermanii.mspct
object_mspct collection object with six object_spct
member objects, each with 651 rows and 3 variables
We thank H. M. Noda for allowing us to include these data in our package. We have included here only data for two leaves from one species (Betula ermanii) and for wavelengths shorter than 1000 nm, from the much larger original data set. The whole data set is publicly available and the data easy to read into R. The data included here where measured with a Li-Cor LI-1800 spectroradiometer equipped with a LI-1800-12 (Li-Cor) integrating sphere, and consequently are for total reflectance and total transmittance. Further details on methods are available through the JaLTER web site. If you use these data in a publication, please cite the original source as given under references and contact the original author. In addition cite this package.
Noda H. 'Reflectance and transmittance spectra of leaves and
shoots of 22 vascular plant species and reflectance spectra of trunks and
branches of 12 tree species in Japan' ERDP-2013-02.1.1
(http://db.cger.nies.go.jp/JaLTER/metacat/metacat/ERDP-2013-02.1.1/jalter-en)
JaLTER, Japan Long Term Ecological Research Network,
http://www.jalter.org/
A dataset containing the wavelengths at an arbitrary nm interval. Tabulated values for the in vitro absorbance spectrum of beta-carotene, lutein, lycopene, 3-4,di-hydro-lycopene, phytoene, phytofluene, violaxanthin and zeaxanthin. Data were digitized from plots downloaded from LipidBase (https://lipidbank.jp/), The official database of Japanese Conference on the Biochemistry of Lipids (JCBL). Data contributed to LipinBank by Takaichi Sinichi.
A filter_mspct with eight member filter_spct objects each
with 300 rows and 2 numeric variables, w.length and A
The variables of the member spectra are as follows:
w.length (nm)
A (spectral absorbance)
If you use these data in a publication, please cite also the original source as given under references in addition to this package.
Watanabe K., Yasugi E. and Oshima M. "How to search the glycolipid data in LIPIDBANK for Web: the newly developed lipid database" Japan Trend Glycosci. and Glycotechnol. 12, 175-184, 2000.
names(carotenoids.mspct) getWhatMeasured(carotenoids.mspct[[1]])names(carotenoids.mspct) getWhatMeasured(carotenoids.mspct[[1]])
Optical absorption spectra of chlorophyll in methanol and chlorophylls
and in diethyl ether containing the wavelengths at 1 nm interval.
A filter_mspct with three member filter_spct objects
each with variable number of rows and 2 numeric variables, w.length
and A
The variables of the member spectra are as follows:
w.length (nm)
A (spectral absorbance)
Data from PhotochemCAD 2.1a has been munged on 2 June 2017 by Scott Prahl (https://omlc.org/) to make the information available to non-Windows users. Although he has tried to be as careful as possible, he may have introduced some error; the cautious user is advised to compare these results with the original sources at https://www.photochemcad.com/ (Du et al., 1998; Dixon et al., 2005).
Fluorescence emission was measured using a Spex FluoroMax. The excitation and emission monochromators were set at 1 mm, giving a spectral bandwidth of 4.25 nm. The data interval was 0.5 nm and the integration time was 2.0 sec. Samples were prepared in 1cm path length quartz cells with absorbance less than 0.1 at the excitation and all emission wavelengths to uniformly illuminate across the sample, and to avoid the inner-filter effect. The dark counts were subtracted and the spectra were corrected for wavelength-dependent instrument sensitivity.
If you use these data in a publication, please cite also the original sources as given under references. For more information please visit https://omlc.org/.
J. M. Dixon, M. Taniguchi and J. S. Lindsey "PhotochemCAD 2. A refined program with accompanying spectral databases for photochemical calculations", Photochem. Photobiol., 81, 212-213, 2005.
H. Du, R. A. Fuh, J. Li, A. Corkan, J. S. Lindsey, "PhotochemCAD: A computer-aided design and research tool in photochemistry," Photochem. Photobiol., 68, 141-142, 1998.
names(chlorophylls_fluorescence.mspct) getWhatMeasured(chlorophylls_fluorescence.mspct[[1]])names(chlorophylls_fluorescence.mspct) getWhatMeasured(chlorophylls_fluorescence.mspct[[1]])
Optical absorption spectra of chlorophyll a in methanol and chlorophylls a and by in diethyl ether containing the wavelengths at 1 nm interval.
