Tools to Standardize Phytoplankton Taxonomic Data and Perform Functional Group Classifications

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Documentation for package ‘algaeClassify’ version 2.0.2

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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_simple Wrapper function for taxize::gnr_resolve() checks species names against a variety of online databases supports fuzzy partial matching
gnr_simple_df Wrapper function to apply gnr_simple across a data.frame or list of species names
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