Package index • eemanalyzeR

Automated EEMs processing

Automated loading, processing, and export of EEMs and and absorbance data.

Functions for loading in EEMs, absorbance, and metadata.

abs_read(): Read a single absorbance file into R
eem_dir_read() abs_dir_read(): Read absorbance and fluorescence data from directory
meta_check(): Run tests to validate metadata
meta_read(): Read metadata from a file

Functions to process and clean data.

Functions to generate EEMs and absorbance indices.

eemanalyzeR_indices(): Default package methods for fluorescence and absorbance indices
eemR_indices(): eemR and staRdom methods for fluorescence and absorbance indices
get_abs_slope(): Calculate spectral slopes
get_absorbance(): Extract absorbance at a given wavelength
get_fluorescence(): Get fluorescence within a specified range
get_indices(): Get fluorescence and absorbance indices
get_ratios(): Safely return ratios values
usgs_indices(): USGS methods for fluorescence and absorbance indices

Functions to plot and export data.

annotate_plot(): Annotate EEM plot with location of indices
export_data(): Export processed absorbance and fluorescence data
plot(<eem>) plot(<eemlist>) plot(<abs>) plot(<abslist>): Default plot methods for optical data with ggplot2
print_readme(): Print `readme`

Functions to aid in QA/QC checks.

check_eem_mdl() check_abs_mdl(): Check whether an EEM or absorbance sample is above the MDL
check_std(): Check if a check standard is consistent with long-term standard
create_mdl(): Calculate method detection limits (MDL)
create_std(): Create long term average check standard
.combine_flags(): Nicely combine data QAQC flags
flag_missing(): QA/QC flags for missing data
format_index(): Format index and flag data
validate_blanks(): Validate the instrument blank(s)
validate_std(): Visually validate the check standard

Functions to create and maintain processing configuration files.

list_config(): List current eemanalyzeR configuration
modify_config(): Modify the eemanalyzeR configuration settings
reset_config(): Reset all eemanalyzeR settings to package defaults
reset_user_config(): Reset all eemanalyzeR settings in the user configuration file to package defaults
edit_user_config() load_user_config(): Set up and apply user defaults for data processing
validate_config(): Validate the eemanalyzeR configuration

Helper functions and internal utilities.

abs_interp(): Interpolate absorbance data
eem_normalize(): Normalize an eem or eemlist based on a normalization factor
eem_transform(): Convert between an eem object and a data.frame
get_sample_info(): Extract components from an eemlist or abslist
subset_samples(): Subset eemlist or abslist based on components
subset_type(): Extract samples by type from an eemlist or abslist
unique(<eemlist>) unique(<abslist>): Get unique EEMs or absorbance samples

Example datasets.

default_config: Default configuration of arguments for eemanalyzeR
example_abs: Down-scaled absorbance data
example_eems: Down-scaled excitation emission matrices
example_processed_abs: Down-scaled and processed absorbance data
example_processed_eems: Down-scaled and processed excitation emission matrices
indice_ranges: Standard ranges for absorbance and EEMs indices
metadata: Example metadata