A filter_mspct with three member filter_spct objects
each with variable number of rows and 2 numeric variables, w.length
and A
The variables of the member spectra are as follows:
w.length (nm)
A (spectral absorbance)
Data from PhotochemCAD 2.1a has been munged on 2 June 2017 by Scott Prahl (https://omlc.org/) to make the information available to non-Windows users. Although he has tried to be as careful as possible, he may have introduced some error; the cautious user is advised to compare these results with the original sources (Du et al., 1998; Dixon et al., 2005).
The spectral absorption measurements of chlorophyll in methanol,
chlorophyll and chlorophyll in diethyl ether were made by J.
Li on 12-11-1997 using a Cary 3 spectrophotometer. The absorption values were
collected using a spectral bandwidth of 1.0 nm, a signal averaging time of
0.133 sec, a data interval of 0.25 nm, and a scan rate of 112.5 nm/min.
Chlorophyll measurements were scaled to make the molar extinction
coefficient match the value of 111700 cm-1/M at 417.8 nm. These values were
then interpolated to report extinction coefficients at regular 1 nm intervals.
The reported molar extinction coefficient is from Strain et al. (1963).
Chlorophyll measurements were scaled to make the molar extinction
coefficient match the value of 159100 cm-1/M at 453.0 nm. These values were
then interpolated to report extinction coefficients at regular 1 nm intervals.
The reported molar extinction coefficient is from Vernon and Seely (1966).
If you use these data in a publication, please cite also the original sources as given under references. For more information please visit https://omlc.org/.
J. M. Dixon, M. Taniguchi and J. S. Lindsey "PhotochemCAD 2. A refined program with accompanying spectral databases for photochemical calculations", Photochem. Photobiol., 81, 212-213, 2005.
H. Du, R. A. Fuh, J. Li, A. Corkan, J. S. Lindsey, "PhotochemCAD: A computer-aided design and research tool in photochemistry," Photochem. Photobiol., 68, 141-142, 1998.
Strain, H. H., M. R. Thomas and J. J. Katz (1963) Spectral absorption properties of ordinary and fully deuteriated chlorophylls a and b. Biochim. Biophys. Acta 75, 306-311.
Vernon, L. P. and G. R. Seely (1966) The chlorophylls. Academic Press, NY.
names(chlorophylls.mspct) getWhatMeasured(chlorophylls.mspct[[1]])names(chlorophylls.mspct) getWhatMeasured(chlorophylls.mspct[[1]])
A dataset containing the wavelengths at an arbitrary nm interval and spectral absorbance for plant cryptochromes 1 (CRY1), 2 (CRY2), and 3 (CRY3 or CRY-DASH). Tabulated values for the in vitro absorbance spectrum for Arabidopsis thaliana. CRY1 data were digitized from figure 1, curve "dark" and curve "30 min illumination" in Zeugnwer et al. (2005). The CRY2 data were digitized from Figure 1.B, curve "dark adapted sample", and curve "irradiated with blue light (450 nm, 50 umol m-2 s-1) during 30 min" in Banerjee et al. (2007). CRY3 data were digitized from figure 2a, curve "cry3" in Song et al. (2006).
A filter_mspct with five member filter_spct objects each
with 300 rows and 2 numeric variables, w.length and A
The variables of the member spectra are as follows:
w.length (nm)
A (spectral absorbance)
If you use these data in a publication, please cite also the original source as given under references in addition to this package.
Banerjee, R., Schleicher, E., Meier, S., Viana, R. M., Pokorny, R., Ahmad, M., ... Batschauer, A. (2007) The signaling state of Arabidopsis cryptochrome 2 contains flavin semiquinone. J Biol Chem, 282(20), 14916-14922. doi:10.1074/jbc.M700616200
SONG, S.-H., B. DICK, , A. PENZKOFER, , R. POKORNY, , A. BATSCHAUER, L.-O. ESSEN (2006) Absorption and fluorescence spectroscopic characterization of cryptochrome 3 from Arabidopsis thaliana. Journal of Photochemistry and Photobiology B: Biology. 85(1):1-16.
