Radiation, astronomy and atmosphere | Naming conventions | High and low level functions | Example data | Spectra | Getting started | Classes | Data assumptions | Querying the class | Construction | Metadata attributes | Attributes supported by all spectral objects | Attributes supported by source_spct objects | Attributes supported by filter_spct objects | Collections of spectra | Constructors | Using as. conversion functions | Converting tidy data | Converting untidy data frames | Conversion into a "wide" data frame | Extract, replace and combine | Extraction based on summary quantities | Random sampling | Transform or apply functions | Summary spectra | Convolution | Wavebands | Retrieving properties | Collections of wavebands | List constructor | Special constructor | Object inspection methods | Printing | Summary | Handling NAs | Transformations: using operators | Binary operators | Unary operators and maths functions | Options | Transformations: methods and functions | Manipulating spectra | Conversions between radiation units | Conversions among transmission quantities | Normalizing a spectrum | Rescaling a spectrum | Shifting the zero of the spectral data scale | Replacing off-range spectral data values | Removing spikes | Smoothing of spectra | Wavelength interpolation | Trimming, clipping and thining | Method clip_wl() | Method trim_wl() | Functions trim2ovelap() and extend2extremes() | Method thin_wl() | Convolving weights | Individual spectra | Tagging with bands and colours | Summaries | Wavelength | Peaks, valleys and spikes | Wavelengths at target value | Irradiance | Fluence | Photon and energy ratios | Transmittance, reflectance, absorptance and absorbance | Normalized difference indexes | Integrated response | Integration over wavelengths | Calculation from individual spectra | Comparison of spectra | Illumination and light as seen by humans | Illuminance | CCT and CRI | RGB colours

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

Introduction | What are autoplot() method specializations for? | What are ggplot specializations for? | What are the different stats useful for? | What is geom_spct useful for? | What are the new scales for? | What are functions color_chart() and black_or_white() for? | What is method autotitle() for? | How can defaults be modified? | Set up | ggplot() methods for spectra | ggplot() methods for collections fof spectra | Scales | Shared features | Wavelength | Raw counts | Counts per second | Spectral irradiance | Response and action | Transmittance | Absorbance | Absorptance | Reflectance | Stats | Peaks, valleys and target values | Color from wavelength | Averages and similar summaries | Summaries producing graphical elements | Name labels | Summaries by wavelength range | Means by waveband | Totals by waveband | Irradiances by waveband | Spectral irradiances by waveband | Labels from wavebands | Wavelength colours at new x-values | Multiple stats in the same plot | Geometries | Packaged stats, geoms plus scales | wl_guide | Color charts | Changing defaults | Using options to change default arguments | Using 'ggplot2' themes

Summary | Introduction | Building this vignette | Measurement of light spectra | Spectral irradiance | Acquiring a single irradiance spectrum | A simple example | Protocols for enhanced performance | Acquiring a time series of irradiance spectra | Spectral fluence | Spectral transmittance, absorptance and reflectance | Rolling your own | Using scripts

Summary | Preliminaries | Introduction | Importing raw counts from R files | Importing raw counts from text files | Reading calibration data from files

Introduction | Functions | Workflow | Additional corrections | Apply slit function correction | Code examples | Measurement of spectral irradiance | Examples | From files | From OceanView files | From "raw_mspct" objects | Measurement of spectral transmittance | From a "raw_mspct" object | From a raw_mspct object with a known reference | Assembling spectral data for an object | Irradiance calibration from Ocean Optics | Calculating calibration constants | Applying calibration constants | High level functions | Defining new protocols

Purpose | Introduction to computed annotations | Statistics | Model equations and other annotations | Fitted lines, confidence bands and residuals | ANOVA and summary tables | Annotations based on package 'broom' | Other data features | Scales | R options | Loading packages | Examples for Statistics | stat_correlation() | stat_poly_eq() and stat_poly_line() | stat_ma_eq() and stat_ma_line() | stat_quant_eq(), stat_quant_line() and stat_quant_band() | stat_distrmix_eq(), stat_distrmix_line() and stat_distrmix_area() | stat_multcomp | stat_fit_residuals | stat_fit_deviations | stat_fit_glance | stat_fit_tb | stat_fit_tidy | stat_fit_augment | Inspecting computed variables and labels | Examples for Scales | scale_color_outcome, scale_fill_outcome | scale_x_FDR, scale_y_FDR, scale_x_logFC, scale_y_logFC, scale_x_Pvalue, scale_y_Pvalue | symmetric_limits | Volcano-plot examples | Quadrant-plot examples

Basics | Correlation | Fitted models | ANOVA or summary tables | Multiple comparisons | Aesthetic mappings | Peaks and valleys | Volcano and quadrant plots | Utility functions

Introduction | Current state | Set up | The data | Split data into chunks | Grouping | Summaries | Statistics | Locating change points | Using diff() | Durand's et al. algorithm | Using a reference | Using a quantile smoother

