Wondering why defaults for lon and lat use lowercase when GBIF downloads use camelCase

[John Waller]

cc_cen <- function(x, 
                   lon = "decimallongitude", 
                   lat = "decimallatitude", 
                   species = "species",
                   buffer = 1000,
                   geod = TRUE,
                   test = "both", 
                   ref = NULL,
                   verify = FALSE,
                   value = "clean", 
                   verbose = TRUE)

gbif_download %>% 
cc_cen(
lon = "decimallongitude", 
lat = "decimallatitude", 
buffer = 2000, 
value = "clean")

error in evaluating the argument 'obj' in selecting a method for function 'coordinates': Can't subset columns that don't exist.
x Columns decimallongitude and decimallatitude don't exist.

[jammah]

Same problem here.
I just used the example given for Panthera leo (https://ropensci.github.io/CoordinateCleaner/articles/Cleaning_GBIF_data_with_CoordinateCleaner.html) and got the same error message:

library(countrycode)
library(CoordinateCleaner)
library(dplyr)

library(ggplot2)
library(rgbif)
library(sp)

#obtain data from GBIF via rgbif

dat <- occ_search(scientificName = "Panthera leo", limit = 5000, hasCoordinate = T)

dat <- dat$data

names(dat) #a lot of columns

#select columns of interest

dat <- dat %>%
  dplyr::select(species, decimalLongitude, decimalLatitude, countryCode, individualCount,
         gbifID, family, taxonRank, coordinateUncertaintyInMeters, year,
         basisOfRecord, institutionCode, datasetName)

remove records without coordinates

dat <- dat%>%
  filter(!is.na(decimalLongitude))%>%
  filter(!is.na(decimalLatitude))

#to avoid specifying it in each function

names(dat)[2:3] <- c("decimallongitude", "decimallatitude")

clean <- dat%>%
  cc_val()%>%
  cc_equ()%>%
  cc_cap()%>%
  cc_cen()%>%
  cc_coun(iso3 = "countryCode")%>%
  cc_gbif()%>%
  cc_inst()%>%
  cc_sea()%>%
  cc_zero()%>%
  cc_outl()%>%
  cc_dupl()

Testing duplicates
Testing zero coordinates
Testing sea coordinates
Testing biodiversity institutions
Testing GBIF headquarters, flagging records around Copenhagen
Testing country centroids
Testing country capitals
Testing equal lat/lon
Testing coordinate validity
Removed 0 records.
Removed 6 records.
Removed 22 records.
Removed 7 records.
Testing country identity
Removed 4618 records.
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'obj' in selecting a method for function 'coordinates': cannot derive coordinates from non-numeric matrix
In addition: Warning message:
In wkt(obj) : CRS object has no comment

[Alexander Zizka]

This seems like a different thing. I opened a new issue and replied there.