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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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plot.spatialvalid minor issue

ThaiseEmilio opened this issue · comments

commented

Hiya,
I am following the tutorial using my own data and found a minor problem with plot.spatialvalid as the attribute the lon and lat columns are not recognized automatically.

flags <- CleanCoordinates(x = gbif, lon = "decimalLongitude", lat = "decimalLatitude",
countries = "countryCode3",
species = "species",
countrycheck = T,
outliers = T) # most test are on by default

plot(flags)
Error in [.data.frame(x, , c("decimallongitude", "decimallatitude")) :
undefined columns selected

My quick-and-dirty solution was renaming the columns in the CleanCoordinates output before plotting.

colnames(flags)[2:3]<-c("decimallongitude", "decimallatitude")
plot(flags)
Regions defined for each Polygons

This works fine but will be easier if it was not necessary and this implementation will be welcome.
Thanks,
Thaise

commented

Hej,
thanks for the issue, that indeed seems unnecessary. Objects of class spatialvalid should have standardized column names. I couldn't reproduce the problem though. Which version of CoordinateCleaner are you using, and could you provide (a few lines) of example data?

commented

Hiya,
Thanks for the reply. I just installed the GitHub version.

packageVersion("CoordinateCleaner")
[1] ‘1.1.1’

Please see below the the full code.

Thanks,
Thaise

rm(list=ls())
install.packages("devtools")
library(devtools)
install_github("azizka/CoordinateCleaner")

library(tidyverse)
library(rgbif)
library(countrycode)
library(CoordinateCleaner)

packageVersion("CoordinateCleaner")

gbif <- occ_search(scientificName = "Phoenix dactylifera", limit = 20000,
return = "data", hasCoordinate = T)

#select columns of interest
gbif <- gbif %>%
dplyr::select(species, decimalLongitude, decimalLatitude, countryCode, individualCount,
gbifID, family, taxonRank, coordinateUncertaintyInMeters, year,
basisOfRecord, institutionCode, datasetName)

#convert country code from ISO2c to ISO3c
gbif$countryCode3 <- countrycode(gbif$countryCode, origin = 'iso2c', destination = 'iso3c')

#flag problems
dat <- data.frame(gbif)
flags <- CleanCoordinates(x = gbif, lon = "decimalLongitude", lat = "decimalLatitude",
countries = "countryCode3",
species = "species",
countrycheck = T,
outliers = T) # most test are on by default

plot(flags) # return error

colnames(flags)[2:3]<-c("decimallongitude", "decimallatitude")
plot(flags) # now ok

commented

fixed in version 2.0-2