Preliminaries | Introduction to the extensions | Data labels, annotations and insets | Annotations in 'ggplot2' | Support of native plot coordinates | When to use annotations and when insets | Highlighting data features | Summary statistics | Positioning data labels | Local density of observations | ggplot methods | List of references | Examples | Geometries | geom_table() and stat_fmt_table() | geom_plot() | geom_grob() | geom_vhlines() | geom_text_s(), geom_label_s(), and geom_point_s() | geom_text_pairwise() and geom_label_pairwise() | Normalised Parent Coordinates | Marginal markings | Statistics | stat_centroid() | stat_group_counts() | stat_quadrant_counts() and geom_quadrant_lines() | stat_apply_group | stat_dens2d_labels() and stat_dens2d_filter() | stat_dens1d_labels() and stat_dens1d_filter() | Simple position functions | position_nudge_keep() and friends | position_nudge_to() | position_nudge_center() | position_nudge_line() | Combined position functions | position_dodgenudge() | position_stacknudge() | position_fillnudge() | position_stack_minmax() | position_jitternudge() | position_jitter_keep() | Appendix A: More on density filtering | Appendix B: try_tibble() | Time series | Other classes

Introduction | The objects containing the data | The transmittance and reflectance data | Accessing individual spectra | Accessing subsets of spectra | Querying metadata | Conversions | Plotting | Calculating summaries | Using the data in other contexts

Introduction | Preliminaries | Spectrometer output files | Ocean Optics spectrometers | SpectraSuite software | OceanView software | Jaz: Raw detector counts | Jaz: Spectral energy irradiance | "Cleaning" spectral data | Wasatch Photonics array spectrometers | Avantes array spectrometers | ASD array spectrometers | MACAM scanning spectrometers | LI-COR spectrometers | LI-180 array dector spectrometer from LI-COR | LI-1800 scanning spectrometer from LI-COR | PSI SpectraPen spectroradiometer | CID Bio-Science leaf spectrometer | Data from loggers and other instruments | Campbell Scientific | Walz Photosynthesis Instruments | YoctoPuce | Output from simulation models | TUV | Quick TUV calculator | libRadtran | Output enriched with time and date data | Scripts developed by Anders Lindfors | Online public repositories of spectral data | FReD Floral Reflectance Database | ASTER spectral database | Other R packages | To 'hyperSpec' | From 'hyperSpec' | From 'colorSpec' | To 'colorSpec' | Wrappers on 'colorSpec' functions. | From 'pavo' | Dealing with odd and bad data | Using locales | Overriding default metadata | Adding additional metadata

Introduction | References | Packages in the suite | Acknowledgements

Radiation, astronomy and atmosphere | Getting started | Introduction | Position of the sun | Times of sunrise, solar noon and sunset | Solar time | Time of day | Relative air mass | Irradiance

Introduction | Accessing individual spectra | Accessing subsets of spectra | Plotting the spectra | Using the data in other contexts

Introduction | Using the autoplot() methods | The basics | Wavelengths | Normalization | "Parallel" summaries | Summary quantities by waveband | Automatic annotations | Handling of off-range data | Editing plots and adding layers | Ploting wavebands

Introduction | Data and metadata | Accessing individual spectra | Accessing subsets of spectra | Calculating summaries from the normalized data | Plotting the spectra | Angular response | Using the data in other contexts

Introduction | References | Packages in the suite | Acknowledgements

The USB module settings | Example CSV files | Example JSON files | Example R data

First steps | YoctoRelay | YoctoMeteo

Introduction | Preliminaries | ggplot construction | Data mappings in ggplots | Data input to geometries | Data input to statistics | Controlling the debug output | Themes

Introduction | Preliminaries | Exploring how ggplots are stored | Manipulation of plot layers | Replacing scales, coordinates, whole themes and data. | Editing theme elements | Removing unused data | Attributes of the embedded data object | Coda

Introduction | References | Packages in the suite | Acknowledgements

Introduction | Using data from lamps.mspct | Accesing individual spectra | Accessing subsets of spectra | Accesing metadata | Rescaling spectral data | Plotting the spectra | Using the data in other contexts | Other data sets | Ultraviolet-B lamps and temperature | Multicolour LED lamp | Video and photography lamps | Night vision video and photography lamp

Introduction | References | Packages in the suite | Acknowledgements

Introduction | References | Packages in the suite | Acknowledgements

Introduction | References | Packages in the suite | Acknowledgements

Introduction | References | Packages in the suite | Acknowledgements

Introduction | References | Packages in the suite | Acknowledgements

Introduction | References | Packages in the suite | Acknowledgements

Introduction | Instalaltion | Using rOmniDriver | High speed acquisition | High resolution time stamps

Introduction | References | Packages in the suite | Acknowledgements

Introduction | References | Packages in the suite | Acknowledgements

Introduction | References | Packages in the suite | Acknowledgements

Introduction | The data | Accessing individual spectra | Accessing subsets of spectra | Querying metadata | Calculating summaries from the normalized data | Plotting | Using the data in other contexts

Package purpose | AC SAF Offline surface ultraviolet (OUV) | Introduction | Time series | File format | Reading one file | Reading multiple files | Using the data | Data on a geographic grid | Format of gridded data | Reading one gridded-data file | Reading multiple gridded-data files | Reading gridded files differing in the variables | References | OMI/Aura Surface UV (OMUVBd) | Data on a geographic grid subset | Data on the original geographic grid

The R Package 'learnrbook' | Installation of the package | Loading the package | Installation of other packages used in the book | Use of R data objects | Use of examples files | R code for code chunks in the book

Introduction | Preliminaries | Waveband constructors for ranges | Waveband constructors for color-based wavelength ranges | Waveband constructors for instrument-based wavelength ranges | Calculating irradiances | Photon ratios | Spectral weighting functions (SWFs) | Waveband constructors for BSWFs | Effective irradiances and exposures | BSWFs function definitions | Luminous flux