hjsimpso/fungarium

An R package for enabling the use of fungarium collection data in comprehensive trait analyses.

fungarium's Issues

add parallel processing option to get_fips

add parallel processing capability using mclapply

improve documentation for collector bias analysis in enrichment function

provide more detail about how collector bias is calculated and what it means

function for getting iso codes of countries, states, provinces

get codes while accounting for misspellings

remove mycoportal "host" field from find_trait and examples

"host" field no longer exists in data sets obtained from MyCoPortal

Error in mycoportal_tab: Mycoportal website unavailable (yet can directly download data from Mycoportal)

When trying to download as specified in the R help & the manual, cannot download the data (tried across many hours), yet it was downloadable from Mycoportal directly at the same time.

Could this be an issue with the mycoportal_tab() regarding timing out? Just in case it is anything somehow related to the function, I bring it to your awareness.

"Error in mycoportal_tab(path.expand("~"), "Pleurotus", taxon_type = "1", :
MyCoPortal website currently unavailable."

"Error in mycoportal_tab(path.expand("~"), "Pholiota", taxon_type = "1", :
MyCoPortal website currently unavailable.

specify @main to install package

One minor issue with installation -- need to specify @main to install package, i.e.,

install_github("hjsimpso/fungarium@main")

add parallel processing capability to taxon_update

utilize mclapply for parallel processing

update examples in all functions

update and test all function examples

add str_clean arg to get_fips

utilize str_clean function within get_fips to aid approximate name matching

add str_clean arg to find_trait

utilize str_clean function within find_trait to aid in regex string matching

get collector bias algorithm in enrichment function to work for GBIF data

Currently, collector bias algorithm uses two specific columns in MyCoPortal data, "recordedBy" and "associatedCollectors". The later is not present in GBIF data. To be more robust for both data types, a new argument will be created for enrichment where user can specify the fields that contain collector info, then the function details will explain the defaults for MyCoPortal and GBIF data.