ZEUGNER, A., MARTIN BYRDIN, JEAN-PIERRE BOULY, NADIA BAKRIM, BALDISSERA GIOVANI, KLAUS BRETTEL, MARGARET AHMAD (2005) Light-induced Electron Transfer in Arabidopsis Cryptochrome-1 Correlates with in Vivo Function. Journal of Biological Chemistry. 280(20):19437-19440.
The 'classical' action spectra of K. J. McCree (1972) for
Amaranthus edulis Speg. var. UCD 1966 and Avena sativa L.
var. Coronado are included in this data set. Response is net
uptake measured on leaf sections umder monochromatic light. The light
source used was a xenon-arc lamp fitted with a monochromator. Irradiance
was in the range 10 to 15 .
A response_mspct object with two member
response_spct
objects each with 300 rows and 2 numeric variables, w.length and
s.e.response.
Digitised from bitmap of from the original publication.
If you use these data in a publication, please cite also the original source as given under references.
McCree, K. J. (1972) Significance of Enhancement for Calculations Based on the Action Spectrum for Photosynthesis. Plant Physiology, 49, 704-706. Fig. 1, AMARANTH.
summary(McCree_photosynthesis.mspct)summary(McCree_photosynthesis.mspct)
A method implemented for objects of different classes.
Pfr_Ptot(x, ...) ## Default S3 method: Pfr_Ptot(x, ...) ## S3 method for class 'numeric' Pfr_Ptot(x, spct.out = length(x) > 20, ...) ## S3 method for class 'source_spct' Pfr_Ptot(x, ...)Pfr_Ptot(x, ...) ## Default S3 method: Pfr_Ptot(x, ...) ## S3 method for class 'numeric' Pfr_Ptot(x, spct.out = length(x) > 20, ...) ## S3 method for class 'source_spct' Pfr_Ptot(x, ...)
x |
an R object |
... |
not used |
spct.out |
logical Flag indicating if the returned object should be of
class |
If x is numeric, giving wavelengths (nm), a vector of
numeric values giving the unitless photon ratio at each wavelength or a
generic_spct object with the wavelength values sorted in ascending
order and the corresponding Pfr_Ptot values in column
s.q.response.
If x is a source_spct object, a single numeric value
giving the unitless photon ratio
Pfr_Ptot(default): Default for generic function
Pfr_Ptot(numeric): Specialization for numeric
Pfr_Ptot(source_spct): Specialization for source_spct
Calculate phytochrome photoequilibrium from spectral (photon) irradiance
If you use these data in a publication, please cite also the original source as given under references.
Mancinelli, A.L. (1994) The physiology of phytochrome action. In Photomorphogenesis in plants, 2nd edition. R.E. Kendrick and G.H.M. Kronenberg, eds. Kluwer Academic Publishers, Dordrecht, pp. 211-269. ISBN 978-0-7923-2551-2 (print), 978-94-011-1884-2 (on-line). doi:10.1007/978-94-011-1884-2_10
Calculation of Pfr:Ptot ratio for Type I Phytochrome from red:far-red photon ratio. "Exact" only for dichromatic irradiation, only approximate for R:FR ratio calculated from a broadband light source.
