Some species names are not capitalized

[Rekyt]

When retrieving species list from their range, I realized by matching the species list to another one, that some species names were not capitalized.
Here is a reprex:

library("dplyr")
#> Warning: le package 'dplyr' a été compilé avec la version R 4.0.3
#> 
#> Attachement du package : 'dplyr'
#> The following objects are masked from 'package:stats':
#> 
#>     filter, lag
#> The following objects are masked from 'package:base':
#> 
#>     intersect, setdiff, setequal, union

BIEN::BIEN_ranges_box(
  min.lat = -55.61831, max.lat = 83.64513,
  min.long = -171.79111, max.long = -12.20855,
  species.names.only = TRUE) %>%
  filter(substr(species, 1, 1) %in% letters)
#>                  species
#> 1  chamomilla_chamomilla
#> 2          dubius_dubius
#> 3           dubius_subsp
#> 4       lachenalii_subsp
#> 5    polytaenium_jenmani
#> 6    syngonanthus_nitens
#> 7             x_Catyclia
#> 8          x_Agrohordeum
#> 9            x_Agropogon
#> 10          x_Elyhordeum
#> 11         x_Elysitanion
#> 12         x_Festulolium
#> 13         x_Pseudelymus
#> 14 xPseudelymus_saxicola
#> 15       x_Stiporyzopsis
#> 16  anthurium_geherrerae

^{Created on 2020-11-24 by the reprex package (v0.3.0)}

Session info

devtools::session_info()
#> - Session info ---------------------------------------------------------------
#>  setting  value                       
#>  version  R version 4.0.2 (2020-06-22)
#>  os       Windows 10 x64              
#>  system   x86_64, mingw32             
#>  ui       RTerm                       
#>  language (EN)                        
#>  collate  French_France.1252          
#>  ctype    French_France.1252          
#>  tz       Europe/Berlin               
#>  date     2020-11-24                  
#> 
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#>  package     * version date       lib source        
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of course for the crossing it is expected that the first letter is not a capital letter, but what about the other species?

[bmaitner]

Pinging @ojalaquellueva on this one. Brad, any ideas? Since the mistake is on the maps and is not present in vfoi, presumably this is a range pipeline issue? I also guess this means that the previous set of maps weren't TNRSed?

[ojalaquellueva]

@bmaitner : This is a legacy of how ranges were built in the past before I came on board. Basically the species names in the ranges table needed to match to the basename (minus extension) of the range file as a single string without spaces (hence the underscores). The genus was also inconsistently converted to lower case.

Email me the SQL used to retrieve the species names and range info and I will come up with a solution. If you are querying the new ranges schema, then there is a separate species table with both the internal species name (with underscores and weird capitalization) and the well-formed binomial. Just query that. If you are querying the old ranges table in the main analytical schema, then I can add a column with the well-formed binomial.

[Rekyt]

Thank you both for the quick answer! @ojalaquellueva how to know if I'm querying the old or the new ranges schema? Which table should I consider?

[ojalaquellueva]

@reykt That was a backend question for Brian. Once I hear back from Brian I'll know whether to push out a fix or if the solution is on Brian's end.