Find peaks in a spectrum
This function finds all peaks (local maxima) in a spectrum, using a user selectable size threshold relative to the tallest peak (global maximum). This a wrapper built on top of function peaks from package splus2R.
find_peaks(x, ignore_threshold = 0, span = 3, strict = TRUE)
numeric value between 0.0 and 1.0 indicating the size threshold below which peaks will be ignored.
a peak is defined as an element in a sequence which is greater than all other elements within a window of width span centered at that element. The default value is 3, meaning that a peak is bigger than both of its neighbors. Default: 3.
ogical flag: if TRUE, an element must be strictly greater than all other values in its window to be considered a peak. Default: TRUE.
an object like s.irrad of logical values. Values that are TRUE correspond to local peaks in the data.
This function is a wrapper built on function
peaks from splus2R and handles non-finite
(including NA) values differently than
peaks, instead of giving an
error they are replaced with the smallest finite value in
Other peaks and valleys functions:
- A2T: Convert absorbance into transmittance
- absorbance: Absorbance
- absorbance_spct: Calculate absorbance from spectral absorbance.
- absorptance: Absorptance
- absorptance_spct: Calculate absorptance from spectral absorptance.
- A.illuminant.spct: CIE A illuminant data
- as_energy: Convert spectral photon irradiance into spectral energy...
- as.generic_mspct: Collection-of-spectra copy-constructor
- as.generic_spct: Spectral-object copy constructor
- as_quantum: Convert spectral energy irradiance into spectral photon...
- as_quantum_mol: Convert spectral energy irradiance into spectral photon...
- as.solar_date: Convert a solar_time object into solar_date object
- as_tod: Convert date to time-of-day in hours, minutes or seconds
- average_spct: Average spectral data.
- beesxyzCMF.spct: Honeybee xyz chromaticity colour matching function data
- black_body.spct: Theoretical black body
- calc_multipliers: Spectral weights
- calc_source_output: Light-source spectral output
- ccd.spct: Spectral response of a back-thinned CCD image sensor.
- c.generic_mspct: Combine collections of spectra
- 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 of a spectrum.
- checkTimeUnit: Check the "time.unit" attribute of an existing source_spct...
- check_w.length: Sanity check of wavelengths (internal function).
- 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 an spectrum
- clean: Clean (=replace) off-range values in a spectrum
- clean_spct: Clean a spectrum
- clear_body.spct: Theoretical clear body
- clear_photobio.cache: clear the spectral weights cache
- clear.spct: Theoretical spectrum of a clear clear material
- clip_wl: Clip head and/or tail of a spectrum
- color: Color of an object
- 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 deuterim lamp output spectrum from fitted constants
- D65.illuminant.spct: CIE D65 illuminant data
- day_night: Times for sun positions
- defunct: Defunct functions and methods
- dim.generic_mspct: Dimensions of an Object
- div-.generic_spct: Arithmetic Operators
- div_spectra: Divide two spectra, even if the wavelengths values differ
- 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_irrad: Energy irradiance
- 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
- 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
- find_peaks: Find peaks in a spectrum
- fluence: Fluence
- format.solar_time: Encode in a Common Format
- 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
- getBSWFUsed: Get the "bswf.used" attribute
- getInstrDesc: Get the "instr.desc" attribute
- getInstrSettings: Get the "instr.settings" attribute
- getMspctVersion: Get the "mspct.version" attribute
- getMultipleWl: Get the "multiple.wl" attribute
- getNormalized: Get the "normalized" attribute
- get_peaks: Get peaks and valleys in a spectrum
- getRfrType: Get the "Rfr.type" attribute
- getScaled: Get the "scaled" attribute
- getSpctVersion: Get the "spct.version" attribute
- getTfrType: Get the "Tfr.type" 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
- 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 (quantum) irradiance from spectral (energy)...
