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ropensci / CoordinateCleaner

Automated flagging of common spatial and temporal errors in biological and palaeontological collection data, for the use in conservation, ecology and palaeontology.

Home Page:https://docs.ropensci.org/CoordinateCleaner/

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Error in clean_coordinates functions

KunalArekar opened this issue · comments

commented

Hi Alex
I am using the following code to clean the GBIF data. This is according to the tutorial (https://ropensci.github.io/CoordinateCleaner/articles/Cleaning_GBIF_data_with_CoordinateCleaner.html)

library(devtools)
library(dplyr)
library(ggplot2)
library(rgbif)
library(sp)
library(countrycode)
library(CoordinateCleaner)
dat <- occ_search(scientificName = "Macaca radiata", limit = 5000,
return = "data", hasCoordinate = T)

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

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

wm <- borders("world", colour="gray50", fill="gray50")
ggplot()+ coord_fixed()+ wm +
geom_point(data = dat, aes(x = decimalLongitude, y = decimalLatitude),
colour = "darkred", size = 0.5)+
theme_bw()

dat$countryCode <- countrycode(dat$countryCode, origin = 'iso2c', destination = 'iso3c')

dat <- data.frame(dat)
flags <- clean_coordinates(x = dat, lon = "decimalLongitude", lat = "decimalLatitude",
countries = "countryCode",
species = "species",
tests = c("capitals", "centroids", "equal","gbif", "institutions",
"zeros"))

After the last code (highlighted above) I get the following error

"Testing country identity
x[i, ] is invalid
Error in RGEOSBinTopoFunc(spgeom1, spgeom2, byid, id, drop_lower_td, unaryUnion_if_byid_false, :
TopologyException: Input geom 0 is invalid: Ring Self-intersection at or near point 78.719726559999998 31.887646480000001 at 78.719726559999998 31.887646480000001"

Can you please help me in resolving this.

Thanks
Kunal

commented

Hi Kunal,

Thanks for reporting. This was due to invalid polygons resulting from internal cropping in cc_coun. It should be fixed as of version 2.0-17. This is working for me now:

library(devtools)
library(dplyr)
library(ggplot2)
library(rgbif)
library(sp)
library(countrycode)
library(CoordinateCleaner)
dat <- occ_search(scientificName = "Macaca radiata", limit = 5000,
                  return = "data", hasCoordinate = T)$data

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

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

wm <- borders("world", colour="gray50", fill="gray50")
ggplot()+ coord_fixed()+ wm +
  geom_point(data = dat, aes(x = decimalLongitude, y = decimalLatitude),
             colour = "darkred", size = 0.5)+
  theme_bw()

dat$countryCode <- countrycode(dat$countryCode, origin = 'iso2c', destination = 'iso3c')

dat <- data.frame(dat)
flags <- clean_coordinates(x = dat, lon = "decimalLongitude", lat = "decimalLatitude",
                           countries = "countryCode",
                           species = "species",
                           tests = c("capitals", "centroids", "equal","gbif", "institutions",
                                     "zeros"))

Please let me know if it is working for you.

Cheers,

Alex

commented