Man pages for photobiology
Photobiological Calculations
| A2T | Convert absorbance into transmittance |
| absorbance | Absorbance |
| absorbance_spct | Calculate absorbance from spectral absorbance. |
| absorptance | Absorptance |
| absorptance_spct | Calculate absorptance from spectral absorptance. |
| adaptive_smoothing | Custom smoothing |
| add_attr2tb | Copy attributes from members of a 'generic_mspct' |
| Afr2T | Convert transmittance into absorptance. |
| A.illuminant.spct | CIE A illuminant data |
| any2T | Convert filter quantities. |
| as.calibration_mspct | Coerce to a collection-of-spectra |
| as.calibration_spct | Coerce to a spectrum |
| as.chroma_mspct | Coerce to a collection-of-spectra |
| as.chroma_spct | Coerce to a spectrum |
| as.cps_mspct | Coerce to a collection-of-spectra |
| as.cps_spct | Coerce to a spectrum |
| as_energy | Convert spectral photon irradiance into spectral energy... |
| as.filter_mspct | Coerce to a collection-of-spectra |
| as.filter_spct | Coerce or convert into a filter spectrum |
| as.generic_mspct | Coerce to a collection-of-spectra |
| as.generic_spct | Coerce to a spectrum |
| as.matrix-mspct | Coerce a collection of spectra into a matrix |
| as.object_mspct | Coerce to a collection-of-spectra |
| as.object_spct | Coerce to a spectrum |
| as_quantum | Convert spectral energy irradiance into spectral photon... |
| as_quantum_mol | Convert spectral energy irradiance into spectral photon... |
| as.raw_mspct | Coerce to a collection-of-spectra |
| as.raw_spct | Coerce to a spectrum |
| as.reflector_mspct | Coerce to a collection-of-spectra |
| as.reflector_spct | Coerce to a spectrum |
| as.response_mspct | Coerce to a collection-of-spectra |
| as.response_spct | Coerce to a spectrum |
| as.solute_mspct | Coerce to a collection-of-spectra |
| as.solute_spct | Coerce to a solute spectrum |
| as.source_mspct | Coerce to a collection-of-spectra |
| as.source_spct | Coerce to a spectrum |
| auto_hinges | Guess whether insertion of hinges is needed or not |
| average_spct | Average spectral data. |
| beesxyzCMF.spct | Honeybee xyz chromaticity colour matching function data |
| black_body.spct | Theoretical optical bodies |
| c | Combine collections of spectra |
| calc_multipliers | Spectral weights |
| calc_source_output | Scaled and/or interpolated light-source spectral output |
| ccd.spct | Spectral response of a back-thinned CCD image sensor. |
| check_and_rename_vars | check and rename variables |
| checkMspctVersion | Check that the "mspct.version" attribute is set |
| check_spct | Check validity of spectral objects |
| checkSpctVersion | Check that the "spct.version" attribute is set |
| check_spectrum | Sanity check a spectrum |
| checkTimeUnit | Check the "time.unit" attribute of an existing source_spct... |
| check_w.length | Sanity check of wavelengths (internal function). |
| check_wl_stepsize | Check consistency of wavelength step size |
| ciev10.spct | Linear energy CIE 2008 luminous efficiency function 10 deg... |
| ciev2.spct | Linear energy CIE 2008 luminous efficiency function 2 deg... |
| ciexyzCC10.spct | CIE xyz chromaticity coordinates (CC) 10 deg data |
| ciexyzCC2.spct | CIE xyz chromaticity coordinates 2 deg data |
| ciexyzCMF10.spct | Linear energy CIE xyz colour matching function (CMF) 10 deg... |
| ciexyzCMF2.spct | Linear energy CIE xyz colour matching function (CMF) 2 deg... |
| class_spct | Query which is the class of a spectrum |
| clean | Clean (=replace) off-range values in a spectrum |
| clean_spct | Clean a spectrum |
| clear_photobio.cache | Clear the spectral weights cache |
| clear.spct | Theoretical spectrum of clear and apaque materials |
| clip_wl | Clip head and/or tail of a spectrum |
| collect2mspct | Form a new collection |
| color_of | Color of an object |
| compare_spct | Coarse-grained comparison of two spectra |
| cone_fundamentals10.spct | Ten-degree cone fundamentals |
| convertTfrType | Convert the "Tfr.type" attribute |
| convertThickness | Convert the "thickness" attribute of an existing filter_spct... |
| convertTimeUnit | Convert the "time.unit" attribute of an existing source_spct... |
| convolve_each | Convolve function for collections of spectra |
| copy_attributes | Copy attributes |
| cps2irrad | Conversion from counts per second to physical quantities |
| D2_spectrum | Calculate deuterium lamp output spectrum from fitted... |
| D2.UV653 | Data for typical calibration lamps |
| D50.illuminant.spct | CIE D50 illuminant data |