Pfr_Ptot_R_FR(R.FR)Pfr_Ptot_R_FR(R.FR)
R.FR |
R:FR a single value or a vector of photon ratio (dimentionless) values |
a single value or a vector of numeric values giving the Pr:Ptot dimensionless ratio
Mancinelli, A.L. (1994) The physiology of phytochrome action. In Photomorphogenesis in plants, 2nd edition. R.E. Kendrick and G.H.M. Kronenberg, eds. Kluwer Academic Publishers, Dordrecht, pp. 211-269. ISBN 978-0-7923-2551-2 (print), 978-94-011-1884-2 (on-line). doi:10.1007/978-94-011-1884-2_10
Pfr_Ptot_R_FR(1.15) Pfr_Ptot_R_FR(0.10) Pfr_Ptot_R_FR(c(0.1,1.15,5.0,20.0))Pfr_Ptot_R_FR(1.15) Pfr_Ptot_R_FR(0.10) Pfr_Ptot_R_FR(c(0.1,1.15,5.0,20.0))
A dataset containing the wavelengths at an arbitrary nm interval for plant photoreceptors phototropin 1 and phototropin 2. Tabulated values for the in vitro absorbance spectrum of PHOT1 LOV2 domain for fluorescence yield of PHOT1 and PHOT2 from Arabidopsis thaliana measured in vitro. PHOT1 fluorescence yield data were digitized from figure 1a curve "LOV1 + LOV2 (WT) and PHOT2 fluorescence yield data were digitized from figure 7a curve "LOV1 + LOV2 (WT) in Christie et al. (2002). PHOT1 LOV2, dark adapted, spectral absorbance data were digitized from figure 3, black curve and PHOT1 LOV2, blue-light adapted spectral absorbance data were digitized from figure 3, blue curve in Christie et al. (2015).
A filter_mspct with five member filter_spct objects each
with 300 rows and 2 numeric variables, w.length and A
The variables of the member spectra are as follows:
w.length (nm)
A (spectral absorbance)
If you use these data in a publication, please cite also the original source as given under references in addition to this package.
CHRISTIE, John M., SWARTZ, Trevor E., BOGOMOLNI, Roberto A., BRIGGS, Winslow R. (2002) Phototropin LOV domains exhibit distinct roles in regulating photoreceptor function. The Plant Journal 32(2):205-219.
CHRISTIE, J. M., BLACKWOOD, L., PETERSEN, J., SULLIVAN, S. (2015) Plant Flavoprotein Photoreceptors. Plant and Cell Physiology. 56(3):401-413.
Rate constants Pr -> Pfr; Pfr -> Pr; photoconversion rate
for Type I Phytochrome.
Phy_reaction_rates( w.length, s.irrad, unit.in = "energy", check.spectrum = TRUE, use.cached.mult = FALSE )Phy_reaction_rates( w.length, s.irrad, unit.in = "energy", check.spectrum = TRUE, use.cached.mult = FALSE )
w.length |
numeric array of wavelength (nm) |
s.irrad |
numeric array of spectral (energy) irradiances (W m-2 nm-1) or (mol s-1 m-2) |
unit.in |
character string with allowed values "energy", and "photon", or its alias "quantum" |
check.spectrum |
logical indicating whether to sanity check input data, default is TRUE |
use.cached.mult |
logical indicating whether multiplier values should be cached between calls |
a list of three numeric values giving the photoconversion rate
() and reaction rates (, ).
Hayward, P. M. (1984) Determination of phytochrome parameters from radiation measurements. In Techniques in Photomorphogenesis, H. Smith and M. G. Holmes (eds). Academic Press, London, pp. 159-173. ISBN 0-12-652990-6.
Mancinelli, A.L. (1994) The physiology of phytochrome action. In Photomorphogenesis in plants, 2nd edition. R.E. Kendrick and G.H.M. Kronenberg, eds. Kluwer Academic Publishers, Dordrecht, pp. 211-269. ISBN 978-0-7923-2551-2 (print), 978-94-011-1884-2 (on-line). doi:10.1007/978-94-011-1884-2_10
library(photobiology) trimmed.sun.spct <- trim_wl(sun.spct, range = c(300, 770)) with(trimmed.sun.spct, Phy_reaction_rates(w.length, s.e.irrad))library(photobiology) trimmed.sun.spct <- trim_wl(sun.spct, range = c(300, 770)) with(trimmed.sun.spct, Phy_reaction_rates(w.length, s.e.irrad))
Phytochrome Sigma as a function of wavelength, calculated by interpolation from data for Type I Phytochrome as compiled by Mancinelli (1994).
