spectrolab

Spectrolab is an R package that provides a class and methods for processing and visualizing high resolution spectra in R. It is licensed under GPL-3.

Installation

You can install spectrolab from Github using:

library("devtools")
install_github("meireles/spectrolab")

Or from CRAN using:

install.packages("spectrolab")

Using spectrolab

This vignette introduces spectrolab, and walks you through the basics of the package.

This vignette shows how to match (splice) sensors.

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Version

Install

install.packages('spectrolab')

Monthly Downloads

249

Version

0.0.18

License

GPL-3

Last Published

February 12th, 2023

Functions in spectrolab (0.0.18)

i_is_increasing

Is increasing
as.matrix.spectra

Convert spectra to matrix
bands

Get spectra band labels
as_spectra.matrix

Convert matrix to spectra
guess_splice_at

Guess splice bands (bounds between senors)
as_spectra

Convert matrix or data frame to spectra
dim.spectra

Get dimension of spectra
i_is_index

Compatible with being an index?
combine

Combine spectral datasets
i_index_pairwise_combn

Pairwise index combinations
i_is_whole

Is whole number?
default_spec_regions

Return default spectral regions matrix
i_plot_boundaries

Find plot boundaries in user space
i_bands

Internal band constructor for spectra
i_names

Internal constructor for sample names
i_find_sensor_overlap_bounds

Find sensor overlap bounds
i_mind_the_gap_smoothing

Warn if gap between bands is too wide
i_meta

Internal metadata constructor for spectra
i_read_asd_spectra

Parser for ASD's `.asd`
i_match_ij_spectra

Get internal indexes for spectra attributes
i_read_ascii_spectra

Internal parser for ASCII format
max.spectra

Maximum value
i_match_label

Match label
plot.spectra

Plot spectra
match_sensors

Match spectra at sensor transitions
is_spectra

Is it a spectra object?
pairwise_ratio

Pairwise value ratios
i_verify_path_and_format

Internal function to verify file paths and format
names.spectra

Get spectra sample names
normalize

Vector normalize spectra
median.spectra

Median spectrum
mean.spectra

Mean spectrum
i_plot_exists

Tests if a plot device exists
i_read_ascii_metadata

Read metadata
quantile.spectra

Compute spectra quantiles
range.spectra

Range of spectral values
i_match_label_or_idx

Match label or index
plot_interactive

Plot spectra interactively
i_trim_sensor_overlap

Trim sensor overlap
i_value

Internal constructor for value matrix
i_mav

Moving Average
plot_quantile

Plot spectra quantiles
smooth.spectra

Smooth spectra
smooth.default

Default smoothing function
meta<-

Set metadata
spec_matrix_example

Example spectral dataset
[<-.spectra

Assign values to spectra
spectra

Spectra object constructor
try_keep_txt

Wrap function to try to keep text
value<-

Set spectra value
meta

Get metadata
sd

Standard deviation
[.spectra

Subset spectra
summary.spectra

Summarize spectra
spectrolab

Spectrolab
print.spectra

Print spectra
resample

Resample spectra
plot_regions

Plot polygons for spectral regions
subset_by

Subset spectra by factor
str.spectra

Structure of the spectra object
sd.default

Default variance
t.spectra

Spectra Transpose
read_spectra

Read files from various formats into `spectra`
var

Variance
value

Get spectra value
split.spectra

Split spectra
min.spectra

Minimum value
smooth

Generic Smoothing function
sd.spectra

Standard deviation spectrum
names<-.spectra

Set spectra sample names
smooth_moving_avg

Smooth moving average for spectra
var.spectra

Variance spectrum
smooth_spline

Smooth spline functions for spectra
var.default

Variance
bands<-

Set band labels
as_spectra.data.frame

Convert data.frame to spectra
as.data.frame.spectra

Convert spectra to data.frame
aggregate.spectra

Aggregate spectra
Ops.spectra

Arithmetic operators for spectra
apply_by_band

Apply numeric function by band