| D65.illuminant.spct | CIE D65 illuminant data |
| defunct | Defunct functions and methods |
| denormalize_spct | Remove a previously applied normalization |
| despike | Remove spikes from spectrum |
| diffraction_single_slit | Diffraction |
| dim.generic_mspct | Dimensions of an Object |
| div-.generic_spct | Arithmetic Operators |
| div_spectra | Divide two spectra, even if the wavelengths values differ |
| drop_user_cols | Drop user columns |
| e2q | Convert energy-based quantities into photon-based quantities. |
| e2qmol_multipliers | Calculate energy to quantum (mol) multipliers |
| e2quantum_multipliers | Calculate energy to quantum multipliers |
| e_fluence | Energy fluence |
| e_fraction | Energy:energy fraction |
| e_irrad | Energy irradiance |
| enable_check_spct | Enable or disable checks |
| energy_as_default | Set spectral-data options |
| energy_irradiance | Calculate (energy) irradiance from spectral irradiance |
| energy_ratio | Energy:energy ratio |
| eq_ratio | Energy:photon ratio |
| e_ratio | Energy:energy ratio |
| e_response | Energy-based photo-response |
| expanse | Expanse |
| extract | Extract or replace parts of a spectrum |
| extract_mspct | Extract or replace members of a collection of spectra |
| f_dispatcher_spct | Math function dispatcher for spectra |
| FEL_spectrum | Incandescent "FEL" lamp emission spectrum |
| filter_cps.mspct | Counts per second from a measurement of a plastic film |
| findMultipleWl | Find repeated w.length values |
| find_peaks | Find local maxima or global maximum (peaks) |
| find_spikes | Find spikes |
| find_wls | Find wavelength values in a spectrum |
| fit_peaks | Refine position and value of extremes by fitting |
| fluence | Fluence |
| formatted_range | Compute range and format it |
| fscale | Rescale a spectrum using a summary function |
| fscale_spct | fscale a spectrum |
| fshift | Shift the scale of a spectrum using a summary function |
| fshift_spct | fshift a spectrum |
| generic_mspct | Collection-of-spectra constructor |
| get_attributes | Get the metadata attributes |
| getFilterProperties | Get the "filter.properties" attribute |
| getHowMeasured | Get the "how.measured" attribute |
| getIdFactor | Get the "idfactor" attribute |
| getInstrDesc | Get the "instr.desc" attribute |
| getInstrSettings | Get the "instr.settings" attribute |
| getKType | Get the "K.type" attribute |
| getMspctVersion | Get the "mspct.version" attribute |
| getMultipleWl | Get the "multiple.wl" attribute |
| getNormalized | Query the "normalized" and "normalization" attributes |
| get_peaks | Get peaks and valleys from a spectrum |
| getScaled | Get the "scaled" attribute |
| getSoluteProperties | Get the "solute.properties" attribute |
| getSpctVersion | Get the "spct.version" attribute |
| getTimeUnit | Get the "time.unit" attribute of an existing source_spct... |
| getWhatMeasured | Get the '"what.measured"' attribute |
| getWhenMeasured | Get the "when.measured" attribute |
| getWhereMeasured | Get the "where.measured" attribute |
| green_leaf.spct | Green birch leaf reflectance. |
| head_tail | Return the First and Last Parts of an Object |
| illuminance | Irradiance |
| insert_hinges | Insert wavelength values into spectral data. |
| insert_spct_hinges | Insert new wavelength values into a spectrum |
| integrate_spct | Integrate spectral data. |
| integrate_xy | Gives irradiance from spectral irradiance. |
| interpolate_spct | Map a spectrum to new wavelength values. |
| interpolate_spectrum | Calculate spectral values at a different set of wavelengths |
| interpolate_wl | Map spectra to new wavelength values. |
| irrad | Irradiance |
| irradiance | Photon or energy irradiance from spectral energy or photon... |
| is_absorbance_based | Query if a spectrum contains absorbance or transmittance data |
| is_effective | Is an R object "effective" |
| is.generic_mspct | Query class of spectrum objects |
| is.generic_spct | Query class of spectrum objects |
| is_mole_based | Query if a spectrum contains mole or mass based data |
| is_normalized | Query whether a generic spectrum has been normalized. |
| is.old_spct | Query if an object has old class names |
| is_photon_based | Query if a spectrum contains photon- or energy-based data. |
| is_scaled | Query whether a generic spectrum has been scaled |
| is.summary_generic_spct | Query class of spectrum summary objects |
| is_tagged | Query if a spectrum is tagged |
| isValidInstrDesc | Check the "instr.desc" attribute |
