Man pages for algaeClassify
Tools to Query the 'Algaebase' Online Database, Standardize Phytoplankton Taxonomic Data, and Perform Functional Group Classifications
| accum | Split a dataframe column with binomial name into genus and... |
| algaebase_genus_search | Search algaebase for information about a genus of... |
| algaebase_output_parse | Helper function for parsing output from algaebase |
| algaebase_search_df | Search algaebase for information about a list of... |
| algaebase_species_search | Retrieve taxonomic information from the algaebase online... |
| bestmatch | fuzzy partial matching between a scientific name and a list... |
| csrTraits | Database of functional traits for MFG classification, derived... |
| date_mat | Transform a phytoplankton timeseries into a matrix of... |
| genus_search_itis | Wrapper function for several functions in ritis:: Searches... |
| genus_species_extract | Split a dataframe column with binomial name into genus and... |
| get_apikey | Get value of algaebase API key from Environment variable... |
| 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... |
| gnr_simple | checks species names against a variety of online databases... |
| itis_search_df | Wrapper function for applying genus_search_itis and... |
| lakegeneva | example dataset from lake Geneva, Switzerland |
| mean_naomit | Compute mean value while ignoring NA's |
| mfg_csr_convert | Returns a CSR classification based on Morphofunctional group... |
| mfg_csr_convert_df | Returns a CSR classification based on Morphofunctional group... |
| mfg_csr_library | MFG-CSR correspondence based on CSR-trait relationships in... |
| mfgTraits | Functional Trait Database derived from Rimet et al. |
| phyto_ts_aggregate | Aggregate phytoplankton timeseries based on abundance. Up to... |
| sampeff | Visually assess change in sampling effort over time (author:... |
| set_algaebase_apikey_header | Add algaebase API key to curl handle |
| species_mfg_library | Trait-based MFG classifications for common Eurasion/North... |
| species_search_itis | Wrapper function for several functions in ritis:: Searches... |
| species_to_mfg | Conversion of a single genus and species name to a single... |
| species_to_mfg_df | Wrapper function to apply species_phyto_convert() across a... |
| traitranges | surface/volume ratio and max linear dimension criteria for... |
| traits_to_csr | Assign phytoplankton species to CSR functional groups, based... |
| traits_to_csr_df | Add CSR functional group classifications to a dataframe of... |
| traits_to_mfg | Assign MFG based on binary functional traits and taxonomy... |
| traits_to_mfg_df | Assign morphofunctional groups to a dataframe of functional... |
