accum                   Split a dataframe column with binomial name
                        into genus and species columns. Plots change in
                        species richness over time, generates species
                        accumulation curve, and compares SAC against
                        simulated idealized curve assuming all unique
                        taxa have equal probability of being sampled at
                        any point in the time series. (author Dietmar
                        Straile)
algaebase_genus_search
                        Search algaebase for information about a genus
                        of phytoplankton
algaebase_output_parse
                        Helper function for parsing output from
                        algaebase
algaebase_search_df     Search algaebase for information about a list
                        of phytoplankton names
algaebase_species_search
                        Retrieve taxonomic information from the
                        algaebase online database (www.algaebase.org)
                        based on a user-specified genus and species
                        name . This function requires a valid API key
                        for algaebase.
bestmatch               fuzzy partial matching between a scientific
                        name and a list of possible matches
csrTraits               Database of functional traits for MFG
                        classification, derived from Rimet et al. 2019
date_mat                Transform a phytoplankton timeseries into a
                        matrix of abundances for ordination
genus_search_itis       Wrapper function for several functions in
                        ritis:: Searches ITIS database for matches to a
                        genus name
genus_species_extract   Split a dataframe column with binomial name
                        into genus and species columns.
get_apikey              Get value of algaebase API key from Environment
                        variable Return an error if variable not set.
get_apikey_fromfile     Get value of algaebase API key from a file
gnr_df                  Wrapper function to apply gnr_simple across a
                        data.frame or list of species names. Modified
                        on 11/18/2025 by Vijay Patil (vpatil@usgs.gov)
                        for algaeClassify v2.0.5 (pending approval on
                        CRAN).
gnr_simple              checks species names against a variety of
                        online databases supports fuzzy partial
                        matching, using the Global Names Resolver
                        (https://resolver.globalnames.org/). Modified
                        on 11/18/2025 by Vijay Patil (vpatil@usgs.gov)
                        for algaeClassify v2.0.5 (pending approval on
                        CRAN).
itis_search_df          Wrapper function for applying genus_search_itis
                        and species_search_itis to a whole data.frame
                        containing scientific names
lakegeneva              example dataset from lake Geneva, Switzerland
mean_naomit             Compute mean value while ignoring NA's
mfgTraits               Functional Trait Database derived from Rimet et
                        al.
mfg_csr_convert         Returns a CSR classification based on
                        Morphofunctional group (MFG). Correspondence
                        based on Salmaso et al. 2015 and Reynolds et
                        al. 1988
mfg_csr_convert_df      Returns a CSR classification based on
                        Morphofunctional group (MFG). Correspondence
                        based on Salmaso et al. 2015 and Reynolds et
                        al. 1988
mfg_csr_library         MFG-CSR correspondence based on CSR-trait
                        relationships in Reynolds et al. 1988 and
                        MFG-trait relationships in Salmaso et al. 2015
phyto_ts_aggregate      Aggregate phytoplankton timeseries based on
                        abundance. Up to 3 grouping variables can be
                        given: e.g. genus, species, stationid, depth
                        range. If no abundance var is given, will
                        aggregate to presence/absence of grouping vars.
sampeff                 Visually assess change in sampling effort over
                        time (author: Dietmar Straile)
set_algaebase_apikey_header
                        Add algaebase API key to curl handle
species_mfg_library     Trait-based MFG classifications for common
                        Eurasion/North American phytoplankton species.
                        See accompanying manuscript for sources
species_search_itis     Wrapper function for several functions in
                        ritis:: Searches ITIS database for matches to a
                        binomial scientific name outputs matches,
                        current accepted names, synonyms, and higher
                        taxonomy
species_to_mfg          Conversion of a single genus and species name
                        to a single MFG. Uses species.mfg.library
species_to_mfg_df       Wrapper function to apply
                        species_phyto_convert() across a data.frame
traitranges             surface/volume ratio and max linear dimension
                        criteria for CSR From Reynolds 1988 and
                        Reynolds 2006
traits_to_csr           Assign phytoplankton species to CSR functional
                        groups, based on surface to volume ratio and
                        maximum linear dimension ranges proposed by
                        Reynolds et al. 1988;2006
traits_to_csr_df        Add CSR functional group classifications to a
                        dataframe of phytoplankton species, based on
                        surface to volume ratio and maximum linear
                        dimension ranges proposed by Reynolds et al.
                        1988;2006
traits_to_mfg           Assign MFG based on binary functional traits
                        and taxonomy (Class and Order)
traits_to_mfg_df        Assign morphofunctional groups to a dataframe
                        of functional traits and higher taxonomy