- 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_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.solar_time: Query class
- is.summary_generic_spct: Query class of spectrum summary objects
- is_tagged: Query if it is an spectrum is tagged
- is.waveband: Query if it is a waveband
- julian_day: Solar astronomy using Meeus' algorithm
- labels: Find labels from "waveband" object
- l_insert_hinges: Insert wavelength values into spectral data.
- log: Logarithms and Exponentials
- MathFun: Miscellaneous Mathematical Functions
- max: Wavelength maximum
- merge.generic_spct: Merge two generic_spct objects
- midpoint: Central wavelength value
- 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
- normalization: Normalization of an R object
- normalize: Normalize spectral data
- normalized_diff_ind: Calculate a normalized index.
- normalize_range_arg: Normalize a range argument into a true numeric range
- opaque.spct: Theoretical spectrum of an opaque material
- oper_spectra: Binary operation on two spectra, even if the wavelengths...
- peaks: Peaks or local maxima
- photobiology-package: 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
- polyester.spct: Transmittance spectrum of clear polyester film
- pow-.generic_spct: Arithmetic Operators
- print: Print a spectral object
- print.solar_time: Print solar time and solar date objects
- print.summary_generic_spct: Print spectral summary
- print.waveband: Print a "waveband" object
- prod_spectra: Multiply two spectra, even if the wavelengths values differ
- q2e: Convert photon-based quantities into energy-based quantities
- qe_ratio: Photon:energy ratio
- q_fluence: Photon fluence
- q_irrad: Photon irradiance
- q_ratio: Photon:photon ratio
- q_response: Photon-based photo-response
- range: Wavelength range
- rbindspct: Row-bind spectra
- reflectance: Reflectance
- reflectance_spct: Calculate reflectance from spectral reflectance
- response: Integrated response
- resp_spct: Calculate response from spectral response
- 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
- s_e_irrad2rgb: Spectrum to rgb color conversion
- setBSWFUsed: Set the "bswf.used" attribute
- setGenericSpct: Convert an R object into a spectrum object.
- setInstrDesc: Set the "instr.desc" attribute
- setInstrSettings: Set the "instr.settings" attribute
- setMultipleWl: Set the "multiple.wl" attribute
- setNormalized: Set the "normalized" attribute
- setRfrType: Set the "Rfr.type" attribute
- setScaled: Set the "scaled" attribute
- setTfrType: Set 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
- slash-.generic_spct: Arithmetic Operators
- smooth_spct: Smooth a spectrum
- solar_time: Local solar time
- source_spct: Spectral-object constructor
- spct_classes: Function that returns a vector containing the names of...
- 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
- spread: Length of object in wavelength units
- stepsize: Stepsize
- subset2mspct: Convert 'long' or tidy spectral data into a collection of...
- subt_spectra: Subtract two spectra
- summary: Summary of a spectral object
- summary_spct_classes: Function that returns a vector containing the names of...
- sum_spectra: Add two spectra
- sun_angles: Solar angles
- sun.daily.data: Daily solar spectral irradiance (simulated)
- sun.daily.spct: Daily solar spectral irradiance (simulated)
- sun.data: Solar spectral irradiance (simulated)
- sun.spct: Solar spectral irradiance (simulated)
- T2A: Convert transmittance into absorbance.
- tag: Tag a spectrum
- times-.generic_spct: Arithmetic Operators
- transmittance: Transmittance
- transmittance_spct: Calculate transmittance from spectral transmittance.
- Trig: Trigonometric Functions
- trim_spct: Trim (or expand) head and/or tail
- 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
- twilight2angle: twilight argument check and conversion
- tz_time_diff: Time difference between two time zones
- untag: Remove tags
- upgrade_spct: Upgrade one spectral object
- upgrade_spectra: Upgrade one or more spectral objects
- valleys: Valleys or local minima
- v_insert_hinges: Insert wavelength values into spectral data.
- 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
- white_body.spct: Theoretical white body
- w_length2rgb: Wavelength to rgb color conversion
- w_length_range2rgb: Wavelength range to rgb color conversion
- yellow_gel.spct: Transmittance spectrum of yellow theatrical gel.