Error in h(simpleError(msg, call)) : error in evaluating the argument 'obj' in selecting a method for function 'coordinates':

[azizka]

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

Originally posted by @jammah in https://github.com/ropensci/CoordinateCleaner/issues/56#issuecomment-803475370

[azizka]

Hi, I suspect this could be because the country test removed all records. If so, this may happen if the country information is coded in ISO-3, CoordianteCleaner needs ISO-3. Try to include the following line that is further up in the tutorial in your pipeline: dat$countryCode <- countrycode(dat$countryCode, origin = 'iso2c', destination = 'iso3c')

Does this fix the issue?

[jammah]

Yes, you are right. Now it works perfectly!! It fixed the issue!

Many thanks for your help!