R/jbd_coordinates_transposed.R
jbd_coordinates_transposed.RdThis function flags and corrects records when latitude and longitude appear
to be transposed.
This function will preferably use the countryCode column generated by
bdc::bdc_country_standardized().
jbd_coordinates_transposed(
data,
idcol = "database_id",
sci_names = "scientificName",
lat = "decimalLatitude",
lon = "decimalLongitude",
country = "country",
countryCode = "countryCode",
border_buffer = 0.2,
save_outputs = FALSE,
fileName = NULL,
scale = "large",
path = NULL,
mc.cores = 1
)A data frame or tibble. Containing a unique identifier for each record, geographical coordinates, and country names. Coordinates must be expressed in decimal degrees and WGS84.
A character string. The column name with a unique record identifier. Default = "database_id".
A character string. The column name with species' scientific names. Default = "scientificName".
A character string. The column name with latitudes. Coordinates must be expressed in decimal degrees and WGS84. Default = "decimalLatitude".
A character string. The column name with longitudes. Coordinates must be expressed in decimal degrees and WGS84. Default = "decimalLongitude".
A character string. The column name with the country assignment of each occurrence record. Default = "country".
A character string. The column name containing an ISO-2 country code for each record.
Numeric. Must have value greater than or equal to 0. A distance in decimal degrees used to created a buffer around each country. Records within a given country and at a specified distance from the border will be not be corrected. Default = 0.2 (~22 km at the equator).
Logical. Indicates if a table containing transposed coordinates should be saved for further inspection. Default = FALSE.
A character string. The out file's name.
Passed to rnaturalearth's ne_countries(). Scale of map to return, one of 110, 50, 10 or 'small', 'medium', 'large'. Default = "large".
A character string. A path as a character vector for where to create the directories
and save the figures. If
no path is provided (the default), the directories will be created using here::here().
Numeric. If > 1, the jbd_correct_coordinates function will run in parallel using mclapply using the number of cores specified. If = 1 then it will be run using a serial loop. NOTE: Windows machines must use a value of 1 (see ?parallel::mclapply). Additionally, be aware that each thread can use large chunks of memory. Default = 1.#'
A tibble containing the column "coordinates_transposed" which indicates if verbatim coordinates were not transposed (TRUE). Otherwise records are flagged as (FALSE) and, in this case, verbatim coordinates are replaced by corrected coordinates.
This test identifies transposed coordinates based on mismatches between the country provided for a record and the record's latitude and longitude coordinates. Transposed coordinates often fall outside of the indicated country (i.e., in other countries or in the sea). Different coordinate transformations are performed to correct country/coordinates mismatches. Importantly, verbatim coordinates are replaced by the corrected ones in the returned database. A database containing verbatim and corrected coordinates is created in "Output/Check/01_coordinates_transposed.csv" if save_outputs == TRUE. The columns "country" and "countryCode" can be retrieved by using the function bdc::bdc_country_standardized.
# \donttest{
if(requireNamespace("rnaturalearthdata")){
database_id <- c(1, 2, 3, 4)
scientificName <- c(
"Rhinella major", "Scinax ruber",
"Siparuna guianensis", "Psychotria vellosiana"
)
decimalLatitude <- c(63.43333, -14.43333, -41.90000, -46.69778)
decimalLongitude <- c(-17.90000, -67.91667, -13.25000, -13.82444)
country <- c("BOLIVIA", "bolivia", "Brasil", "Brazil")
x <- data.frame(
database_id, scientificName, decimalLatitude,
decimalLongitude, country
)
# Get country codes
x <- bdc::bdc_country_standardized(data = x, country = "country")
jbd_coordinates_transposed(
data = x,
idcol = "database_id",
sci_names = "scientificName",
lat = "decimalLatitude",
lon = "decimalLongitude",
country = "country_suggested",
countryCode = "countryCode",
border_buffer = 0.2,
save_outputs = FALSE,
scale = "medium"
)
}
#> Loading auxiliary data: country names
#> Standardizing country names
#> country found: Bolivia
#> country found: Brazil
#>
#> bdc_country_standardized:
#> The country names of 3 records were standardized.
#> Two columns ('country_suggested' and 'countryCode') were added to the database.
#> Spherical geometry (s2) switched on
#> Correcting latitude and longitude transposed
#> 3 occurrences will be tested
#>
#> jbd_coordinates_transposed:
#> Corrected 3 records.
#> One columns were added to the database.
#> # A tibble: 4 × 8
#> database_id scientificName decimalLatitude decimalLongitude country
#> <dbl> <chr> <dbl> <dbl> <chr>
#> 1 1 Rhinella major -17.9 -63.4 BOLIVIA
#> 2 2 Scinax ruber -14.4 -67.9 bolivia
#> 3 3 Siparuna guianensis -13.2 -41.9 Brasil
#> 4 4 Psychotria vellosiana -13.8 -46.7 Brazil
#> # ℹ 3 more variables: country_suggested <chr>, countryCode <chr>,
#> # coordinates_transposed <lgl>
# } # END if require