Phy_Sigma(w.length)Phy_Sigma(w.length)
w.length |
numeric array of wavelength (nm) |
a numeric array with values for Sigma
Mancinelli, A.L. (1994) The physiology of phytochrome action. In Photomorphogenesis in plants, 2nd edition. R.E. Kendrick and G.H.M. Kronenberg, eds. Kluwer Academic Publishers, Dordrecht, pp. 211-269. ISBN 978-0-7923-2551-2 (print), 978-94-011-1884-2 (on-line). doi:10.1007/978-94-011-1884-2_10
with(sun.data, Phy_Sigma(w.length))with(sun.data, Phy_Sigma(w.length))
Pfr Sigma as a function of wavelength, calculated by interpolation from data for Type I Phytochrome as compiled by Mancinelli (1994).
Phy_Sigma_FR(w.length, use.cached.mult = FALSE)Phy_Sigma_FR(w.length, use.cached.mult = FALSE)
w.length |
numeric array of wavelength (nm) |
use.cached.mult |
logical ignored |
a numeric array with values for Sigma
Mancinelli, A.L. (1994) The physiology of phytochrome action. In Photomorphogenesis in plants, 2nd edition. R.E. Kendrick and G.H.M. Kronenberg, eds. Kluwer Academic Publishers, Dordrecht, pp. 211-269. ISBN 978-0-7923-2551-2 (print), 978-94-011-1884-2 (on-line). doi:10.1007/978-94-011-1884-2_10
Phy_Sigma,
Pfr_Ptot and
Pfr_Ptot_R_FR
with(sun.spct, Phy_Sigma_FR(w.length)) with(sun.spct, Phy_Sigma_FR(w.length, TRUE))with(sun.spct, Phy_Sigma_FR(w.length)) with(sun.spct, Phy_Sigma_FR(w.length, TRUE))
Pr Sigma as a function of wavelength, calculated by interpolation from data for Type I Phytochrome as compiled by Mancinelli (1994).
Phy_Sigma_R(w.length, use.cached.mult = FALSE)Phy_Sigma_R(w.length, use.cached.mult = FALSE)
w.length |
numeric array of wavelength (nm) |
use.cached.mult |
logical ignored |
a numeric array with values for Sigma
Mancinelli, A.L. (1994) The physiology of phytochrome action. In Photomorphogenesis in plants, 2nd edition. R.E. Kendrick and G.H.M. Kronenberg, eds. Kluwer Academic Publishers, Dordrecht, pp. 211-269. ISBN 978-0-7923-2551-2 (print), 978-94-011-1884-2 (on-line). doi:10.1007/978-94-011-1884-2_10
Phy_Sigma,
Pfr_Ptot and
Pfr_Ptot_R_FR
with(sun.data, Phy_Sigma_R(w.length)) with(sun.data, Phy_Sigma_R(w.length, TRUE))with(sun.data, Phy_Sigma_R(w.length)) with(sun.data, Phy_Sigma_R(w.length, TRUE))
A dataset containing the wavelengths at a 1 nm interval. Tabulated values for Sigma R and Sigma FR for Type I Phytochrome as compiled by Mancinelli (1994).
The variables are as follows:
wavelength (nm)
Sigma.R (quantum effectiveness)
Sigma.FR (quantum effectiveness)
A generic_mspct with one member generic_spct object
with 49 rows and 3 numeric variables, w.length, Sigma.R and
Sigma.FR.
If you use these data in a publication, please cite also the original source as given under references in addition to this package.
Mancinelli, A.L. (1994) The physiology of phytochrome action. In Photomorphogenesis in plants, 2nd edition. R.E. Kendrick and G.H.M. Kronenberg, eds. Kluwer Academic Publishers, Dordrecht, pp. 211-269. ISBN 978-0-7923-2551-2 (print), 978-94-011-1884-2 (on-line). doi:10.1007/978-94-011-1884-2_10
This function returns the red:far-red photon ratio of a light source spectrum.
R_FR(spct, std = "Smith10", use.cached.mult = FALSE, use.hinges = TRUE)R_FR(spct, std = "Smith10", use.cached.mult = FALSE, use.hinges = TRUE)
spct |
an object of class "source.spct". |
std |
select which definition of red and far-red should be used, defaults to "Smith". |
use.cached.mult |
logical indicating whether multiplier values should be cached between calls. |
use.hinges |
logical indicating whether to use hinges to reduce interpolation errors. |
a single numeric dimensionless value giving the R:FR photon ratio, with name attribute set to the name of the wavebands, with "(q:q)" appended.
