check_classification: Checks classification mismatches between a dataframe and the...
In BLE-LTER/BLE-LTER-utils: Utility functions for BLE LTER IM team
View source: R/check_classification.R
check_classification R Documentation
Checks classification mismatches between a dataframe and the WoRMS database
This function verifies the taxonomic classification of rows in a dataframe against data from the WoRMS API based on AphiaID. It iterates over each unique AphiaID in the dataframe, fetches the corresponding classification from WoRMS, and compares it against the dataframe values.
Mismatches are collected and printed. If no dataframe is provided or the input is not a dataframe, the function will stop with an error.
Description
Checks classification mismatches between a dataframe and the WoRMS database
This function verifies the taxonomic classification of rows in a dataframe against data from the WoRMS API based on AphiaID. It iterates over each unique AphiaID in the dataframe, fetches the corresponding classification from WoRMS, and compares it against the dataframe values.
Mismatches are collected and printed. If no dataframe is provided or the input is not a dataframe, the function will stop with an error.
Usage
check_classification(input_dataframe, file_path)
Arguments
input_dataframe
A dataframe with at least one column named 'aphia_ID' and other columns corresponding to taxonomic levels (kingdom, phylum, class, order, family, genus, species). Taxa levels columns must be lower case.
file_path
A character string representing the file path where the output will be saved, e.g., "C:/Users/YourName/Documents/output.txt".
Value
Returns a list of mismatches, where each mismatch is a list containing the AphiaID and the discrepancies between the dataframe and the WoRMS data. Each mismatch specifies the dataframe value and the WoRMS value for each differing taxonomic level.
BLE-LTER/BLE-LTER-utils documentation built on Feb. 26, 2025, 12:20 a.m.
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View source: R/check_classification.R
| check_classification | R Documentation |
Checks classification mismatches between a dataframe and the WoRMS database This function verifies the taxonomic classification of rows in a dataframe against data from the WoRMS API based on AphiaID. It iterates over each unique AphiaID in the dataframe, fetches the corresponding classification from WoRMS, and compares it against the dataframe values. Mismatches are collected and printed. If no dataframe is provided or the input is not a dataframe, the function will stop with an error.
Description
Checks classification mismatches between a dataframe and the WoRMS database This function verifies the taxonomic classification of rows in a dataframe against data from the WoRMS API based on AphiaID. It iterates over each unique AphiaID in the dataframe, fetches the corresponding classification from WoRMS, and compares it against the dataframe values. Mismatches are collected and printed. If no dataframe is provided or the input is not a dataframe, the function will stop with an error.
Usage
check_classification(input_dataframe, file_path)
Arguments
input_dataframe |
A dataframe with at least one column named 'aphia_ID' and other columns corresponding to taxonomic levels (kingdom, phylum, class, order, family, genus, species). Taxa levels columns must be lower case. |
file_path |
A character string representing the file path where the output will be saved, e.g., "C:/Users/YourName/Documents/output.txt". |
Value
Returns a list of mismatches, where each mismatch is a list containing the AphiaID and the discrepancies between the dataframe and the WoRMS data. Each mismatch specifies the dataframe value and the WoRMS value for each differing taxonomic level.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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