Graphical User Interface (GUI) for standardizing plant names with WorldFlora

How to get started...

(Roeland Kindt, World Agroforestry, Nairobi, June 2020)
   

The suggested citation of the World Flora Online (WFO) is:
	WFO ([Year]): World Flora Online. Version [Year].[Month]. Published on the Internet; 
	http://www.worldfloraonline.org. Accessed on:[Date]".

The suggested citation of the WorldFlora package is:

	Kindt R. 2020. WorldFlora: An R package for exact and fuzzy matching of plant names against the 
	World Flora Online Taxonomic Backbone data. 
	Applications in Plant Sciences 8(9): e11388.
	https://doi.org/10.1002/aps3.11388


1. Change the working directory
	This is especially important as location where results will be saved.
	When downloading the World Flora Online taxonomic backbone, it will be placed in the working dir
    
2. Import the data set with plant names to be checked
	The WorldFlora GUI will select variables from the 'active data set' of the R Commander.
	This data can be imported via Data or WorldFlora menu options.
	The ideal method of importing is to import the variables as character vectors, not as factors.
	To import MS Excel files, you need to have the readxl package installed.
	Note that the R Commander Data menu provides various methods of manipulating the active data set.
    
3. Download or 'remember' the World Flora Online taxonomic backbone data set.
	Option WFO.download will download the backbone data set to the working directory.
	Option WFO.remember will remember the location from the previous download.
	The WFO taxonomic backbone will be available as data set 'WFO.data'.
	Note that it will take some time to load all the data.

4. Test WorldFlora with menu option of Taxon lookup
	Type a name of a taxon in the Explore taxon field and select browse, synonyms and/or family.
	Results will be available as new data sets.
	To see or save these resuls, make these new data sets the active data set in the R Commander.
    
5. Prepare the data set, especially if the plant names include the authority
	Use function WFO.prepare after selecting the right active data set.
	The result of this function will become the new active data set, with suffix of '.prep'.

6. Check for matching names
	Use function WFO.match after selecting the right active data set.
	The result of this function will become the new active data set, with suffix of '.match'.
	For large data sets, it may take long before the final results are ready.

7. Check for the best single match for each submitted plant name
	Use function WFO.one after selecting the right active data set.
	The result of this function will become the new active data set, with suffix of '.one'.

8. As steps 5-7 generate a large number of messages with verbose=TRUE, it may be easier to explore these 
by only generating the scripts, then pasting these scripts into the R GUI.

9. Save the results
	To check on the pipeline, it is advisable to immediately inspect the intermediate results of
	functions WFO.prepare, WFO.match and WFO.one. Note that each of these functions will add extra
	columns to the input data set.
	To export to MS Excel, you need to have installed the writexl package.

10. Once that you are familiar with the scripts, you may find it more efficient to directly make scripts
for the WorldFlora package.