R_FR(sun.spct)R_FR(sun.spct)
A dataset containing for wavelengths at a 1 nm interval in the range 350 to 1000 nm, tabulated values for total reflectance and total transmittance, for the upper and lower epidermis of one leaf from the upper part of a shoot and another one from the lower part of a shoot of tall goldenrod (Solidago altissima).
The variables in each spectrum are as follows:
w.length (nm)
Rfr
Tfr
Solidago_altissima.mspctSolidago_altissima.mspct
object_mspct collection object with four object_spct
member objects, each with 651 rows and 3 variables
We thank H. M. Noda for allowing us to include these data in our package. We have included here only data for two leaves from one species (Solidago altissima) and for wavelengths shorter than 1000 nm, from the much larger original data set. The whole data set is publicly available and the data easy to read into R. The data included here where measured with a Li-Cor LI-1800 spectroradiometer equipped with a LI-1800-12 (Li-Cor) integrating sphere, and consequently are for total reflectance and total transmittance. Further details on methods are available through the JaLTER web site. If you use these data in a publication, please cite the original source as given under references and contact the original author. In addition cite this package.
Noda H. 'Reflectance and transmittance spectra of leaves and
shoots of 22 vascular plant species and reflectance spectra of trunks and
branches of 12 tree species in Japan' ERDP-2013-02.1.1
(http://db.cger.nies.go.jp/JaLTER/metacat/metacat/ERDP-2013-02.1.1/jalter-en)
JaLTER, Japan Long Term Ecological Research Network,
http://www.jalter.org/
This function returns the UV:PAR photon ratio of a light source spectrum.
UV_PAR(spct, std = "ISO", use.cached.mult = FALSE, use.hinges = TRUE)UV_PAR(spct, std = "ISO", use.cached.mult = FALSE, use.hinges = TRUE)
spct |
an object of class "source.spct". |
std |
select which definition of UV should be used, defaults to "ISO". |
use.cached.mult |
logical indicating whether multiplier values should be cached between calls. |
use.hinges |
logical indicating whether to use hinges to reduce interpolation errors. |
a single numeric dimensionless value giving the UV:PAR photon ratio, with name attribute set to the name of the wavebands, with "(q:q)" appended.
UV_PAR(sun.spct)UV_PAR(sun.spct)
This function returns the UVA:PAR photon ratio of a light source spectrum.
UVA_PAR(spct, std = "ISO", use.cached.mult = FALSE, use.hinges = TRUE)UVA_PAR(spct, std = "ISO", use.cached.mult = FALSE, use.hinges = TRUE)
spct |
an object of class "source.spct". |
std |
select which definition of UVA should be used, defaults to "ISO". |
use.cached.mult |
logical indicating whether multiplier values should be cached between calls. |
use.hinges |
logical indicating whether to use hinges to reduce interpolation errors. |
a single numeric dimensionless value giving the UVA:PAR photon ratio, with name attribute set to the name of the wavebands, with "(q:q)" appended.
UVA_PAR(sun.spct)UVA_PAR(sun.spct)
This function returns the UVA:UV photon ratio of a light source spectrum.
UVA_UV(spct, std = "ISO", use.cached.mult = FALSE, use.hinges = TRUE)UVA_UV(spct, std = "ISO", use.cached.mult = FALSE, use.hinges = TRUE)
spct |
an object of class "source.spct". |
std |
select which definition of UVB and UV should be used, defaults to "ISO". |
use.cached.mult |
logical indicating whether multiplier values should be cached between calls. |
use.hinges |
logical indicating whether to use hinges to reduce interpolation errors. |
a single numeric dimensionless value giving the UVA:UV photon ratio, with name attribute set to the name of the wavebands, with "(q:q)" appended.
UVA_UV(sun.spct)UVA_UV(sun.spct)
This function returns the UVA1:UV photon ratio of a light source spectrum.