| isValidInstrSettings | Check the "instr.settings" attribute |
| is.waveband | Query if it is a waveband |
| join_mspct | Join all spectra in a collection |
| julian_day | Solar astronomy using Meeus' algorithm |
| labels | Find labels from "waveband" object |
| Ler_leaf.spct | Green Arabidopsis leaf reflectance and transmittance. |
| l_insert_hinges | Insert wavelength values into spectral data. |
| log | Logarithms and Exponentials |
| make_var_labels | Column or variable labels |
| make_wl_consistent | Make wavelengths consistent |
| MathFun | Miscellaneous Mathematical Functions |
| max | Wavelength maximum |
| merge2object_spct | Merge into object_spct |
| merge_attributes | Merge and copy attributes |
| midpoint | Midpoint |
| min | Wavelength minimum |
| minus-.generic_spct | Arithmetic Operators |
| mod-.generic_spct | Arithmetic Operators |
| msmsply | Multi-spct transform methods |
| mspct_classes | Names of multi-spectra classes |
| na.omit | Handle Missing Values in Objects |
| normalization | Normalization of an R object |
| normalize | Normalize spectral data |
| normalized_diff_ind | Calculate a normalized difference. |
| normalize_range_arg | Normalize a range argument into a true numeric range |
| oper_spectra | Binary operation on two spectra, even if the wavelengths... |
| peaks | Peaks or local maxima |
| phenylalanine.spct | Molar spectral attenuation coefficient of phenylalanine |
| photobiology-package | photobiology: Photobiological Calculations |
| photodiode.spct | Spectral response of a GaAsP photodiode |
| photon_irradiance | Photon irradiance |
| photon_ratio | Photo:photon ratio |
| photons_energy_ratio | Photon:energy ratio |
| plus-.generic_spct | Arithmetic Operators |
| pow-.generic_spct | Arithmetic Operators |
| print.generic_spct | Print spectral objects |
| print.metadata | Print methods for metadata records |
| print.summary_generic_spct | Print spectral summary |
| print.waveband | Print a "waveband" object |
| prod_spectra | Multiply two spectra, even if the wavelengths values differ |
| pull_sample | Random sample of spectra |
| q2e | Convert photon-based quantities into energy-based quantities |
| qe_ratio | Photon:energy ratio |
| q_fluence | Photon fluence |
| q_fraction | Photon:photon fraction |
| q_irrad | Photon irradiance |
| q_ratio | Photon:photon ratio |
| q_response | Photon-based photo-response |
| r4p_pkgs | Packages in R for Photobiology suite |
| range | Wavelength range |
| range_check_Tfr | Internal utility range-check functions |
| rbindspct | Row-bind spectra |
| reflectance | Reflectance |
| reflectance_spct | Calculate reflectance from spectral reflectance |
| replace_bad_pixs | Replace bad pixels in a spectrum |
| response | Integrated response |
| resp_spct | Calculate response from spectral response |
| Rfr_fraction | reflectance:reflectance fraction |
| Rfr_from_n | Reflectance at a planar boundary |
| Rfr_normdiff | reflectance:reflectance normalised difference |
| Rfr_ratio | reflectance:reflectance ratio |
| rgb_spct | RGB color values |
| rmDerivedMspct | Remove "generic_mspct" and derived class attributes. |
| rmDerivedSpct | Remove "generic_spct" and derived class attributes. |
| round | Rounding of Numbers |
| rowwise | rowwise functions for collections of spectra |
| se | Standard error of the mean |
| s_e_irrad2rgb | Spectral irradiance to rgb color conversion |
| select_spct_attributes | Merge user supplied attribute names with default ones |
| se.m | Standard error of the mean |
| se.p | Standard error of the mean |
| setBSWFUsed | The "bswf.used" attribute |
| setFilterProperties | Set the "filter.properties" attribute |
| setGenericSpct | Convert an R object into a spectrum object. |
| setHowMeasured | Set the "how.measured" attribute |
| setIdFactor | Set the "idfactor" attribute |
| setInstrDesc | Set the "instr.desc" attribute |
| setInstrSettings | Set the "instr.settings" attribute |
| setKType | Set the "K.type" attribute |
| setMultipleWl | Set the "multiple.wl" attribute |
| setNormalized | Set the "normalized" and "normalization" attributes |
| setResponseType | Set the "response.type" attribute |
| setRfrType | The "Rfr.type" attribute |
| setScaled | Set the "scaled" attribute |
| setSoluteProperties | Set the "solute.properties" attribute |
| setTfrType | The "Tfr.type" attribute |
| setTimeUnit | Set the "time.unit" attribute of an existing source_spct... |
| setWhatMeasured | Set the "what.measured" attribute |
