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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.
https://docs.ropensci.org/CoordinateCleaner/
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plot.spatialvalid minor issue #3

Closed ThaiseEmilio closed 6 years ago

ThaiseEmilio commented 6 years ago

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

azizka commented 6 years ago

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?

ThaiseEmilio commented 6 years ago

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

azizka commented 6 years ago

fixed in version 2.0-2