UVA1_UV(spct, std = "CIE", use.cached.mult = FALSE, use.hinges = TRUE)UVA1_UV(spct, std = "CIE", use.cached.mult = FALSE, use.hinges = TRUE)
spct |
an object of class "source.spct". |
std |
select which definition of UVA1 should be used, defaults to "CIE". For UV "ISO" is always used. |
use.cached.mult |
logical indicating whether multiplier values should be cached between calls. |
use.hinges |
logical indicating whether to use hinges to reduce interpolation errors. |
a single numeric dimensionless value giving the UVA:UV photon ratio, with name attribute set to the name of the wavebands, with "(q:q)" appended.
UVA1_UV(sun.spct)UVA1_UV(sun.spct)
This function returns the UVA2:UV photon ratio of a light source spectrum.
UVA2_UV(spct, std = "CIE", use.cached.mult = FALSE, use.hinges = TRUE)UVA2_UV(spct, std = "CIE", use.cached.mult = FALSE, use.hinges = TRUE)
spct |
an object of class "source.spct". |
std |
select which definition of UVA1 should be used, defaults to "CIE". For UV "ISO" is always used. |
use.cached.mult |
logical indicating whether multiplier values should be cached between calls. |
use.hinges |
logical indicating whether to use hinges to reduce interpolation errors. |
a single numeric dimensionless value giving the UVA:UV photon ratio, with name attribute set to the name of the wavebands, with "(q:q)" appended.
UVA2_UV(sun.spct)UVA2_UV(sun.spct)
This function returns the UVA:UV photon ratio of a light source spectrum.
UVAlw_UV(spct, std = "plants", use.cached.mult = FALSE, use.hinges = TRUE)UVAlw_UV(spct, std = "plants", use.cached.mult = FALSE, use.hinges = TRUE)
spct |
an object of class "source.spct". |
std |
select which definition of UVAlw should be used, defaults to "plants". For UV "ISO" is always used. |
use.cached.mult |
logical indicating whether multiplier values should be cached between calls. |
use.hinges |
logical indicating whether to use hinges to reduce interpolation errors. |
a single numeric dimensionless value giving the UVA:UV photon ratio, with name attribute set to the name of the wavebands, with "(q:q)" appended.
Whenever possible use UVA1 instead of UVAlw and UVA2 instead of UVAsw as UVA1 and UVA2 are frequently used definitions, even if not standardised, while UVAlw and UVAsw are ad-hoc definitions used in some publications for specific optical filters.
UVA_UV(sun.spct)UVA_UV(sun.spct)
This function returns the UVAsw:UV photon ratio of a light source spectrum.
UVAsw_UV(spct, std = "plants", use.cached.mult = FALSE, use.hinges = TRUE)UVAsw_UV(spct, std = "plants", use.cached.mult = FALSE, use.hinges = TRUE)
spct |
an object of class "source.spct". |
std |
select which definition of UVAsw should be used, defaults to "plants". For UV "ISO" is always used. |
use.cached.mult |
logical indicating whether multiplier values should be cached between calls. |
use.hinges |
logical indicating whether to use hinges to reduce interpolation errors. |
a single numeric dimensionless value giving the UVA:UV photon ratio, with name attribute set to the name of the wavebands, with "(q:q)" appended.
Whenever possible use UVA1 instead of UVAlw and UVA2 instead of UVAsw as UVA1 and UVA2 are frequently used definitions, even if not standardised, while UVAlw and UVAsw are ad-hoc definitions used in some publications for specific optical filters.
UVAsw_UV(sun.spct)UVAsw_UV(sun.spct)
This function returns the UVB:PAR photon ratio of a light source spectrum.
UVB_PAR(spct, std = "ISO", use.cached.mult = FALSE, use.hinges = TRUE)UVB_PAR(spct, std = "ISO", use.cached.mult = FALSE, use.hinges = TRUE)
spct |
an object of class "source.spct". |
std |
select which definition of UVB should be used, defaults to "ISO". |
use.cached.mult |
logical indicating whether multiplier values should be cached between calls. |
use.hinges |
logical indicating whether to use hinges to reduce interpolation errors. |
a single numeric dimensionless value giving the UVB:UV photon ratio, with name attribute set to the name of the wavebands, with "(q:q)" appended.