| setWhenMeasured | Set the "when.measured" attribute |
| setWhereMeasured | Set the "where.measured" attribute |
| shared_member_class | Classes common to all collection members. |
| sign | Sign |
| sinc | sinc |
| slash-.generic_spct | Arithmetic Operators |
| s_mean | Mean from collection of spectra |
| s_mean_se | Mean and standard error from collection of spectra |
| s_mean_se_band | Mean plus and minus standard error from collection of spectra |
| s_median | Median of a collection of spectra |
| smooth_spct | Smooth a spectrum |
| source_spct | Spectral-object constructors |
| spct_attr2tb | Copy attributes into a tibble |
| spct_classes | Function returning a vector containing the names of spectra... |
| spct_metadata | Access metadata |
| spct_wide2long | Convert spectrum from wide to long form |
| spikes | Spikes |
| split2mspct | Convert a 'wide' or untidy data frame into a collection of... |
| split_bands | List-of-wavebands constructor |
| split_energy_irradiance | Energy irradiance for split spectrum regions |
| split_irradiance | Energy or photon irradiance for split spectrum regions |
| split_photon_irradiance | Photon irradiance for split spectrum regions |
| s_prod | Product from collection of spectra |
| s_range | Range of a collection of spectra |
| s_sd | Standard Deviation of a collection of spectra |
| s_se | Standard Error of a collection of spectra |
| s_sum | Sum from collection of spectra |
| stepsize | Stepsize |
| subset | Subsetting spectra |
| subset2mspct | Convert 'long' or tidy spectral data into a collection of... |
| subset_attributes | Subset the metadata attributes |
| subt_spectra | Subtract two spectra |
| summary.generic_spct | Summary of one or more spectra |
| summary_spct_classes | Function that returns a vector containing the names of... |
| sum_spectra | Add two spectra |
| sun_daily.spct | Daily solar spectral irradiance (simulated) |
| sun_evening.spct | Time series of solar spectral irradiance (measured) |
| sun.spct | Solar spectral irradiance (simulated) |
| s_var | Variance of a collection of spectra |
| T2A | Convert transmittance into absorbance. |
| T2Afr | Convert transmittance into absorptance. |
| tag | Tag a spectrum |
| Tfr_fraction | transmittance:transmittance fraction |
| Tfr_normdiff | transmittance:transmittance normalised difference |
| Tfr_ratio | transmittance:transmittance ratio |
| thin_wl | Thin the density of wavelength values |
| times-.generic_spct | Arithmetic Operators |
| transmittance | Transmittance |
| transmittance_spct | Calculate transmittance from spectral transmittance. |
| Trig | Trigonometric Functions |
| trimInstrDesc | Trim the "instr.desc" attribute |
| trimInstrSettings | Trim the "instr.settings" attribute |
| trim_spct | Trim (or expand) head and/or tail of a spectrum |
| trim_tails | Trim (or expand) head and/or tail |
| trim_waveband | Trim (or expand) head and/or tail |
| trim_wl | Trim head and/or tail of a spectrum |
| two_filters.spct | Transmittance spectrum of plastic films |
| two_irrads | Compute two irrads for ratio, fraction or normalised... |
| two_reflectances | Compute two reflectances for ratio, fraction or normalised... |
| two_sensors.mspct | Spectral response of two light sensors. |
| two_transmittances | Compute two transmittances for ratio, fraction or normalised... |
| uncollect2spct | Extract all members from a collection |
| untag | Remove tags |
| upgrade_spct | Upgrade one spectral object |
| upgrade_spectra | Upgrade one or more spectral objects |
| using_Tfr | Use photobiology options |
| valleys | Valleys or local minima |
| verbose_as_default | Set error reporting options |
| v_insert_hinges | Insert spectral data values at new wavelength values. |
| v_replace_hinges | Overwrite spectral data values at existing wavelength values. |
| water.spct | Molar spectral attenuation coefficient of water |
| waveband | Waveband constructor method |
| waveband_ratio | Photon or energy ratio |
| wb2rect_spct | Create tagged spectrum from wavebands |
| wb2spct | Create spectrum from wavebands |
| wb2tagged_spct | Create tagged spectrum from wavebands |
| wb_trim_as_default | Set computation options |
| white_led.source_spct | White led bulb spectrum |
| wl2wavenumber | Wavelength conversions |
| w_length2rgb | Wavelength to rgb color conversion |
| w_length_range2rgb | Wavelength range to rgb color conversion |
| wls_at_target | Find wavelengths values corresponding to a target spectral... |