UVB_PAR(sun.spct)UVB_PAR(sun.spct)
This function returns the UVB:UV photon ratio of a light source spectrum.
UVB_UV(spct, std = "ISO", use.cached.mult = FALSE, use.hinges = TRUE)UVB_UV(spct, std = "ISO", use.cached.mult = FALSE, use.hinges = TRUE)
spct |
an object of class "source.spct". |
std |
select which definition of UVB and UV should be used, defaults to "ISO". |
use.cached.mult |
logical indicating whether multiplier values should be cached between calls. |
use.hinges |
logical indicating whether to use hinges to reduce interpolation errors. |
a single numeric dimensionless value giving the UVB:UV photon ratio, with name attribute set to the name of the wavebands, with "(q:q)" appended.
UVB_UV(sun.spct)UVB_UV(sun.spct)
This function returns the UVB:UVA photon ratio of a light source spectrum.
UVB_UVA(spct, std = "ISO", use.cached.mult = FALSE, use.hinges = TRUE)UVB_UVA(spct, std = "ISO", use.cached.mult = FALSE, use.hinges = TRUE)
spct |
an object of class "source.spct". |
std |
select which definition of UVB and UVA should be used, defaults to "ISO". |
use.cached.mult |
logical indicating whether multiplier values should be cached between calls. |
use.hinges |
logical indicating whether to use hinges to reduce interpolation errors. |
a single numeric dimensionless value giving the UVB:UVA photon ratio, with name attribute set to the name of the wavebands, with "(q:q)" appended.
UVB_UVA(sun.spct)UVB_UVA(sun.spct)
A dataset containing the wavelengths at an arbitrary nm interval. Tabulated values for the in vitro absorbance spectrum of UVR8.
A filter_spct object with two member filter_spct
objects.
The variables are as follows:
w.length (nm)
A (spectral absorbance)
If you use these data in a publication, please cite also the original source as given under references in addition to this package.
Christie, J. M., A. S. Arvai, K. J. Baxter, M. Heilmann, A. J. Pratt, A. O'Hara, S. M. Kelly, M. Hothorn, B. O. Smith, K. Hitomi, et al. (2012). Plant UVR8 photoreceptor senses UV-B by tryptophan-mediated disruption of cross-dimer salt bridges. In: Science (New York, N.Y.) 335.6075, pp. 1492-1496. doi:10.1126/science.1218091. (Figure S3)
Neha Rai Andrew O'Hara Daniel Farkas Omid Safronov Khuanpiroon Ratanasopa Fang Wang Anders V. Lindfors Gareth I. Jenkins Tarja Lehto Jarkko Salojärvi Mikael Brosché Åke Strid Pedro J. Aphalo Luis O. Morales (2020) The photoreceptor UVR8 mediates the perception of both UV‐B and UV‐A wavelengths up to 350 nm of sunlight with responsivity moderated by cryptochromes. Plant Cell and Environment, early on-line. doi:10.1111/pce.13752. (Figure S7)
names(UVR8s.mspct) getWhatMeasured(UVR8s.mspct[[1]])names(UVR8s.mspct) getWhatMeasured(UVR8s.mspct[[1]])
A dataset containing the wavelengths at an arbitrary nm interval. Tabulated values for the in vitro absorbance spectrum of ZTL LOV2 domain from Arabidopsis measured in vitro. Data were digitized from figure 2B in Zoltowski and Imaizumi (2014).
A filter_mspct with five member filter_spct objects each
with 300 rows and 2 numeric variables, w.length and A
The variables of the member spectra are as follows:
w.length (nm)
A (spectral absorbance)
If you use these data in a publication, please cite also the original source as given under references in addition to this package.
Zoltowski, B. D., Imaizumi, T. (2014). Structure and Function of the ZTL/FKF1/LKP2 Group Proteins in Arabidopsis. Enzymes, 35, 213-39.